Staying Cool when Things Get Hot: Emotion Regulation Modulates Neural Mechanisms of Memory Encoding

PubMed Central

Hayes, Jasmeet Pannu; Morey, Rajendra A.; Petty, Christopher M.; Seth, Srishti; Smoski, Moria J.; McCarthy, Gregory; LaBar, Kevin S.

2010-01-01

During times of emotional stress, individuals often engage in emotion regulation to reduce the experiential and physiological impact of negative emotions. Interestingly, emotion regulation strategies also influence memory encoding of the event. Cognitive reappraisal is associated with enhanced memory while expressive suppression is associated with impaired explicit memory of the emotional event. However, the mechanism by which these emotion regulation strategies affect memory is unclear. We used event-related fMRI to investigate the neural mechanisms that give rise to memory formation during emotion regulation. Twenty-five participants viewed negative pictures while alternately engaging in cognitive reappraisal, expressive suppression, or passive viewing. As part of the subsequent memory design, participants returned to the laboratory two weeks later for a surprise memory test. Behavioral results showed a reduction in negative affect and a retention advantage for reappraised stimuli relative to the other conditions. Imaging results showed that successful encoding during reappraisal was uniquely associated with greater co-activation of the left inferior frontal gyrus, amygdala, and hippocampus, suggesting a possible role for elaborative encoding of negative memories. This study provides neurobehavioral evidence that engaging in cognitive reappraisal is advantageous to both affective and mnemonic processes. PMID:21212840

Memory Dynamics in Cross-linked Actin Networks

NASA Astrophysics Data System (ADS)

Scheff, Danielle; Majumdar, Sayantan; Gardel, Margaret

Cells demonstrate the remarkable ability to adapt to mechanical stimuli through rearrangement of the actin cytoskeleton, a cross-linked network of actin filaments. In addition to its importance in cell biology, understanding this mechanical response provides strategies for creation of novel materials. A recent study has demonstrated that applied stress can encode mechanical memory in these networks through changes in network geometry, which gives rise to anisotropic shear response. Under later shear, the network is stiffer in the direction of the previously applied stress. However, the dynamics behind the encoding of this memory are unknown. To address this question, we explore the effect of varying either the rigidity of the cross-linkers or the length of actin filament on the time scales required for both memory encoding and over which it later decays. While previous experiments saw only a long-lived memory, initial results suggest another mechanism where memories relax relatively quickly. Overall, our study is crucial for understanding the process by which an external stress can impact network arrangement and thus the dynamics of memory formation.

Encoding sensory and motor patterns as time-invariant trajectories in recurrent neural networks

PubMed Central

2018-01-01

Much of the information the brain processes and stores is temporal in nature—a spoken word or a handwritten signature, for example, is defined by how it unfolds in time. However, it remains unclear how neural circuits encode complex time-varying patterns. We show that by tuning the weights of a recurrent neural network (RNN), it can recognize and then transcribe spoken digits. The model elucidates how neural dynamics in cortical networks may resolve three fundamental challenges: first, encode multiple time-varying sensory and motor patterns as stable neural trajectories; second, generalize across relevant spatial features; third, identify the same stimuli played at different speeds—we show that this temporal invariance emerges because the recurrent dynamics generate neural trajectories with appropriately modulated angular velocities. Together our results generate testable predictions as to how recurrent networks may use different mechanisms to generalize across the relevant spatial and temporal features of complex time-varying stimuli. PMID:29537963

Encoding sensory and motor patterns as time-invariant trajectories in recurrent neural networks.

PubMed

Goudar, Vishwa; Buonomano, Dean V

2018-03-14

Much of the information the brain processes and stores is temporal in nature-a spoken word or a handwritten signature, for example, is defined by how it unfolds in time. However, it remains unclear how neural circuits encode complex time-varying patterns. We show that by tuning the weights of a recurrent neural network (RNN), it can recognize and then transcribe spoken digits. The model elucidates how neural dynamics in cortical networks may resolve three fundamental challenges: first, encode multiple time-varying sensory and motor patterns as stable neural trajectories; second, generalize across relevant spatial features; third, identify the same stimuli played at different speeds-we show that this temporal invariance emerges because the recurrent dynamics generate neural trajectories with appropriately modulated angular velocities. Together our results generate testable predictions as to how recurrent networks may use different mechanisms to generalize across the relevant spatial and temporal features of complex time-varying stimuli. © 2018, Goudar et al.

Neural mechanisms of motivated forgetting

PubMed Central

Anderson, Michael C.; Hanslmayr, Simon

2014-01-01

Not all memories are equally welcome in awareness. People limit the time they spend thinking about unpleasant experiences, a process that begins during encoding, but that continues when cues later remind someone of the memory. Here, we review the emerging behavioural and neuroimaging evidence that suppressing awareness of an unwelcome memory, at encoding or retrieval, is achieved by inhibitory control processes mediated by the lateral prefrontal cortex. These mechanisms interact with neural structures that represent experiences in memory, disrupting traces that support retention. Thus, mechanisms engaged to regulate momentary awareness introduce lasting biases in which experiences remain accessible. We argue that theories of forgetting that neglect the motivated control of awareness omit a powerful force shaping the retention of our past. PMID:24747000

Differential Encoding of Time by Prefrontal and Striatal Network Dynamics.

PubMed

Bakhurin, Konstantin I; Goudar, Vishwa; Shobe, Justin L; Claar, Leslie D; Buonomano, Dean V; Masmanidis, Sotiris C

2017-01-25

Telling time is fundamental to many forms of learning and behavior, including the anticipation of rewarding events. Although the neural mechanisms underlying timing remain unknown, computational models have proposed that the brain represents time in the dynamics of neural networks. Consistent with this hypothesis, changing patterns of neural activity dynamically in a number of brain areas-including the striatum and cortex-has been shown to encode elapsed time. To date, however, no studies have explicitly quantified and contrasted how well different areas encode time by recording large numbers of units simultaneously from more than one area. Here, we performed large-scale extracellular recordings in the striatum and orbitofrontal cortex of mice that learned the temporal relationship between a stimulus and a reward and reported their response with anticipatory licking. We used a machine-learning algorithm to quantify how well populations of neurons encoded elapsed time from stimulus onset. Both the striatal and cortical networks encoded time, but the striatal network outperformed the orbitofrontal cortex, a finding replicated both in simultaneously and nonsimultaneously recorded corticostriatal datasets. The striatal network was also more reliable in predicting when the animals would lick up to ∼1 s before the actual lick occurred. Our results are consistent with the hypothesis that temporal information is encoded in a widely distributed manner throughout multiple brain areas, but that the striatum may have a privileged role in timing because it has a more accurate "clock" as it integrates information across multiple cortical areas. The neural representation of time is thought to be distributed across multiple functionally specialized brain structures, including the striatum and cortex. However, until now, the neural code for time has not been compared quantitatively between these areas. Here, we performed large-scale recordings in the striatum and orbitofrontal cortex of mice trained on a stimulus-reward association task involving a delay period and used a machine-learning algorithm to quantify how well populations of simultaneously recorded neurons encoded elapsed time from stimulus onset. We found that, although both areas encoded time, the striatum consistently outperformed the orbitofrontal cortex. These results suggest that the striatum may refine the code for time by integrating information from multiple inputs. Copyright © 2017 the authors 0270-6474/17/370854-17$15.00/0.

Working memory accuracy for multiple targets is driven by reward expectation and stimulus contrast with different time-courses.

PubMed

Klink, P Christiaan; Jeurissen, Danique; Theeuwes, Jan; Denys, Damiaan; Roelfsema, Pieter R

2017-08-22

The richness of sensory input dictates that the brain must prioritize and select information for further processing and storage in working memory. Stimulus salience and reward expectations influence this prioritization but their relative contributions and underlying mechanisms are poorly understood. Here we investigate how the quality of working memory for multiple stimuli is determined by priority during encoding and later memory phases. Selective attention could, for instance, act as the primary gating mechanism when stimuli are still visible. Alternatively, observers might still be able to shift priorities across memories during maintenance or retrieval. To distinguish between these possibilities, we investigated how and when reward cues determine working memory accuracy and found that they were only effective during memory encoding. Previously learned, but currently non-predictive, color-reward associations had a similar influence, which gradually weakened without reinforcement. Finally, we show that bottom-up salience, manipulated through varying stimulus contrast, influences memory accuracy during encoding with a fundamentally different time-course than top-down reward cues. While reward-based effects required long stimulus presentation, the influence of contrast was strongest with brief presentations. Our results demonstrate how memory resources are distributed over memory targets and implicates selective attention as a main gating mechanism between sensory and memory systems.

Exploring the influence of encoding format on subsequent memory.

PubMed

Turney, Indira C; Dennis, Nancy A; Maillet, David; Rajah, M Natasha

2017-05-01

Distinctive encoding is greatly influenced by gist-based processes and has been shown to suffer when highly similar items are presented in close succession. Thus, elucidating the mechanisms underlying how presentation format affects gist processing is essential in determining the factors that influence these encoding processes. The current study utilised multivariate partial least squares (PLS) analysis to identify encoding networks directly associated with retrieval performance in a blocked and intermixed presentation condition. Subsequent memory analysis for successfully encoded items indicated no significant differences between reaction time and retrieval performance and presentation format. Despite no significant behavioural differences, behaviour PLS revealed differences in brain-behaviour correlations and mean condition activity in brain regions associated with gist-based vs. distinctive encoding. Specifically, the intermixed format encouraged more distinctive encoding, showing increased activation of regions associated with strategy use and visual processing (e.g., frontal and visual cortices, respectively). Alternatively, the blocked format exhibited increased gist-based processes, accompanied by increased activity in the right inferior frontal gyrus. Together, results suggest that the sequence that information is presented during encoding affects the degree to which distinctive encoding is engaged. These findings extend our understanding of the Fuzzy Trace Theory and the role of presentation format on encoding processes.

Population clocks: motor timing with neural dynamics

PubMed Central

Buonomano, Dean V.; Laje, Rodrigo

2010-01-01

An understanding of sensory and motor processing will require elucidation of the mechanisms by which the brain tells time. Open questions relate to whether timing relies on dedicated or intrinsic mechanisms and whether distinct mechanisms underlie timing across scales and modalities. Although experimental and theoretical studies support the notion that neural circuits are intrinsically capable of sensory timing on short scales, few general models of motor timing have been proposed. For one class of models, population clocks, it is proposed that time is encoded in the time-varying patterns of activity of a population of neurons. We argue that population clocks emerge from the internal dynamics of recurrently connected networks, are biologically realistic and account for many aspects of motor timing. PMID:20889368

Compensating for Language Deficits in Amnesia II: H.M.’s Spared versus Impaired Encoding Categories

PubMed Central

MacKay, Donald G.; Johnson, Laura W.; Hadley, Chris

2013-01-01

Although amnesic H.M. typically could not recall where or when he met someone, he could recall their topics of conversation after long interference-filled delays, suggesting impaired encoding for some categories of novel events but not others. Similarly, H.M. successfully encoded into internal representations (sentence plans) some novel linguistic structures but not others in the present language production studies. For example, on the Test of Language Competence (TLC), H.M. produced uncorrected errors when encoding a wide range of novel linguistic structures, e.g., violating reliably more gender constraints than memory-normal controls when encoding referent-noun, pronoun-antecedent, and referent-pronoun anaphora, as when he erroneously and without correction used the gender-inappropriate pronoun “her” to refer to a man. In contrast, H.M. never violated corresponding referent-gender constraints for proper names, suggesting that his mechanisms for encoding proper name gender-agreement were intact. However, H.M. produced no more dysfluencies, off-topic comments, false starts, neologisms, or word and phonological sequencing errors than controls on the TLC. Present results suggest that: (a) frontal mechanisms for retrieving and sequencing word, phrase, and phonological categories are intact in H.M., unlike in category-specific aphasia; (b) encoding mechanisms in the hippocampal region are category-specific rather than item-specific, applying to, e.g., proper names rather than words; (c) H.M.’s category-specific mechanisms for encoding referents into words, phrases, and propositions are impaired, with the exception of referent gender, person, and number for encoding proper names; and (d) H.M. overuses his intact proper name encoding mechanisms to compensate for his impaired mechanisms for encoding other functionally equivalent linguistic information. PMID:24961410

Compensating for Language Deficits in Amnesia II: H.M.'s Spared versus Impaired Encoding Categories.

PubMed

MacKay, Donald G; Johnson, Laura W; Hadley, Chris

2013-03-27

Although amnesic H.M. typically could not recall where or when he met someone, he could recall their topics of conversation after long interference-filled delays, suggesting impaired encoding for some categories of novel events but not others. Similarly, H.M. successfully encoded into internal representations (sentence plans) some novel linguistic structures but not others in the present language production studies. For example, on the Test of Language Competence (TLC), H.M. produced uncorrected errors when encoding a wide range of novel linguistic structures, e.g., violating reliably more gender constraints than memory-normal controls when encoding referent-noun, pronoun-antecedent, and referent-pronoun anaphora, as when he erroneously and without correction used the gender-inappropriate pronoun "her" to refer to a man. In contrast, H.M. never violated corresponding referent-gender constraints for proper names, suggesting that his mechanisms for encoding proper name gender-agreement were intact. However, H.M. produced no more dysfluencies, off-topic comments, false starts, neologisms, or word and phonological sequencing errors than controls on the TLC. Present results suggest that: (a) frontal mechanisms for retrieving and sequencing word, phrase, and phonological categories are intact in H.M., unlike in category-specific aphasia; (b) encoding mechanisms in the hippocampal region are category-specific rather than item-specific, applying to, e.g., proper names rather than words; (c) H.M.'s category-specific mechanisms for encoding referents into words, phrases, and propositions are impaired, with the exception of referent gender, person, and number for encoding proper names; and (d) H.M. overuses his intact proper name encoding mechanisms to compensate for his impaired mechanisms for encoding other functionally equivalent linguistic information.

Differential effects of acute cortisol administration on deep and shallow episodic memory traces: a study on healthy males.

PubMed

Cioncoloni, David; Galli, Giulia; Mazzocchio, Riccardo; Feurra, Matteo; Giovannelli, Fabio; Santarnecchi, Emiliano; Bonifazi, Marco; Rossi, Alessandro; Rossi, Simone

2014-10-01

We aimed at investigating rapid effects of plasma cortisol elevations on the episodic memory phase of encoding or retrieval, and on the strength of the memory trace. Participants were asked either to select a word containing the letter "e" (shallow encoding task) or to judge if a word referred to a living entity (deep encoding task). We intravenously administered a bolus of 20mg of cortisol either 5 min before encoding or 5 min before retrieval, in a between-subjects design. The study included only male participants tested in the late afternoon, and neutral words as stimuli. When cortisol administration occurred prior to retrieval, a main effect of group emerged. Recognition accuracy was higher for individuals who received cortisol compared to placebo. The higher discrimination accuracy for the cortisol group was significant for words encoded during deep but not shallow task. Cortisol administration before encoding did not affect subsequent retrieval performance (either for deep or shallow stimuli) despite a facilitatory trend. Because genomic mechanisms take some time to develop, such a mechanism cannot apply to our findings where the memory task was performed shortly after the enhancement of glucocorticoid levels. Therefore, glucocorticoids, through non-genomic fast effects, determine an enhancement in episodic memory if administered immediately prior to retrieval. This effect is more evident if the memory trace is laid down through deep encoding operations involving the recruitment of specific neural networks. Copyright © 2014 Elsevier Inc. All rights reserved.

Mental reinstatement of encoding context improves episodic remembering.

PubMed

Bramão, Inês; Karlsson, Anna; Johansson, Mikael

2017-09-01

This study investigates context-dependent memory retrieval. Previous work has shown that physically re-experiencing the encoding context at retrieval improves memory accessibility. The current study examined if mental reconstruction of the original encoding context would yield parallel memory benefits. Participants performed a cued-recall memory task, preceded either by a mental or by a physical context reinstatement task, and we manipulated whether the context reinstated at retrieval overlapped with the context of the target episode. Both behavioral and electrophysiological measures of brain activity showed strong encoding-retrieval (E-R) overlap effects, with facilitated episodic retrieval when the encoding and retrieval contexts overlapped. The electrophysiological E-R overlap effect was more sustained and involved more posterior regions when context was mentally compared with physically reinstated. Additionally, a time-frequency analysis revealed that context reinstatement alone engenders recollection of the target episode. However, while recollection of the target memory is readily prompted by a physical reinstatement, target recollection during mental reinstatement is delayed and depends on the gradual reconstruction of the context. Taken together, our results show facilitated episodic remembering also when mentally reinstating the encoding context; and that such benefits are supported by both shared and partially non-overlapping neural mechanisms when the encoding context is mentally reconstructed as compared with physically presented at the time of retrieval. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular mechanisms for protein-encoded inheritance

PubMed Central

Wiltzius, Jed J. W.; Landau, Meytal; Nelson, Rebecca; Sawaya, Michael R.; Apostol, Marcin I.; Goldschmidt, Lukasz; Soriaga, Angela B.; Cascio, Duilio; Rajashankar, Kanagalaghatta; Eisenberg, David

2013-01-01

Strains are phenotypic variants, encoded by nucleic acid sequences in chromosomal inheritance and by protein “conformations” in prion inheritance and transmission. But how is a protein “conformation” stable enough to endure transmission between cells or organisms? Here new polymorphic crystal structures of segments of prion and other amyloid proteins offer structural mechanisms for prion strains. In packing polymorphism, prion strains are encoded by alternative packings (polymorphs) of β-sheets formed by the same segment of a protein; in a second mechanism, segmental polymorphism, prion strains are encoded by distinct β-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring “conformations,” capable of encoding strains. These molecular mechanisms for transfer of information into prion strains share features with the familiar mechanism for transfer of information by nucleic acid inheritance, including sequence specificity and recognition by non-covalent bonds. PMID:19684598

Asymptotic theory of time varying networks with burstiness and heterogeneous activation patterns

NASA Astrophysics Data System (ADS)

Burioni, Raffaella; Ubaldi, Enrico; Vezzani, Alessandro

2017-05-01

The recent availability of large-scale, time-resolved and high quality digital datasets has allowed for a deeper understanding of the structure and properties of many real-world networks. The empirical evidence of a temporal dimension prompted the switch of paradigm from a static representation of networks to a time varying one. In this work we briefly review the framework of time-varying-networks in real world social systems, especially focusing on the activity-driven paradigm. We develop a framework that allows for the encoding of three generative mechanisms that seem to play a central role in the social networks’ evolution: the individual’s propensity to engage in social interactions, its strategy in allocate these interactions among its alters and the burstiness of interactions amongst social actors. The functional forms and probability distributions encoding these mechanisms are typically data driven. A natural question arises if different classes of strategies and burstiness distributions, with different local scale behavior and analogous asymptotics can lead to the same long time and large scale structure of the evolving networks. We consider the problem in its full generality, by investigating and solving the system dynamics in the asymptotic limit, for general classes of ties allocation mechanisms and waiting time probability distributions. We show that the asymptotic network evolution is driven by a few characteristics of these functional forms, that can be extracted from direct measurements on large datasets.

QR encoded smart oral dosage forms by inkjet printing.

PubMed

Edinger, Magnus; Bar-Shalom, Daniel; Sandler, Niklas; Rantanen, Jukka; Genina, Natalja

2018-01-30

The use of inkjet printing (IJP) technology enables the flexible manufacturing of personalized medicine with the doses tailored for each patient. In this study we demonstrate, for the first time, the applicability of IJP in the production of edible dosage forms in the pattern of a quick response (QR) code. This printed pattern contains the drug itself and encoded information relevant to the patient and/or healthcare professionals. IJP of the active pharmaceutical ingredient (API)-containing ink in the pattern of QR code was performed onto a newly developed porous and flexible, but mechanically stable substrate with a good absorption capacity. The printing did not affect the mechanical properties of the substrate. The actual drug content of the printed dosage forms was in accordance with the encoded drug content. The QR encoded dosage forms had a good print definition without significant edge bleeding. They were readable by a smartphone even after storage in harsh conditions. This approach of efficient data incorporation and data storage combined with the use of smart devices can lead to safer and more patient-friendly drug products in the future. Copyright © 2017 Elsevier B.V. All rights reserved.

Principles of Discrete Time Mechanics

NASA Astrophysics Data System (ADS)

Jaroszkiewicz, George

2014-04-01

1. Introduction; 2. The physics of discreteness; 3. The road to calculus; 4. Temporal discretization; 5. Discrete time dynamics architecture; 6. Some models; 7. Classical cellular automata; 8. The action sum; 9. Worked examples; 10. Lee's approach to discrete time mechanics; 11. Elliptic billiards; 12. The construction of system functions; 13. The classical discrete time oscillator; 14. Type 2 temporal discretization; 15. Intermission; 16. Discrete time quantum mechanics; 17. The quantized discrete time oscillator; 18. Path integrals; 19. Quantum encoding; 20. Discrete time classical field equations; 21. The discrete time Schrodinger equation; 22. The discrete time Klein-Gordon equation; 23. The discrete time Dirac equation; 24. Discrete time Maxwell's equations; 25. The discrete time Skyrme model; 26. Discrete time quantum field theory; 27. Interacting discrete time scalar fields; 28. Space, time and gravitation; 29. Causality and observation; 30. Concluding remarks; Appendix A. Coherent states; Appendix B. The time-dependent oscillator; Appendix C. Quaternions; Appendix D. Quantum registers; References; Index.

Early remodeling of the neocortex upon episodic memory encoding

PubMed Central

Bero, Adam W.; Meng, Jia; Cho, Sukhee; Shen, Abra H.; Canter, Rebecca G.; Ericsson, Maria; Tsai, Li-Huei

2014-01-01

Understanding the mechanisms by which long-term memories are formed and stored in the brain represents a central aim of neuroscience. Prevailing theory suggests that long-term memory encoding involves early plasticity within hippocampal circuits, whereas reorganization of the neocortex is thought to occur weeks to months later to subserve remote memory storage. Here we report that long-term memory encoding can elicit early transcriptional, structural, and functional remodeling of the neocortex. Parallel studies using genome-wide RNA sequencing, ultrastructural imaging, and whole-cell recording in wild-type mice suggest that contextual fear conditioning initiates a transcriptional program in the medial prefrontal cortex (mPFC) that is accompanied by rapid expansion of the synaptic active zone and postsynaptic density, enhanced dendritic spine plasticity, and increased synaptic efficacy. To address the real-time contribution of the mPFC to long-term memory encoding, we performed temporally precise optogenetic inhibition of excitatory mPFC neurons during contextual fear conditioning. Using this approach, we found that real-time inhibition of the mPFC inhibited activation of the entorhinal–hippocampal circuit and impaired the formation of long-term associative memory. These findings suggest that encoding of long-term episodic memory is associated with early remodeling of neocortical circuits, identify the prefrontal cortex as a critical regulator of encoding-induced hippocampal activation and long-term memory formation, and have important implications for understanding memory processing in healthy and diseased brain states. PMID:25071187

Automatic semantic encoding in verbal short-term memory: evidence from the concreteness effect.

PubMed

Campoy, Guillermo; Castellà, Judit; Provencio, Violeta; Hitch, Graham J; Baddeley, Alan D

2015-01-01

The concreteness effect in verbal short-term memory (STM) tasks is assumed to be a consequence of semantic encoding in STM, with immediate recall of concrete words benefiting from richer semantic representations. We used the concreteness effect to test the hypothesis that semantic encoding in standard verbal STM tasks is a consequence of controlled, attention-demanding mechanisms of strategic semantic retrieval and encoding. Experiment 1 analysed the effect of presentation rate, with slow presentations being assumed to benefit strategic, time-dependent semantic encoding. Experiments 2 and 3 provided a more direct test of the strategic hypothesis by introducing three different concurrent attention-demanding tasks. Although Experiment 1 showed a larger concreteness effect with slow presentations, the following two experiments yielded strong evidence against the strategic hypothesis. Limiting available attention resources by concurrent tasks reduced global memory performance, but the concreteness effect was equivalent to that found in control conditions. We conclude that semantic effects in STM result from automatic semantic encoding and provide tentative explanations for the interaction between the concreteness effect and the presentation rate.

Normative shifts of cortical mechanisms of encoding contribute to adult age differences in visual-spatial working memory.

PubMed

Störmer, Viola S; Li, Shu-Chen; Heekeren, Hauke R; Lindenberger, Ulman

2013-06-01

The capacity of visual-spatial working memory (WM) declines from early to late adulthood. Recent attempts at identifying neural correlates of WM capacity decline have focused on the maintenance phase of WM. Here, we investigate neural mechanisms during the encoding phase as another potential mechanism contributing to adult age differences in WM capacity. We used electroencephalography to track neural activity during encoding and maintenance on a millisecond timescale in 35 younger and 35 older adults performing a visual-spatial WM task. As predicted, we observed pronounced age differences in ERP indicators of WM encoding: Younger adults showed attentional selection during item encoding (N2pc component), but this selection mechanism was greatly attenuated in older adults. Conversely, older adults showed more pronounced signs of early perceptual stimulus processing (N1 component) than younger adults. The amplitude modulation of the N1 component predicted WM capacity in older adults, whereas the attentional amplitude modulation of the N2pc component predicted WM capacity in younger adults. Our findings suggest that adult age differences in mechanisms of WM encoding contribute to adult age differences in limits of visual-spatial WM capacity. Copyright © 2013 Elsevier Inc. All rights reserved.

Fly Photoreceptors Encode Phase Congruency

PubMed Central

Friederich, Uwe; Billings, Stephen A.; Hardie, Roger C.; Juusola, Mikko; Coca, Daniel

2016-01-01

More than five decades ago it was postulated that sensory neurons detect and selectively enhance behaviourally relevant features of natural signals. Although we now know that sensory neurons are tuned to efficiently encode natural stimuli, until now it was not clear what statistical features of the stimuli they encode and how. Here we reverse-engineer the neural code of Drosophila photoreceptors and show for the first time that photoreceptors exploit nonlinear dynamics to selectively enhance and encode phase-related features of temporal stimuli, such as local phase congruency, which are invariant to changes in illumination and contrast. We demonstrate that to mitigate for the inherent sensitivity to noise of the local phase congruency measure, the nonlinear coding mechanisms of the fly photoreceptors are tuned to suppress random phase signals, which explains why photoreceptor responses to naturalistic stimuli are significantly different from their responses to white noise stimuli. PMID:27336733

Stimulation of the human medial temporal lobe between learning and recall selectively enhances forgetting

PubMed Central

Merkow, Maxwell B.; Burke, John F.; Ramayya, Ashwin G.; Sharan, Ashwini D.; Sperling, Michael R.; Kahana, Michael J.

2017-01-01

Background Direct electrical stimulation applied to the human medial temporal lobe (MTL) typically disrupts performance on memory tasks, however, the mechanism underlying this effect is not known. Objective To study the effects of MTL stimulation on memory performance Methods We studied the effects of MTL stimulation on memory in five patients undergoing invasive electrocorticographic monitoring during various phases of a memory task (encoding, distractor, recall). Results We found that MTL stimulation disrupted memory performance in a timing-dependent manner; we observed greater forgetting when applying stimulation during the delay between encoding and recall, compared to when it was applied during encoding or recall. Conclusions The results suggest that recall is most dependent on the MTL between learning and retrieval. PMID:28073638

Accelerated Slice Encoding for Metal Artifact Correction

PubMed Central

Hargreaves, Brian A.; Chen, Weitian; Lu, Wenmiao; Alley, Marcus T.; Gold, Garry E.; Brau, Anja C. S.; Pauly, John M.; Pauly, Kim Butts

2010-01-01

Purpose To demonstrate accelerated imaging with artifact reduction near metallic implants and different contrast mechanisms. Materials and Methods Slice-encoding for metal artifact correction (SEMAC) is a modified spin echo sequence that uses view-angle tilting and slice-direction phase encoding to correct both in-plane and through-plane artifacts. Standard spin echo trains and short-TI inversion recovery (STIR) allow efficient PD-weighted imaging with optional fat suppression. A completely linear reconstruction allows incorporation of parallel imaging and partial Fourier imaging. The SNR effects of all reconstructions were quantified in one subject. 10 subjects with different metallic implants were scanned using SEMAC protocols, all with scan times below 11 minutes, as well as with standard spin echo methods. Results The SNR using standard acceleration techniques is unaffected by the linear SEMAC reconstruction. In all cases with implants, accelerated SEMAC significantly reduced artifacts compared with standard imaging techniques, with no additional artifacts from acceleration techniques. The use of different contrast mechanisms allowed differentiation of fluid from other structures in several subjects. Conclusion SEMAC imaging can be combined with standard echo-train imaging, parallel imaging, partial-Fourier imaging and inversion recovery techniques to offer flexible image contrast with a dramatic reduction of metal-induced artifacts in scan times under 11 minutes. PMID:20373445

Accelerated slice encoding for metal artifact correction.

PubMed

Hargreaves, Brian A; Chen, Weitian; Lu, Wenmiao; Alley, Marcus T; Gold, Garry E; Brau, Anja C S; Pauly, John M; Pauly, Kim Butts

2010-04-01

To demonstrate accelerated imaging with both artifact reduction and different contrast mechanisms near metallic implants. Slice-encoding for metal artifact correction (SEMAC) is a modified spin echo sequence that uses view-angle tilting and slice-direction phase encoding to correct both in-plane and through-plane artifacts. Standard spin echo trains and short-TI inversion recovery (STIR) allow efficient PD-weighted imaging with optional fat suppression. A completely linear reconstruction allows incorporation of parallel imaging and partial Fourier imaging. The signal-to-noise ratio (SNR) effects of all reconstructions were quantified in one subject. Ten subjects with different metallic implants were scanned using SEMAC protocols, all with scan times below 11 minutes, as well as with standard spin echo methods. The SNR using standard acceleration techniques is unaffected by the linear SEMAC reconstruction. In all cases with implants, accelerated SEMAC significantly reduced artifacts compared with standard imaging techniques, with no additional artifacts from acceleration techniques. The use of different contrast mechanisms allowed differentiation of fluid from other structures in several subjects. SEMAC imaging can be combined with standard echo-train imaging, parallel imaging, partial-Fourier imaging, and inversion recovery techniques to offer flexible image contrast with a dramatic reduction of metal-induced artifacts in scan times under 11 minutes. (c) 2010 Wiley-Liss, Inc.

An Efficient Supervised Training Algorithm for Multilayer Spiking Neural Networks

PubMed Central

Xie, Xiurui; Qu, Hong; Liu, Guisong; Zhang, Malu; Kurths, Jürgen

2016-01-01

The spiking neural networks (SNNs) are the third generation of neural networks and perform remarkably well in cognitive tasks such as pattern recognition. The spike emitting and information processing mechanisms found in biological cognitive systems motivate the application of the hierarchical structure and temporal encoding mechanism in spiking neural networks, which have exhibited strong computational capability. However, the hierarchical structure and temporal encoding approach require neurons to process information serially in space and time respectively, which reduce the training efficiency significantly. For training the hierarchical SNNs, most existing methods are based on the traditional back-propagation algorithm, inheriting its drawbacks of the gradient diffusion and the sensitivity on parameters. To keep the powerful computation capability of the hierarchical structure and temporal encoding mechanism, but to overcome the low efficiency of the existing algorithms, a new training algorithm, the Normalized Spiking Error Back Propagation (NSEBP) is proposed in this paper. In the feedforward calculation, the output spike times are calculated by solving the quadratic function in the spike response model instead of detecting postsynaptic voltage states at all time points in traditional algorithms. Besides, in the feedback weight modification, the computational error is propagated to previous layers by the presynaptic spike jitter instead of the gradient decent rule, which realizes the layer-wised training. Furthermore, our algorithm investigates the mathematical relation between the weight variation and voltage error change, which makes the normalization in the weight modification applicable. Adopting these strategies, our algorithm outperforms the traditional SNN multi-layer algorithms in terms of learning efficiency and parameter sensitivity, that are also demonstrated by the comprehensive experimental results in this paper. PMID:27044001

Trading Speed and Accuracy by Coding Time: A Coupled-circuit Cortical Model

PubMed Central

Standage, Dominic; You, Hongzhi; Wang, Da-Hui; Dorris, Michael C.

2013-01-01

Our actions take place in space and time, but despite the role of time in decision theory and the growing acknowledgement that the encoding of time is crucial to behaviour, few studies have considered the interactions between neural codes for objects in space and for elapsed time during perceptual decisions. The speed-accuracy trade-off (SAT) provides a window into spatiotemporal interactions. Our hypothesis is that temporal coding determines the rate at which spatial evidence is integrated, controlling the SAT by gain modulation. Here, we propose that local cortical circuits are inherently suited to the relevant spatial and temporal coding. In simulations of an interval estimation task, we use a generic local-circuit model to encode time by ‘climbing’ activity, seen in cortex during tasks with a timing requirement. The model is a network of simulated pyramidal cells and inhibitory interneurons, connected by conductance synapses. A simple learning rule enables the network to quickly produce new interval estimates, which show signature characteristics of estimates by experimental subjects. Analysis of network dynamics formally characterizes this generic, local-circuit timing mechanism. In simulations of a perceptual decision task, we couple two such networks. Network function is determined only by spatial selectivity and NMDA receptor conductance strength; all other parameters are identical. To trade speed and accuracy, the timing network simply learns longer or shorter intervals, driving the rate of downstream decision processing by spatially non-selective input, an established form of gain modulation. Like the timing network's interval estimates, decision times show signature characteristics of those by experimental subjects. Overall, we propose, demonstrate and analyse a generic mechanism for timing, a generic mechanism for modulation of decision processing by temporal codes, and we make predictions for experimental verification. PMID:23592967

Learning to Encode Timing: Mechanisms of Plasticity in the Auditory Brainstem

PubMed Central

Tzounopoulos, Thanos; Kraus, Nina

2009-01-01

Mechanisms of plasticity have traditionally been ascribed to higher-order sensory processing areas such as the cortex, whereas early sensory processing centers have been considered largely hard-wired. In agreement with this view, the auditory brainstem has been viewed as a nonplastic site, important for preserving temporal information and minimizing transmission delays. However, recent groundbreaking results from animal models and human studies have revealed remarkable evidence for cellular and behavioral mechanisms for learning and memory in the auditory brainstem. PMID:19477149

[Expression changes of major outer membrane protein antigens in Leptospira interrogans during infection and its mechanism].

PubMed

Zheng, Linli; Ge, Yumei; Hu, Weilin; Yan, Jie

2013-03-01

To determine expression changes of major outer membrane protein(OMP) antigens of Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai strain Lai during infection of human macrophages and its mechanism. OmpR encoding genes and OmpR-related histidine kinase (HK) encoding gene of L.interrogans strain Lai and their functional domains were predicted using bioinformatics technique. mRNA level changes of the leptospiral major OMP-encoding genes before and after infection of human THP-1 macrophages were detected by real-time fluorescence quantitative RT-PCR. Effects of the OmpR-encoding genes and HK-encoding gene on the expression of leptospiral OMPs during infection were determined by HK-peptide antiserum block assay and closantel inhibitive assays. The bioinformatics analysis indicated that LB015 and LB333 were referred to OmpR-encoding genes of the spirochete, while LB014 might act as a OmpR-related HK-encoding gene. After the spirochete infecting THP-1 cells, mRNA levels of leptospiral lipL21, lipL32 and lipL41 genes were rapidly and persistently down-regulated (P <0.01), whereas mRNA levels of leptospiral groEL, mce, loa22 and ligB genes were rapidly but transiently up-regulated (P<0.01). The treatment with closantel and HK-peptide antiserum partly reversed the infection-based down-regulated mRNA levels of lipL21 and lipL48 genes (P <0.01). Moreover, closantel caused a decrease of the infection-based up-regulated mRNA levels of groEL, mce, loa22 and ligB genes (P <0.01). Expression levels of L.interrogans strain Lai major OMP antigens present notable changes during infection of human macrophages. There is a group of OmpR-and HK-encoding genes which may play a major role in down-regulation of expression levels of partial OMP antigens during infection.

Musicians change their tune: how hearing loss alters the neural code.

PubMed

Parbery-Clark, Alexandra; Anderson, Samira; Kraus, Nina

2013-08-01

Individuals with sensorineural hearing loss have difficulty understanding speech, especially in background noise. This deficit remains even when audibility is restored through amplification, suggesting that mechanisms beyond a reduction in peripheral sensitivity contribute to the perceptual difficulties associated with hearing loss. Given that normal-hearing musicians have enhanced auditory perceptual skills, including speech-in-noise perception, coupled with heightened subcortical responses to speech, we aimed to determine whether similar advantages could be observed in middle-aged adults with hearing loss. Results indicate that musicians with hearing loss, despite self-perceptions of average performance for understanding speech in noise, have a greater ability to hear in noise relative to nonmusicians. This is accompanied by more robust subcortical encoding of sound (e.g., stimulus-to-response correlations and response consistency) as well as more resilient neural responses to speech in the presence of background noise (e.g., neural timing). Musicians with hearing loss also demonstrate unique neural signatures of spectral encoding relative to nonmusicians: enhanced neural encoding of the speech-sound's fundamental frequency but not of its upper harmonics. This stands in contrast to previous outcomes in normal-hearing musicians, who have enhanced encoding of the harmonics but not the fundamental frequency. Taken together, our data suggest that although hearing loss modifies a musician's spectral encoding of speech, the musician advantage for perceiving speech in noise persists in a hearing-impaired population by adaptively strengthening underlying neural mechanisms for speech-in-noise perception. Copyright © 2013 Elsevier B.V. All rights reserved.

ERP markers of target selection discriminate children with high vs. low working memory capacity.

PubMed

Shimi, Andria; Nobre, Anna Christina; Scerif, Gaia

2015-01-01

Selective attention enables enhancing a subset out of multiple competing items to maximize the capacity of our limited visual working memory (VWM) system. Multiple behavioral and electrophysiological studies have revealed the cognitive and neural mechanisms supporting adults' selective attention of visual percepts for encoding in VWM. However, research on children is more limited. What are the neural mechanisms involved in children's selection of incoming percepts in service of VWM? Do these differ from the ones subserving adults' selection? Ten-year-olds and adults used a spatial arrow cue to select a colored item for later recognition from an array of four colored items. The temporal dynamics of selection were investigated through EEG signals locked to the onset of the memory array. Both children and adults elicited significantly more negative activity over posterior scalp locations contralateral to the item to-be-selected for encoding (N2pc). However, this activity was elicited later and for longer in children compared to adults. Furthermore, although children as a group did not elicit a significant N2pc during the time-window in which N2pc was elicited in adults, the magnitude of N2pc during the "adult time-window" related to their behavioral performance during the later recognition phase of the task. This in turn highlights how children's neural activity subserving attention during encoding relates to better subsequent VWM performance. Significant differences were observed when children were divided into groups of high vs. low VWM capacity as a function of cueing benefit. Children with large cue benefits in VWM capacity elicited an adult-like contralateral negativity following attentional selection of the to-be-encoded item, whereas children with low VWM capacity did not. These results corroborate the close coupling between selective attention and VWM from childhood and elucidate further the attentional mechanisms constraining VWM performance in children.

Irregular Speech Rate Dissociates Auditory Cortical Entrainment, Evoked Responses, and Frontal Alpha

PubMed Central

Kayser, Stephanie J.; Ince, Robin A.A.; Gross, Joachim

2015-01-01

The entrainment of slow rhythmic auditory cortical activity to the temporal regularities in speech is considered to be a central mechanism underlying auditory perception. Previous work has shown that entrainment is reduced when the quality of the acoustic input is degraded, but has also linked rhythmic activity at similar time scales to the encoding of temporal expectations. To understand these bottom-up and top-down contributions to rhythmic entrainment, we manipulated the temporal predictive structure of speech by parametrically altering the distribution of pauses between syllables or words, thereby rendering the local speech rate irregular while preserving intelligibility and the envelope fluctuations of the acoustic signal. Recording EEG activity in human participants, we found that this manipulation did not alter neural processes reflecting the encoding of individual sound transients, such as evoked potentials. However, the manipulation significantly reduced the fidelity of auditory delta (but not theta) band entrainment to the speech envelope. It also reduced left frontal alpha power and this alpha reduction was predictive of the reduced delta entrainment across participants. Our results show that rhythmic auditory entrainment in delta and theta bands reflect functionally distinct processes. Furthermore, they reveal that delta entrainment is under top-down control and likely reflects prefrontal processes that are sensitive to acoustical regularities rather than the bottom-up encoding of acoustic features. SIGNIFICANCE STATEMENT The entrainment of rhythmic auditory cortical activity to the speech envelope is considered to be critical for hearing. Previous work has proposed divergent views in which entrainment reflects either early evoked responses related to sound encoding or high-level processes related to expectation or cognitive selection. Using a manipulation of speech rate, we dissociated auditory entrainment at different time scales. Specifically, our results suggest that delta entrainment is controlled by frontal alpha mechanisms and thus support the notion that rhythmic auditory cortical entrainment is shaped by top-down mechanisms. PMID:26538641

Stimulation of the human medial temporal lobe between learning and recall selectively enhances forgetting.

PubMed

Merkow, Maxwell B; Burke, John F; Ramayya, Ashwin G; Sharan, Ashwini D; Sperling, Michael R; Kahana, Michael J

Direct electrical stimulation applied to the human medial temporal lobe (MTL) typically disrupts performance on memory tasks, however, the mechanism underlying this effect is not known. To study the effects of MTL stimulation on memory performance. We studied the effects of MTL stimulation on memory in five patients undergoing invasive electrocorticographic monitoring during various phases of a memory task (encoding, distractor, recall). We found that MTL stimulation disrupted memory performance in a timing-dependent manner; we observed greater forgetting when applying stimulation during the delay between encoding and recall, compared to when it was applied during encoding or recall. The results suggest that recall is most dependent on the MTL between learning and retrieval. Copyright © 2017 Elsevier Inc. All rights reserved.

Electrophysiological correlates of encoding and retrieving emotional events.

PubMed

Koenig, Stefanie; Mecklinger, Axel

2008-04-01

This study examined the impact of emotional content on encoding and retrieval processes. Event-related potentials were recorded in a source recognition memory task. During encoding, a posterior positivity for positive and negative pictures (250-450 ms) that presumably reflects attentional capturing of emotionally valenced stimuli was found. Additionally, positive events, which were also rated as less arousing than negative events, gave rise to anterior and posterior slow wave activity as compared with neutral and negative events and also showed enhanced recognition memory. It is assumed that positive low-arousing events enter controlled and elaborated encoding processes that are beneficial for recognition memory performance. The high arousal of negative events may interfere with controlled encoding mechanisms and attenuate item recognition and the quality of remembering. Moreover, topographically distinct late posterior negativities were obtained for the retrieval of the context features location and time that support the view that this component reflects processes in service of reconstructing the study episode by binding together contextual details with an item and that varies with the kind of episodic detail to be retrieved. (Copyright) 2008 APA.

Determining the Neural Substrate for Encoding a Memory of Human Pain and the Influence of Anxiety

PubMed Central

Kong, Yazhuo; Tracey, Irene

2017-01-01

To convert a painful stimulus into a briefly maintainable construct when the painful stimulus is no longer accessible is essential to guide human behavior and avoid dangerous situations. Because of the aversive nature of pain, this encoding process might be influenced by emotional aspects and could thus vary across individuals, but we have yet to understand both the basic underlying neural mechanisms as well as potential interindividual differences. Using fMRI in combination with a delayed-discrimination task in healthy volunteers of both sexes, we discovered that brain regions involved in this working memory encoding process were dissociable according to whether the to-be-remembered stimulus was painful or not, with the medial thalamus and the rostral anterior cingulate cortex encoding painful and the primary somatosensory cortex encoding nonpainful stimuli. Encoding of painful stimuli furthermore significantly enhanced functional connectivity between the thalamus and medial prefrontal cortex (mPFC). With regards to emotional aspects influencing encoding processes, we observed that more anxious participants showed significant performance advantages when encoding painful stimuli. Importantly, only during the encoding of pain, the interindividual differences in anxiety were associated with the strength of coupling between medial thalamus and mPFC, which was furthermore related to activity in the amygdala. These results indicate not only that there is a distinct signature for the encoding of a painful experience in humans, but also that this encoding process involves a strong affective component. SIGNIFICANCE STATEMENT To convert the sensation of pain into a briefly maintainable construct is essential to guide human behavior and avoid dangerous situations. Although this working memory encoding process is implicitly contained in the majority of studies, the underlying neural mechanisms remain unclear. Using fMRI in a delayed-discrimination task, we found that the encoding of pain engaged the activation of the medial thalamus and the functional connectivity between the thalamus and medial prefrontal cortex. These fMRI data were directly and indirectly related to participants' self-reported trait and state anxiety. Our findings indicate that the mechanisms responsible for the encoding of noxious stimuli differ from those for the encoding of innocuous stimuli, and that these mechanisms are shaped by an individual's anxiety levels. PMID:29097595

Determining the Neural Substrate for Encoding a Memory of Human Pain and the Influence of Anxiety.

PubMed

Tseng, Ming-Tsung; Kong, Yazhuo; Eippert, Falk; Tracey, Irene

2017-12-06

To convert a painful stimulus into a briefly maintainable construct when the painful stimulus is no longer accessible is essential to guide human behavior and avoid dangerous situations. Because of the aversive nature of pain, this encoding process might be influenced by emotional aspects and could thus vary across individuals, but we have yet to understand both the basic underlying neural mechanisms as well as potential interindividual differences. Using fMRI in combination with a delayed-discrimination task in healthy volunteers of both sexes, we discovered that brain regions involved in this working memory encoding process were dissociable according to whether the to-be-remembered stimulus was painful or not, with the medial thalamus and the rostral anterior cingulate cortex encoding painful and the primary somatosensory cortex encoding nonpainful stimuli. Encoding of painful stimuli furthermore significantly enhanced functional connectivity between the thalamus and medial prefrontal cortex (mPFC). With regards to emotional aspects influencing encoding processes, we observed that more anxious participants showed significant performance advantages when encoding painful stimuli. Importantly, only during the encoding of pain, the interindividual differences in anxiety were associated with the strength of coupling between medial thalamus and mPFC, which was furthermore related to activity in the amygdala. These results indicate not only that there is a distinct signature for the encoding of a painful experience in humans, but also that this encoding process involves a strong affective component. SIGNIFICANCE STATEMENT To convert the sensation of pain into a briefly maintainable construct is essential to guide human behavior and avoid dangerous situations. Although this working memory encoding process is implicitly contained in the majority of studies, the underlying neural mechanisms remain unclear. Using fMRI in a delayed-discrimination task, we found that the encoding of pain engaged the activation of the medial thalamus and the functional connectivity between the thalamus and medial prefrontal cortex. These fMRI data were directly and indirectly related to participants' self-reported trait and state anxiety. Our findings indicate that the mechanisms responsible for the encoding of noxious stimuli differ from those for the encoding of innocuous stimuli, and that these mechanisms are shaped by an individual's anxiety levels. Copyright © 2017 Tseng et al.

Experience with proactive interference diminishes its effects: mechanisms of change.

PubMed

Wahlheim, Christopher N; Jacoby, Larry L

2011-02-01

In three experiments, we examined the mechanisms by which prior experience with proactive interference (PI) diminished its effects. Cued recall tasks conforming to an A-B, A-D paradigm were used to induce PI effects. Experiment 1 showed that reduced PI was not due to a reduction in attention to the source of PI. Experiment 2 revealed that participants' awareness of PI effects on memory performance increased with experience, resulting in a shift in encoding processes. Experiment 3 demonstrated that changes in encoding provided additional support for recollection that further enhanced participants' ability to constrain their retrieval processing to the appropriate source of information at the time of test. These results can be interpreted as showing that experience with PI enhances awareness of its effects and allows individuals to adjust their learning and retrieval strategies to compensate for such effects.

Spike count, spike timing and temporal information in the cortex of awake, freely moving rats

PubMed Central

Scaglione, Alessandro; Foffani, Guglielmo; Moxon, Karen A.

2014-01-01

Objective Sensory processing of peripheral information is not stationary but is, in general, a dynamic process related to the behavioral state of the animal. Yet the link between the state of the behavior and the encoding properties of neurons is unclear. This report investigates the impact of the behavioral state on the encoding mechanisms used by cortical neurons for both detection and discrimination of somatosensory stimuli in awake, freely moving, rats. Approach Neuronal activity was recorded from the primary somatosensory cortex of five rats under two different behavioral states (quiet vs. whisking) while electrical stimulation of increasing stimulus strength was delivered to the mystacial pad. Information theoretical measures were then used to measure the contribution of different encoding mechanisms to the information carried by neurons in response to the whisker stimulation. Main Results We found that the behavioral state of the animal modulated the total amount of information conveyed by neurons and that the timing of individual spikes increased the information compared to the total count of spikes alone. However, the temporal information, i.e. information exclusively related to when the spikes occur, was not modulated by behavioral state. Significance We conclude that information about somatosensory stimuli is modulated by the behavior of the animal and this modulation is mainly expressed in the spike count while the temporal information is more robust to changes in behavioral state. PMID:25024291

Cryogenic Optical Position Encoders for Mechanisms in the JWST Optical Telescope Element Simulator (OSIM)

NASA Technical Reports Server (NTRS)

Leviton, Douglas B.; Anderjaska, Thomas; Badger, James (Inventor); Capon, Tom; Davis, CLinton; Dicks, Brent (Inventor); Eichhorn, William; Garza, Mario; Guishard, Corina; Haghani, Shadan;

Inferring genome-wide interplay landscape between DNA methylation and transcriptional regulation.

PubMed

Tang, Binhua; Wang, Xin

2015-01-01

DNA methylation and transcriptional regulation play important roles in cancer cell development and differentiation processes. Based on the currently available cell line profiling information from the ENCODE Consortium, we propose a Bayesian inference model to infer and construct genome-wide interaction landscape between DNA methylation and transcriptional regulation, which sheds light on the underlying complex functional mechanisms important within the human cancer and disease context. For the first time, we select all the currently available cell lines (>=20) and transcription factors (>=80) profiling information from the ENCODE Consortium portal. Through the integration of those genome-wide profiling sources, our genome-wide analysis detects multiple functional loci of interest, and indicates that DNA methylation is cell- and region-specific, due to the interplay mechanisms with transcription regulatory activities. We validate our analysis results with the corresponding RNA-sequencing technique for those detected genomic loci. Our results provide novel and meaningful insights for the interplay mechanisms of transcriptional regulation and gene expression for the human cancer and disease studies.

Slow cortical potentials and "inner time consciousness" - A neuro-phenomenal hypothesis about the "width of present".

PubMed

Northoff, Georg

2016-05-01

William James postulated a "stream of consciousness" that presupposes temporal continuity. The neuronal mechanisms underlying the construction of such temporal continuity remain unclear, however, in my contribution, I propose a neuro-phenomenal hypothesis that is based on slow cortical potentials and their extension of the present moment as described in the phenomenal term of "width of present". More specifically, I focus on the way the brain's neural activity needs to be encoded in order to make possible the "stream of consciousness." This leads us again to the low-frequency fluctuations of the brain's neural activity and more specifically to slow cortical potentials (SCPs). Due to their long phase duration as low-frequency fluctuations, SCPs can integrate different stimuli and their associated neural activity from different regions in one converging region. Such integration may be central for consciousness to occur, as it was recently postulated by He and Raichle. They leave open, however, the question of the exact neuronal mechanisms, like the encoding strategy, that make possible the association of the otherwise purely neuronal SCP with consciousness and its phenomenal features. I hypothesize that SCPs allow for linking and connecting different discrete points in physical time by encoding their statistically based temporal differences rather than the single discrete time points by themselves. This presupposes difference-based coding rather than stimulus-based coding. The encoding of such statistically based temporal differences makes it possible to "go beyond" the merely physical features of the stimuli; that is, their single discrete time points and their conduction delays (as related to their neural processing in the brain). This, in turn, makes possible the constitution of "local temporal continuity" of neural activity in one particular region. The concept of "local temporal continuity" signifies the linkage and integration of different discrete time points into one neural activity in a particular region. How does such local temporal continuity predispose the experience of time in consciousness? For that, I turn to phenomenological philosopher Edmund Husserl and his description of what he calls "inner time consciousness" (Husserl and Brough, 1990). One hallmark of humans' "inner time consciousness" is that we experience events and objects in succession and duration in our consciousness; according to Husserl, this amounts to what he calls the "width of [the] present." The concept of the width of present describes the extension of the present beyond the single discrete time point, such as, for instance, when we perceive different tones as a melody. I now hypothesize the degree of the width of present to be directly dependent upon and thus predisposed by the degree of the temporal differences between two (or more) discrete time points as they are encoded into neural activity. I therefore conclude that the SCPs and their encoding of neural activity in terms of temporal differences must be regarded a neural predisposition of consciousness (NPC) as distinguished from a neural correlate of consciousness (NCC). Copyright © 2015 Elsevier B.V. All rights reserved.

CA1 subfield contributions to memory integration and inference

PubMed Central

Schlichting, Margaret L.; Zeithamova, Dagmar; Preston, Alison R.

2014-01-01

The ability to combine information acquired at different times to make novel inferences is a powerful function of episodic memory. One perspective suggests that by retrieving related knowledge during new experiences, existing memories can be linked to the new, overlapping information as it is encoded. The resulting memory traces would thus incorporate content across event boundaries, representing important relationships among items encountered during separate experiences. While prior work suggests that the hippocampus is involved in linking memories experienced at different times, the involvement of specific subfields in this process remains unknown. Using both univariate and multivariate analyses of high-resolution functional magnetic resonance imaging (fMRI) data, we localized this specialized encoding mechanism to human CA1. Specifically, right CA1 responses during encoding of events that overlapped with prior experience predicted subsequent success on a test requiring inferences about the relationships among events. Furthermore, we employed neural pattern similarity analysis to show that patterns of activation evoked during overlapping event encoding were later reinstated in CA1 during successful inference. The reinstatement of CA1 patterns during inference was specific to those trials that were performed quickly and accurately, consistent with the notion that linking memories during learning facilitates novel judgments. These analyses provide converging evidence that CA1 plays a unique role in encoding overlapping events and highlight the dynamic interactions between hippocampal-mediated encoding and retrieval processes. More broadly, our data reflect the adaptive nature of episodic memories, in which representations are derived across events in anticipation of future judgments. PMID:24888442

Programming temporal shapeshifting

NASA Astrophysics Data System (ADS)

Hu, Xiaobo; Zhou, Jing; Vatankhah-Varnosfaderani, Mohammad; Daniel, William F. M.; Li, Qiaoxi; Zhushma, Aleksandr P.; Dobrynin, Andrey V.; Sheiko, Sergei S.

2016-09-01

Shapeshifting enables a wide range of engineering and biomedical applications, but until now transformations have required external triggers. This prerequisite limits viability in closed or inert systems and puts forward the challenge of developing materials with intrinsically encoded shape evolution. Herein we demonstrate programmable shape-memory materials that perform a sequence of encoded actuations under constant environment conditions without using an external trigger. We employ dual network hydrogels: in the first network, covalent crosslinks are introduced for elastic energy storage, and in the second one, temporary hydrogen-bonds regulate the energy release rate. Through strain-induced and time-dependent reorganization of the reversible hydrogen-bonds, this dual network allows for encoding both the rate and pathway of shape transformations on timescales from seconds to hours. This generic mechanism for programming trigger-free shapeshifting opens new ways to design autonomous actuators, drug-release systems and active implants.

Evaluating dedicated and intrinsic models of temporal encoding by varying context

PubMed Central

Spencer, Rebecca M.C.; Karmarkar, Uma; Ivry, Richard B.

2009-01-01

Two general classes of models have been proposed to account for how people process temporal information in the milliseconds range. Dedicated models entail a mechanism in which time is explicitly encoded; examples include clock–counter models and functional delay lines. Intrinsic models, such as state-dependent networks (SDN), represent time as an emergent property of the dynamics of neural processing. An important property of SDN is that the encoding of duration is context dependent since the representation of an interval will vary as a function of the initial state of the network. Consistent with this assumption, duration discrimination thresholds for auditory intervals spanning 100 ms are elevated when an irrelevant tone is presented at varying times prior to the onset of the test interval. We revisit this effect in two experiments, considering attentional issues that may also produce such context effects. The disruptive effect of a variable context was eliminated or attenuated when the intervals between the irrelevant tone and test interval were made dissimilar or the duration of the test interval was increased to 300 ms. These results indicate how attentional processes can influence the perception of brief intervals, as well as point to important constraints for SDN models. PMID:19487188

Is the survival-processing memory advantage due to richness of encoding?

PubMed

Röer, Jan P; Bell, Raoul; Buchner, Axel

2013-07-01

Memory for words rated according to their relevance in a grassland survival context is exceptionally good. According to Nairne, Thompson, and Pandeirada's (2007) evolutionary-based explanation, natural selection processes have tuned the human memory system to prioritize the processing of fitness-relevant information. The survival-processing memory advantage has been replicated numerous times, but very little is known about the proximate mechanisms behind it. The richness-of-encoding hypothesis (Kroneisen & Erdfelder, 2011) implies that rating the usefulness of items in a survival context leads to the generation of a large number of ideas that may be used as retrieval cues at test to boost recall. In Experiment 1, the typical survival-processing recall advantage was obtained when words were rated according to their usefulness in 1 of 3 fictional contexts. In Experiment 2, participants were asked to write down any ideas that came to mind when thinking about the usefulness of the words. Consistent with the richness-of-encoding hypothesis, participants generated more ideas in the survival condition than in the fitness-irrelevant control conditions. In Experiment 3, participants generated more ideas for congruent than for incongruent words, demonstrating that the richness-of-encoding hypothesis can also account for the previously obtained congruency effect on recall (Butler, Kang, & Roediger, 2009). In both experiments the number of ideas written down predicted future recall performance well. Our results provide further evidence for the assumption that richness of encoding is an important proximate mechanism involved in memory performance in the survival-processing paradigm. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Hall effect encoding of brushless dc motors

NASA Technical Reports Server (NTRS)

Berard, C. A.; Furia, T. J.; Goldberg, E. A.; Greene, R. C.

1970-01-01

Encoding mechanism integral to the motor and using the permanent magnets embedded in the rotor eliminates the need for external devices to encode information relating the position and velocity of the rotating member.

Memorization and recall of very long lists accounted for within the Long-Term Working Memory framework.

PubMed

Hu, Yi; Ericsson, K Anders

2012-06-01

In a recent paper, Hu, Ericsson, Yang, and Lu (2009) found that an ability to memorize very long lists of digits is not mediated by the same mechanisms as exceptional memory for rapidly presented lists, which has been the traditional focus of laboratory research. Chao Lu is the holder of the Guinness World Record for reciting the most decimal positions of pi, yet he lacks an exceptional memory span for digits. In the first part of this paper we analyzed the reliability and structure of his reported encodings for lists of 300 digits and his application of the story mnemonic. Next, his study and recall times for lists of digits were analyzed to test hypotheses about his detailed encoding processes, and cued-recall performance was used to assess the structure of his encodings. Three experiments were then designed to interfere with the uniqueness of Chao Lu's story encodings, and evidence was found for his remarkable ability to adapt his encoding processes to reduce the interference. Finally, we show how his skills for encoding and recalling long lists can be accounted for within the theoretical framework of Ericsson and Kintsch's (1995) Long-Term Working Memory. Copyright © 2012 Elsevier Inc. All rights reserved.

Mechanisms of viral mutation.

PubMed

Sanjuán, Rafael; Domingo-Calap, Pilar

2016-12-01

The remarkable capacity of some viruses to adapt to new hosts and environments is highly dependent on their ability to generate de novo diversity in a short period of time. Rates of spontaneous mutation vary amply among viruses. RNA viruses mutate faster than DNA viruses, single-stranded viruses mutate faster than double-strand virus, and genome size appears to correlate negatively with mutation rate. Viral mutation rates are modulated at different levels, including polymerase fidelity, sequence context, template secondary structure, cellular microenvironment, replication mechanisms, proofreading, and access to post-replicative repair. Additionally, massive numbers of mutations can be introduced by some virus-encoded diversity-generating elements, as well as by host-encoded cytidine/adenine deaminases. Our current knowledge of viral mutation rates indicates that viral genetic diversity is determined by multiple virus- and host-dependent processes, and that viral mutation rates can evolve in response to specific selective pressures.

Dynamical information encoding in neural adaptation.

PubMed

Luozheng Li; Wenhao Zhang; Yuanyuan Mi; Dahui Wang; Xiaohan Lin; Si Wu

2016-08-01

Adaptation refers to the general phenomenon that a neural system dynamically adjusts its response property according to the statistics of external inputs. In response to a prolonged constant stimulation, neuronal firing rates always first increase dramatically at the onset of the stimulation; and afterwards, they decrease rapidly to a low level close to background activity. This attenuation of neural activity seems to be contradictory to our experience that we can still sense the stimulus after the neural system is adapted. Thus, it prompts a question: where is the stimulus information encoded during the adaptation? Here, we investigate a computational model in which the neural system employs a dynamical encoding strategy during the neural adaptation: at the early stage of the adaptation, the stimulus information is mainly encoded in the strong independent firings; and as time goes on, the information is shifted into the weak but concerted responses of neurons. We find that short-term plasticity, a general feature of synapses, provides a natural mechanism to achieve this goal. Furthermore, we demonstrate that with balanced excitatory and inhibitory inputs, this correlation-based information can be read out efficiently. The implications of this study on our understanding of neural information encoding are discussed.

Conduction Delay Learning Model for Unsupervised and Supervised Classification of Spatio-Temporal Spike Patterns

PubMed Central

Matsubara, Takashi

2017-01-01

Precise spike timing is considered to play a fundamental role in communications and signal processing in biological neural networks. Understanding the mechanism of spike timing adjustment would deepen our understanding of biological systems and enable advanced engineering applications such as efficient computational architectures. However, the biological mechanisms that adjust and maintain spike timing remain unclear. Existing algorithms adopt a supervised approach, which adjusts the axonal conduction delay and synaptic efficacy until the spike timings approximate the desired timings. This study proposes a spike timing-dependent learning model that adjusts the axonal conduction delay and synaptic efficacy in both unsupervised and supervised manners. The proposed learning algorithm approximates the Expectation-Maximization algorithm, and classifies the input data encoded into spatio-temporal spike patterns. Even in the supervised classification, the algorithm requires no external spikes indicating the desired spike timings unlike existing algorithms. Furthermore, because the algorithm is consistent with biological models and hypotheses found in existing biological studies, it could capture the mechanism underlying biological delay learning. PMID:29209191

Conduction Delay Learning Model for Unsupervised and Supervised Classification of Spatio-Temporal Spike Patterns.

PubMed

Matsubara, Takashi

2017-01-01

Precise spike timing is considered to play a fundamental role in communications and signal processing in biological neural networks. Understanding the mechanism of spike timing adjustment would deepen our understanding of biological systems and enable advanced engineering applications such as efficient computational architectures. However, the biological mechanisms that adjust and maintain spike timing remain unclear. Existing algorithms adopt a supervised approach, which adjusts the axonal conduction delay and synaptic efficacy until the spike timings approximate the desired timings. This study proposes a spike timing-dependent learning model that adjusts the axonal conduction delay and synaptic efficacy in both unsupervised and supervised manners. The proposed learning algorithm approximates the Expectation-Maximization algorithm, and classifies the input data encoded into spatio-temporal spike patterns. Even in the supervised classification, the algorithm requires no external spikes indicating the desired spike timings unlike existing algorithms. Furthermore, because the algorithm is consistent with biological models and hypotheses found in existing biological studies, it could capture the mechanism underlying biological delay learning.

Microelectromechanical timer

DOEpatents

Polosky, Marc A.; Garcia, Ernest J.; Plummer, David W.

2001-01-01

A microminiature timer having an optical readout is disclosed. The timer can be formed by surface micromachining or LIGA processes on a silicon substrate. The timer includes an integral motor (e.g. an electrostatic motor) that can intermittently wind a mainspring to store mechanical energy for driving a train of meshed timing gears at a rate that is regulated by a verge escapement. Each timing gear contains an optical encoder that can be read out with one or more light beams (e.g. from a laser or light-emitting diode) to recover timing information. In the event that electrical power to the timer is temporarily interrupted, the mechanical clock formed by the meshed timing gears and verge escapement can continue to operate, generating accurate timing information that can be read out when the power is restored.

Qubits, qutrits, and ququads stored in single photons from an atom-cavity system

NASA Astrophysics Data System (ADS)

Holleczek, Annemarie; Barter, Oliver; Langfahl-Klabes, Gunnar; Kuhn, Axel

2015-03-01

One of today's challenge to realize computing based on quantum mechanics is to reliably and scalably encode information in quantum systems. Here, we present a photon source to on-demand deliver photonic quantum bits of information based on a strongly coupled atom-cavity system. It operates intermittently for periods of up to 100μs, with a single-photon repetition rate of 1MHz, and an intra-cavity production e!ciency of up to 85%. Due to the photons inherent coherence time of 500ns and our ability to arbitrarily shape their amplitude and phase profile we time-bin encode information within one photon. To do so, the spatio-temporal envelope of a single photon is sub-divided in d time bins which allows for the delivery of arbitrary qu-d-its. The latter is done with a fidelity of > 95% for qubits, and 94% for qutrits verified using a newly developed time-resolved quantum-homodyne technique.

Sensory adaptation for timing perception.

PubMed

Roseboom, Warrick; Linares, Daniel; Nishida, Shin'ya

2015-04-22

Recent sensory experience modifies subjective timing perception. For example, when visual events repeatedly lead auditory events, such as when the sound and video tracks of a movie are out of sync, subsequent vision-leads-audio presentations are reported as more simultaneous. This phenomenon could provide insights into the fundamental problem of how timing is represented in the brain, but the underlying mechanisms are poorly understood. Here, we show that the effect of recent experience on timing perception is not just subjective; recent sensory experience also modifies relative timing discrimination. This result indicates that recent sensory history alters the encoding of relative timing in sensory areas, excluding explanations of the subjective phenomenon based only on decision-level changes. The pattern of changes in timing discrimination suggests the existence of two sensory components, similar to those previously reported for visual spatial attributes: a lateral shift in the nonlinear transducer that maps relative timing into perceptual relative timing and an increase in transducer slope around the exposed timing. The existence of these components would suggest that previous explanations of how recent experience may change the sensory encoding of timing, such as changes in sensory latencies or simple implementations of neural population codes, cannot account for the effect of sensory adaptation on timing perception.

Encoding-related brain activity dissociates between the recollective processes underlying successful recall and recognition: a subsequent-memory study.

PubMed

Sadeh, Talya; Maril, Anat; Goshen-Gottstein, Yonatan

2012-07-01

The subsequent-memory (SM) paradigm uncovers brain mechanisms that are associated with mnemonic activity during encoding by measuring participants' neural activity during encoding and classifying the encoding trials according to performance in the subsequent retrieval phase. The majority of these studies have converged on the notion that the mechanism supporting recognition is mediated by familiarity and recollection. The process of recollection is often assumed to be a recall-like process, implying that the active search for the memory trace is similar, if not identical, for recall and recognition. Here we challenge this assumption and hypothesize - based on previous findings obtained in our lab - that the recollective processes underlying recall and recognition might show dissociative patterns of encoding-related brain activity. To this end, our design controlled for familiarity, thereby focusing on contextual, recollective processes. We found evidence for dissociative neurocognitive encoding mechanisms supporting subsequent-recall and subsequent-recognition. Specifically, the contrast of subsequent-recognition versus subsequent-recall revealed activation in the Parahippocampal cortex (PHc) and the posterior hippocampus--regions associated with contextual processing. Implications of our findings and their relation to current cognitive models of recollection are discussed. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

Hu, Xiaobo; Zhou, Jing; Vatankhah-Varnosfaderani, Mohammad

Shapeshifting enables a wide range of engineering and biomedical applications, but until now transformations have required external triggers. This prerequisite limits viability in closed or inert systems and puts forward the challenge of developing materials with intrinsically encoded shape evolution. Herein we demonstrate programmable shape-memory materials that perform a sequence of encoded actuations under constant environment conditions without using an external trigger. We employ dual network hydrogels: in the first network, covalent crosslinks are introduced for elastic energy storage, and in the second one, temporary hydrogen-bonds regulate the energy release rate. Through strain-induced and time-dependent reorganization of the reversible hydrogen-bonds,more » this dual network allows for encoding both the rate and pathway of shape transformations on timescales from seconds to hours. In conclusion, this generic mechanism for programming trigger-free shapeshifting opens new ways to design autonomous actuators, drug-release systems and active implants.« less

Programming temporal shapeshifting

DOE PAGES

Hu, Xiaobo; Zhou, Jing; Vatankhah-Varnosfaderani, Mohammad; ...

2016-09-27

Shapeshifting enables a wide range of engineering and biomedical applications, but until now transformations have required external triggers. This prerequisite limits viability in closed or inert systems and puts forward the challenge of developing materials with intrinsically encoded shape evolution. Herein we demonstrate programmable shape-memory materials that perform a sequence of encoded actuations under constant environment conditions without using an external trigger. We employ dual network hydrogels: in the first network, covalent crosslinks are introduced for elastic energy storage, and in the second one, temporary hydrogen-bonds regulate the energy release rate. Through strain-induced and time-dependent reorganization of the reversible hydrogen-bonds,more » this dual network allows for encoding both the rate and pathway of shape transformations on timescales from seconds to hours. In conclusion, this generic mechanism for programming trigger-free shapeshifting opens new ways to design autonomous actuators, drug-release systems and active implants.« less

Cyclic Tensile Strain Upregulates Pro-Inflammatory Cytokine Expression Via FAK-MAPK Signaling in Chondrocytes.

PubMed

Yanoshita, Makoto; Hirose, Naoto; Okamoto, Yuki; Sumi, Chikako; Takano, Mami; Nishiyama, Sayuri; Asakawa-Tanne, Yuki; Horie, Kayo; Onishi, Azusa; Yamauchi, Yuka; Mitsuyoshi, Tomomi; Kunimatsu, Ryo; Tanimoto, Kotaro

2018-05-08

Excessive mechanical stimulation is considered an important factor in the destruction of chondrocytes. Focal adhesion kinase (FAK) is non-receptor tyrosine kinase related to a number of different signaling proteins. Little is known about the function of FAK in chondrocytes under mechanical stimulation. In the present study, we investigated the function of FAK in mechanical signal transduction and the mechanism through which cyclic tensile strain (CTS) induces expression of inflammation-related factors. Mouse ATDC5 chondrogenic cells were subjected to CTS of 0.5 Hz to 10% cell elongation with an FAK inhibitor. The expression of genes encoding COX-2, IL-1β, and TNF-α was examined using real-time RT-PCR after CTS application with FAK inhibitor. Phosphorylation of p-38, ERK, and JNK was analyzed by Western blotting. Differences in COX-2 expression following pretreatment with FAK, p-38, ERK, and JNK inhibitors were compared by Western blotting. We found that CTS increased the expression of genes encoding COX-2, IL-1β, and TNF-α and activated the phosphorylation of FAK, p-38, ERK, and JNK. Pretreatment with an FAK inhibitor for 2 h reduced the expression of genes encoding COX-2, IL-1β, and TNF-α induced by CTS-associated inflammation and decreased phosphorylation of FAK, p-38, ERK, and JNK. Pretreatment with FAK, p-38, ERK, and JNK inhibitors markedly suppressed COX-2 and IL-1β protein expression. In conclusion, FAK appears to regulate inflammation in chondrocytes under CTS via MAPK pathways.

Learning to recognize face shapes through serial exploration.

PubMed

Wallraven, Christian; Whittingstall, Lisa; Bülthoff, Heinrich H

2013-05-01

Human observers are experts at visual face recognition due to specialized visual mechanisms for face processing that evolve with perceptual expertize. Such expertize has long been attributed to the use of configural processing, enabled by fast, parallel information encoding of the visual information in the face. Here we tested whether participants can learn to efficiently recognize faces that are serially encoded-that is, when only partial visual information about the face is available at any given time. For this, ten participants were trained in gaze-restricted face recognition in which face masks were viewed through a small aperture controlled by the participant. Tests comparing trained with untrained performance revealed (1) a marked improvement in terms of speed and accuracy, (2) a gradual development of configural processing strategies, and (3) participants' ability to rapidly learn and accurately recognize novel exemplars. This performance pattern demonstrates that participants were able to learn new strategies to compensate for the serial nature of information encoding. The results are discussed in terms of expertize acquisition and relevance for other sensory modalities relying on serial encoding.

Oscillatory EEG dynamics underlying automatic chunking during sentence processing.

PubMed

Bonhage, Corinna E; Meyer, Lars; Gruber, Thomas; Friederici, Angela D; Mueller, Jutta L

2017-05-15

Sentences are easier to remember than random word sequences, likely because linguistic regularities facilitate chunking of words into meaningful groups. The present electroencephalography study investigated the neural oscillations modulated by this so-called sentence superiority effect during the encoding and maintenance of sentence fragments versus word lists. We hypothesized a chunking-related modulation of neural processing during the encoding and retention of sentences (i.e., sentence fragments) as compared to word lists. Time-frequency analysis revealed a two-fold oscillatory pattern for the memorization of sentences: Sentence encoding was accompanied by higher delta amplitude (4Hz), originating both from regions processing syntax as well as semantics (bilateral superior/middle temporal regions and fusiform gyrus). Subsequent sentence retention was reflected in decreased theta (6Hz) and beta/gamma (27-32Hz) amplitude instead. Notably, whether participants simply read or properly memorized the sentences did not impact chunking-related activity during encoding. Therefore, we argue that the sentence superiority effect is grounded in highly automatized language processing mechanisms, which generate meaningful memory chunks irrespective of task demands. Copyright © 2017 Elsevier Inc. All rights reserved.

Observation of development of breast cancer cell lines in real time by fluorescence microscopy under simulated microgravity

NASA Astrophysics Data System (ADS)

Lavan, David; Valdivia-Silva, Julio E.; Sanabria, Gabriela; Orihuela, Diego; Suarez, Juan; Quispe, Marco; Chuchon, Mariano; Martin, David; Maroto, Marcos; Egea, Javier

2016-07-01

This project consist in the implementation of a fluorescence microscope for the in real time monitoring of biological labeled samples by several fluorophores in microgravity conditions keeping the temperature, humidity, and (CO)2 controlled by an electronic platform. The system (fluorescence microscope and incubator) is integrated to a microgravity simulator machine which was presented on the "30th Annual American Society for Gravitation and Space Research Meeting" October 2014 in Pasadena, CA, USA. Currently, we have the microgravity machine biologically validated by genetic expression studies in pupal stage of Drosophila melanogaster. The fluorescence microscope has a platform designed to hold a culture flask, and a fluorescence camera (Leica DFC3000 G) connected to an optical system (Fluorescence Light source Leica EL6000, optic fiber, fiber adapter, and fluorescence filter) in order to take images in real time. The mechanical system of the fluorescence microsc ope is designed to allow the displacement of the fluorescence camera through a parallel plane to the culture flask's plane and also the movement of the platform through a perpendicular axis to the culture flask in order to focus the samples to the optical system. The mechanical system is propelled by four DC moto-reductors with encoder (A-max 26 Maxon motor, GP 32S screw and MR encoder) that generate displacements in the order of micrometers. The angular position control of the DC motoreductor's shaft of all the DC moto-reductors is done by PWM signals based on the interpretation of the signals provided by the encoders during the movement. The system is remotely operated by a graphic interface installed on a personal computer or any mobile device (smartphone, laptop or tablet) by using the internet. Acknowledgments: Grant of INNOVATE PERU (Formerly FINCYT)

Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors.

PubMed

Shah, Firoz; Nicolás, César; Bentzer, Johan; Ellström, Magnus; Smits, Mark; Rineau, Francois; Canbäck, Björn; Floudas, Dimitrios; Carleer, Robert; Lackner, Gerald; Braesel, Jana; Hoffmeister, Dirk; Henrissat, Bernard; Ahrén, Dag; Johansson, Tomas; Hibbett, David S; Martin, Francis; Persson, Per; Tunlid, Anders

2016-03-01

Ectomycorrhizal fungi are thought to have a key role in mobilizing organic nitrogen that is trapped in soil organic matter (SOM). However, the extent to which ectomycorrhizal fungi decompose SOM and the mechanism by which they do so remain unclear, considering that they have lost many genes encoding lignocellulose-degrading enzymes that are present in their saprotrophic ancestors. Spectroscopic analyses and transcriptome profiling were used to examine the mechanisms by which five species of ectomycorrhizal fungi, representing at least four origins of symbiosis, decompose SOM extracted from forest soils. In the presence of glucose and when acquiring nitrogen, all species converted the organic matter in the SOM extract using oxidative mechanisms. The transcriptome expressed during oxidative decomposition has diverged over evolutionary time. Each species expressed a different set of transcripts encoding proteins associated with oxidation of lignocellulose by saprotrophic fungi. The decomposition 'toolbox' has diverged through differences in the regulation of orthologous genes, the formation of new genes by gene duplications, and the recruitment of genes from diverse but functionally similar enzyme families. The capacity to oxidize SOM appears to be common among ectomycorrhizal fungi. We propose that the ancestral decay mechanisms used primarily to obtain carbon have been adapted in symbiosis to scavenge nutrients instead. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

DELAY OF GERMINATION 1 mediates a conserved coat-dormancy mechanism for the temperature- and gibberellin-dependent control of seed germination.

PubMed

Graeber, Kai; Linkies, Ada; Steinbrecher, Tina; Mummenhoff, Klaus; Tarkowská, Danuše; Turečková, Veronika; Ignatz, Michael; Sperber, Katja; Voegele, Antje; de Jong, Hans; Urbanová, Terezie; Strnad, Miroslav; Leubner-Metzger, Gerhard

2014-08-26

Seed germination is an important life-cycle transition because it determines subsequent plant survival and reproductive success. To detect optimal spatiotemporal conditions for germination, seeds act as sophisticated environmental sensors integrating information such as ambient temperature. Here we show that the delay of germination 1 (DOG1) gene, known for providing dormancy adaptation to distinct environments, determines the optimal temperature for seed germination. By reciprocal gene-swapping experiments between Brassicaceae species we show that the DOG1-mediated dormancy mechanism is conserved. Biomechanical analyses show that this mechanism regulates the material properties of the endosperm, a seed tissue layer acting as germination barrier to control coat dormancy. We found that DOG1 inhibits the expression of gibberellin (GA)-regulated genes encoding cell-wall remodeling proteins in a temperature-dependent manner. Furthermore we demonstrate that DOG1 causes temperature-dependent alterations in the seed GA metabolism. These alterations in hormone metabolism are brought about by the temperature-dependent differential expression of genes encoding key enzymes of the GA biosynthetic pathway. These effects of DOG1 lead to a temperature-dependent control of endosperm weakening and determine the optimal temperature for germination. The conserved DOG1-mediated coat-dormancy mechanism provides a highly adaptable temperature-sensing mechanism to control the timing of germination.

Microarray analysis of toxicogenomic effects of Ortho-phenylphenol in Staphylococcus aureus

PubMed Central

Jang, Hyeung-Jin; Nde, Chantal; Toghrol, Freshteh; Bentley, William E

2008-01-01

Background Staphylococcus aureus (S. aureus), is responsible for many infectious diseases, ranging from benign skin infections to life-threatening endocarditis and toxic shock syndrome. Ortho-phenylphenol (OPP) is an antimicrobial agent and an active ingredient of EPA-registered disinfectants with wide human exposure in various agricultural, hospital and veterinary disinfectant products. Despite many uses, an understanding of a cellular response to OPP and it's mechanism of action, targeted genes, and the connectivity between targeted genes and the rest of cell metabolism remains obscure. Results Herein, we performed a genome-wide transcriptome analysis of the cellular responses of S. aureus when exposed to 0.82 mM of OPP for 20 and 60 min. Our data indicated that OPP downregulated the biosynthesis of many amino acids, which are required for protein synthesis. In particular, the genes encoding the enzymes of the diaminopimelate (DAP) pathway which results in lysine biosynthesis were significantly downregualted. Intriguingly, we revealed that the transcription of genes encoding ribosomal proteins was upregulated by OPP and at the same time, the genes encoding iron acquisition and transport were downregulated. The genes encoding virulence factors were upregulated and genes encoding phospholipids were downregulated upon 20 min exposure to OPP. Conclusion By using microarray analysis that enables us to simultaneously and globally examine the complete transcriptome during cellular responses, we have revealed novel information regarding the mode of action of OPP on Staphylococcus: OPP inhibits anabolism of many amino acids and highly downregulates the genes that encode the enzymes involved in the DAP pathway. Lysine and DAP are essential for building up the peptidoglycan cell wall. It was concluded that the mode of action of OPP is similar to the mechanism of action of some antibiotics. The discovery of this phenomenon provides useful information that will benefit further antimicrobial research on S. aureus. PMID:18793396

Selective attention neutralizes the adverse effects of low socioeconomic status on memory in 9-month-old infants

PubMed Central

Markant, Julie; Ackerman, Laura K.; Nussenbaum, Kate; Amso, Dima

2015-01-01

Socioeconomic status (SES) has a documented impact on brain and cognitive development. We demonstrate that engaging spatial selective attention mechanisms may counteract this negative influence of impoverished environments on early learning. We previously used a spatial cueing task to compare target object encoding in the context of basic orienting (“facilitation”) versus a spatial selective attention orienting mechanism that engages distractor suppression (“IOR”). This work showed that object encoding in the context of IOR boosted 9-month-old infants’ recognition memory relative to facilitation (Markant and Amso, 2013). Here we asked whether this attention-memory links further interacted with SES in infancy. Results indicated that SES was related to memory but not attention orienting efficacy. However, the correlation between SES and memory performance was moderated by the attention mechanism engaged during encoding. SES predicted memory performance when objects were encoded with basic orienting processes, with infants from low-SES environments showing poorer memory than those from high-SES environments. However, SES did not predict memory performance among infants who engaged selective attention during encoding. Spatial selective attention engagement mitigated the effects of SES on memory and may offer an effective mechanism for promoting learning among infants at risk for poor cognitive outcomes related to SES. PMID:26597046

Encoding and Retrieval Interference in Sentence Comprehension: Evidence from Agreement

PubMed Central

Villata, Sandra; Tabor, Whitney; Franck, Julie

2018-01-01

Long-distance verb-argument dependencies generally require the integration of a fronted argument when the verb is encountered for sentence interpretation. Under a parsing model that handles long-distance dependencies through a cue-based retrieval mechanism, retrieval is hampered when retrieval cues also resonate with non-target elements (retrieval interference). However, similarity-based interference may also stem from interference arising during the encoding of elements in memory (encoding interference), an effect that is not directly accountable for by a cue-based retrieval mechanism. Although encoding and retrieval interference are clearly distinct at the theoretical level, it is difficult to disentangle the two on empirical grounds, since encoding interference may also manifest at the retrieval region. We report two self-paced reading experiments aimed at teasing apart the role of each component in gender and number subject-verb agreement in Italian and English object relative clauses. In Italian, the verb does not agree in gender with the subject, thus providing no cue for retrieval. In English, although present tense verbs agree in number with the subject, past tense verbs do not, allowing us to test the role of number as a retrieval cue within the same language. Results from both experiments converge, showing similarity-based interference at encoding, and some evidence for an effect at retrieval. After having pointed out the non-negligible role of encoding in sentence comprehension, and noting that Lewis and Vasishth’s (2005) ACT-R model of sentence processing, the most fully developed cue-based retrieval approach to sentence processing does not predict encoding effects, we propose an augmentation of this model that predicts these effects. We then also propose a self-organizing sentence processing model (SOSP), which has the advantage of accounting for retrieval and encoding interference with a single mechanism. PMID:29403414

Instantaneous speed jitter detection via encoder signal and its application for the diagnosis of planetary gearbox

NASA Astrophysics Data System (ADS)

Zhao, Ming; Jia, Xiaodong; Lin, Jing; Lei, Yaguo; Lee, Jay

2018-01-01

In modern rotating machinery, rotary encoders have been widely used for the purpose of positioning and dynamic control. The study in this paper indicates that, the encoder signal, after proper processing, can be also effectively used for the health monitoring of rotating machines. In this work, a Kurtosis-guided local polynomial differentiator (KLPD) is proposed to estimate the instantaneous angular speed (IAS) of rotating machines based on the encoder signal. Compared with the central difference method, the KLPD is more robust to noise and it is able to precisely capture the weak speed jitters introduced by mechanical defects. The fault diagnosis of planetary gearbox has proven to be a challenging issue in both industry and academia. Based on the proposed KLPD, a systematic method for the fault diagnosis of planetary gearbox is proposed. In this method, residual time synchronous time averaging (RTSA) is first employed to remove the operation-related IAS components that come from normal gear meshing and non-stationary load variations, KLPD is then utilized to detect and enhance the speed jitter from the IAS residual in a data-driven manner. The effectiveness of proposed method has been validated by both simulated data and experimental data. The results demonstrate that the proposed KLPD-RTSA could not only detect fault signatures but also identify defective components, thus providing a promising tool for the health monitoring of planetary gearbox.

Involvement of the ornithine decarboxylase gene in acid stress response in probiotic Lactobacillus delbrueckii UFV H2b20.

PubMed

Ferreira, A B; Oliveira, M N V de; Freitas, F S; Paiva, A D; Alfenas-Zerbini, P; Silva, D F da; Queiroz, M V de; Borges, A C; Moraes, C A de

2015-01-01

Amino acid decarboxylation is important for the maintenance of intracellular pH under acid stress. This study aims to carry out phylogenetic and expression analysis by real-time PCR of two genes that encode proteins involved in ornithine decarboxylation in Lactobacillus delbrueckii UFV H2b20 exposed to acid stress. Sequencing and phylogeny analysis of genes encoding ornithine decarboxylase and amino acid permease in L. delbrueckii UFV H2b20 showed their high sequence identity (99%) and grouping with those of L. delbrueckii subsp. bulgaricus ATCC 11842. Exposure of L. delbrueckii UFV H2b20 cells in MRS pH 3.5 for 30 and 60 min caused a significant increase in expression of the gene encoding ornithine decarboxylase (up to 8.1 times higher when compared to the control treatment). Increased expression of the ornithine decarboxylase gene demonstrates its involvement in acid stress response in L. delbrueckii UFV H2b20, evidencing that the protein encoded by that gene could be involved in intracellular pH regulation. The results obtained show ornithine decarboxylation as a possible mechanism of adaptation to an acidic environmental condition, a desirable and necessary characteristic for probiotic cultures and certainly important to the survival and persistence of the L. delbrueckii UFV H2b20 in the human gastrointestinal tract.

Dynamic Information Encoding With Dynamic Synapses in Neural Adaptation

PubMed Central

Li, Luozheng; Mi, Yuanyuan; Zhang, Wenhao; Wang, Da-Hui; Wu, Si

2018-01-01

Adaptation refers to the general phenomenon that the neural system dynamically adjusts its response property according to the statistics of external inputs. In response to an invariant stimulation, neuronal firing rates first increase dramatically and then decrease gradually to a low level close to the background activity. This prompts a question: during the adaptation, how does the neural system encode the repeated stimulation with attenuated firing rates? It has been suggested that the neural system may employ a dynamical encoding strategy during the adaptation, the information of stimulus is mainly encoded by the strong independent spiking of neurons at the early stage of the adaptation; while the weak but synchronized activity of neurons encodes the stimulus information at the later stage of the adaptation. The previous study demonstrated that short-term facilitation (STF) of electrical synapses, which increases the synchronization between neurons, can provide a mechanism to realize dynamical encoding. In the present study, we further explore whether short-term plasticity (STP) of chemical synapses, an interaction form more common than electrical synapse in the cortex, can support dynamical encoding. We build a large-size network with chemical synapses between neurons. Notably, facilitation of chemical synapses only enhances pair-wise correlations between neurons mildly, but its effect on increasing synchronization of the network can be significant, and hence it can serve as a mechanism to convey the stimulus information. To read-out the stimulus information, we consider that a downstream neuron receives balanced excitatory and inhibitory inputs from the network, so that the downstream neuron only responds to synchronized firings of the network. Therefore, the response of the downstream neuron indicates the presence of the repeated stimulation. Overall, our study demonstrates that STP of chemical synapse can serve as a mechanism to realize dynamical neural encoding. We believe that our study shed lights on the mechanism underlying the efficient neural information processing via adaptation. PMID:29636675

Emergence of band-pass filtering through adaptive spiking in the owl's cochlear nucleus

PubMed Central

MacLeod, Katrina M.; Lubejko, Susan T.; Steinberg, Louisa J.; Köppl, Christine; Peña, Jose L.

2014-01-01

In the visual, auditory, and electrosensory modalities, stimuli are defined by first- and second-order attributes. The fast time-pressure signal of a sound, a first-order attribute, is important, for instance, in sound localization and pitch perception, while its slow amplitude-modulated envelope, a second-order attribute, can be used for sound recognition. Ascending the auditory pathway from ear to midbrain, neurons increasingly show a preference for the envelope and are most sensitive to particular envelope modulation frequencies, a tuning considered important for encoding sound identity. The level at which this tuning property emerges along the pathway varies across species, and the mechanism of how this occurs is a matter of debate. In this paper, we target the transition between auditory nerve fibers and the cochlear nucleus angularis (NA). While the owl's auditory nerve fibers simultaneously encode the fast and slow attributes of a sound, one synapse further, NA neurons encode the envelope more efficiently than the auditory nerve. Using in vivo and in vitro electrophysiology and computational analysis, we show that a single-cell mechanism inducing spike threshold adaptation can explain the difference in neural filtering between the two areas. We show that spike threshold adaptation can explain the increased selectivity to modulation frequency, as input level increases in NA. These results demonstrate that a spike generation nonlinearity can modulate the tuning to second-order stimulus features, without invoking network or synaptic mechanisms. PMID:24790170

Syllabic encoding during overt speech production in Cantonese: Evidence from temporal brain responses.

PubMed

Wong, Andus Wing-Kuen; Wang, Jie; Ng, Tin-Yan; Chen, Hsuan-Chih

2016-10-01

The time course of phonological encoding in overt Cantonese disyllabic word production was investigated using a picture-word interference task with concurrent recording of the event-related brain potentials (ERPs). Participants were asked to name aloud individually presented pictures and ignore a distracting Chinese character. Participants' naming responses were faster, relative to an unrelated control, when the distractor overlapped with the target's word-initial or word-final syllables. Furthermore, ERP waves in the syllable-related conditions were more positive-going than those in the unrelated control conditions from 500ms to 650ms post target onset (i.e., a late positivity). The mean and peak amplitudes of this late positivity correlated with the size of phonological facilitation. More importantly, the onset of the late positivity associated with word-initial syllable priming was 44ms earlier than that associated with word-final syllable priming, suggesting that phonological encoding in overt speech runs incrementally and the encoding duration for one syllable unit is approximately 44ms. Although the size of effective phonological units might vary across languages, as suggested by previous speech production studies, the present data indicate that the incremental nature of phonological encoding is a universal mechanism. Copyright © 2016 Elsevier B.V. All rights reserved.

Level of processing modulates the neural correlates of emotional memory formation

PubMed Central

Ritchey, Maureen; LaBar, Kevin S.; Cabeza, Roberto

2010-01-01

Emotion is known to influence multiple aspects of memory formation, including the initial encoding of the memory trace and its consolidation over time. However, the neural mechanisms whereby emotion impacts memory encoding remain largely unexplored. The present study employed a levels-of-processing manipulation to characterize the impact of emotion on encoding with and without the influence of elaborative processes. Participants viewed emotionally negative, neutral, and positive scenes under two conditions: a shallow condition focused on the perceptual features of the scenes and a deep condition that queried their semantic meaning. Recognition memory was tested 2 days later. Results showed that emotional memory enhancements were greatest in the shallow condition. FMRI analyses revealed that the right amygdala predicted subsequent emotional memory in the shallow more than deep condition, whereas the right ventrolateral prefrontal cortex demonstrated the reverse pattern. Furthermore, the association of these regions with the hippocampus was modulated by valence: the amygdala-hippocampal link was strongest for negative stimuli, whereas the prefrontal-hippocampal link was strongest for positive stimuli. Taken together, these results suggest two distinct activation patterns underlying emotional memory formation: an amygdala component that promotes memory during shallow encoding, especially for negative information, and a prefrontal component that provides extra benefits during deep encoding, especially for positive information. PMID:20350176

Level of processing modulates the neural correlates of emotional memory formation.

PubMed

Ritchey, Maureen; LaBar, Kevin S; Cabeza, Roberto

2011-04-01

Emotion is known to influence multiple aspects of memory formation, including the initial encoding of the memory trace and its consolidation over time. However, the neural mechanisms whereby emotion impacts memory encoding remain largely unexplored. The present study used a levels-of-processing manipulation to characterize the impact of emotion on encoding with and without the influence of elaborative processes. Participants viewed emotionally negative, neutral, and positive scenes under two conditions: a shallow condition focused on the perceptual features of the scenes and a deep condition that queried their semantic meaning. Recognition memory was tested 2 days later. Results showed that emotional memory enhancements were greatest in the shallow condition. fMRI analyses revealed that the right amygdala predicted subsequent emotional memory in the shallow more than deep condition, whereas the right ventrolateral PFC demonstrated the reverse pattern. Furthermore, the association of these regions with the hippocampus was modulated by valence: the amygdala-hippocampal link was strongest for negative stimuli, whereas the prefrontal-hippocampal link was strongest for positive stimuli. Taken together, these results suggest two distinct activation patterns underlying emotional memory formation: an amygdala component that promotes memory during shallow encoding, especially for negative information, and a prefrontal component that provides extra benefits during deep encoding, especially for positive information.

Binding and strategic selection in working memory: a lifespan dissociation.

PubMed

Sander, Myriam C; Werkle-Bergner, Markus; Lindenberger, Ulman

2011-09-01

Working memory (WM) shows a gradual increase during childhood, followed by accelerating decline from adulthood to old age. To examine these lifespan differences more closely, we asked 34 children (10-12 years), 40 younger adults (20-25 years), and 39 older adults (70-75 years) to perform a color change detection task. Load levels and encoding durations were varied for displays including targets only (Experiment 1) or targets plus distracters (Experiment 2, investigating a subsample of Experiment 1). WM performance was lower in older adults and children than in younger adults. Longer presentation times were associated with better performance in all age groups, presumably reflecting increasing effects of strategic selection mechanisms on WM performance. Children outperformed older adults when encoding times were short, and distracter effects were larger in children and older adults than in younger adults. We conclude that strategic selection in WM develops more slowly during childhood than basic binding operations, presumably reflecting the delay in maturation of frontal versus medio-temporal brain networks. In old age, both sets of mechanisms decline, reflecting senescent change in both networks. We discuss similarities to episodic memory development and address open questions for future research.

Deterministic folding: The role of entropic forces and steric specificities

NASA Astrophysics Data System (ADS)

da Silva, Roosevelt A.; da Silva, M. A. A.; Caliri, A.

2001-03-01

The inverse folding problem of proteinlike macromolecules is studied by using a lattice Monte Carlo (MC) model in which steric specificities (nearest-neighbors constraints) are included and the hydrophobic effect is treated explicitly by considering interactions between the chain and solvent molecules. Chemical attributes and steric peculiarities of the residues are encoded in a 10-letter alphabet and a correspondent "syntax" is provided in order to write suitable sequences for the specified target structures; twenty-four target configurations, chosen in order to cover all possible values of the average contact order χ (0.2381⩽χ⩽0.4947 for this system), were encoded and analyzed. The results, obtained by MC simulations, are strongly influenced by geometrical properties of the native configuration, namely χ and the relative number φ of crankshafts-type structures: For χ<0.35 the folding is deterministic, that is, the syntax is able to encode successful sequences: The system presents larger encodability, minimum sequence-target degeneracies and smaller characteristic folding time τf. For χ⩾0.35 the above results are not reproduced any more: The folding success is severely reduced, showing strong correlation with φ. Additionally, the existence of distinct characteristic folding times suggests that different mechanisms are acting at the same time in the folding process. The results (all obtained from the same single model, under the same "physiological conditions") resemble some general features of the folding problem, supporting the premise that the steric specificities, in association with the entropic forces (hydrophobic effect), are basic ingredients in the protein folding process.

Decoupling kinematics and mechanics reveals coding properties of trigeminal ganglion neurons in the rat vibrissal system

PubMed Central

Bush, Nicholas E; Schroeder, Christopher L; Hobbs, Jennifer A; Yang, Anne ET; Huet, Lucie A; Solla, Sara A; Hartmann, Mitra JZ

2016-01-01

Tactile information available to the rat vibrissal system begins as external forces that cause whisker deformations, which in turn excite mechanoreceptors in the follicle. Despite the fundamental mechanical origin of tactile information, primary sensory neurons in the trigeminal ganglion (Vg) have often been described as encoding the kinematics (geometry) of object contact. Here we aimed to determine the extent to which Vg neurons encode the kinematics vs. mechanics of contact. We used models of whisker bending to quantify mechanical signals (forces and moments) at the whisker base while simultaneously monitoring whisker kinematics and recording single Vg units in both anesthetized rats and awake, body restrained rats. We employed a novel manual stimulation technique to deflect whiskers in a way that decouples kinematics from mechanics, and used Generalized Linear Models (GLMs) to show that Vg neurons more directly encode mechanical signals when the whisker is deflected in this decoupled stimulus space. DOI: http://dx.doi.org/10.7554/eLife.13969.001 PMID:27348221

Nonlinear inversion of potential-field data using a hybrid-encoding genetic algorithm

USGS Publications Warehouse

Chen, C.; Xia, J.; Liu, J.; Feng, G.

2006-01-01

Using a genetic algorithm to solve an inverse problem of complex nonlinear geophysical equations is advantageous because it does not require computer gradients of models or "good" initial models. The multi-point search of a genetic algorithm makes it easier to find the globally optimal solution while avoiding falling into a local extremum. As is the case in other optimization approaches, the search efficiency for a genetic algorithm is vital in finding desired solutions successfully in a multi-dimensional model space. A binary-encoding genetic algorithm is hardly ever used to resolve an optimization problem such as a simple geophysical inversion with only three unknowns. The encoding mechanism, genetic operators, and population size of the genetic algorithm greatly affect search processes in the evolution. It is clear that improved operators and proper population size promote the convergence. Nevertheless, not all genetic operations perform perfectly while searching under either a uniform binary or a decimal encoding system. With the binary encoding mechanism, the crossover scheme may produce more new individuals than with the decimal encoding. On the other hand, the mutation scheme in a decimal encoding system will create new genes larger in scope than those in the binary encoding. This paper discusses approaches of exploiting the search potential of genetic operations in the two encoding systems and presents an approach with a hybrid-encoding mechanism, multi-point crossover, and dynamic population size for geophysical inversion. We present a method that is based on the routine in which the mutation operation is conducted in the decimal code and multi-point crossover operation in the binary code. The mix-encoding algorithm is called the hybrid-encoding genetic algorithm (HEGA). HEGA provides better genes with a higher probability by a mutation operator and improves genetic algorithms in resolving complicated geophysical inverse problems. Another significant result is that final solution is determined by the average model derived from multiple trials instead of one computation due to the randomness in a genetic algorithm procedure. These advantages were demonstrated by synthetic and real-world examples of inversion of potential-field data. ?? 2005 Elsevier Ltd. All rights reserved.

The inactivation of RNase G reduces the Stenotrophomonas maltophilia susceptibility to quinolones by triggering the heat shock response.

PubMed

Bernardini, Alejandra; Corona, Fernando; Dias, Ricardo; Sánchez, Maria B; Martínez, Jose L

2015-01-01

Quinolone resistance is usually due to mutations in the genes encoding bacterial topoisomerases. However, different reports have shown that neither clinical quinolone resistant isolates nor in vitro obtained Stenotrophomonas maltophilia mutants present mutations in such genes. The mechanisms so far described consist on efflux pumps' overexpression. Our objective is to get information on novel mechanisms of S. maltophilia quinolone resistance. For this purpose, a transposon-insertion mutant library was obtained in S. maltophilia D457. One mutant presenting reduced susceptibility to nalidixic acid was selected. Inverse PCR showed that the inactivated gene encodes RNase G. Complementation of the mutant with wild-type RNase G allele restored the susceptibility to quinolones. Transcriptomic and real-time RT-PCR analyses showed that several genes encoding heat-shock response proteins were expressed at higher levels in the RNase defective mutant than in the wild-type strain. In agreement with this situation, heat-shock reduces the S. maltophilia susceptibility to quinolone. We can then conclude that the inactivation of the RNase G reduces the susceptibility of S. maltophilia to quinolones, most likely by regulating the expression of heat-shock response genes. Heat-shock induces a transient phenotype of quinolone resistance in S. maltophilia.

Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data.

PubMed

Li, Ruichao; Xie, Miaomiao; Dong, Ning; Lin, Dachuan; Yang, Xuemei; Wong, Marcus Ho Yin; Chan, Edward Wai-Chi; Chen, Sheng

2018-03-01

Multidrug resistance (MDR)-encoding plasmids are considered major molecular vehicles responsible for transmission of antibiotic resistance genes among bacteria of the same or different species. Delineating the complete sequences of such plasmids could provide valuable insight into the evolution and transmission mechanisms underlying bacterial antibiotic resistance development. However, due to the presence of multiple repeats of mobile elements, complete sequencing of MDR plasmids remains technically complicated, expensive, and time-consuming. Here, we demonstrate a rapid and efficient approach to obtaining multiple MDR plasmid sequences through the use of the MinION nanopore sequencing platform, which is incorporated in a portable device. By assembling the long sequencing reads generated by a single MinION run according to a rapid barcoding sequencing protocol, we obtained the complete sequences of 20 plasmids harbored by multiple bacterial strains. Importantly, single long reads covering a plasmid end-to-end were recorded, indicating that de novo assembly may be unnecessary if the single reads exhibit high accuracy. This workflow represents a convenient and cost-effective approach for systematic assessment of MDR plasmids responsible for treatment failure of bacterial infections, offering the opportunity to perform detailed molecular epidemiological studies to probe the evolutionary and transmission mechanisms of MDR-encoding elements.

To search or to like: Mapping fixations to differentiate two forms of incidental scene memory.

PubMed

Choe, Kyoung Whan; Kardan, Omid; Kotabe, Hiroki P; Henderson, John M; Berman, Marc G

2017-10-01

We employed eye-tracking to investigate how performing different tasks on scenes (e.g., intentionally memorizing them, searching for an object, evaluating aesthetic preference) can affect eye movements during encoding and subsequent scene memory. We found that scene memorability decreased after visual search (one incidental encoding task) compared to intentional memorization, and that preference evaluation (another incidental encoding task) produced better memory, similar to the incidental memory boost previously observed for words and faces. By analyzing fixation maps, we found that although fixation map similarity could explain how eye movements during visual search impairs incidental scene memory, it could not explain the incidental memory boost from aesthetic preference evaluation, implying that implicit mechanisms were at play. We conclude that not all incidental encoding tasks should be taken to be similar, as different mechanisms (e.g., explicit or implicit) lead to memory enhancements or decrements for different incidental encoding tasks.

Modulation by geraniol of gene expression involved in lipid metabolism leading to a reduction of serum-cholesterol and triglyceride levels.

PubMed

Galle, Marianela; Kladniew, Boris Rodenak; Castro, María Agustina; Villegas, Sandra Montero; Lacunza, Ezequiel; Polo, Mónica; de Bravo, Margarita García; Crespo, Rosana

2015-07-15

Geraniol (G) is a natural isoprenoid present in the essential oils of several aromatic plants, with various biochemical and pharmacologic properties. Nevertheless, the mechanisms of action of G on cellular metabolism are largely unknown. We propose that G could be a potential agent for the treatment of hyperlipidemia that could contribute to the prevention of cardiovascular disease. The aim of the present study was to advance our understanding of its mechanism of action on cholesterol and TG metabolism. NIH mice received supplemented diets containing 25, 50, and 75 mmol G/kg chow. After a 3-week treatment, serum total-cholesterol and triglyceride levels were measured by commercial kits and lipid biosynthesis determined by the [(14)C] acetate incorporated into fatty acids plus nonsaponifiable and total hepatic lipids of the mice. The activity of the mRNA encoding HMGCR-the rate-limiting step in cholesterol biosynthesis-along with the enzyme levels and catalysis were assessed by real-time RT-PCR, Western blotting, and HMG-CoA-conversion assays, respectively. In-silico analysis of several genes involved in lipid metabolism and regulated by G in cultured cells was also performed. Finally, the mRNA levels encoded by the genes for the low-density-lipoprotein receptor (LDLR), the sterol-regulatory-element-binding transcription factor (SREBF2), the very-low-density-lipoprotein receptor (VLDLR), and the acetyl-CoA carboxylase (ACACA) were determined by real-time RT-PCR. Plasma total-cholesterol and triglyceride levels plus hepatic fatty-acid, total-lipid, and nonsaponifiable-lipid biosynthesis were significantly reduced by feeding with G. Even though an up-regulation of the mRNA encoding HMGCR occurred in the G treated mouse livers, the protein levels and specific activity of the enzyme were both inhibited. G also enhanced the mRNAs encoding the LDL and VLDL receptors and reduced ACACA mRNA, without altering the transcription of the mRNA encoding the SREBF2. The following mechanisms may have mediated the decrease in plasma lipids levels in mice: a down-regulation of hepatocyte-cholesterol synthesis occurred as a result of decreased HMGCR protein levels and catalytic activity; the levels of LDLR mRNA became elevated, thus suggesting an increase in the uptake of serum LDL, especially by the liver; and TG synthesis became reduced very likely because of a decrease in fatty-acid synthesis. Copyright © 2015 Elsevier GmbH. All rights reserved.

Locus Coeruleus Activity Strengthens Prioritized Memories Under Arousal.

PubMed

Clewett, David V; Huang, Ringo; Velasco, Rico; Lee, Tae-Ho; Mather, Mara

2018-02-07

Recent models posit that bursts of locus ceruleus (LC) activity amplify neural gain such that limited attention and encoding resources focus even more on prioritized mental representations under arousal. Here, we tested this hypothesis in human males and females using fMRI, neuromelanin MRI, and pupil dilation, a biomarker of arousal and LC activity. During scanning, participants performed a monetary incentive encoding task in which threat of punishment motivated them to prioritize encoding of scene images over superimposed objects. Threat of punishment elicited arousal and selectively enhanced memory for goal-relevant scenes. Furthermore, trial-level pupil dilations predicted better scene memory under threat, but were not related to object memory outcomes. fMRI analyses revealed that greater threat-evoked pupil dilations were positively associated with greater scene encoding activity in LC and parahippocampal cortex, a region specialized to process scene information. Across participants, this pattern of LC engagement for goal-relevant encoding was correlated with neuromelanin signal intensity, providing the first evidence that LC structure relates to its activation pattern during cognitive processing. Threat also reduced dynamic functional connectivity between high-priority (parahippocampal place area) and lower-priority (lateral occipital cortex) category-selective visual cortex in ways that predicted increased memory selectivity. Together, these findings support the idea that, under arousal, LC activity selectively strengthens prioritized memory representations by modulating local and functional network-level patterns of information processing. SIGNIFICANCE STATEMENT Adaptive behavior relies on the ability to select and store important information amid distraction. Prioritizing encoding of task-relevant inputs is especially critical in threatening or arousing situations, when forming these memories is essential for avoiding danger in the future. However, little is known about the arousal mechanisms that support such memory selectivity. Using fMRI, neuromelanin MRI, and pupil measures, we demonstrate that locus ceruleus (LC) activity amplifies neural gain such that limited encoding resources focus even more on prioritized mental representations under arousal. For the first time, we also show that LC structure relates to its involvement in threat-related encoding processes. These results shed new light on the brain mechanisms by which we process important information when it is most needed. Copyright © 2018 the authors 0270-6474/18/381558-17$15.00/0.

Neural Mechanisms of Encoding Social and Non-Social Context Information in Autism Spectrum Disorder

ERIC Educational Resources Information Center

Greimel, Ellen; Nehrkorn, Barbara; Fink, Gereon R.; Kukolja, Juraj; Kohls, Gregor; Muller, Kristin; Piefke, Martina; Kamp-Becker, Inge; Remschmidt, Helmut; Herpertz-Dahlmann, Beate; Konrad, Kerstin; Schulte-Ruther, Martin

2012-01-01

Individuals with autism spectrum disorder (ASD) often fail to attach context to their memories and are specifically impaired in processing social aspects of contextual information. The aim of the present study was to investigate the modulatory influence of social vs. non-social context on neural mechanisms during encoding in ASD. Using…

Selective attention neutralizes the adverse effects of low socioeconomic status on memory in 9-month-old infants.

PubMed

Markant, Julie; Ackerman, Laura K; Nussenbaum, Kate; Amso, Dima

2016-04-01

Socioeconomic status (SES) has a documented impact on brain and cognitive development. We demonstrate that engaging spatial selective attention mechanisms may counteract this negative influence of impoverished environments on early learning. We previously used a spatial cueing task to compare target object encoding in the context of basic orienting ("facilitation") versus a spatial selective attention orienting mechanism that engages distractor suppression ("IOR"). This work showed that object encoding in the context of IOR boosted 9-month-old infants' recognition memory relative to facilitation (Markant and Amso, 2013). Here we asked whether this attention-memory link further interacted with SES in infancy. Results indicated that SES was related to memory but not attention orienting efficacy. However, the correlation between SES and memory performance was moderated by the attention mechanism engaged during encoding. SES predicted memory performance when objects were encoded with basic orienting processes, with infants from low-SES environments showing poorer memory than those from high-SES environments. However, SES did not predict memory performance among infants who engaged selective attention during encoding. Spatial selective attention engagement mitigated the effects of SES on memory and may offer an effective mechanism for promoting learning among infants at risk for poor cognitive outcomes related to SES. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Robust high-resolution quantification of time signals encoded by in vivo magnetic resonance spectroscopy

NASA Astrophysics Data System (ADS)

Belkić, Dževad; Belkić, Karen

2018-01-01

This paper on molecular imaging emphasizes improving specificity of magnetic resonance spectroscopy (MRS) for early cancer diagnostics by high-resolution data analysis. Sensitivity of magnetic resonance imaging (MRI) is excellent, but specificity is insufficient. Specificity is improved with MRS by going beyond morphology to assess the biochemical content of tissue. This is contingent upon accurate data quantification of diagnostically relevant biomolecules. Quantification is spectral analysis which reconstructs chemical shifts, amplitudes and relaxation times of metabolites. Chemical shifts inform on electronic shielding of resonating nuclei bound to different molecular compounds. Oscillation amplitudes in time signals retrieve the abundance of MR sensitive nuclei whose number is proportional to metabolite concentrations. Transverse relaxation times, the reciprocal of decay probabilities of resonances, arise from spin-spin coupling and reflect local field inhomogeneities. In MRS single voxels are used. For volumetric coverage, multi-voxels are employed within a hybrid of MRS and MRI called magnetic resonance spectroscopic imaging (MRSI). Common to MRS and MRSI is encoding of time signals and subsequent spectral analysis. Encoded data do not provide direct clinical information. Spectral analysis of time signals can yield the quantitative information, of which metabolite concentrations are the most clinically important. This information is equivocal with standard data analysis through the non-parametric, low-resolution fast Fourier transform and post-processing via fitting. By applying the fast Padé transform (FPT) with high-resolution, noise suppression and exact quantification via quantum mechanical signal processing, advances are made, presented herein, focusing on four areas of critical public health importance: brain, prostate, breast and ovarian cancers.

The role of cortical beta oscillations in time estimation.

PubMed

Kulashekhar, Shrikanth; Pekkola, Johanna; Palva, Jaakko Matias; Palva, Satu

2016-09-01

Estimation of time is central to perception, action, and cognition. Human functional magnetic resonance imaging (fMRI) and positron emission topography (PET) have revealed a positive correlation between the estimation of multi-second temporal durations and neuronal activity in a circuit of sensory and motor areas, prefrontal and temporal cortices, basal ganglia, and cerebellum. The systems-level mechanisms coordinating the collective neuronal activity in these areas have remained poorly understood. Synchronized oscillations regulate communication in neuronal networks and could hence serve such coordination, but their role in the estimation and maintenance of multi-second time intervals has remained largely unknown. We used source-reconstructed magnetoencephalography (MEG) to address the functional significance of local neuronal synchronization, as indexed by the amplitudes of cortical oscillations, in time-estimation. MEG was acquired during a working memory (WM) task where the subjects first estimated and then memorized the durations, or in the contrast condition, the colors of dynamic visual stimuli. Time estimation was associated with stronger beta (β, 14 - 30 Hz) band oscillations than color estimation in sensory regions and attentional cortical structures that earlier have been associated with time processing. In addition, the encoding of duration information was associated with strengthened gamma- (γ, 30 - 120 Hz), and the retrieval and maintenance with alpha- (α, 8 - 14 Hz) band oscillations. These data suggest that β oscillations may provide a mechanism for estimating short temporal durations, while γ and α oscillations support their encoding, retrieval, and maintenance in memory. Hum Brain Mapp 37:3262-3281, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Neural Correlates of Early Sound Encoding and their Relationship to Speech-in-Noise Perception

PubMed Central

Coffey, Emily B. J.; Chepesiuk, Alexander M. P.; Herholz, Sibylle C.; Baillet, Sylvain; Zatorre, Robert J.

2017-01-01

Speech-in-noise (SIN) perception is a complex cognitive skill that affects social, vocational, and educational activities. Poor SIN ability particularly affects young and elderly populations, yet varies considerably even among healthy young adults with normal hearing. Although SIN skills are known to be influenced by top-down processes that can selectively enhance lower-level sound representations, the complementary role of feed-forward mechanisms and their relationship to musical training is poorly understood. Using a paradigm that minimizes the main top-down factors that have been implicated in SIN performance such as working memory, we aimed to better understand how robust encoding of periodicity in the auditory system (as measured by the frequency-following response) contributes to SIN perception. Using magnetoencephalograpy, we found that the strength of encoding at the fundamental frequency in the brainstem, thalamus, and cortex is correlated with SIN accuracy. The amplitude of the slower cortical P2 wave was previously also shown to be related to SIN accuracy and FFR strength; we use MEG source localization to show that the P2 wave originates in a temporal region anterior to that of the cortical FFR. We also confirm that the observed enhancements were related to the extent and timing of musicianship. These results are consistent with the hypothesis that basic feed-forward sound encoding affects SIN perception by providing better information to later processing stages, and that modifying this process may be one mechanism through which musical training might enhance the auditory networks that subserve both musical and language functions. PMID:28890684

Reduction of nuclear encoded enzymes of mitochondrial energy metabolism in cells devoid of mitochondrial DNA

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

Mueller, Edith E., E-mail: ed.mueller@salk.at; Mayr, Johannes A., E-mail: h.mayr@salk.at; Zimmermann, Franz A., E-mail: f.zimmermann@salk.at

2012-01-20

Highlights: Black-Right-Pointing-Pointer We examined OXPHOS and citrate synthase enzyme activities in HEK293 cells devoid of mtDNA. Black-Right-Pointing-Pointer Enzymes partially encoded by mtDNA show reduced activities. Black-Right-Pointing-Pointer Also the entirely nuclear encoded complex II and citrate synthase exhibit reduced activities. Black-Right-Pointing-Pointer Loss of mtDNA induces a feedback mechanism that downregulates complex II and citrate synthase. -- Abstract: Mitochondrial DNA (mtDNA) depletion syndromes are generally associated with reduced activities of oxidative phosphorylation (OXPHOS) enzymes that contain subunits encoded by mtDNA. Conversely, entirely nuclear encoded mitochondrial enzymes in these syndromes, such as the tricarboxylic acid cycle enzyme citrate synthase (CS) and OXPHOS complexmore » II, usually exhibit normal or compensatory enhanced activities. Here we report that a human cell line devoid of mtDNA (HEK293 {rho}{sup 0} cells) has diminished activities of both complex II and CS. This finding indicates the existence of a feedback mechanism in {rho}{sup 0} cells that downregulates the expression of entirely nuclear encoded components of mitochondrial energy metabolism.« less

The role of encoding and attention in facial emotion memory: an EEG investigation.

PubMed

Brenner, Colleen A; Rumak, Samuel P; Burns, Amy M N; Kieffaber, Paul D

2014-09-01

Facial expressions are encoded via sensory mechanisms, but meaning extraction and salience of these expressions involve cognitive functions. We investigated the time course of sensory encoding and subsequent maintenance in memory via EEG. Twenty-nine healthy participants completed a facial emotion delayed match-to-sample task. P100, N170 and N250 ERPs were measured in response to the first stimulus, and evoked theta power (4-7Hz) was measured during the delay interval. Negative facial expressions produced larger N170 amplitudes and greater theta power early in the delay. N170 amplitude correlated with theta power, however larger N170 amplitude coupled with greater theta power only predicted behavioural performance for one emotion condition (very happy) out of six tested (see Supplemental Data). These findings indicate that the N170 ERP may be sensitive to emotional facial expressions when task demands require encoding and retention of this information. Furthermore, sustained theta activity may represent continued attentional processing that supports short-term memory, especially of negative facial stimuli. Further study is needed to investigate the potential influence of these measures, and their interaction, on behavioural performance. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Human Amygdala Represents the Complete Spectrum of Subjective Valence

PubMed Central

Jin, Jingwen; Zelano, Christina; Gottfried, Jay A.

2015-01-01

Although the amygdala is a major locus for hedonic processing, how it encodes valence information is poorly understood. Given the hedonic potency of odor stimuli and the amygdala's anatomical proximity to the peripheral olfactory system, we combined high-resolution fMRI with pattern-based multivariate techniques to examine how valence information is encoded in the amygdala. Ten human subjects underwent fMRI scanning while smelling 9 odorants that systematically varied in perceived valence. Representational similarity analyses showed that amygdala codes the entire dimension of valence, ranging from pleasantness to unpleasantness. This unidimensional representation significantly correlated with self-reported valence ratings but not with intensity ratings. Furthermore, within-trial valence representations evolved over time, prioritizing earlier differentiation of unpleasant stimuli. Together, these findings underscore the idea that both spatial and temporal features uniquely encode pleasant and unpleasant odor valence in the amygdala. The availability of a unidimensional valence code in the amygdala, distributed in both space and time, would create greater flexibility in determining the pleasantness or unpleasantness of stimuli, providing a mechanism by which expectation, context, attention, and learning could influence affective boundaries for guiding behavior. SIGNIFICANCE STATEMENT Our findings elucidate the mechanisms of affective processing in the amygdala by demonstrating that this brain region represents the entire valence dimension from pleasant to unpleasant. An important implication of this unidimensional valence code is that pleasant and unpleasant valence cannot coexist in the amygdale because overlap of fMRI ensemble patterns for these two valence extremes obscures their unique content. This functional architecture, whereby subjective valence maps onto a pattern continuum between pleasant and unpleasant poles, offers a robust mechanism by which context, expectation, and experience could alter the set-point for valence-based behavior. Finally, identification of spatial and temporal differentiation of valence in amygdala may shed new insights into individual differences in emotional responding, with potential relevance for affective disorders. PMID:26558785

Information transfer during the universal gravitational decoherence

NASA Astrophysics Data System (ADS)

Korbicz, J. K.; Tuziemski, J.

2017-12-01

Recently Pikovski et al. (Nat Phys 11:668, 2015) have proposed in an intriguing universal decoherence mechanism, suggesting that gravitation may play a conceptually important role in the quantum-to-classical transition, albeit vanishingly small in everyday situations. Here we analyze information transfer induced by this mechanism. We show that generically on short time-scales, gravitational decoherence leads to a redundant information encoding, which results in a form of objectivization of the center-of-mass position in the gravitational field. We derive the relevant time-scales of this process, given in terms of energy dispersion and quantum Fisher information. As an example we study thermal coherent states and show certain robustness of the effect with the temperature. Finally, we draw an analogy between our objectivization mechanism and the fundamental problem of point individuation in General Relativity as emphasized by the Einstein's Hole argument.

DELAY OF GERMINATION 1 mediates a conserved coat-dormancy mechanism for the temperature- and gibberellin-dependent control of seed germination

PubMed Central

Graeber, Kai; Linkies, Ada; Steinbrecher, Tina; Mummenhoff, Klaus; Tarkowská, Danuše; Turečková, Veronika; Ignatz, Michael; Sperber, Katja; Voegele, Antje; de Jong, Hans; Urbanová, Terezie; Strnad, Miroslav; Leubner-Metzger, Gerhard

2014-01-01

Seed germination is an important life-cycle transition because it determines subsequent plant survival and reproductive success. To detect optimal spatiotemporal conditions for germination, seeds act as sophisticated environmental sensors integrating information such as ambient temperature. Here we show that the DELAY OF GERMINATION 1 (DOG1) gene, known for providing dormancy adaptation to distinct environments, determines the optimal temperature for seed germination. By reciprocal gene-swapping experiments between Brassicaceae species we show that the DOG1-mediated dormancy mechanism is conserved. Biomechanical analyses show that this mechanism regulates the material properties of the endosperm, a seed tissue layer acting as germination barrier to control coat dormancy. We found that DOG1 inhibits the expression of gibberellin (GA)-regulated genes encoding cell-wall remodeling proteins in a temperature-dependent manner. Furthermore we demonstrate that DOG1 causes temperature-dependent alterations in the seed GA metabolism. These alterations in hormone metabolism are brought about by the temperature-dependent differential expression of genes encoding key enzymes of the GA biosynthetic pathway. These effects of DOG1 lead to a temperature-dependent control of endosperm weakening and determine the optimal temperature for germination. The conserved DOG1-mediated coat-dormancy mechanism provides a highly adaptable temperature-sensing mechanism to control the timing of germination. PMID:25114251

Common capacity-limited neural mechanisms of selective attention and spatial working memory encoding

PubMed Central

Fusser, Fabian; Linden, David E J; Rahm, Benjamin; Hampel, Harald; Haenschel, Corinna; Mayer, Jutta S

2011-01-01

One characteristic feature of visual working memory (WM) is its limited capacity, and selective attention has been implicated as limiting factor. A possible reason why attention constrains the number of items that can be encoded into WM is that the two processes share limited neural resources. Functional magnetic resonance imaging (fMRI) studies have indeed demonstrated commonalities between the neural substrates of WM and attention. Here we investigated whether such overlapping activations reflect interacting neural mechanisms that could result in capacity limitations. To independently manipulate the demands on attention and WM encoding within one single task, we combined visual search and delayed discrimination of spatial locations. Participants were presented with a search array and performed easy or difficult visual search in order to encode one, three or five positions of target items into WM. Our fMRI data revealed colocalised activation for attention-demanding visual search and WM encoding in distributed posterior and frontal regions. However, further analysis yielded two patterns of results. Activity in prefrontal regions increased additively with increased demands on WM and attention, indicating regional overlap without functional interaction. Conversely, the WM load-dependent activation in visual, parietal and premotor regions was severely reduced during high attentional demand. We interpret this interaction as indicating the sites of shared capacity-limited neural resources. Our findings point to differential contributions of prefrontal and posterior regions to the common neural mechanisms that support spatial WM encoding and attention, providing new imaging evidence for attention-based models of WM encoding. PMID:21781193

A Neural Model for Temporal Order Judgments and Their Active Recalibration: A Common Mechanism for Space and Time?

PubMed Central

Cai, Mingbo; Stetson, Chess; Eagleman, David M.

2012-01-01

When observers experience a constant delay between their motor actions and sensory feedback, their perception of the temporal order between actions and sensations adapt (Stetson et al., 2006). We present here a novel neural model that can explain temporal order judgments (TOJs) and their recalibration. Our model employs three ubiquitous features of neural systems: (1) information pooling, (2) opponent processing, and (3) synaptic scaling. Specifically, the model proposes that different populations of neurons encode different delays between motor-sensory events, the outputs of these populations feed into rivaling neural populations (encoding “before” and “after”), and the activity difference between these populations determines the perceptual judgment. As a consequence of synaptic scaling of input weights, motor acts which are consistently followed by delayed sensory feedback will cause the network to recalibrate its point of subjective simultaneity. The structure of our model raises the possibility that recalibration of TOJs is a temporal analog to the motion aftereffect (MAE). In other words, identical neural mechanisms may be used to make perceptual determinations about both space and time. Our model captures behavioral recalibration results for different numbers of adapting trials and different adapting delays. In line with predictions of the model, we additionally demonstrate that temporal recalibration can last through time, in analogy to storage of the MAE. PMID:23130010

Zipf's Law in Short-Time Timbral Codings of Speech, Music, and Environmental Sound Signals

PubMed Central

Haro, Martín; Serrà, Joan; Herrera, Perfecto; Corral, Álvaro

2012-01-01

Timbre is a key perceptual feature that allows discrimination between different sounds. Timbral sensations are highly dependent on the temporal evolution of the power spectrum of an audio signal. In order to quantitatively characterize such sensations, the shape of the power spectrum has to be encoded in a way that preserves certain physical and perceptual properties. Therefore, it is common practice to encode short-time power spectra using psychoacoustical frequency scales. In this paper, we study and characterize the statistical properties of such encodings, here called timbral code-words. In particular, we report on rank-frequency distributions of timbral code-words extracted from 740 hours of audio coming from disparate sources such as speech, music, and environmental sounds. Analogously to text corpora, we find a heavy-tailed Zipfian distribution with exponent close to one. Importantly, this distribution is found independently of different encoding decisions and regardless of the audio source. Further analysis on the intrinsic characteristics of most and least frequent code-words reveals that the most frequent code-words tend to have a more homogeneous structure. We also find that speech and music databases have specific, distinctive code-words while, in the case of the environmental sounds, this database-specific code-words are not present. Finally, we find that a Yule-Simon process with memory provides a reasonable quantitative approximation for our data, suggesting the existence of a common simple generative mechanism for all considered sound sources. PMID:22479497

Identifying different mechanisms in the control of a nitrogen-vacancy center system

NASA Astrophysics Data System (ADS)

Li, Shouzhi; Yang, Ling; Cao, Dewen; Wang, Yaoxiong; Shuang, Feng; Gao, Fang

2017-10-01

The nitrogen-vacancy (NV) center system has shown great potential in quantum computing due to its long decoherence time at room temperature by encoding the qubit in dressed states [28]. The corresponding control mechanisms, which is expressed by the pathways linking the initial and target states, can be naturally investigated with the Hamiltonian-encoding and observable-decoding (HE-OD) method in the interaction adiabatic representation. This is proved by the fact that the mechanisms change slightly with different detunings, magnetic and driving field intensities, and the dominant pathway is always | g 〉 → | d 〉 → | g 〉 , with | g 〉 and | d 〉 as the first two lowest dressed states. Cases are different in the diabatic representation. The orders of dominant pathways increase the driving field intensities. Tendencies of quantum pathway amplitudes with driving fields, magnetic fields and detunings change at different conditions, which can be analyzed from the Dyson series. HE-OD analysis show that the two states | g 〉 and | d 〉 in the interaction adiabatic representation are preferable to be employed as a qubit than the state pair |0〉 and | - 1 〉 in the diabatic representation under the current Hamiltonian and parameters.

Regulation Mechanism Mediated by Trans-Encoded sRNA Nc117 in Short Chain Alcohols Tolerance in Synechocystis sp. PCC 6803.

PubMed

Bi, Yanqi; Pei, Guangsheng; Sun, Tao; Chen, Zixi; Chen, Lei; Zhang, Weiwen

2018-01-01

Microbial small RNAs (sRNAs) play essential roles against many stress conditions in cyanobacteria. However, little is known on their regulatory mechanisms on biofuels tolerance. In our previous sRNA analysis, a trans -encoded sRNA Nc117 was found involved in the tolerance to ethanol and 1-butanol in Synechocystis sp. PCC 6803. However, its functional mechanism is yet to be determined. In this study, functional characterization of sRNA Nc117 was performed. Briefly, the exact length of the trans -encoded sRNA Nc117 was determined to be 102 nucleotides using 3' RACE, and the positive regulation of Nc117 on short chain alcohols tolerance was further confirmed. Then, computational target prediction and transcriptomic analysis were integrated to explore the potential targets of Nc117. A total of 119 up-regulated and 116 down-regulated genes were identified in nc117 overexpression strain compared with the wild type by comparative transcriptomic analysis, among which the upstream regions of five genes were overlapped with those predicted by computational target approach. Based on the phenotype analysis of gene deletion and overexpression strains under short chain alcohols stress, one gene slr0007 encoding D-glycero-alpha-D-manno-heptose 1-phosphate guanylyltransferase was determined as a potential target of Nc117, suggesting that the synthesis of LPS or S-layer glycoprotein may be responsible for the tolerance enhancement. As the first reported trans -encoded sRNA positively regulating biofuels tolerance in cyanobacteria, this study not only provided evidence for a new regulatory mechanism of trans -encoded sRNA in cyanobacteria, but also valuable information for rational construction of high-tolerant cyanobacterial chassis.

Time-resolved neuroimaging of visual short term memory consolidation by post-perceptual attention shifts.

PubMed

Hecht, Marcus; Thiemann, Ulf; Freitag, Christine M; Bender, Stephan

2016-01-15

Post-perceptual cues can enhance visual short term memory encoding even after the offset of the visual stimulus. However, both the mechanisms by which the sensory stimulus characteristics are buffered as well as the mechanisms by which post-perceptual selective attention enhances short term memory encoding remain unclear. We analyzed late post-perceptual event-related potentials (ERPs) in visual change detection tasks (100ms stimulus duration) by high-resolution ERP analysis to elucidate these mechanisms. The effects of early and late auditory post-cues (300ms or 850ms after visual stimulus onset) as well as the effects of a visual interference stimulus were examined in 27 healthy right-handed adults. Focusing attention with post-perceptual cues at both latencies significantly improved memory performance, i.e. sensory stimulus characteristics were available for up to 850ms after stimulus presentation. Passive watching of the visual stimuli without auditory cue presentation evoked a slow negative wave (N700) over occipito-temporal visual areas. N700 was strongly reduced by a visual interference stimulus which impeded memory maintenance. In contrast, contralateral delay activity (CDA) still developed in this condition after the application of auditory post-cues and was thereby dissociated from N700. CDA and N700 seem to represent two different processes involved in short term memory encoding. While N700 could reflect visual post processing by automatic attention attraction, CDA may reflect the top-down process of searching selectively for the required information through post-perceptual attention. Copyright © 2015 Elsevier Inc. All rights reserved.

Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

PubMed

Mehedi, Masfique; Hoenen, Thomas; Robertson, Shelly; Ricklefs, Stacy; Dolan, Michael A; Taylor, Travis; Falzarano, Darryl; Ebihara, Hideki; Porcella, Stephen F; Feldmann, Heinz

2013-01-01

Ebolavirus (EBOV), the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. In this study, we report for the first time that minigenomes containing the glycoprotein gene editing site can undergo RNA editing, thereby eliminating the requirement for a biosafety level 4 laboratory to study EBOV RNA editing. Using a newly developed dual-reporter minigenome, we have characterized the mechanism of EBOV RNA editing, and have identified cis-acting sequences that are required for editing, located between 9 nt upstream and 9 nt downstream of the editing site. Moreover, we show that a secondary structure in the upstream cis-acting sequence plays an important role in RNA editing. EBOV RNA editing is glycoprotein gene-specific, as a stretch encoding for 7 adenosine residues located in the viral polymerase gene did not serve as an editing site, most likely due to an absence of the necessary cis-acting sequences. Finally, the EBOV protein VP30 was identified as a trans-acting factor for RNA editing, constituting a novel function for this protein. Overall, our results provide novel insights into the RNA editing mechanism of EBOV, further understanding of which might result in novel intervention strategies against this viral pathogen.

Mechanical dynamics in live cells and fluorescence-based force/tension sensors

PubMed Central

Yang, Chao; Zhang, Xiaohan; Guo, Yichen; Meng, Fanjie; Sachs, Frederick; Guo, Jun

2016-01-01

Three signaling systems play the fundamental roles in modulating cell activities: chemical, electrical, and mechanical. While the former two are well studied, the mechanical signaling system is still elusive because of the lack of methods to measure structural forces in real time at cellular and subcellular levels. Indeed, almost all biological processes are responsive to modulation by mechanical forces that trigger dispersive downstream electrical and biochemical pathways. Communication among the three systems is essential to make cells and tissues receptive to environmental changes. Cells have evolved many sophisticated mechanisms for the generation, perception and transduction of mechanical forces, including motor proteins and mechanosensors. In this review, we introduce some background information about mechanical dynamics in live cells, including the ubiquitous mechanical activity, various types of mechanical stimuli exerted on cells and the different mechanosensors. We also summarize recent results obtained using genetically encoded FRET (fluorescence resonance energy transfer)-based force/tension sensors; a new technique used to measure mechanical forces in structural proteins. The sensors have been incorporated into many specific structural proteins and have measured the force gradients in real time within live cells, tissues, and animals. PMID:25958335

Selective Memories: Infants' Encoding Is Enhanced in Selection via Suppression

ERIC Educational Resources Information Center

Markant, Julie; Amso, Dima

2013-01-01

The present study examined the hypothesis that inhibitory visual selection mechanisms play a vital role in memory by limiting distractor interference during item encoding. In Experiment 1a we used a modified spatial cueing task in which 9-month-old infants encoded multiple category exemplars in the contexts of an attention orienting mechanism…

Controlling the Messenger: Regulated Translation of Maternal mRNAs in Xenopus laevis Development

PubMed Central

Fox, Catherine A.; Dowdle, Megan E.; Blaser, Susanne Imboden; Chung, Andy; Park, Sookhee

2017-01-01

The selective translation of maternal mRNAs encoding cell-fate determinants drives the earliest decisions of embryogenesis that establish the vertebrate body plan. This chapter will discuss studies in Xenopus laevis that provide insights into mechanisms underlying this translational control. Xenopus has been a powerful model organism for many discoveries relevant to the translational control of maternal mRNAs because of the large size of its oocytes and eggs that allow for microinjection of molecules and the relative ease of manipulating the oocyte to egg transition (maturation) and fertilization in culture. Consequently, many key studies have focused on the expression of maternal mRNAs during the oocyte to egg transition (the meiotic cell cycle) and the rapid cell divisions immediately following fertilization. This research has made seminal contributions to our understanding of translational regulatory mechanisms, but while some of the mRNAs under consideration at these stages encode cell-fate determinants, many encode cell cycle regulatory proteins that drive these early cell cycles. In contrast, while maternal mRNAs encoding key developmental (i.e., cell-fate) regulators that function after the first cleavage stages may exploit aspects of these foundational mechanisms, studies reveal that these mRNAs must also rely on distinct and, as of yet, incompletely understood mechanisms. These findings are logical because the functions of such developmental regulatory proteins have requirements distinct from cell cycle regulators, including becoming relevant only after fertilization and then only in specific cells of the embryo. Indeed, key maternal cell-fate determinants must be made available in exquisitely precise amounts (usually low), only at specific times and in specific cells during embryogenesis. To provide an appreciation for the regulation of maternal cell-fate determinant expression, an overview of the maternal phase of Xenopus embryogenesis will be presented. This section will be followed by a review of translational mechanisms operating in oocytes, eggs, and early cleavage-stage embryos and conclude with a discussion of how the regulation of key maternal cell-fate determinants at the level of translation functions in Xenopus embryogenesis. A key theme is that the molecular asymmetries critical for forming the body axes are established and further elaborated upon by the selective temporal and spatial regulation of maternal mRNA translation. PMID:27975270

Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level.

PubMed

Kardyńska, Małgorzata; Paszek, Anna; Śmieja, Jarosław; Spiller, David; Widłak, Wiesława; White, Michael R H; Paszek, Pawel; Kimmel, Marek

2018-04-01

Elevated temperature induces the heat shock (HS) response, which modulates cell proliferation, apoptosis, the immune and inflammatory responses. However, specific mechanisms linking the HS response pathways to major cellular signaling systems are not fully understood. Here we used integrated computational and experimental approaches to quantitatively analyze the crosstalk mechanisms between the HS-response and a master regulator of inflammation, cell proliferation, and apoptosis the Nuclear Factor κB (NF-κB) system. We found that populations of human osteosarcoma cells, exposed to a clinically relevant 43°C HS had an attenuated NF-κB p65 response to Tumor Necrosis Factor α (TNFα) treatment. The degree of inhibition of the NF-κB response depended on the HS exposure time. Mathematical modeling of single cells indicated that individual crosstalk mechanisms differentially encode HS-mediated NF-κB responses while being consistent with the observed population-level responses. In particular "all-or-nothing" encoding mechanisms were involved in the HS-dependent regulation of the IKK activity and IκBα phosphorylation, while others involving transport were "analogue". In order to discriminate between these mechanisms, we used live-cell imaging of nuclear translocations of the NF-κB p65 subunit. The single cell responses exhibited "all-or-nothing" encoding. While most cells did not respond to TNFα stimulation after a 60 min HS, 27% showed responses similar to those not receiving HS. We further demonstrated experimentally and theoretically that the predicted inhibition of IKK activity was consistent with the observed HS-dependent depletion of the IKKα and IKKβ subunits in whole cell lysates. However, a combination of "all-or-nothing" crosstalk mechanisms was required to completely recapitulate the single cell data. We postulate therefore that the heterogeneity of the single cell responses might be explained by the cell-intrinsic variability of HS-modulated IKK signaling. In summary, we show that high temperature modulates NF-κB responses in single cells in a complex and unintuitive manner, which needs to be considered in hyperthermia-based treatment strategies.

[Brain Mechanisms for Measuring Time: Population Coding of Durations].

PubMed

Hayashi, Masamichi J

2016-11-01

Temporal processing is crucial in many aspects of our perception and action. While there is mounting evidence for the encoding mechanisms of spatial ("where") and identity ("what") information, those of temporal information ("when") remain largely unknown. Recent studies suggested that, similarly to the basic visual stimulus features such as orientation, motion direction, and numerical quantity, event durations are also represented by a population of neurons that are tuned for specific, preferred durations. This paper first reviews recent psychophysical studies on duration aftereffect. Changes in the three parameters (response gain, shift, and width of tuning curves) are then discussed that may need to be taken into account in the putative duration-channel model. Next, the potential neural basis of the duration channels is examined by overviewing recent neuroimaging and electrophysiological studies on time perception. Finally, this paper proposes a general neural basis of timing that commonly represents time-differences independent of stimulus types (e.g., a single duration v.s. multiple brief events). This extends the idea of the "when pathway" from the perception of temporal order to the general timing mechanisms for the perception of duration, temporal frequency, and synchrony.

Encoding mechano-memories in filamentous-actin networks

NASA Astrophysics Data System (ADS)

Majumdar, Sayantan; Foucard, Louis; Levine, Alex; Gardel, Margaret L.

History-dependent adaptation is a central feature of learning and memory. Incorporating such features into `adaptable materials' that can modify their mechanical properties in response to external cues, remains an outstanding challenge in materials science. Here, we study a novel mechanism of mechano-memory in cross-linked F-actin networks, the essential determinants of the mechanical behavior of eukaryotic cells. We find that the non-linear mechanical response of such networks can be reversibly programmed through induction of mechano-memories. In particular, the direction, magnitude, and duration of previously applied shear stresses can be encoded into the network architecture. The `memory' of the forcing history is long-lived, but it can be erased by force applied in the opposite direction. These results demonstrate that F-actin networks can encode analog read-write mechano-memories which can be used for adaptation to mechanical stimuli. We further show that the mechano-memory arises from changes in the nematic order of the constituent filaments. Our results suggest a new mechanism of mechanical sensing in eukaryotic cells and provide a strategy for designing a novel class of materials. S.M. acknowledges U. Chicago MRSEC for support through a Kadanoff-Rice fellowship.

Not All Attention Orienting is Created Equal: Recognition Memory is Enhanced When Attention Orienting Involves Distractor Suppression

PubMed Central

Markant, Julie; Worden, Michael S.; Amso, Dima

2015-01-01

Learning through visual exploration often requires orienting of attention to meaningful information in a cluttered world. Previous work has shown that attention modulates visual cortex activity, with enhanced activity for attended targets and suppressed activity for competing inputs, thus enhancing the visual experience. Here we examined the idea that learning may be engaged differentially with variations in attention orienting mechanisms that drive driving eye movements during visual search and exploration. We hypothesized that attention orienting mechanisms that engaged suppression of a previously attended location will boost memory encoding of the currently attended target objects to a greater extent than those that involve target enhancement alone To test this hypothesis we capitalized on the classic spatial cueing task and the inhibition of return (IOR) mechanism (Posner, Rafal, & Choate, 1985; Posner, 1980) to demonstrate that object images encoded in the context of concurrent suppression at a previously attended location were encoded more effectively and remembered better than those encoded without concurrent suppression. Furthermore, fMRI analyses revealed that this memory benefit was driven by attention modulation of visual cortex activity, as increased suppression of the previously attended location in visual cortex during target object encoding predicted better subsequent recognition memory performance. These results suggest that not all attention orienting impacts learning and memory equally. PMID:25701278

Posterior parietal cortex and episodic encoding: insights from fMRI subsequent memory effects and dual-attention theory.

PubMed

Uncapher, Melina R; Wagner, Anthony D

2009-02-01

The formation of episodic memories--memories for life events--is affected by attention during event processing. A leading neurobiological model of attention posits two separate yet interacting systems that depend on distinct regions in lateral posterior parietal cortex (PPC). From this dual-attention perspective, dorsal PPC is thought to support the goal-directed allocation of attention, whereas ventral PPC is thought to support reflexive orienting to information that automatically captures attention. To advance understanding of how parietal mechanisms may impact event encoding, we review functional MRI studies that document the relationship between lateral PPC activation during encoding and subsequent memory performance (e.g., later remembering or forgetting). This review reveals that (a) encoding-related activity is frequently observed in human lateral PPC, (b) increased activation in dorsal PPC is associated with later memory success, and (c) increased activation in ventral PPC predominantly correlates with later memory failure. From a dual-attention perspective, these findings suggest that allocating goal-directed attention during event processing increases the probability that the event will be remembered later, whereas the capture of reflexive attention during event processing may have negative consequences for event encoding. The prevalence of encoding-related activation in parietal cortex suggests that neurobiological models of episodic memory should consider how parietal-mediated attentional mechanisms regulate encoding.

The Andes hantavirus NSs protein is expressed from the viral small mRNA by a leaky scanning mechanism.

PubMed

Vera-Otarola, Jorge; Solis, Loretto; Soto-Rifo, Ricardo; Ricci, Emiliano P; Pino, Karla; Tischler, Nicole D; Ohlmann, Théophile; Darlix, Jean-Luc; López-Lastra, Marcelo

2012-02-01

The small mRNA (SmRNA) of all Bunyaviridae encodes the nucleocapsid (N) protein. In 4 out of 5 genera in the Bunyaviridae, the smRNA encodes an additional nonstructural protein denominated NSs. In this study, we show that Andes hantavirus (ANDV) SmRNA encodes an NSs protein. Data show that the NSs protein is expressed in the context of an ANDV infection. Additionally, our results suggest that translation initiation from the NSs initiation codon is mediated by ribosomal subunits that have bypassed the upstream N protein initiation codon through a leaky scanning mechanism.

The Andes Hantavirus NSs Protein Is Expressed from the Viral Small mRNA by a Leaky Scanning Mechanism

PubMed Central

Vera-Otarola, Jorge; Solis, Loretto; Soto-Rifo, Ricardo; Ricci, Emiliano P.; Pino, Karla; Tischler, Nicole D.; Ohlmann, Théophile; Darlix, Jean-Luc

2012-01-01

The small mRNA (SmRNA) of all Bunyaviridae encodes the nucleocapsid (N) protein. In 4 out of 5 genera in the Bunyaviridae, the smRNA encodes an additional nonstructural protein denominated NSs. In this study, we show that Andes hantavirus (ANDV) SmRNA encodes an NSs protein. Data show that the NSs protein is expressed in the context of an ANDV infection. Additionally, our results suggest that translation initiation from the NSs initiation codon is mediated by ribosomal subunits that have bypassed the upstream N protein initiation codon through a leaky scanning mechanism. PMID:22156529

Optical delay encoding for fast timing and detector signal multiplexing in PET

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

Grant, Alexander M.; Levin, Craig S., E-mail: cslevin@stanford.edu; Molecular Imaging Program at Stanford

2015-08-15

Purpose: The large number of detector channels in modern positron emission tomography (PET) scanners poses a challenge in terms of readout electronics complexity. Multiplexing schemes are typically implemented to reduce the number of physical readout channels, but often result in performance degradation. Novel methods of multiplexing in PET must be developed to avoid this data degradation. The preservation of fast timing information is especially important for time-of-flight PET. Methods: A new multiplexing scheme based on encoding detector interaction events with a series of extremely fast overlapping optical pulses with precise delays is demonstrated in this work. Encoding events in thismore » way potentially allows many detector channels to be simultaneously encoded onto a single optical fiber that is then read out by a single digitizer. A two channel silicon photomultiplier-based prototype utilizing this optical delay encoding technique along with dual threshold time-over-threshold is demonstrated. Results: The optical encoding and multiplexing prototype achieves a coincidence time resolution of 160 ps full width at half maximum (FWHM) and an energy resolution of 13.1% FWHM at 511 keV with 3 × 3 × 5 mm{sup 3} LYSO crystals. All interaction information for both detectors, including timing, energy, and channel identification, is encoded onto a single optical fiber with little degradation. Conclusions: Optical delay encoding and multiplexing technology could lead to time-of-flight PET scanners with fewer readout channels and simplified data acquisition systems.« less

A reaction time advantage for calculating beliefs over public representations signals domain specificity for 'theory of mind'.

PubMed

Cohen, Adam S; German, Tamsin C

2010-06-01

In a task where participants' overt task was to track the location of an object across a sequence of events, reaction times to unpredictable probes requiring an inference about a social agent's beliefs about the location of that object were obtained. Reaction times to false belief situations were faster than responses about the (false) contents of a map showing the location of the object (Experiment 1) and about the (false) direction of an arrow signaling the location of the object (Experiment 2). These results are consistent with developmental, neuro-imaging and neuropsychological evidence that there exist domain specific mechanisms within human cognition for encoding and reasoning about mental states. Specialization of these mechanisms may arise from either core cognitive architecture or via the accumulation of expertise in the social domain.

Fully phase-encoded MRI near metallic implants using ultrashort echo times and broadband excitation.

PubMed

Wiens, Curtis N; Artz, Nathan S; Jang, Hyungseok; McMillan, Alan B; Koch, Kevin M; Reeder, Scott B

2018-04-01

To develop a fully phase-encoded MRI method for distortion-free imaging near metallic implants, in clinically feasible acquisition times. An accelerated 3D fully phase-encoded acquisition with broadband excitation and ultrashort echo times is presented, which uses a broadband radiofrequency pulse to excite the entire off-resonance induced by the metallic implant. Furthermore, fully phase-encoded imaging is used to prevent distortions caused by frequency encoding, and to obtain ultrashort echo times for rapidly decaying signal. Phantom and in vivo acquisitions were used to describe the relationship among excitation bandwidth, signal loss near metallic implants, and T 1 weighting. Shorter radiofrequency pulses captured signal closer to the implant by improving spectral coverage and allowing shorter echo times, whereas longer pulses improved T 1 weighting through larger maximum attainable flip angles. Comparisons of fully phase-encoded acquisition with broadband excitation and ultrashort echo times to T 1 -weighted multi-acquisition with variable resonance image combination selective were performed in phantoms and subjects with metallic knee and hip prostheses. These acquisitions had similar contrast and acquisition efficiency. Accelerated fully phase-encoded acquisitions with ultrashort echo times and broadband excitation can generate distortion free images near metallic implants in clinically feasible acquisition times. Magn Reson Med 79:2156-2163, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Fully Phase-Encoded MRI Near Metallic Implants Using Ultrashort Echo Times and Broadband Excitation

PubMed Central

Wiens, Curtis N.; Artz, Nathan S.; Jang, Hyungseok; McMillan, Alan B.; Koch, Kevin M.; Reeder, Scott B.

2017-01-01

Purpose To develop a fully phase-encoded MRI method for distortion-free imaging near metallic implants, in clinically feasible acquisition times. Theory and Methods An accelerated 3D fully phase-encoded acquisition with broadband excitation and ultrashort echo times is presented, which uses a broadband radiofrequency pulse to excite the entire off-resonance induced by the metallic implant. Furthermore, fully phase-encoded imaging is used to prevent distortions caused by frequency encoding, and to obtain ultrashort echo times for rapidly decaying signal. Results Phantom and in vivo acquisitions were used to describe the relationship among excitation bandwidth, signal loss near metallic implants, and T1 weighting. Shorter radiofrequency pulses captured signal closer to the implant by improving spectral coverage and allowing shorter echo times, whereas longer pulses improved T1 weighting through larger maximum attainable flip angles. Comparisons of fully phase-encoded acquisition with broadband excitation and ultrashort echo times to T1-weighted multi-acquisition with variable resonance image combination selective were performed in phantoms and subjects with metallic knee and hip prostheses. These acquisitions had similar contrast and acquisition efficiency. Conclusions Accelerated fully phase-encoded acquisitions with ultrashort echo times and broadband excitation can generate distortion free images near metallic implants in clinically feasible acquisition times. Magn Reson Med 000:000–000, 2017. PMID:28833407

The Bean Pod Mottle Virus RNA2-Encoded 58-Kilodalton Protein P58 Is Required in cis for RNA2 Accumulation

PubMed Central

Lin, Junyan; Guo, Jiangbo; Finer, John; Dorrance, Anne E.; Redinbaugh, Margaret G.

2014-01-01

ABSTRACT Bean pod mottle virus (BPMV) is a bipartite, positive-sense (+) RNA plant virus in the Secoviridae family. Its RNA1 encodes proteins required for genome replication, whereas RNA2 primarily encodes proteins needed for virion assembly and cell-to-cell movement. However, the function of a 58-kDa protein (P58) encoded by RNA2 has not been resolved. P58 and the movement protein (MP) of BPMV are two largely identical proteins differing only at their N termini, with P58 extending MP upstream by 102 amino acid residues. In this report, we unveil a unique role for P58. We show that BPMV RNA2 accumulation in infected cells was abolished when the start codon of P58 was eliminated. The role of P58 does not require the region shared by MP, as RNA2 accumulation in individual cells remained robust even when most of the MP coding sequence was removed. Importantly, the function of P58 required the P58 protein, rather than its coding RNA, as compensatory mutants could be isolated that restored RNA2 accumulation by acquiring new start codons upstream of the original one. Most strikingly, loss of P58 function could not be complemented by P58 provided in trans, suggesting that P58 functions in cis to selectively promote the accumulation of RNA2 copies that encode a functional P58 protein. Finally, we found that all RNA1-encoded proteins are cis-acting relative to RNA1. Together, our results suggest that P58 probably functions by recruiting the RNA1-encoded polyprotein to RNA2 to enable RNA2 reproduction. IMPORTANCE Bean pod mottle virus (BPMV) is one of the most important pathogens of the crop plant soybean, yet its replication mechanism is not well understood, hindering the development of knowledge-based control measures. The current study examined the replication strategy of BPMV RNA2, one of the two genomic RNA segments of this virus, and established an essential role for P58, one of the RNA2-encoded proteins, in the process of RNA2 replication. Our study demonstrates for the first time that P58 functions preferentially with the very RNA from which it is translated, thus greatly advancing our understanding of the replication mechanisms of this and related viruses. Furthermore, this study is important because it provides a potential target for BPMV-specific control, and hence could help to mitigate soybean production losses caused by this virus. PMID:24390330

Method and apparatus for optical encoding with compressible imaging

NASA Technical Reports Server (NTRS)

Leviton, Douglas B. (Inventor)

2006-01-01

The present invention presents an optical encoder with increased conversion rates. Improvement in the conversion rate is a result of combining changes in the pattern recognition encoder's scale pattern with an image sensor readout technique which takes full advantage of those changes, and lends itself to operation by modern, high-speed, ultra-compact microprocessors and digital signal processors (DSP) or field programmable gate array (FPGA) logic elements which can process encoder scale images at the highest speeds. Through these improvements, all three components of conversion time (reciprocal conversion rate)--namely exposure time, image readout time, and image processing time--are minimized.

Perceiving while acting: action affects perception.

PubMed

Schubö, Anna; Prinz, Wolfgang; Aschersleben, Gisa

2004-08-01

In two experiments we studied how motor responses affect stimulus encoding when stimuli and responses are functionally unrelated and merely overlap in time. Such R-S effects across S-R assignments have been reported by Schubö, Aschersleben, and Prinz (2001), who found that stimulus encoding was affected by concurrent response execution in the sense of a contrast (i.e., emphasizing differences). The present study aimed at elucidating the mechanisms underlying this effect. Experiment 1 studied the time course of the R-S effect. Contrast was only obtained for short intertrial intervals (ITIs). With long ITIs contrast turned into assimilation (i.e., emphasizing similarities). Experiment 2 excluded an interpretation of the assimilation effect in terms of motor repetition. Our findings support the notion of a shared representational domain for perception and action control, and suggest that contrast between stimulus and response codes emerges when two S-R assignments compete with each other in perception. When perceptual competition is over, assimilation emerges in memory.

Neural pattern change during encoding of a narrative predicts retrospective duration estimates

PubMed Central

Lositsky, Olga; Chen, Janice; Toker, Daniel; Honey, Christopher J; Shvartsman, Michael; Poppenk, Jordan L; Hasson, Uri; Norman, Kenneth A

2016-01-01

What mechanisms support our ability to estimate durations on the order of minutes? Behavioral studies in humans have shown that changes in contextual features lead to overestimation of past durations. Based on evidence that the medial temporal lobes and prefrontal cortex represent contextual features, we related the degree of fMRI pattern change in these regions with people’s subsequent duration estimates. After listening to a radio story in the scanner, participants were asked how much time had elapsed between pairs of clips from the story. Our ROI analyses found that duration estimates were correlated with the neural pattern distance between two clips at encoding in the right entorhinal cortex. Moreover, whole-brain searchlight analyses revealed a cluster spanning the right anterior temporal lobe. Our findings provide convergent support for the hypothesis that retrospective time judgments are driven by 'drift' in contextual representations supported by these regions. DOI: http://dx.doi.org/10.7554/eLife.16070.001 PMID:27801645

The inner experience of time

PubMed Central

Wittmann, Marc

2009-01-01

The striking diversity of psychological and neurophysiological models of ‘time perception’ characterizes the debate on how and where in the brain time is processed. In this review, the most prominent models of time perception will be critically discussed. Some of the variation across the proposed models will be explained, namely (i) different processes and regions of the brain are involved depending on the length of the processed time interval, and (ii) different cognitive processes may be involved that are not necessarily part of a core timekeeping system but, nevertheless, influence the experience of time. These cognitive processes are distributed over the brain and are difficult to discern from timing mechanisms. Recent developments in the research on emotional influences on time perception, which succeed decades of studies on the cognition of temporal processing, will be highlighted. Empirical findings on the relationship between affect and time, together with recent conceptualizations of self- and body processes, are integrated by viewing time perception as entailing emotional and interoceptive (within the body) states. To date, specific neurophysiological mechanisms that would account for the representation of human time have not been identified. It will be argued that neural processes in the insular cortex that are related to body signals and feeling states might constitute such a neurophysiological mechanism for the encoding of duration. PMID:19487197

Treatment with MOG-DNA vaccines induces CD4+CD25+FoxP3+ regulatory T cells and up-regulates genes with neuroprotective functions in experimental autoimmune encephalomyelitis

PubMed Central

2012-01-01

Background DNA vaccines represent promising therapeutic strategies in autoimmune disorders such as multiple sclerosis (MS). However, the precise mechanisms by which DNA vaccines induce immune regulation remain largely unknown. Here, we aimed to expand previous knowledge existing on the mechanisms of action of DNA vaccines in the animal model of MS, experimental autoimmune encephalomyelitis (EAE), by treating EAE mice with a DNA vaccine encoding the myelin oligodendrocyte glycoprotein (MOG), and exploring the therapeutic effects on the disease-induced inflammatory and neurodegenerative changes. Methods EAE was induced in C57BL6/J mice by immunization with MOG35-55 peptide. Mice were intramuscularly treated with a MOG-DNA vaccine or vehicle in prophylactic and therapeutic approaches. Histological studies were performed in central nervous system (CNS) tissue. Cytokine production and regulatory T cell (Treg) quantification were achieved by flow cytometry. Gene expression patterns were determined using microarrays, and the main findings were validated by real-time PCR. Results MOG-DNA treatment reduced the clinical and histopathological signs of EAE when administered in both prophylactic and therapeutic settings. Suppression of clinical EAE was associated with dampening of antigen (Ag)-specific proinflammatory Th1 and Th17 immune responses and, interestingly, expansion of Treg in the periphery and upregulation in the CNS of genes encoding neurotrophic factors and proteins involved in remyelination. Conclusions These results suggest for the first time that the beneficial effects of DNA vaccines in EAE are not limited to anti-inflammatory mechanisms, and DNA vaccines may also exert positive effects through hitherto unknown neuroprotective mechanisms. PMID:22727044

The cognitive processing of film and musical soundtracks.

PubMed

Boltz, Marilyn G

2004-10-01

Previous research has demonstrated that musical soundtracks can influence the interpretation, emotional impact, and remembering of film information. The intent here was to examine how music is encoded into the cognitive system and subsequently represented relative to its accompanying visual action. In Experiment 1, participants viewed a set of music/film clips that were either congruent or incongruent in their emotional affects. Selective attending was also systematically manipulated by instructing viewers to attend to and remember the music, film, or both in tandem. The results from tune recognition, film recall, and paired discrimination tasks collectively revealed that mood-congruent pairs lead to a joint encoding of music/film information as well as an integrated memory code. Incongruent pairs, on the other hand, result in an independent encoding in which a given dimension, music or film, is only remembered well if it was selectively attended to at the time of encoding. Experiment 2 extended these findings by showing that tunes from mood-congruent pairs are better recognized when cued by their original scenes, while those from incongruent pairs are better remembered in the absence of scene information. These findings both support and extend the "Congruence Associationist Model" (A. J. Cohen, 2001), which addresses those cognitive mechanisms involved in the processing of music/film information.

Posterior Parietal Cortex and Episodic Encoding: Insights from fMRI Subsequent Memory Effects and Dual Attention Theory

PubMed Central

Uncapher, Melina; Wagner, Anthony D.

2010-01-01

The formation of episodic memories –– memories for life events –– is affected by attention during event processing. A leading neurobiological model of attention posits two separate yet interacting systems that depend on distinct regions in lateral posterior parietal cortex (PPC). From this dual-attention perspective, dorsal PPC is thought to support the goal-directed allocation of attention, whereas ventral PPC is thought to support reflexive orienting to information that automatically captures attention. To advance understanding of how parietal mechanisms may impact event encoding, we review functional MRI studies that document the relationship between lateral PPC activation during encoding and subsequent memory performance (e.g., later remembering or forgetting). This review reveals that (a) encoding-related activity is frequently observed in human lateral PPC, (b) increased activation in dorsal PPC is associated with later memory success, and (c) increased activation in ventral PPC predominantly correlates with later memory failure. From a dual-attention perspective, these findings suggest that allocating goal-directed attention during event processing increases the probability that the event will be remembered later, whereas the capture of reflexive attention during event processing may have negative consequences for event encoding. The prevalence of encoding-related activation in parietal cortex suggests that neurobiological models of episodic memory should consider how parietal-mediated attentional mechanisms regulate encoding. PMID:19028591

Selecting for memory? The influence of selective attention on the mnemonic binding of contextual information.

PubMed

Uncapher, Melina R; Rugg, Michael D

2009-06-24

Not all of what is experienced is remembered later. Behavioral evidence suggests that the manner in which an event is processed influences which aspects of the event will later be remembered. The present experiment investigated the neural correlates of "selective encoding," or the mechanisms that support the encoding of some elements of an event in preference to others. Event-related MRI data were acquired while volunteers selectively attended to one of two different contextual features of study items (color or location). A surprise memory test for the items and both contextual features was subsequently administered to determine the influence of selective attention on the neural correlates of contextual encoding. Activity in several cortical regions indexed later memory success selectively for color or location information, and this encoding-related activity was enhanced by selective attention to the relevant feature. Critically, a region in the hippocampus responded selectively to attended source information (whether color or location), demonstrating encoding-related activity for attended but not for nonattended source features. Together, the findings suggest that selective attention modulates the magnitude of activity in cortical regions engaged by different aspects of an event, and hippocampal encoding mechanisms seem to be sensitive to this modulation. Thus, the information that is encoded into a memory representation is biased by selective attention, and this bias is mediated by cortical-hippocampal interactions.

Fast Coding of Orientation in Primary Visual Cortex

PubMed Central

Shriki, Oren; Kohn, Adam; Shamir, Maoz

2012-01-01

Understanding how populations of neurons encode sensory information is a major goal of systems neuroscience. Attempts to answer this question have focused on responses measured over several hundred milliseconds, a duration much longer than that frequently used by animals to make decisions about the environment. How reliably sensory information is encoded on briefer time scales, and how best to extract this information, is unknown. Although it has been proposed that neuronal response latency provides a major cue for fast decisions in the visual system, this hypothesis has not been tested systematically and in a quantitative manner. Here we use a simple ‘race to threshold’ readout mechanism to quantify the information content of spike time latency of primary visual (V1) cortical cells to stimulus orientation. We find that many V1 cells show pronounced tuning of their spike latency to stimulus orientation and that almost as much information can be extracted from spike latencies as from firing rates measured over much longer durations. To extract this information, stimulus onset must be estimated accurately. We show that the responses of cells with weak tuning of spike latency can provide a reliable onset detector. We find that spike latency information can be pooled from a large neuronal population, provided that the decision threshold is scaled linearly with the population size, yielding a processing time of the order of a few tens of milliseconds. Our results provide a novel mechanism for extracting information from neuronal populations over the very brief time scales in which behavioral judgments must sometimes be made. PMID:22719237

Not all attention orienting is created equal: recognition memory is enhanced when attention orienting involves distractor suppression.

PubMed

Markant, Julie; Worden, Michael S; Amso, Dima

2015-04-01

Learning through visual exploration often requires orienting of attention to meaningful information in a cluttered world. Previous work has shown that attention modulates visual cortex activity, with enhanced activity for attended targets and suppressed activity for competing inputs, thus enhancing the visual experience. Here we examined the idea that learning may be engaged differentially with variations in attention orienting mechanisms that drive eye movements during visual search and exploration. We hypothesized that attention orienting mechanisms that engaged suppression of a previously attended location would boost memory encoding of the currently attended target objects to a greater extent than those that involve target enhancement alone. To test this hypothesis we capitalized on the classic spatial cueing task and the inhibition of return (IOR) mechanism (Posner, 1980; Posner, Rafal, & Choate, 1985) to demonstrate that object images encoded in the context of concurrent suppression at a previously attended location were encoded more effectively and remembered better than those encoded without concurrent suppression. Furthermore, fMRI analyses revealed that this memory benefit was driven by attention modulation of visual cortex activity, as increased suppression of the previously attended location in visual cortex during target object encoding predicted better subsequent recognition memory performance. These results suggest that not all attention orienting impacts learning and memory equally. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparative assessment of H.265/MPEG-HEVC, VP9, and H.264/MPEG-AVC encoders for low-delay video applications

NASA Astrophysics Data System (ADS)

Grois, Dan; Marpe, Detlev; Nguyen, Tung; Hadar, Ofer

2014-09-01

The popularity of low-delay video applications dramatically increased over the last years due to a rising demand for realtime video content (such as video conferencing or video surveillance), and also due to the increasing availability of relatively inexpensive heterogeneous devices (such as smartphones and tablets). To this end, this work presents a comparative assessment of the two latest video coding standards: H.265/MPEG-HEVC (High-Efficiency Video Coding), H.264/MPEG-AVC (Advanced Video Coding), and also of the VP9 proprietary video coding scheme. For evaluating H.264/MPEG-AVC, an open-source x264 encoder was selected, which has a multi-pass encoding mode, similarly to VP9. According to experimental results, which were obtained by using similar low-delay configurations for all three examined representative encoders, it was observed that H.265/MPEG-HEVC provides significant average bit-rate savings of 32.5%, and 40.8%, relative to VP9 and x264 for the 1-pass encoding, and average bit-rate savings of 32.6%, and 42.2% for the 2-pass encoding, respectively. On the other hand, compared to the x264 encoder, typical low-delay encoding times of the VP9 encoder, are about 2,000 times higher for the 1-pass encoding, and are about 400 times higher for the 2-pass encoding.

Analysis of gene expression provides insights into the mechanism of cadmium tolerance in Acidithiobacillus ferrooxidans.

PubMed

Chen, Minjie; Li, Yanjun; Zhang, Li; Wang, Jianying; Zheng, Chunli; Zhang, Xuefeng

2015-02-01

Acidithiobacillus ferrooxidans plays a critical role in metal solubilization in the biomining industry, and occupies an ecological niche characterized by high acidity and high concentrations of toxic heavy metal ions. In order to investigate the possible metal resistance mechanism, the cellular distribution of cadmium was tested. The result indicated that Cd(2+) entered the cells upon initial exposure resulting in increased intracellular concentrations, followed by its excretion from the cells during subsequent growth and adaptation. Sequence homology analyses were used to identify 10 genes predicted to participate in heavy metal homeostasis, and the expression of these genes was investigated in cells cultured in the presence of increasing concentrations of toxic divalent cadmium (Cd(2+)). The results suggested that one gene (cmtR A.f ) encoded a putative Cd(2+)/Pb(2+)-responsive transcriptional regulator; four genes (czcA1 A.f , czcA2 A.f , czcB1 A.f ; and czcC1 A.f ) encoded heavy metal efflux proteins for Cd(2+); two genes (cadA1 A.f and cadB1 A.f ) encoded putative cation channel proteins related to the transport of Cd(2+). No significant enhancement of gene expression was observed at low concentrations of Cd(2+) (5 mM) and most of the putative metal resistance genes were up-regulated except cmtR A.f , cadB3 A.f ; and czcB1 A.f at higher concentrations (15 and 30 mM) according to real-time polymerase chain reaction. A model was developed for the mechanism of resistance to cadmium ions based on homology analyses of the predicted genes, the transcription of putative Cd(2+) resistance genes, and previous work.

Distinct Sources of Deterministic and Stochastic Components of Action Timing Decisions in Rodent Frontal Cortex.

PubMed

Murakami, Masayoshi; Shteingart, Hanan; Loewenstein, Yonatan; Mainen, Zachary F

2017-05-17

The selection and timing of actions are subject to determinate influences such as sensory cues and internal state as well as to effectively stochastic variability. Although stochastic choice mechanisms are assumed by many theoretical models, their origin and mechanisms remain poorly understood. Here we investigated this issue by studying how neural circuits in the frontal cortex determine action timing in rats performing a waiting task. Electrophysiological recordings from two regions necessary for this behavior, medial prefrontal cortex (mPFC) and secondary motor cortex (M2), revealed an unexpected functional dissociation. Both areas encoded deterministic biases in action timing, but only M2 neurons reflected stochastic trial-by-trial fluctuations. This differential coding was reflected in distinct timescales of neural dynamics in the two frontal cortical areas. These results suggest a two-stage model in which stochastic components of action timing decisions are injected by circuits downstream of those carrying deterministic bias signals. Copyright © 2017 Elsevier Inc. All rights reserved.

Impaired memory for material related to a problem solved prior to encoding: suppression at learning or interference at recall?

PubMed

Kowalczyk, Marek

2017-07-01

Earlier research by the author revealed that material encoded incidentally in a speeded affective classification task and related to the demands of a divergent problem tends to be recalled worse in participants who solved the problem prior to encoding than in participants in the control, no-problem condition. The aim of the present experiment was to replicate this effect with a new, size-comparison orienting task, and to test for possible mechanisms of impaired recall. Participants either solved a problem before the orienting task or not, and classified each item in this task either once or three times. There was a reliable effect of impaired recall of problem-related items in the repetition condition, but not in the no-repetition condition. Solving the problem did not influence repetition priming for these items. These results support an account that attributes the impaired recall to inhibitory processes at learning and speak against a proactive interference explanation. However, they can be also accommodated by an account that refers to inefficient context cues and competitor interference at retrieval.

Quantum Darwinism Requires an Extra-Theoretical Assumption of Encoding Redundancy

NASA Astrophysics Data System (ADS)

Fields, Chris

2010-10-01

Observers restricted to the observation of pointer states of apparatus cannot conclusively demonstrate that the pointer of an apparatus mathcal{A} registers the state of a system of interest S without perturbing S. Observers cannot, therefore, conclusively demonstrate that the states of a system S are redundantly encoded by pointer states of multiple independent apparatus without destroying the redundancy of encoding. The redundancy of encoding required by quantum Darwinism must, therefore, be assumed from outside the quantum-mechanical formalism and without the possibility of experimental demonstration.

Decomposing ADHD-Related Effects in Response Speed and Variability

PubMed Central

Karalunas, Sarah L.; Huang-Pollock, Cynthia L.; Nigg, Joel T.

2012-01-01

Objective Slow and variable reaction times (RTs) on fast tasks are such a prominent feature of Attention Deficit Hyperactivity Disorder (ADHD) that any theory must account for them. However, this has proven difficult because the cognitive mechanisms responsible for this effect remain unexplained. Although speed and variability are typically correlated, it is unclear whether single or multiple mechanisms are responsible for group differences in each. RTs are a result of several semi-independent processes, including stimulus encoding, rate of information processing, speed-accuracy trade-offs, and motor response, which have not been previously well characterized. Method A diffusion model was applied to RTs from a forced-choice RT paradigm in two large, independent case-control samples (NCohort 1= 214 and N Cohort 2=172). The decomposition measured three validated parameters that account for the full RT distribution, and assessed reproducibility of ADHD effects. Results In both samples, group differences in traditional RT variables were explained by slow information processing speed, and unrelated to speed-accuracy trade-offs or non-decisional processes (e.g. encoding, motor response). Conclusions RT speed and variability in ADHD may be explained by a single information processing parameter, potentially simplifying explanations that assume different mechanisms are required to account for group differences in the mean and variability of RTs. PMID:23106115

A neural mechanism for background information-gated learning based on axonal-dendritic overlaps.

PubMed

Mainetti, Matteo; Ascoli, Giorgio A

2015-03-01

Experiencing certain events triggers the acquisition of new memories. Although necessary, however, actual experience is not sufficient for memory formation. One-trial learning is also gated by knowledge of appropriate background information to make sense of the experienced occurrence. Strong neurobiological evidence suggests that long-term memory storage involves formation of new synapses. On the short time scale, this form of structural plasticity requires that the axon of the pre-synaptic neuron be physically proximal to the dendrite of the post-synaptic neuron. We surmise that such "axonal-dendritic overlap" (ADO) constitutes the neural correlate of background information-gated (BIG) learning. The hypothesis is based on a fundamental neuroanatomical constraint: an axon must pass close to the dendrites that are near other neurons it contacts. The topographic organization of the mammalian cortex ensures that nearby neurons encode related information. Using neural network simulations, we demonstrate that ADO is a suitable mechanism for BIG learning. We model knowledge as associations between terms, concepts or indivisible units of thought via directed graphs. The simplest instantiation encodes each concept by single neurons. Results are then generalized to cell assemblies. The proposed mechanism results in learning real associations better than spurious co-occurrences, providing definitive cognitive advantages.

A Neural Mechanism for Background Information-Gated Learning Based on Axonal-Dendritic Overlaps

PubMed Central

Mainetti, Matteo; Ascoli, Giorgio A.

2015-01-01

Experiencing certain events triggers the acquisition of new memories. Although necessary, however, actual experience is not sufficient for memory formation. One-trial learning is also gated by knowledge of appropriate background information to make sense of the experienced occurrence. Strong neurobiological evidence suggests that long-term memory storage involves formation of new synapses. On the short time scale, this form of structural plasticity requires that the axon of the pre-synaptic neuron be physically proximal to the dendrite of the post-synaptic neuron. We surmise that such “axonal-dendritic overlap” (ADO) constitutes the neural correlate of background information-gated (BIG) learning. The hypothesis is based on a fundamental neuroanatomical constraint: an axon must pass close to the dendrites that are near other neurons it contacts. The topographic organization of the mammalian cortex ensures that nearby neurons encode related information. Using neural network simulations, we demonstrate that ADO is a suitable mechanism for BIG learning. We model knowledge as associations between terms, concepts or indivisible units of thought via directed graphs. The simplest instantiation encodes each concept by single neurons. Results are then generalized to cell assemblies. The proposed mechanism results in learning real associations better than spurious co-occurrences, providing definitive cognitive advantages. PMID:25767887

Training to Improve Hearing Speech in Noise: Biological Mechanisms

PubMed Central

Song, Judy H.; Skoe, Erika; Banai, Karen

2012-01-01

We investigated training-related improvements in listening in noise and the biological mechanisms mediating these improvements. Training-related malleability was examined using a program that incorporates cognitively based listening exercises to improve speech-in-noise perception. Before and after training, auditory brainstem responses to a speech syllable were recorded in quiet and multitalker noise from adults who ranged in their speech-in-noise perceptual ability. Controls did not undergo training but were tested at intervals equivalent to the trained subjects. Trained subjects exhibited significant improvements in speech-in-noise perception that were retained 6 months later. Subcortical responses in noise demonstrated training-related enhancements in the encoding of pitch-related cues (the fundamental frequency and the second harmonic), particularly for the time-varying portion of the syllable that is most vulnerable to perceptual disruption (the formant transition region). Subjects with the largest strength of pitch encoding at pretest showed the greatest perceptual improvement. Controls exhibited neither neurophysiological nor perceptual changes. We provide the first demonstration that short-term training can improve the neural representation of cues important for speech-in-noise perception. These results implicate and delineate biological mechanisms contributing to learning success, and they provide a conceptual advance to our understanding of the kind of training experiences that can influence sensory processing in adulthood. PMID:21799207

Face-Name Association Learning and Brain Structural Substrates in Alcoholism

PubMed Central

Pitel, Anne-Lise; Chanraud, Sandra; Rohlfing, Torsten; Pfefferbaum, Adolf; Sullivan, Edith V.

2011-01-01

Background Associative learning is required for face-name association and is impaired in alcoholism, but the cognitive processes and brain structural components underlying this deficit remain unclear. It is also unknown whether prompting alcoholics to implement a deep level of processing during face-name encoding would enhance performance. Methods Abstinent alcoholics and controls performed a levels-of-processing face-name learning task. Participants indicated whether the face was that of an honest person (deep encoding) or that of a man (shallow encoding). Retrieval was examined using an associative (face-name) recognition task and a single-item (face or name only) recognition task. Participants also underwent a 3T structural MRI. Results Compared with controls, alcoholics had poorer associative and single-item recognition, each impaired to the same extent. Level of processing at encoding had little effect on recognition performance but affected reaction time. Correlations with brain volumes were generally modest and based primarily on reaction time in alcoholics, where the deeper the processing at encoding, the more restricted the correlations with brain volumes. In alcoholics, longer control task reaction times correlated modestly with volumes across several anterior to posterior brain regions; shallow encoding correlated with calcarine and striatal volumes; deep encoding correlated with precuneus and parietal volumes; associative recognition RT correlated with cerebellar volumes. In controls, poorer associative recognition with deep encoding correlated significantly with smaller volumes of frontal and striatal structures. Conclusions Despite prompting, alcoholics did not take advantage of encoding memoranda at a deep level to enhance face-name recognition accuracy. Nonetheless, conditions of deeper encoding resulted in faster reaction times and more specific relations with regional brain volumes than did shallow encoding. The normal relation between associative recognition and corticostriatal volumes was not present in alcoholics. Rather, their speeded reaction time occurred at the expense of accuracy and was related most robustly to cerebellar volumes. PMID:22509954

Balanced ionotropic receptor dynamics support signal estimation via voltage-dependent membrane noise.

PubMed

Marcoux, Curtis M; Clarke, Stephen E; Nesse, William H; Longtin, Andre; Maler, Leonard

2016-01-01

Encoding behaviorally relevant stimuli in a noisy background is critical for animals to survive in their natural environment. We identify core biophysical and synaptic mechanisms that permit the encoding of low-frequency signals in pyramidal neurons of the weakly electric fish Apteronotus leptorhynchus, an animal that can accurately encode even miniscule amplitude modulations of its self-generated electric field. We demonstrate that slow NMDA receptor (NMDA-R)-mediated excitatory postsynaptic potentials (EPSPs) are able to summate over many interspike intervals (ISIs) of the primary electrosensory afferents (EAs), effectively eliminating the baseline EA ISI correlations from the pyramidal cell input. Together with a dynamic balance of NMDA-R and GABA-A-R currents, this permits stimulus-evoked changes in EA spiking to be transmitted efficiently to target electrosensory lobe (ELL) pyramidal cells, for encoding low-frequency signals. Interestingly, AMPA-R activity is depressed and appears to play a negligible role in the generation of action potentials. Instead, we hypothesize that cell-intrinsic voltage-dependent membrane noise supports the encoding of perithreshold sensory input; this noise drives a significant proportion of pyramidal cell spikes. Together, these mechanisms may be sufficient for the ELL to encode signals near the threshold of behavioral detection. Copyright © 2016 the American Physiological Society.

Hypothesis driven single cell dual oscillator mathematical model of circadian rhythms

PubMed Central

S, Shiju

2017-01-01

Molecular mechanisms responsible for 24 h circadian oscillations, entrainment to external cues, encoding of day length and the time-of-day effects have been well studied experimentally. However, it is still debated from the molecular network point of view whether each cell in suprachiasmatic nuclei harbors two molecular oscillators, where one tracks dawn and the other tracks dusk activities. A single cell dual morning and evening oscillator was proposed by Daan et al., based on the molecular network that has two sets of similar non-redundant per1/cry1 and per2/cry2 circadian genes and each can independently maintain their endogenous oscillations. Understanding of dual oscillator dynamics in a single cell at molecular level may provide insight about the circadian mechanisms that encodes day length variations and its response to external zeitgebers. We present here a realistic dual oscillator model of circadian rhythms based on the series of hypotheses proposed by Daan et al., in which they conjectured that the circadian genes per1/cry1 track dawn while per2/cry2 tracks dusk and they together constitute the morning and evening oscillators (dual oscillator). Their hypothesis also provides explanations about the encoding of day length in terms of molecular mechanisms of per/cry expression. We frame a minimal mathematical model with the assumption that per1 acts a morning oscillator and per2 acts as an evening oscillator and to support and interpret this assumption we fit the model to the experimental data of per1/per2 circadian temporal dynamics, phase response curves (PRC's), and entrainment phenomena under various light-dark conditions. We also capture different patterns of splitting phenomena by coupling two single cell dual oscillators with neuropeptides vasoactive intestinal polypeptide (VIP) and arginine vasopressin (AVP) as the coupling agents and provide interpretation for the occurrence of splitting in terms of ME oscillators, though they are not required to explain the morning and evening oscillators. The proposed dual oscillator model based on Daan's hypothesis supports per1 and per2 playing the role of morning and evening oscillators respectively and this may be the first step towards the understanding of the core molecular mechanism responsible for encoding the day length. PMID:28486525

Hypothesis driven single cell dual oscillator mathematical model of circadian rhythms.

PubMed

S, Shiju; Sriram, K

2017-01-01

Molecular mechanisms responsible for 24 h circadian oscillations, entrainment to external cues, encoding of day length and the time-of-day effects have been well studied experimentally. However, it is still debated from the molecular network point of view whether each cell in suprachiasmatic nuclei harbors two molecular oscillators, where one tracks dawn and the other tracks dusk activities. A single cell dual morning and evening oscillator was proposed by Daan et al., based on the molecular network that has two sets of similar non-redundant per1/cry1 and per2/cry2 circadian genes and each can independently maintain their endogenous oscillations. Understanding of dual oscillator dynamics in a single cell at molecular level may provide insight about the circadian mechanisms that encodes day length variations and its response to external zeitgebers. We present here a realistic dual oscillator model of circadian rhythms based on the series of hypotheses proposed by Daan et al., in which they conjectured that the circadian genes per1/cry1 track dawn while per2/cry2 tracks dusk and they together constitute the morning and evening oscillators (dual oscillator). Their hypothesis also provides explanations about the encoding of day length in terms of molecular mechanisms of per/cry expression. We frame a minimal mathematical model with the assumption that per1 acts a morning oscillator and per2 acts as an evening oscillator and to support and interpret this assumption we fit the model to the experimental data of per1/per2 circadian temporal dynamics, phase response curves (PRC's), and entrainment phenomena under various light-dark conditions. We also capture different patterns of splitting phenomena by coupling two single cell dual oscillators with neuropeptides vasoactive intestinal polypeptide (VIP) and arginine vasopressin (AVP) as the coupling agents and provide interpretation for the occurrence of splitting in terms of ME oscillators, though they are not required to explain the morning and evening oscillators. The proposed dual oscillator model based on Daan's hypothesis supports per1 and per2 playing the role of morning and evening oscillators respectively and this may be the first step towards the understanding of the core molecular mechanism responsible for encoding the day length.

Goal-directed mechanisms that constrain retrieval predict subsequent memory for new "foil" information.

PubMed

Vogelsang, David A; Bonnici, Heidi M; Bergström, Zara M; Ranganath, Charan; Simons, Jon S

2016-08-01

To remember a previous event, it is often helpful to use goal-directed control processes to constrain what comes to mind during retrieval. Behavioral studies have demonstrated that incidental learning of new "foil" words in a recognition test is superior if the participant is trying to remember studied items that were semantically encoded compared to items that were non-semantically encoded. Here, we applied subsequent memory analysis to fMRI data to understand the neural mechanisms underlying the "foil effect". Participants encoded information during deep semantic and shallow non-semantic tasks and were tested in a subsequent blocked memory task to examine how orienting retrieval towards different types of information influences the incidental encoding of new words presented as foils during the memory test phase. To assess memory for foils, participants performed a further surprise old/new recognition test involving foil words that were encountered during the previous memory test blocks as well as completely new words. Subsequent memory effects, distinguishing successful versus unsuccessful incidental encoding of foils, were observed in regions that included the left inferior frontal gyrus and posterior parietal cortex. The left inferior frontal gyrus exhibited disproportionately larger subsequent memory effects for semantic than non-semantic foils, and significant overlap in activity during semantic, but not non-semantic, initial encoding and foil encoding. The results suggest that orienting retrieval towards different types of foils involves re-implementing the neurocognitive processes that were involved during initial encoding. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon “Candidatus Nitrosotalea devanaterra”

PubMed Central

Sayavedra-Soto, Luis A.; Gallois, Nicolas; Schouten, Stefan; Stein, Lisa Y.; Prosser, James I.; Nicol, Graeme W.

2016-01-01

Ammonia oxidation is the first and rate-limiting step in nitrification and is dominated by two distinct groups of microorganisms in soil: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). AOA are often more abundant than AOB and dominate activity in acid soils. The mechanism of ammonia oxidation under acidic conditions has been a long-standing paradox. While high rates of ammonia oxidation are frequently measured in acid soils, cultivated ammonia oxidizers grew only at near-neutral pH when grown in standard laboratory culture. Although a number of mechanisms have been demonstrated to enable neutrophilic AOB growth at low pH in the laboratory, these have not been demonstrated in soil, and the recent cultivation of the obligately acidophilic ammonia oxidizer “Candidatus Nitrosotalea devanaterra” provides a more parsimonious explanation for the observed high rates of activity. Analysis of the sequenced genome, transcriptional activity, and lipid content of “Ca. Nitrosotalea devanaterra” reveals that previously proposed mechanisms used by AOB for growth at low pH are not essential for archaeal ammonia oxidation in acidic environments. Instead, the genome indicates that “Ca. Nitrosotalea devanaterra” contains genes encoding both a predicted high-affinity substrate acquisition system and potential pH homeostasis mechanisms absent in neutrophilic AOA. Analysis of mRNA revealed that candidate genes encoding the proposed homeostasis mechanisms were all expressed during acidophilic growth, and lipid profiling by high-performance liquid chromatography–mass spectrometry (HPLC-MS) demonstrated that the membrane lipids of “Ca. Nitrosotalea devanaterra” were not dominated by crenarchaeol, as found in neutrophilic AOA. This study for the first time describes a genome of an obligately acidophilic ammonia oxidizer and identifies potential mechanisms enabling this unique phenotype for future biochemical characterization. PMID:26896134

Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon "Candidatus Nitrosotalea devanaterra".

PubMed

Lehtovirta-Morley, Laura E; Sayavedra-Soto, Luis A; Gallois, Nicolas; Schouten, Stefan; Stein, Lisa Y; Prosser, James I; Nicol, Graeme W

2016-05-01

Ammonia oxidation is the first and rate-limiting step in nitrification and is dominated by two distinct groups of microorganisms in soil: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). AOA are often more abundant than AOB and dominate activity in acid soils. The mechanism of ammonia oxidation under acidic conditions has been a long-standing paradox. While high rates of ammonia oxidation are frequently measured in acid soils, cultivated ammonia oxidizers grew only at near-neutral pH when grown in standard laboratory culture. Although a number of mechanisms have been demonstrated to enable neutrophilic AOB growth at low pH in the laboratory, these have not been demonstrated in soil, and the recent cultivation of the obligately acidophilic ammonia oxidizer "Candidatus Nitrosotalea devanaterra" provides a more parsimonious explanation for the observed high rates of activity. Analysis of the sequenced genome, transcriptional activity, and lipid content of "Ca Nitrosotalea devanaterra" reveals that previously proposed mechanisms used by AOB for growth at low pH are not essential for archaeal ammonia oxidation in acidic environments. Instead, the genome indicates that "Ca Nitrosotalea devanaterra" contains genes encoding both a predicted high-affinity substrate acquisition system and potential pH homeostasis mechanisms absent in neutrophilic AOA. Analysis of mRNA revealed that candidate genes encoding the proposed homeostasis mechanisms were all expressed during acidophilic growth, and lipid profiling by high-performance liquid chromatography-mass spectrometry (HPLC-MS) demonstrated that the membrane lipids of "Ca Nitrosotalea devanaterra" were not dominated by crenarchaeol, as found in neutrophilic AOA. This study for the first time describes a genome of an obligately acidophilic ammonia oxidizer and identifies potential mechanisms enabling this unique phenotype for future biochemical characterization. Copyright © 2016 Lehtovirta-Morley et al.

Cyclic stretch-induced the cytoskeleton rearrangement and gene expression of cytoskeletal regulators in human periodontal ligament cells.

PubMed

Wu, Yaqin; Zhuang, Jiabao; Zhao, Dan; Zhang, Fuqiang; Ma, Jiayin; Xu, Chun

2017-10-01

This study aimed to explore the mechanism of the stretch-induced cell realignment and cytoskeletal rearrangement by identifying several mechanoresponsive genes related to cytoskeletal regulators in human PDL cells. After the cells were stretched by 1, 10 and 20% strains for 0.5, 1, 2, 4, 6, 12 or 24 h, the changes of the morphology and content of microfilaments were recorded and calculated. Meanwhile, the expression of 84 key genes encoding cytoskeletal regulators after 6 and 24 h stretches with 20% strain was detected by using real-time PCR array. Western blot was applied to identify the protein expression level of several cytoskeletal regulators encoded by these differentially expressed genes. The confocal fluorescent staining results confirmed that stretch-induced realignment of cells and rearrangement of microfilaments. Among the 84 genes screened, one gene was up-regulated while two genes were down-regulated after 6 h stretch. Meanwhile, three genes were up-regulated while two genes were down-regulated after 24 h stretch. These genes displaying differential expression included genes regulating polymerization/depolymerization of microfilaments (CDC42EP2, FNBP1L, NCK2, PIKFYVE, WASL), polymerization/depolymerization of microtubules (STMN1), interacting between microfilaments and microtubules (MACF1), as well as a phosphatase (PPP1R12B). Among the proteins encoded by these genes, the protein expression level of Cdc42 effector protein-2 (encoded by CDC42EP2) and Stathmin-1 (encoded by STMN1) was down-regulated, while the protein expression level of N-WASP (encoded by WASL) was up-regulated. The present study confirmed the cyclic stretch-induced cellular realignment and rearrangement of microfilaments in the human PDL cells and indicated several force-sensitive genes with regard to cytoskeletal regulators.

Movement Interferes with Visuospatial Working Memory during the Encoding: An ERP Study

PubMed Central

Gunduz Can, Rumeysa; Schack, Thomas; Koester, Dirk

2017-01-01

The present study focuses on the functional interactions of cognition and manual action control. Particularly, we investigated the neurophysiological correlates of the dual-task costs of a manual-motor task (requiring grasping an object, holding it, and subsequently placing it on a target) for working memory (WM) domains (verbal and visuospatial) and processes (encoding and retrieval). Thirty participants were tested in a cognitive-motor dual-task paradigm, in which a single block (a verbal or visuospatial WM task) was compared with a dual block (concurrent performance of a WM task and a motor task). Event-related potentials (ERPs) were analyzed separately for the encoding and retrieval processes of verbal and visuospatial WM domains both in single and dual blocks. The behavioral analyses show that the motor task interfered with WM and decreased the memory performance. The performance decrease was larger for the visuospatial task compared with the verbal task, i.e., domain-specific memory costs were obtained. The ERP analyses show the domain-specific interference also at the neurophysiological level, which is further process-specific to encoding. That is, comparing the patterns of WM-related ERPs in the single block and dual block, we showed that visuospatial ERPs changed only for the encoding process when a motor task was performed at the same time. Generally, the present study provides evidence for domain- and process-specific interactions of a prepared manual-motor movement with WM (visuospatial domain during the encoding process). This study, therefore, provides an initial neurophysiological characterization of functional interactions of WM and manual actions in a cognitive-motor dual-task setting, and contributes to a better understanding of the neuro-cognitive mechanisms of motor action control. PMID:28611714

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE.

PubMed

Trinh, Quang M; Jen, Fei-Yang Arthur; Zhou, Ziru; Chu, Kar Ming; Perry, Marc D; Kephart, Ellen T; Contrino, Sergio; Ruzanov, Peter; Stein, Lincoln D

2013-07-22

Funded by the National Institutes of Health (NIH), the aim of the Model Organism ENCyclopedia of DNA Elements (modENCODE) project is to provide the biological research community with a comprehensive encyclopedia of functional genomic elements for both model organisms C. elegans (worm) and D. melanogaster (fly). With a total size of just under 10 terabytes of data collected and released to the public, one of the challenges faced by researchers is to extract biologically meaningful knowledge from this large data set. While the basic quality control, pre-processing, and analysis of the data has already been performed by members of the modENCODE consortium, many researchers will wish to reinterpret the data set using modifications and enhancements of the original protocols, or combine modENCODE data with other data sets. Unfortunately this can be a time consuming and logistically challenging proposition. In recognition of this challenge, the modENCODE DCC has released uniform computing resources for analyzing modENCODE data on Galaxy (https://github.com/modENCODE-DCC/Galaxy), on the public Amazon Cloud (http://aws.amazon.com), and on the private Bionimbus Cloud for genomic research (http://www.bionimbus.org). In particular, we have released Galaxy workflows for interpreting ChIP-seq data which use the same quality control (QC) and peak calling standards adopted by the modENCODE and ENCODE communities. For convenience of use, we have created Amazon and Bionimbus Cloud machine images containing Galaxy along with all the modENCODE data, software and other dependencies. Using these resources provides a framework for running consistent and reproducible analyses on modENCODE data, ultimately allowing researchers to use more of their time using modENCODE data, and less time moving it around.

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE

PubMed Central

2013-01-01

Background Funded by the National Institutes of Health (NIH), the aim of the Model Organism ENCyclopedia of DNA Elements (modENCODE) project is to provide the biological research community with a comprehensive encyclopedia of functional genomic elements for both model organisms C. elegans (worm) and D. melanogaster (fly). With a total size of just under 10 terabytes of data collected and released to the public, one of the challenges faced by researchers is to extract biologically meaningful knowledge from this large data set. While the basic quality control, pre-processing, and analysis of the data has already been performed by members of the modENCODE consortium, many researchers will wish to reinterpret the data set using modifications and enhancements of the original protocols, or combine modENCODE data with other data sets. Unfortunately this can be a time consuming and logistically challenging proposition. Results In recognition of this challenge, the modENCODE DCC has released uniform computing resources for analyzing modENCODE data on Galaxy (https://github.com/modENCODE-DCC/Galaxy), on the public Amazon Cloud (http://aws.amazon.com), and on the private Bionimbus Cloud for genomic research (http://www.bionimbus.org). In particular, we have released Galaxy workflows for interpreting ChIP-seq data which use the same quality control (QC) and peak calling standards adopted by the modENCODE and ENCODE communities. For convenience of use, we have created Amazon and Bionimbus Cloud machine images containing Galaxy along with all the modENCODE data, software and other dependencies. Conclusions Using these resources provides a framework for running consistent and reproducible analyses on modENCODE data, ultimately allowing researchers to use more of their time using modENCODE data, and less time moving it around. PMID:23875683

Integrated devices for quantum information and quantum simulation with polarization encoded qubits

NASA Astrophysics Data System (ADS)

Sansoni, Linda; Sciarrino, Fabio; Mataloni, Paolo; Crespi, Andrea; Ramponi, Roberta; Osellame, Roberto

2012-06-01

The ability to manipulate quantum states of light by integrated devices may open new perspectives both for fundamental tests of quantum mechanics and for novel technological applications. The technology for handling polarization-encoded qubits, the most commonly adopted approach, was still missing in quantum optical circuits until the ultrafast laser writing (ULW) technique was adopted for the first time to realize integrated devices able to support and manipulate polarization encoded qubits.1 Thanks to this method, polarization dependent and independent devices can be realized. In particular the maintenance of polarization entanglement was demonstrated in a balanced polarization independent integrated beam splitter1 and an integrated CNOT gate for polarization qubits was realized and carachterized.2 We also exploited integrated optics for quantum simulation tasks: by adopting the ULW technique an integrated quantum walk circuit was realized3 and, for the first time, we investigate how the particle statistics, either bosonic or fermionic, influences a two-particle discrete quantum walk. Such experiment has been realized by adopting two-photon entangled states and an array of integrated symmetric directional couplers. The polarization entanglement was exploited to simulate the bunching-antibunching feature of non interacting bosons and fermions. To this scope a novel three-dimensional geometry for the waveguide circuit is introduced, which allows accurate polarization independent behaviour, maintaining a remarkable control on both phase and balancement of the directional couplers.

Semantic encoding and retrieval in the left inferior prefrontal cortex: a functional MRI study of task difficulty and process specificity.

PubMed

Demb, J B; Desmond, J E; Wagner, A D; Vaidya, C J; Glover, G H; Gabrieli, J D

1995-09-01

Prefrontal cortical function was examined during semantic encoding and repetition priming using functional magnetic resonance imaging (fMRI), a noninvasive technique for localizing regional changes in blood oxygenation, a correlate of neural activity. Words studied in a semantic (deep) encoding condition were better remembered than words studied in both easier and more difficult nonsemantic (shallow) encoding conditions, with difficulty indexed by response time. The left inferior prefrontal cortex (LIPC) (Brodmann's areas 45, 46, 47) showed increased activation during semantic encoding relative to nonsemantic encoding regardless of the relative difficulty of the nonsemantic encoding task. Therefore, LIPC activation appears to be related to semantic encoding and not task difficulty. Semantic encoding decisions are performed faster the second time words are presented. This represents semantic repetition priming, a facilitation in semantic processing for previously encoded words that is not dependent on intentional recollection. The same LIPC area activated during semantic encoding showed decreased activation during repeated semantic encoding relative to initial semantic encoding of the same words. This decrease in activation during repeated encoding was process specific; it occurred when words were semantically reprocessed but not when words were nonsemantically reprocessed. The results were apparent in both individual and averaged functional maps. These findings suggest that the LIPC is part of a semantic executive system that contributes to the on-line retrieval of semantic information.

Semantic and Phonological Encoding Times in Adults Who Stutter: Brain Electrophysiological Evidence.

PubMed

Maxfield, Nathan D

2017-10-17

Some psycholinguistic theories of stuttering propose that language production operates along a different time course in adults who stutter (AWS) versus typically fluent adults (TFA). However, behavioral evidence for such a difference has been mixed. Here, the time course of semantic and phonological encoding in picture naming was compared in AWS (n = 16) versus TFA (n = 16) by measuring 2 event-related potential (ERP) components: NoGo N200, an ERP index of response inhibition, and lateralized readiness potential, an ERP index of response preparation. Each trial required a semantic judgment about a picture in addition to a phonemic judgment about the target label of the picture. Judgments were mapped onto a dual-choice (Go-NoGo/left-right) push-button response paradigm. On each trial, ERP activity time-locked to picture onset was recorded at 32 scalp electrodes. NoGo N200 was detected earlier to semantic NoGo trials than to phonemic NoGo trials in both groups, replicating previous evidence that semantic encoding generally precedes phonological encoding in language production. Moreover, N200 onset was earlier to semantic NoGo trials in TFA than in AWS, indicating that semantic information triggering response inhibition became available earlier in TFA versus AWS. In contrast, the time course of N200 activity to phonemic NoGo trials did not differ between groups. Lateralized readiness potential activity was influenced by strategic response preparation and, thus, could not be used to index real-time semantic and phonological encoding. NoGo N200 results point to slowed semantic encoding in AWS versus TFA. Discussion considers possible factors in slowed semantic encoding in AWS and how fluency might be impacted by slowed semantic encoding.

Semantic and Phonological Encoding Times in Adults Who Stutter: Brain Electrophysiological Evidence

PubMed Central

2017-01-01

Purpose Some psycholinguistic theories of stuttering propose that language production operates along a different time course in adults who stutter (AWS) versus typically fluent adults (TFA). However, behavioral evidence for such a difference has been mixed. Here, the time course of semantic and phonological encoding in picture naming was compared in AWS (n = 16) versus TFA (n = 16) by measuring 2 event-related potential (ERP) components: NoGo N200, an ERP index of response inhibition, and lateralized readiness potential, an ERP index of response preparation. Method Each trial required a semantic judgment about a picture in addition to a phonemic judgment about the target label of the picture. Judgments were mapped onto a dual-choice (Go–NoGo/left–right) push-button response paradigm. On each trial, ERP activity time-locked to picture onset was recorded at 32 scalp electrodes. Results NoGo N200 was detected earlier to semantic NoGo trials than to phonemic NoGo trials in both groups, replicating previous evidence that semantic encoding generally precedes phonological encoding in language production. Moreover, N200 onset was earlier to semantic NoGo trials in TFA than in AWS, indicating that semantic information triggering response inhibition became available earlier in TFA versus AWS. In contrast, the time course of N200 activity to phonemic NoGo trials did not differ between groups. Lateralized readiness potential activity was influenced by strategic response preparation and, thus, could not be used to index real-time semantic and phonological encoding. Conclusion NoGo N200 results point to slowed semantic encoding in AWS versus TFA. Discussion considers possible factors in slowed semantic encoding in AWS and how fluency might be impacted by slowed semantic encoding. PMID:28973156

Accelerated radial Fourier-velocity encoding using compressed sensing.

PubMed

Hilbert, Fabian; Wech, Tobias; Hahn, Dietbert; Köstler, Herbert

2014-09-01

Phase Contrast Magnetic Resonance Imaging (MRI) is a tool for non-invasive determination of flow velocities inside blood vessels. Because Phase Contrast MRI only measures a single mean velocity per voxel, it is only applicable to vessels significantly larger than the voxel size. In contrast, Fourier Velocity Encoding measures the entire velocity distribution inside a voxel, but requires a much longer acquisition time. For accurate diagnosis of stenosis in vessels on the scale of spatial resolution, it is important to know the velocity distribution of a voxel. Our aim was to determine velocity distributions with accelerated Fourier Velocity Encoding in an acquisition time required for a conventional Phase Contrast image. We imaged the femoral artery of healthy volunteers with ECG-triggered, radial CINE acquisition. Data acquisition was accelerated by undersampling, while missing data were reconstructed by Compressed Sensing. Velocity spectra of the vessel were evaluated by high resolution Phase Contrast images and compared to spectra from fully sampled and undersampled Fourier Velocity Encoding. By means of undersampling, it was possible to reduce the scan time for Fourier Velocity Encoding to the duration required for a conventional Phase Contrast image. Acquisition time for a fully sampled data set with 12 different Velocity Encodings was 40 min. By applying a 12.6-fold retrospective undersampling, a data set was generated equal to 3:10 min acquisition time, which is similar to a conventional Phase Contrast measurement. Velocity spectra from fully sampled and undersampled Fourier Velocity Encoded images are in good agreement and show the same maximum velocities as compared to velocity maps from Phase Contrast measurements. Compressed Sensing proved to reliably reconstruct Fourier Velocity Encoded data. Our results indicate that Fourier Velocity Encoding allows an accurate determination of the velocity distribution in vessels in the order of the voxel size. Thus, compared to normal Phase Contrast measurements delivering only mean velocities, no additional scan time is necessary to retrieve meaningful velocity spectra in small vessels. Copyright © 2013. Published by Elsevier GmbH.

Spatial attention improves the quality of population codes in human visual cortex.

PubMed

Saproo, Sameer; Serences, John T

2010-08-01

Selective attention enables sensory input from behaviorally relevant stimuli to be processed in greater detail, so that these stimuli can more accurately influence thoughts, actions, and future goals. Attention has been shown to modulate the spiking activity of single feature-selective neurons that encode basic stimulus properties (color, orientation, etc.). However, the combined output from many such neurons is required to form stable representations of relevant objects and little empirical work has formally investigated the relationship between attentional modulations on population responses and improvements in encoding precision. Here, we used functional MRI and voxel-based feature tuning functions to show that spatial attention induces a multiplicative scaling in orientation-selective population response profiles in early visual cortex. In turn, this multiplicative scaling correlates with an improvement in encoding precision, as evidenced by a concurrent increase in the mutual information between population responses and the orientation of attended stimuli. These data therefore demonstrate how multiplicative scaling of neural responses provides at least one mechanism by which spatial attention may improve the encoding precision of population codes. Increased encoding precision in early visual areas may then enhance the speed and accuracy of perceptual decisions computed by higher-order neural mechanisms.

[Cloning, mutagenesis and symbiotic phenotype of three lipid transfer protein encoding genes from Mesorhizobium huakuii 7653R].

PubMed

Li, Yanan; Zeng, Xiaobo; Zhou, Xuejuan; Li, Youguo

2016-12-04

Lipid transfer protein superfamily is involved in lipid transport and metabolism. This study aimed to construct mutants of three lipid transfer protein encoding genes in Mesorhizobium huakuii 7653R, and to study the phenotypes and function of mutations during symbiosis with Astragalus sinicus. We used bioinformatics to predict structure characteristics and biological functions of lipid transfer proteins, and conducted semi-quantitative and fluorescent quantitative real-time PCR to analyze the expression levels of target genes in free-living and symbiotic conditions. Using pK19mob insertion mutagenesis to construct mutants, we carried out pot plant experiments to observe symbiotic phenotypes. MCHK-5577, MCHK-2172 and MCHK-2779 genes encoding proteins belonged to START/RHO alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) superfamily, involved in lipid transport or metabolism, and were identical to M. loti at 95% level. Gene relative transcription level of the three genes all increased compared to free-living condition. We obtained three mutants. Compared with wild-type 7653R, above-ground biomass of plants and nodulenitrogenase activity induced by the three mutants significantly decreased. Results indicated that lipid transfer protein encoding genes of Mesorhizobium huakuii 7653R may play important roles in symbiotic nitrogen fixation, and the mutations significantly affected the symbiotic phenotypes. The present work provided a basis to study further symbiotic function mechanism associated with lipid transfer proteins from rhizobia.

The Effect of Aging on the Stages of Processing in a Choice Reaction Time Task

ERIC Educational Resources Information Center

Simon, J. Richard; Pouraghabagher, A. Reza

1978-01-01

Two experiments were conducted to determine the effect of aging on encoding and response selection stages of a choice reaction time task. Results suggested reducing stimulus discriminability may affect information processing prior to the encoding stage, but the encoding stage is the primary locus of the slowing which accompanied aging. (Author)

The mitochondrial gene encoding ribosomal protein S12 has been translocated to the nuclear genome in Oenothera.

PubMed Central

Grohmann, L; Brennicke, A; Schuster, W

1992-01-01

The Oenothera mitochondrial genome contains only a gene fragment for ribosomal protein S12 (rps12), while other plants encode a functional gene in the mitochondrion. The complete Oenothera rps12 gene is located in the nucleus. The transit sequence necessary to target this protein to the mitochondrion is encoded by a 5'-extension of the open reading frame. Comparison of the amino acid sequence encoded by the nuclear gene with the polypeptides encoded by edited mitochondrial cDNA and genomic sequences of other plants suggests that gene transfer between mitochondrion and nucleus started from edited mitochondrial RNA molecules. Mechanisms and requirements of gene transfer and activation are discussed. Images PMID:1454526

Selecting for memory? The influence of selective attention on the mnemonic binding of contextual information

PubMed Central

Uncapher, Melina R.; Rugg, Michael D.

2009-01-01

Not all of what is experienced is remembered later. Behavioral evidence suggests that the manner in which an event is processed influences which aspects of the event will later be remembered. The present experiment investigated the neural correlates of ‘selective encoding’, or the mechanisms that support the encoding of some elements of an event in preference to others. Event-related functional magnetic resonance imaging (fMRI) data were acquired while volunteers selectively attended to one of two different contextual features of study items (color or location). A surprise memory test for the items and both contextual features was subsequently administered to determine the influence of selective attention on the neural correlates of contextual encoding. Activity in several cortical regions indexed later memory success selectively for color or location information, and this encoding-related activity was enhanced by selective attention to the relevant feature. Critically, a region in the hippocampus responded selectively to attended source information (whether color or location), demonstrating encoding-related activity for attended but not for nonattended source features. Together, the findings suggest that selective attention modulates the magnitude of activity in cortical regions engaged by different aspects of an event, and hippocampal encoding mechanisms seem to be sensitive to this modulation. Thus, the information that is encoded into a memory representation is biased by selective attention, and this bias is mediated by cortico-hippocampal interactions. PMID:19553466

Analysis of decoherence mechanisms in a single-atom quantum memory

NASA Astrophysics Data System (ADS)

Koerber, Matthias; Langenfeld, Stefan; Morin, Olivier; Neuzner, Andreas; Ritter, Stephan; Rempe, Gerhard

2017-04-01

While photons are ideal for the transmission of quantum information, they require dedicated memories for long-term storage. The challenge for such a photonic quantum memory is the combination of an efficient light-matter interface with a low-decoherence encoding. To increase the time before the quantum information is lost, a thorough analysis of the relevant decoherence mechanisms is indispensable. Our optical quantum memory consists of a single rubidium atom trapped in a two dimensional optical lattice in a high-finesse Fabry-Perot-type optical resonator. The qubit is initially stored in a superposition of Zeeman states, making magnetic field fluctuations the dominant source of decoherence. The impact to this type of noise is greatly reduced by transferring the qubit into a subspace less susceptible to magnetic field fluctuations. In this configuration, the achievable coherence times are no longer limited by those fluctuations, but decoherence mechanisms induced by the trapping beams pose a new limit. We will discuss the origin and magnitude of the relevant effects and strategies for possible resolutions.

Decoding spike timing: the differential reverse correlation method

PubMed Central

Tkačik, Gašper; Magnasco, Marcelo O.

2009-01-01

It is widely acknowledged that detailed timing of action potentials is used to encode information, for example in auditory pathways; however the computational tools required to analyze encoding through timing are still in their infancy. We present a simple example of encoding, based on a recent model of time-frequency analysis, in which units fire action potentials when a certain condition is met, but the timing of the action potential depends also on other features of the stimulus. We show that, as a result, spike-triggered averages are smoothed so much they do not represent the true features of the encoding. Inspired by this example, we present a simple method, differential reverse correlations, that can separate an analysis of what causes a neuron to spike, and what controls its timing. We analyze with this method the leaky integrate-and-fire neuron and show the method accurately reconstructs the model's kernel. PMID:18597928

A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease

PubMed Central

Bacci, Giovanni; Fiscarelli, Ersilia; Taccetti, Giovanni; Dolce, Daniela; Paganin, Patrizia; Morelli, Patrizia; Tuccio, Vanessa; De Alessandri, Alessandra; Lucidi, Vincenzina

2017-01-01

In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease. PMID:28758937

Real-time monitoring of the Trojan-horse effect of silver nanoparticles by using a genetically encoded fluorescent cell sensor.

PubMed

You, Fang; Tang, Wenqin; Yung, Lin-Yue Lanry

2018-04-26

Silver nanoparticles (AgNPs) are widely incorporated into commercial products due to their antimicrobial properties. As a consequence, concerns about the adverse effects induced by AgNPs to humans and the environment need to be carefully examined. The existing literature reveals that AgNPs exhibit certain toxic effects, but it remains to be proved whether AgNPs or the ionic silver (Ag+) released from AgNPs are the main toxic species. Here, a genetically encoded fluorescent protein sensor with high affinity to Ag+ was developed. The resulting sensor, MT2a-FRET, was found to be ratiometric, sensitive and selective toward only Ag+ but inert against AgNPs. This makes this sensor a potential useful tool for monitoring the real-time intracellular dissolutions of AgNPs. Our data supported that AgNPs display the "Trojan-horse" mechanism, where AgNPs are internalized by cells and undergo dissolution intracellularly. We further found that cells exhibited a detoxification ability to remove active Ag+ from cells in 48 hours.

Face Encoding and Recognition in the Human Brain

NASA Astrophysics Data System (ADS)

Haxby, James V.; Ungerleider, Leslie G.; Horwitz, Barry; Maisog, Jose Ma.; Rapoport, Stanley I.; Grady, Cheryl L.

1996-01-01

A dissociation between human neural systems that participate in the encoding and later recognition of new memories for faces was demonstrated by measuring memory task-related changes in regional cerebral blood flow with positron emission tomography. There was almost no overlap between the brain structures associated with these memory functions. A region in the right hippocampus and adjacent cortex was activated during memory encoding but not during recognition. The most striking finding in neocortex was the lateralization of prefrontal participation. Encoding activated left prefrontal cortex, whereas recognition activated right prefrontal cortex. These results indicate that the hippocampus and adjacent cortex participate in memory function primarily at the time of new memory encoding. Moreover, face recognition is not mediated simply by recapitulation of operations performed at the time of encoding but, rather, involves anatomically dissociable operations.

Comparison of H.265/HEVC encoders

NASA Astrophysics Data System (ADS)

Trochimiuk, Maciej

2016-09-01

The H.265/HEVC is the state-of-the-art video compression standard, which allows the bitrate reduction up to 50% compared with its predecessor, H.264/AVC, maintaining equal perceptual video quality. The growth in coding efficiency was achieved by increasing the number of available intra- and inter-frame prediction features and improvements in existing ones, such as entropy encoding and filtering. Nevertheless, to achieve real-time performance of the encoder, simplifications in algorithm are inevitable. Some features and coding modes shall be skipped, to reduce time needed to evaluate modes forwarded to rate-distortion optimisation. Thus, the potential acceleration of the encoding process comes at the expense of coding efficiency. In this paper, a trade-off between video quality and encoding speed of various H.265/HEVC encoders is discussed.

The Effect of Coded Healing Abutments on Treatment Duration and Clinical Outcome: A Randomized Controlled Clinical Trial Comparing Encode and Conventional Impression Protocols.

PubMed

Abduo, Jaafar; Chen, Chen; Le Breton, Eugene; Radu, Alexandra; Szeto, Josephine; Judge, Roy; Darby, Ivan

To compare the Encode impression protocol (Biomet 3i) with the conventional impression protocol in terms of treatment duration, clinical accuracy, and outcome up to the first postplacement review of single-implant crowns. A total of 45 implants were included in this study. The implants were randomly allocated to the Encode group (23 implants) or the conventional group (22 implants). At the time of surgery, all implants received two-piece Encode healing abutments. The implants were restored 3 months after insertion. In the conventional protocol, open-tray implant-level impressions were taken and the implants were restored with prefabricated abutments and porcelain-fused-to-metal (PFM) crowns. For the implants in the Encode group, closed-tray impressions of the healing abutments were taken. The generated casts were sent to the Biomet 3i scanning/milling center for custom abutment manufacturing on which PFM crowns were fabricated. Treatment duration (laboratory and clinical), clinical accuracy of occlusal and proximal contacts, and outcome (esthetics, patient satisfaction, and crown contour) were evaluated with the aid of a series of questionnaires. The Encode protocol required significantly less laboratory time (18 minutes) than the conventional protocol for adjustment of the abutments. The impression pour time, time for the laboratory to return the crown, time for crown insertion at the final appointment, and total clinical time for crown insertion did not differ significantly between the two protocols. Likewise, clinical accuracy, esthetics, and patient satisfaction were similar for the two protocols. The two protocols were clinically comparable. The Encode protocol is advantageous in reducing the laboratory time before crown fabrication.

Time Course of Grammatical Encoding in Agrammatism

ERIC Educational Resources Information Center

Lee, Jiyeon

2011-01-01

Producing a sentence involves encoding a preverbal message into a grammatical structure by retrieving lexical items and integrating them into a functional (semantic-to-grammatical) structure. Individuals with agrammatism are impaired in this grammatical encoding process. However, it is unclear what aspect of grammatical encoding is impaired and…

Efficient Encoding and Rendering of Time-Varying Volume Data

NASA Technical Reports Server (NTRS)

Ma, Kwan-Liu; Smith, Diann; Shih, Ming-Yun; Shen, Han-Wei

1998-01-01

Visualization of time-varying volumetric data sets, which may be obtained from numerical simulations or sensing instruments, provides scientists insights into the detailed dynamics of the phenomenon under study. This paper describes a coherent solution based on quantization, coupled with octree and difference encoding for visualizing time-varying volumetric data. Quantization is used to attain voxel-level compression and may have a significant influence on the performance of the subsequent encoding and visualization steps. Octree encoding is used for spatial domain compression, and difference encoding for temporal domain compression. In essence, neighboring voxels may be fused into macro voxels if they have similar values, and subtrees at consecutive time steps may be merged if they are identical. The software rendering process is tailored according to the tree structures and the volume visualization process. With the tree representation, selective rendering may be performed very efficiently. Additionally, the I/O costs are reduced. With these combined savings, a higher level of user interactivity is achieved. We have studied a variety of time-varying volume datasets, performed encoding based on data statistics, and optimized the rendering calculations wherever possible. Preliminary tests on workstations have shown in many cases tremendous reduction by as high as 90% in both storage space and inter-frame delay.

The pine Pschi4 promoter directs wound-induced transcription

Treesearch

Haiguo Wu; Charles H. Michler; Liborio LaRussa; John M. Davis

1999-01-01

Mechanical wounding stimulates the accumulation of Pschi4 transcripts (encoding a putative extracellular chitinase) in pine trees. To gain insight into the transcriptional regulatory region(s) in this gymnosperm defense gene, the 5'-flanking region of Pschi4 was fused to the uidA reporter gene encoding -...

Spatial Learning and Action Planning in a Prefrontal Cortical Network Model

PubMed Central

Martinet, Louis-Emmanuel; Sheynikhovich, Denis; Benchenane, Karim; Arleo, Angelo

2011-01-01

The interplay between hippocampus and prefrontal cortex (PFC) is fundamental to spatial cognition. Complementing hippocampal place coding, prefrontal representations provide more abstract and hierarchically organized memories suitable for decision making. We model a prefrontal network mediating distributed information processing for spatial learning and action planning. Specific connectivity and synaptic adaptation principles shape the recurrent dynamics of the network arranged in cortical minicolumns. We show how the PFC columnar organization is suitable for learning sparse topological-metrical representations from redundant hippocampal inputs. The recurrent nature of the network supports multilevel spatial processing, allowing structural features of the environment to be encoded. An activation diffusion mechanism spreads the neural activity through the column population leading to trajectory planning. The model provides a functional framework for interpreting the activity of PFC neurons recorded during navigation tasks. We illustrate the link from single unit activity to behavioral responses. The results suggest plausible neural mechanisms subserving the cognitive “insight” capability originally attributed to rodents by Tolman & Honzik. Our time course analysis of neural responses shows how the interaction between hippocampus and PFC can yield the encoding of manifold information pertinent to spatial planning, including prospective coding and distance-to-goal correlates. PMID:21625569

Irradiation properties of T0 chopper components

NASA Astrophysics Data System (ADS)

Itoh, Shinichi; Ueno, Kenji; Ohkubo, Ryuji; Sagehashi, Hidenori; Funahashi, Yoshisato; Yokoo, Tetsuya

2011-10-01

We investigated the irradiation properties of the components of a T0 chopper. The organic materials in the rotor bearing grease, the magnetic fluids in seals, and the rubber in the timing belt, as well as the semiconductor materials in the rotation sensor and motor encoder, were all irradiated with high-energy γ-rays up to 100 kGy. No significant damage that shortens the lifetime of a T0 chopper was observed for the mechanical components. However, the semiconductor components were damaged by the irradiation. For the rotation sensor system detecting the rotor phase, the signal from a marker on the rotor shaft was transmitted outside the shielding by an optical fiber with radiation-proofing and the electrical circuits were removed from the beamline shielding. The lifetime of the motor encoder possibly meets the requirement for the maintenance period of the T0 chopper.

Does Top-Down Feedback Modulate the Encoding of Orthographic Representations During Visual-Word Recognition?

PubMed

Perea, Manuel; Marcet, Ana; Vergara-Martínez, Marta

2016-09-01

In masked priming lexical decision experiments, there is a matched-case identity advantage for nonwords, but not for words (e.g., ERTAR-ERTAR <  ertar-ERTAR; ALTAR-ALTAR = altar-ALTAR). This dissociation has been interpreted in terms of feedback from higher levels of processing during orthographic encoding. Here, we examined whether a matched-case identity advantage also occurs for words when top-down feedback is minimized. We employed a task that taps prelexical orthographic processes: the masked prime same-different task. For "same" trials, results showed faster response times for targets when preceded by a briefly presented matched-case identity prime than when preceded by a mismatched-case identity prime. Importantly, this advantage was similar in magnitude for nonwords and words. This finding constrains the interplay of bottom-up versus top-down mechanisms in models of visual-word identification.

Schemes for efficient transmission of encoded video streams on high-speed networks

NASA Astrophysics Data System (ADS)

Ramanathan, Srinivas; Vin, Harrick M.; Rangan, P. Venkat

1994-04-01

In this paper, we argue that significant performance benefits can accrue if integrated networks implement application-specific mechanisms that account for the diversities in media compression schemes. Towards this end, we propose a simple, yet effective, strategy called Frame Induced Packet Discarding (FIPD), in which, upon detection of loss of a threshold number (determined by an application's video encoding scheme) of packets belonging to a video frame, the network attempts to discard all the remaining packets of that frame. In order to analytically quantify the performance of FIPD so as to obtain fractional frame losses that can be guaranteed to video channels, we develop a finite state, discrete time markov chain model of the FIPD strategy. The fractional frame loss thus computed can serve as the criterion for admission control at the network. Performance evaluations demonstrate the utility of the FIPD strategy.

Episodic sequence memory is supported by a theta-gamma phase code.

PubMed

Heusser, Andrew C; Poeppel, David; Ezzyat, Youssef; Davachi, Lila

2016-10-01

The meaning we derive from our experiences is not a simple static extraction of the elements but is largely based on the order in which those elements occur. Models propose that sequence encoding is supported by interactions between high- and low-frequency oscillations, such that elements within an experience are represented by neural cell assemblies firing at higher frequencies (gamma) and sequential order is encoded by the specific timing of firing with respect to a lower frequency oscillation (theta). During episodic sequence memory formation in humans, we provide evidence that items in different sequence positions exhibit greater gamma power along distinct phases of a theta oscillation. Furthermore, this segregation is related to successful temporal order memory. Our results provide compelling evidence that memory for order, a core component of an episodic memory, capitalizes on the ubiquitous physiological mechanism of theta-gamma phase-amplitude coupling.

Mutations in genes encoding condensin complex proteins cause microcephaly through decatenation failure at mitosis

PubMed Central

Martin, Carol-Anne; Murray, Jennie E.; Carroll, Paula; Leitch, Andrea; Mackenzie, Karen J.; Halachev, Mihail; Fetit, Ahmed E.; Keith, Charlotte; Bicknell, Louise S.; Fluteau, Adeline; Gautier, Philippe; Hall, Emma A.; Joss, Shelagh; Soares, Gabriela; Silva, João; Bober, Michael B.; Duker, Angela; Wise, Carol A.; Quigley, Alan J.; Phadke, Shubha R.; Wood, Andrew J.; Vagnarelli, Paola; Jackson, Andrew P.

2016-01-01

Compaction of chromosomes is essential for accurate segregation of the genome during mitosis. In vertebrates, two condensin complexes ensure timely chromosome condensation, sister chromatid disentanglement, and maintenance of mitotic chromosome structure. Here, we report that biallelic mutations in NCAPD2, NCAPH, or NCAPD3, encoding subunits of these complexes, cause microcephaly. In addition, hypomorphic Ncaph2 mice have significantly reduced brain size, with frequent anaphase chromatin bridge formation observed in apical neural progenitors during neurogenesis. Such DNA bridges also arise in condensin-deficient patient cells, where they are the consequence of failed sister chromatid disentanglement during chromosome compaction. This results in chromosome segregation errors, leading to micronucleus formation and increased aneuploidy in daughter cells. These findings establish “condensinopathies” as microcephalic disorders, with decatenation failure as an additional disease mechanism for microcephaly, implicating mitotic chromosome condensation as a key process ensuring mammalian cerebral cortex size. PMID:27737959

Dopaminergic inputs in the dentate gyrus direct the choice of memory encoding.

PubMed

Du, Huiyun; Deng, Wei; Aimone, James B; Ge, Minyan; Parylak, Sarah; Walch, Keenan; Zhang, Wei; Cook, Jonathan; Song, Huina; Wang, Liping; Gage, Fred H; Mu, Yangling

2016-09-13

Rewarding experiences are often well remembered, and such memory formation is known to be dependent on dopamine modulation of the neural substrates engaged in learning and memory; however, it is unknown how and where in the brain dopamine signals bias episodic memory toward preceding rather than subsequent events. Here we found that photostimulation of channelrhodopsin-2-expressing dopaminergic fibers in the dentate gyrus induced a long-term depression of cortical inputs, diminished theta oscillations, and impaired subsequent contextual learning. Computational modeling based on this dopamine modulation indicated an asymmetric association of events occurring before and after reward in memory tasks. In subsequent behavioral experiments, preexposure to a natural reward suppressed hippocampus-dependent memory formation, with an effective time window consistent with the duration of dopamine-induced changes of dentate activity. Overall, our results suggest a mechanism by which dopamine enables the hippocampus to encode memory with reduced interference from subsequent experience.

Entrainment, transport and concentration of meteorites in polar ice sheets

NASA Technical Reports Server (NTRS)

Drewry, D. J.

1986-01-01

Glaciers and ice sheets act as slow-moving conveyancing systems for material added to both their upper and lower surfaces. Because the transit time for most materials is extremely long the ice acts as a major global storage facility. The effects of horizontal and vertical motions on the flow patterns of Antarctic ice sheets are summarized. The determination of the source areas of meteorites and their transport paths is a problem of central importance since it relates not only directly to concentration mechanisms but also to the wider issues in glaciology and meteorites. The ice and snow into which a meteorite falls, and which moves with it to the concentration area, encodes information about the infall area. The principle environmental conditions being former elevation, temperature (also related to elevation), and age of the ice. This encoded information could be used to identify the infall area.

Dopaminergic inputs in the dentate gyrus direct the choice of memory encoding

PubMed Central

Du, Huiyun; Deng, Wei; Aimone, James B.; Ge, Minyan; Parylak, Sarah; Walch, Keenan; Zhang, Wei; Cook, Jonathan; Song, Huina; Wang, Liping; Gage, Fred H.; Mu, Yangling

2016-01-01

Rewarding experiences are often well remembered, and such memory formation is known to be dependent on dopamine modulation of the neural substrates engaged in learning and memory; however, it is unknown how and where in the brain dopamine signals bias episodic memory toward preceding rather than subsequent events. Here we found that photostimulation of channelrhodopsin-2–expressing dopaminergic fibers in the dentate gyrus induced a long-term depression of cortical inputs, diminished theta oscillations, and impaired subsequent contextual learning. Computational modeling based on this dopamine modulation indicated an asymmetric association of events occurring before and after reward in memory tasks. In subsequent behavioral experiments, preexposure to a natural reward suppressed hippocampus-dependent memory formation, with an effective time window consistent with the duration of dopamine-induced changes of dentate activity. Overall, our results suggest a mechanism by which dopamine enables the hippocampus to encode memory with reduced interference from subsequent experience. PMID:27573822

Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus Pneumocystis jirovecii.

PubMed

Schmid-Siegert, Emanuel; Richard, Sophie; Luraschi, Amanda; Mühlethaler, Konrad; Pagni, Marco; Hauser, Philippe M

2017-11-07

Microbial pathogens commonly escape the human immune system by varying surface proteins. We investigated the mechanisms used for that purpose by Pneumocystis jirovecii This uncultivable fungus is an obligate pulmonary pathogen that in immunocompromised individuals causes pneumonia, a major life-threatening infection. Long-read PacBio sequencing was used to assemble a core of subtelomeres of a single P. jirovecii strain from a bronchoalveolar lavage fluid specimen from a single patient. A total of 113 genes encoding surface proteins were identified, including 28 pseudogenes. These genes formed a subtelomeric gene superfamily, which included five families encoding adhesive glycosylphosphatidylinositol (GPI)-anchored glycoproteins and one family encoding excreted glycoproteins. Numerical analyses suggested that diversification of the glycoproteins relies on mosaic genes created by ectopic recombination and occurs only within each family. DNA motifs suggested that all genes are expressed independently, except those of the family encoding the most abundant surface glycoproteins, which are subject to mutually exclusive expression. PCR analyses showed that exchange of the expressed gene of the latter family occurs frequently, possibly favored by the location of the genes proximal to the telomere because this allows concomitant telomere exchange. Our observations suggest that (i) the P. jirovecii cell surface is made of a complex mixture of different surface proteins, with a majority of a single isoform of the most abundant glycoprotein, (ii) genetic mosaicism within each family ensures variation of the glycoproteins, and (iii) the strategy of the fungus consists of the continuous production of new subpopulations composed of cells that are antigenically different. IMPORTANCE Pneumocystis jirovecii is a fungus causing severe pneumonia in immunocompromised individuals. It is the second most frequent life-threatening invasive fungal infection. We have studied the mechanisms of antigenic variation used by this pathogen to escape the human immune system, a strategy commonly used by pathogenic microorganisms. Using a new DNA sequencing technology generating long reads, we could characterize the highly repetitive gene families encoding the proteins that are present on the cellular surface of this pest. These gene families are localized in the regions close to the ends of all chromosomes, the subtelomeres. Such chromosomal localization was found to favor genetic recombinations between members of each gene family and to allow diversification of these proteins continuously over time. This pathogen seems to use a strategy of antigenic variation consisting of the continuous production of new subpopulations composed of cells that are antigenically different. Such a strategy is unique among human pathogens. Copyright © 2017 Schmid-Siegert et al.

Locomotion Enhances Neural Encoding of Visual Stimuli in Mouse V1

PubMed Central

2017-01-01

Neurons in mouse primary visual cortex (V1) are selective for particular properties of visual stimuli. Locomotion causes a change in cortical state that leaves their selectivity unchanged but strengthens their responses. Both locomotion and the change in cortical state are thought to be initiated by projections from the mesencephalic locomotor region, the latter through a disinhibitory circuit in V1. By recording simultaneously from a large number of single neurons in alert mice viewing moving gratings, we investigated the relationship between locomotion and the information contained within the neural population. We found that locomotion improved encoding of visual stimuli in V1 by two mechanisms. First, locomotion-induced increases in firing rates enhanced the mutual information between visual stimuli and single neuron responses over a fixed window of time. Second, stimulus discriminability was improved, even for fixed population firing rates, because of a decrease in noise correlations across the population. These two mechanisms contributed differently to improvements in discriminability across cortical layers, with changes in firing rates most important in the upper layers and changes in noise correlations most important in layer V. Together, these changes resulted in a threefold to fivefold reduction in the time needed to precisely encode grating direction and orientation. These results support the hypothesis that cortical state shifts during locomotion to accommodate an increased load on the visual system when mice are moving. SIGNIFICANCE STATEMENT This paper contains three novel findings about the representation of information in neurons within the primary visual cortex of the mouse. First, we show that locomotion reduces by at least a factor of 3 the time needed for information to accumulate in the visual cortex that allows the distinction of different visual stimuli. Second, we show that the effect of locomotion is to increase information in cells of all layers of the visual cortex. Third, we show that the means by which information is enhanced by locomotion differs between the upper layers, where the major effect is the increasing of firing rates, and in layer V, where the major effect is the reduction in noise correlations. PMID:28264980

New insights into non-conventional epitopes as T cell targets: The missing link for breaking immune tolerance in autoimmune disease?

PubMed

Harbige, James; Eichmann, Martin; Peakman, Mark

2017-11-01

The mechanism by which immune tolerance is breached in autoimmune disease is poorly understood. One possibility is that post-translational modification of self-antigens leads to peripheral recognition of neo-epitopes against which central and peripheral tolerance is inadequate. Accumulating evidence points to multiple mechanisms through which non-germline encoded sequences can give rise to these non-conventional epitopes which in turn engage the immune system as T cell targets. In particular, where these modifications alter the rules of epitope engagement with MHC molecules, such non-conventional epitopes offer a persuasive explanation for associations between specific HLA alleles and autoimmune diseases. In this review article, we discuss current understanding of mechanisms through which non-conventional epitopes may be generated, focusing on several recently described pathways that can transpose germline-encoded sequences. We contextualise these discoveries around type 1 diabetes, the prototypic organ-specific autoimmune disease in which specific HLA-DQ molecules confer high risk. Non-conventional epitopes have the potential to act as tolerance breakers or disease drivers in type 1 diabetes, prompting a timely re-evaluation of models of a etiopathogenesis. Future studies are required to elucidate the disease-relevance of a range of potential non-germline epitopes and their relationship to the natural peptide repertoire. Copyright © 2017 Elsevier Ltd. All rights reserved.

Time in the eye of the beholder: Gaze position reveals spatial-temporal associations during encoding and memory retrieval of future and past.

PubMed

Martarelli, Corinna S; Mast, Fred W; Hartmann, Matthias

2017-01-01

Time is grounded in various ways, and previous studies point to a "mental time line" with past associated with the left, and future with the right side. In this study, we investigated whether spontaneous eye movements on a blank screen would follow a mental timeline during encoding, free recall, and recognition of past and future items. In all three stages of processing, gaze position was more rightward during future items compared to past items. Moreover, horizontal gaze position during encoding predicted horizontal gaze position during free recall and recognition. We conclude that mental time line and the stored gaze position during encoding assist memory retrieval of past versus future items. Our findings highlight the spatial nature of temporal representations.

Ribbon synapses compute temporal contrast and encode luminance in retinal rod bipolar cells

PubMed Central

Oesch, Nicholas W.; Diamond, Jeffrey S.

2011-01-01

Contrast is computed throughout the nervous system to encode changing inputs efficiently. The retina encodes luminance and contrast over a wide range of visual conditions and so must adapt its responses to maintain sensitivity and avoid saturation. Here we show how one type of adaptation allows individual synapses to compute contrast and encode luminance in biphasic responses to step changes in light levels. Light-evoked depletion of the readily releasable vesicle pool (RRP) at rod bipolar cell (RBC) ribbon synapses in rat retina limits the dynamic range available to encode transient but not sustained responses, thereby allowing the transient and sustained components of release to compute temporal contrast and encode mean light levels, respectively. A release/replenishment model shows that a single, homogeneous pool of synaptic vesicles is sufficient to generate this behavior and reveals that the dominant mechanism shaping the biphasic contrast/luminance response is the partial depletion of the RRP. PMID:22019730

Costs and benefits in item-method directed forgetting: differential effects of encoding and retrieval.

PubMed

Lee, Yuh-Shiow

2013-01-01

This study examined how encoding and retrieval factors affected directed forgetting costs and benefits in an item-method procedure. Experiment 1 used a typical item-method procedure and revealed a levels-of-processing effect in overall recall. However, the deep encoding condition showed a smaller directed forgetting effect than the shallow encoding conditions. More importantly, "remember" (R) words were selectively rehearsed as indicated by greater recall from the primacy portion of the list and more apt to be recalled before "forget" (F) words. Experiment 2 showed that a deep encoding operation reduced directed forgetting costs and that directed forgetting benefits occurred only when R words were recalled before F words. These findings supported the hypotheses that encoding manipulation affected directed forgetting costs and that directed forgetting benefits were associated with output order bias. Results were discussed in terms of mechanisms that produce item-method directed forgetting.

A Spiking Neural Network System for Robust Sequence Recognition.

PubMed

Yu, Qiang; Yan, Rui; Tang, Huajin; Tan, Kay Chen; Li, Haizhou

2016-03-01

This paper proposes a biologically plausible network architecture with spiking neurons for sequence recognition. This architecture is a unified and consistent system with functional parts of sensory encoding, learning, and decoding. This is the first systematic model attempting to reveal the neural mechanisms considering both the upstream and the downstream neurons together. The whole system is a consistent temporal framework, where the precise timing of spikes is employed for information processing and cognitive computing. Experimental results show that the system is competent to perform the sequence recognition, being robust to noisy sensory inputs and invariant to changes in the intervals between input stimuli within a certain range. The classification ability of the temporal learning rule used in the system is investigated through two benchmark tasks that outperform the other two widely used learning rules for classification. The results also demonstrate the computational power of spiking neurons over perceptrons for processing spatiotemporal patterns. In summary, the system provides a general way with spiking neurons to encode external stimuli into spatiotemporal spikes, to learn the encoded spike patterns with temporal learning rules, and to decode the sequence order with downstream neurons. The system structure would be beneficial for developments in both hardware and software.

Memory: Ironing Out a Wrinkle in Time.

PubMed

Miller, Adam M P; Frankland, Paul W; Josselyn, Sheena A

2018-05-21

Individual hippocampal neurons encode time over seconds, whereas large-scale changes in population activity of hippocampal neurons encode time over minutes and days. New research shows how the hippocampus represents these multiple timescales simultaneously. Copyright © 2018 Elsevier Ltd. All rights reserved.

Integration of remote sensing and GIS: Data and data access

USGS Publications Warehouse

Ehlers, M.; Greenlee, D.D.; Smith, T.; Star, J.

1991-01-01

CT: Theintegration of remote sensing tools and technology with the spatial analysis orientation of geographic information systems is a complex task. In this paper, we focus on the issues of making data available and useful to the user. In part, this involves a set of problems which reflect on the physical and logical structures used to encode the data. At the same time, however, the mechanisms and protocols which provide information about the data, and which maintain the data through time, have become increasingly important. We discuss these latter issues from the viewpoint of the functions which must be provided by archives of spatial data.

Robust encoding of stimulus identity and concentration in the accessory olfactory system.

PubMed

Arnson, Hannah A; Holy, Timothy E

2013-08-14

Sensory systems represent stimulus identity and intensity, but in the neural periphery these two variables are typically intertwined. Moreover, stable detection may be complicated by environmental uncertainty; stimulus properties can differ over time and circumstance in ways that are not necessarily biologically relevant. We explored these issues in the context of the mouse accessory olfactory system, which specializes in detection of chemical social cues and infers myriad aspects of the identity and physiological state of conspecifics from complex mixtures, such as urine. Using mixtures of sulfated steroids, key constituents of urine, we found that spiking responses of individual vomeronasal sensory neurons encode both individual compounds and mixtures in a manner consistent with a simple model of receptor-ligand interactions. Although typical neurons did not accurately encode concentration over a large dynamic range, from population activity it was possible to reliably estimate the log-concentration of pure compounds over several orders of magnitude. For binary mixtures, simple models failed to accurately segment the individual components, largely because of the prevalence of neurons responsive to both components. By accounting for such overlaps during model tuning, we show that, from neuronal firing, one can accurately estimate log-concentration of both components, even when tested across widely varying concentrations. With this foundation, the difference of logarithms, log A - log B = log A/B, provides a natural mechanism to accurately estimate concentration ratios. Thus, we show that a biophysically plausible circuit model can reconstruct concentration ratios from observed neuronal firing, representing a powerful mechanism to separate stimulus identity from absolute concentration.

Kaposi's Sarcoma-Associated Herpesvirus Utilizes and Manipulates RNA N6-Adenosine Methylation To Promote Lytic Replication

PubMed Central

Chen, E. Ricky; Nilsen, Timothy W.

2017-01-01

ABSTRACT N6-adenosine methylation (m6A) is the most common posttranscriptional RNA modification in mammalian cells. We found that most transcripts encoded by the Kaposi's sarcoma-associated herpesvirus (KSHV) genome undergo m6A modification. The levels of m6A-modified mRNAs increased substantially upon stimulation for lytic replication. The blockage of m6A inhibited splicing of the pre-mRNA encoding the replication transcription activator (RTA), a key KSHV lytic switch protein, and halted viral lytic replication. We identified several m6A sites in RTA pre-mRNA crucial for splicing through interactions with YTH domain containing 1 (YTHDC1), an m6A nuclear reader protein, in conjunction with serine/arginine-rich splicing factor 3 (SRSF3) and SRSF10. Interestingly, RTA induced m6A and enhanced its own pre-mRNA splicing. Our results not only demonstrate an essential role of m6A in regulating RTA pre-mRNA splicing but also suggest that KSHV has evolved a mechanism to manipulate the host m6A machinery to its advantage in promoting lytic replication. IMPORTANCE KSHV productive lytic replication plays a pivotal role in the initiation and progression of Kaposi's sarcoma tumors. Previous studies suggested that the KSHV switch from latency to lytic replication is primarily controlled at the chromatin level through histone and DNA modifications. The present work reports for the first time that KSHV genome-encoded mRNAs undergo m6A modification, which represents a new mechanism at the posttranscriptional level in the control of viral replication. PMID:28592530

Information recall using relative spike timing in a spiking neural network.

PubMed

Sterne, Philip

2012-08-01

We present a neural network that is capable of completing and correcting a spiking pattern given only a partial, noisy version. It operates in continuous time and represents information using the relative timing of individual spikes. The network is capable of correcting and recalling multiple patterns simultaneously. We analyze the network's performance in terms of information recall. We explore two measures of the capacity of the network: one that values the accurate recall of individual spike times and another that values only the presence or absence of complete patterns. Both measures of information are found to scale linearly in both the number of neurons and the period of the patterns, suggesting these are natural measures of network information. We show a smooth transition from encodings that provide precise spike times to flexible encodings that can encode many scenes. This makes it plausible that many diverse tasks could be learned with such an encoding.

Fast and memory efficient text image compression with JBIG2.

PubMed

Ye, Yan; Cosman, Pamela

2003-01-01

In this paper, we investigate ways to reduce encoding time, memory consumption and substitution errors for text image compression with JBIG2. We first look at page striping where the encoder splits the input image into horizontal stripes and processes one stripe at a time. We propose dynamic dictionary updating procedures for page striping to reduce the bit rate penalty it incurs. Experiments show that splitting the image into two stripes can save 30% of encoding time and 40% of physical memory with a small coding loss of about 1.5%. Using more stripes brings further savings in time and memory but the return diminishes. We also propose an adaptive way to update the dictionary only when it has become out-of-date. The adaptive updating scheme can resolve the time versus bit rate tradeoff and the memory versus bit rate tradeoff well simultaneously. We then propose three speedup techniques for pattern matching, the most time-consuming encoding activity in JBIG2. When combined together, these speedup techniques can save up to 75% of the total encoding time with at most 1.7% of bit rate penalty. Finally, we look at improving reconstructed image quality for lossy compression. We propose enhanced prescreening and feature monitored shape unifying to significantly reduce substitution errors in the reconstructed images.

Enhancing Young Infants' Representations of Physical Events through Improved Retrieval (Not Encoding) of Information

ERIC Educational Resources Information Center

Wang, Su-hua; Onishi, Kristine H.

2017-01-01

Infants' representations of physical events are surprisingly flexible. Brief exposure to one event can immediately enhance infants' representations of another event. The present experiments tested two potential mechanisms underlying this priming: enhanced encoding or improved retrieval. Five-month-olds saw a target block become hidden inside a…

Binding an Event to Its Source at Encoding Improves Children's Source Monitoring

ERIC Educational Resources Information Center

Roberts, Kim P.; Evans, Angela D.; Duncanson, Sara

2016-01-01

Children learn information from a variety of sources and often remember the content but forget the source. Whereas the majority of research has focused on retrieval mechanisms for such difficulties, the present investigation examines whether the way in which sources are "encoded" influences future source monitoring. In Study 1, 86…

Sensitivity quantification of remote detection NMR and MRI

NASA Astrophysics Data System (ADS)

Granwehr, J.; Seeley, J. A.

2006-04-01

A sensitivity analysis is presented of the remote detection NMR technique, which facilitates the spatial separation of encoding and detection of spin magnetization. Three different cases are considered: remote detection of a transient signal that must be encoded point-by-point like a free induction decay, remote detection of an experiment where the transient dimension is reduced to one data point like phase encoding in an imaging experiment, and time-of-flight (TOF) flow visualization. For all cases, the sensitivity enhancement is proportional to the relative sensitivity between the remote detector and the circuit that is used for encoding. It is shown for the case of an encoded transient signal that the sensitivity does not scale unfavorably with the number of encoded points compared to direct detection. Remote enhancement scales as the square root of the ratio of corresponding relaxation times in the two detection environments. Thus, remote detection especially increases the sensitivity of imaging experiments of porous materials with large susceptibility gradients, which cause a rapid dephasing of transverse spin magnetization. Finally, TOF remote detection, in which the detection volume is smaller than the encoded fluid volume, allows partial images corresponding to different time intervals between encoding and detection to be recorded. These partial images, which contain information about the fluid displacement, can be recorded, in an ideal case, with the same sensitivity as the full image detected in a single step with a larger coil.

Quantum Image Processing and Its Application to Edge Detection: Theory and Experiment

NASA Astrophysics Data System (ADS)

Yao, Xi-Wei; Wang, Hengyan; Liao, Zeyang; Chen, Ming-Cheng; Pan, Jian; Li, Jun; Zhang, Kechao; Lin, Xingcheng; Wang, Zhehui; Luo, Zhihuang; Zheng, Wenqiang; Li, Jianzhong; Zhao, Meisheng; Peng, Xinhua; Suter, Dieter

2017-07-01

Processing of digital images is continuously gaining in volume and relevance, with concomitant demands on data storage, transmission, and processing power. Encoding the image information in quantum-mechanical systems instead of classical ones and replacing classical with quantum information processing may alleviate some of these challenges. By encoding and processing the image information in quantum-mechanical systems, we here demonstrate the framework of quantum image processing, where a pure quantum state encodes the image information: we encode the pixel values in the probability amplitudes and the pixel positions in the computational basis states. Our quantum image representation reduces the required number of qubits compared to existing implementations, and we present image processing algorithms that provide exponential speed-up over their classical counterparts. For the commonly used task of detecting the edge of an image, we propose and implement a quantum algorithm that completes the task with only one single-qubit operation, independent of the size of the image. This demonstrates the potential of quantum image processing for highly efficient image and video processing in the big data era.

Camouflage and visual perception

PubMed Central

Troscianko, Tom; Benton, Christopher P.; Lovell, P. George; Tolhurst, David J.; Pizlo, Zygmunt

2008-01-01

How does an animal conceal itself from visual detection by other animals? This review paper seeks to identify general principles that may apply in this broad area. It considers mechanisms of visual encoding, of grouping and object encoding, and of search. In most cases, the evidence base comes from studies of humans or species whose vision approximates to that of humans. The effort is hampered by a relatively sparse literature on visual function in natural environments and with complex foraging tasks. However, some general constraints emerge as being potentially powerful principles in understanding concealment—a ‘constraint’ here means a set of simplifying assumptions. Strategies that disrupt the unambiguous encoding of discontinuities of intensity (edges), and of other key visual attributes, such as motion, are key here. Similar strategies may also defeat grouping and object-encoding mechanisms. Finally, the paper considers how we may understand the processes of search for complex targets in complex scenes. The aim is to provide a number of pointers towards issues, which may be of assistance in understanding camouflage and concealment, particularly with reference to how visual systems can detect the shape of complex, concealed objects. PMID:18990671

Temporal coding in a silicon network of integrate-and-fire neurons.

PubMed

Liu, Shih-Chii; Douglas, Rodney

2004-09-01

Spatio-temporal processing of spike trains by neuronal networks depends on a variety of mechanisms distributed across synapses, dendrites, and somata. In natural systems, the spike trains and the processing mechanisms cohere though their common physical instantiation. This coherence is lost when the natural system is encoded for simulation on a general purpose computer. By contrast, analog VLSI circuits are, like neurons, inherently related by their real-time physics, and so, could provide a useful substrate for exploring neuronlike event-based processing. Here, we describe a hybrid analog-digital VLSI chip comprising a set of integrate-and-fire neurons and short-term dynamical synapses that can be configured into simple network architectures with some properties of neocortical neuronal circuits. We show that, despite considerable fabrication variance in the properties of individual neurons, the chip offers a viable substrate for exploring real-time spike-based processing in networks of neurons.

Large-scale network integration in the human brain tracks temporal fluctuations in memory encoding performance.

PubMed

Keerativittayayut, Ruedeerat; Aoki, Ryuta; Sarabi, Mitra Taghizadeh; Jimura, Koji; Nakahara, Kiyoshi

2018-06-18

Although activation/deactivation of specific brain regions have been shown to be predictive of successful memory encoding, the relationship between time-varying large-scale brain networks and fluctuations of memory encoding performance remains unclear. Here we investigated time-varying functional connectivity patterns across the human brain in periods of 30-40 s, which have recently been implicated in various cognitive functions. During functional magnetic resonance imaging, participants performed a memory encoding task, and their performance was assessed with a subsequent surprise memory test. A graph analysis of functional connectivity patterns revealed that increased integration of the subcortical, default-mode, salience, and visual subnetworks with other subnetworks is a hallmark of successful memory encoding. Moreover, multivariate analysis using the graph metrics of integration reliably classified the brain network states into the period of high (vs. low) memory encoding performance. Our findings suggest that a diverse set of brain systems dynamically interact to support successful memory encoding. © 2018, Keerativittayayut et al.

Imitation learning based on an intrinsic motivation mechanism for efficient coding

PubMed Central

Triesch, Jochen

2013-01-01

A hypothesis regarding the development of imitation learning is presented that is rooted in intrinsic motivations. It is derived from a recently proposed form of intrinsically motivated learning (IML) for efficient coding in active perception, wherein an agent learns to perform actions with its sense organs to facilitate efficient encoding of the sensory data. To this end, actions of the sense organs that improve the encoding of the sensory data trigger an internally generated reinforcement signal. Here it is argued that the same IML mechanism might also support the development of imitation when general actions beyond those of the sense organs are considered: The learner first observes a tutor performing a behavior and learns a model of the the behavior's sensory consequences. The learner then acts itself and receives an internally generated reinforcement signal reflecting how well the sensory consequences of its own behavior are encoded by the sensory model. Actions that are more similar to those of the tutor will lead to sensory signals that are easier to encode and produce a higher reinforcement signal. Through this, the learner's behavior is progressively tuned to make the sensory consequences of its actions match the learned sensory model. I discuss this mechanism in the context of human language acquisition and bird song learning where similar ideas have been proposed. The suggested mechanism also offers an account for the development of mirror neurons and makes a number of predictions. Overall, it establishes a connection between principles of efficient coding, intrinsic motivations and imitation. PMID:24204350

Emotional arousal and memory after deep encoding.

PubMed

Leventon, Jacqueline S; Camacho, Gabriela L; Ramos Rojas, Maria D; Ruedas, Angelica

2018-05-22

Emotion often enhances long-term memory. One mechanism for this enhancement is heightened arousal during encoding. However, reducing arousal, via emotion regulation (ER) instructions, has not been associated with reduced memory. In fact, the opposite pattern has been observed: stronger memory for emotional stimuli encoded with an ER instruction to reduce arousal. This pattern may be due to deeper encoding required by ER instructions. In the current research, we examine the effects of emotional arousal and deep-encoding on memory across three studies. In Study 1, adult participants completed a writing task (deep-encoding) for encoding negative, neutral, and positive picture stimuli, whereby half the emotion stimuli had the ER instruction to reduce the emotion. Memory was strong across conditions, and no memory enhancement was observed for any condition. In Study 2, adult participants completed the same writing task as Study 1, as well as a shallow-encoding task for one-third of negative, neutral, and positive trials. Memory was strongest for deep vs. shallow encoding trials, with no effects of emotion or ER instruction. In Study 3, adult participants completed a shallow-encoding task for negative, neutral, and positive stimuli, with findings indicating enhanced memory for negative emotional stimuli. Findings suggest that deep encoding must be acknowledged as a source of memory enhancement when examining manipulations of emotion-related arousal. Copyright © 2018. Published by Elsevier B.V.

Single-Molecule Encoders for Tracking Motor Proteins on DNA

NASA Astrophysics Data System (ADS)

Lipman, Everett A.

2012-02-01

Devices such as inkjet printers and disk drives track position and velocity using optical encoders, which produce periodic signals precisely synchronized with linear or rotational motion. We have implemented this technique at the nanometer scale by labeling DNA with regularly spaced fluorescent dyes. The resulting molecular encoders can be used in several ways for high-resolution continuous tracking of individual motor proteins. These measurements do not require mechanical coupling to macroscopic instrumentation, are automatically calibrated by the underlying structure of DNA, and depend on signal periodicity rather than absolute level. I will describe the synthesis of single-molecule encoders, data from and modeling of experiments on a helicase and a DNA polymerase, and some ideas for future work.

Grammatical constraints on phonological encoding in speech production.

PubMed

Heller, Jordana R; Goldrick, Matthew

2014-12-01

To better understand the influence of grammatical encoding on the retrieval and encoding of phonological word-form information during speech production, we examine how grammatical class constraints influence the activation of phonological neighbors (words phonologically related to the target--e.g., MOON, TWO for target TUNE). Specifically, we compare how neighbors that share a target's grammatical category (here, nouns) influence its planning and retrieval, assessed by picture naming latencies, and phonetic encoding, assessed by word productions in picture names, when grammatical constraints are strong (in sentence contexts) versus weak (bare naming). Within-category (noun) neighbors influenced planning time and phonetic encoding more strongly in sentence contexts. This suggests that grammatical encoding constrains phonological processing; the influence of phonological neighbors is grammatically dependent. Moreover, effects on planning times could not fully account for phonetic effects, suggesting that phonological interaction affects articulation after speech onset. These results support production theories integrating grammatical, phonological, and phonetic processes.

Photo-Induced Deformations of Liquid Crystal Elastomers

NASA Astrophysics Data System (ADS)

Dawson, Nathan; Kuzyk, Mark; Neal, Jeremy; Luchette, Paul; Palffy-Muhoray, Peter

2010-10-01

Over a century ago, Alexander Graham Bell transmitted mechanical information on a beam of light using the ``photophone.'' We report on the use of a Fabry-Perot interferometer to encode and detect mechanical information of an illuminated liquid crystal elastomer (LCE) that is placed at a critical point between the reflectors. Furthermore, we show that cascading of macroscopic LCE-interferometer devices is possible. These are the first steps in the creation of ultra smart materials. Such applications require materials with a large photomechanical response. Thus, understanding the underlying mechanisms is critical. Only limited studies of the mechanisms of photomechanical effects have been studied in azo-dye-doped LCEs. The focus of our present work is to use the Fabry-Perot transducer geometry to study the underlying mechanisms and to determine the relevant material parameters that are used to develop theoretical models of the response. We use various intensity-modulated optical wave forms to determine the frequency response of the material, which are used to predict the material response in the time domain.

Concurrent encoding of frequency and amplitude modulation in human auditory cortex: encoding transition.

PubMed

Luo, Huan; Wang, Yadong; Poeppel, David; Simon, Jonathan Z

2007-12-01

Complex natural sounds (e.g., animal vocalizations or speech) can be characterized by specific spectrotemporal patterns the components of which change in both frequency (FM) and amplitude (AM). The neural coding of AM and FM has been widely studied in humans and animals but typically with either pure AM or pure FM stimuli. The neural mechanisms employed to perceptually unify AM and FM acoustic features remain unclear. Using stimuli with simultaneous sinusoidal AM (at rate f(AM) = 37 Hz) and FM (with varying rates f(FM)), magnetoencephalography (MEG) is used to investigate the elicited auditory steady-state response (aSSR) at relevant frequencies (f(AM), f(FM), f(AM) + f(FM)). Previous work demonstrated that for sounds with slower FM dynamics (f(FM) < 5 Hz), the phase of the aSSR at f(AM) tracked the FM; in other words, AM and FM features were co-tracked and co-represented by "phase modulation" encoding. This study explores the neural coding mechanism for stimuli with faster FM dynamics (< or =30 Hz), demonstrating that at faster rates (f(FM) > 5 Hz), there is a transition from pure phase modulation encoding to a single-upper-sideband (SSB) response (at frequency f(AM) + f(FM)) pattern. We propose that this unexpected SSB response can be explained by the additional involvement of subsidiary AM encoding responses simultaneously to, and in quadrature with, the ongoing phase modulation. These results, using MEG to reveal a possible neural encoding of specific acoustic properties, demonstrate more generally that physiological tests of encoding hypotheses can be performed noninvasively on human subjects, complementing invasive, single-unit recordings in animals.

Characterization and developmental expression of genes encoding the early carotenoid biosynthetic enzymes in Citrus paradisi Macf.

PubMed

Costa, Marcio G C; Moreira, Cristina D; Melton, John R; Otoni, Wagner C; Moore, Gloria A

2012-02-01

In the present study, the full-length cDNA sequences of PSY, PDS, and ZDS, encoding the early carotenoid biosynthetic enzymes in the carotenoid pathway of grapefruit (Citrus paradisi), were isolated and characterized for the first time. CpPSY contained a 1311-bp open reading frame (ORF) encoding a polypeptide of 436 amino acids, CpPDS contained a 1659-bp ORF encoding a polypeptide of 552 amino acids, and CpZDS contained a 1713-bp ORF encoding a polypeptide of 570 amino acids. Phylogenetic analysis indicated that CpPSY shares homology with PSYs from Citrus, tomato, pepper, Arabidopsis, and the monocot PSY1 group, while CpPDS and CpZDS are most closely related to orthologs from Citrus and tomato. Expression analysis revealed fluctuations in CpPSY, CpPDS, and CpZDS transcript abundance and a non-coordinated regulation between the former and the two latter genes during fruit development in albedo and juice vesicles of white ('Duncan') and red ('Flame') grapefruits. A 3× higher upregulation of CpPSY expression in juice vesicles of red-fleshed 'Flame' as compared to white-fruited 'Duncan' was observed in the middle stages of fruit development, which correlates with the well documented accumulation pattern of lycopene in red grapefruit. Together with previous data, our results suggest that the primary mechanism controlling lycopene accumulation in red grapefruit involves the transcriptional upregulation of CpPSY, which controls the flux into the carotenoid pathway, and the downregulated expression of CpLCYB2, which controls the step of cyclization of lycopene in chromoplasts during fruit ripening. A correlation between CpPSY expression and fruit color evolution in red grapefruit is demonstrated.

Identification and Characterization of Three Differentially Expressed Genes, Encoding S-Adenosylhomocysteine Hydrolase, Methionine Aminopeptidase, and a Histone-Like Protein, in the Toxic Dinoflagellate Alexandrium fundyense†

PubMed Central

Taroncher-Oldenburg, Gaspar; Anderson, Donald M.

2000-01-01

Genes showing differential expression related to the early G1 phase of the cell cycle during synchronized circadian growth of the toxic dinoflagellate Alexandrium fundyense were identified and characterized by differential display (DD). The determination in our previous work that toxin production in Alexandrium is relegated to a narrow time frame in early G1 led to the hypothesis that transcriptionally up- or downregulated genes during this subphase of the cell cycle might be related to toxin biosynthesis. Three genes, encoding S-adenosylhomocysteine hydrolase (Sahh), methionine aminopeptidase (Map), and a histone-like protein (HAf), were isolated. Sahh was downregulated, while Map and HAf were upregulated, during the early G1 phase of the cell cycle. Sahh and Map encoded amino acid sequences with about 90 and 70% similarity to those encoded by several eukaryotic and prokaryotic Sahh and Map genes, respectively. The partial Map sequence also contained three cobalt binding motifs characteristic of all Map genes. HAf encoded an amino acid sequence with 60% similarity to those of two histone-like proteins from the dinoflagellate Crypthecodinium cohnii Biecheler. This study documents the potential of applying DD to the identification of genes that are related to physiological processes or cell cycle events in phytoplankton under conditions where small sample volumes represent an experimental constraint. The identification of an additional 21 genes with various cell cycle-related DD patterns also provides evidence for the importance of pretranslational or transcriptional regulation in dinoflagellates, contrary to previous reports suggesting the possibility that translational mechanisms are the primary means of circadian regulation in this group of organisms. PMID:10788388

Timing: An Attribute of Associative Learning

PubMed Central

Molet, Mikael; Miller, Ralph R.

2013-01-01

The evidence reviewed in this paper suggests that when two events occur in spatiotemporal proximity to one another, an association between the two events is formed which encodes the timing of the events in relation to one another (including duration, order, and interval). The primary evidence supporting the view that temporal relationships are encoded is that subsequent presentation of one event ordinarily elicits behavior indicative of an expectation of the other event at a specific time. Thus, temporal relationships appear to be one of several attributes encoded at acquisition. PMID:23751257

Episodic Memory Encoding Interferes with Reward Learning and Decreases Striatal Prediction Errors

PubMed Central

Braun, Erin Kendall; Daw, Nathaniel D.

2014-01-01

Learning is essential for adaptive decision making. The striatum and its dopaminergic inputs are known to support incremental reward-based learning, while the hippocampus is known to support encoding of single events (episodic memory). Although traditionally studied separately, in even simple experiences, these two types of learning are likely to co-occur and may interact. Here we sought to understand the nature of this interaction by examining how incremental reward learning is related to concurrent episodic memory encoding. During the experiment, human participants made choices between two options (colored squares), each associated with a drifting probability of reward, with the goal of earning as much money as possible. Incidental, trial-unique object pictures, unrelated to the choice, were overlaid on each option. The next day, participants were given a surprise memory test for these pictures. We found that better episodic memory was related to a decreased influence of recent reward experience on choice, both within and across participants. fMRI analyses further revealed that during learning the canonical striatal reward prediction error signal was significantly weaker when episodic memory was stronger. This decrease in reward prediction error signals in the striatum was associated with enhanced functional connectivity between the hippocampus and striatum at the time of choice. Our results suggest a mechanism by which memory encoding may compete for striatal processing and provide insight into how interactions between different forms of learning guide reward-based decision making. PMID:25378157

Transcriptome analysis of Neisseria meningitidis in human whole blood and mutagenesis studies identify virulence factors involved in blood survival.

PubMed

Echenique-Rivera, Hebert; Muzzi, Alessandro; Del Tordello, Elena; Seib, Kate L; Francois, Patrice; Rappuoli, Rino; Pizza, Mariagrazia; Serruto, Davide

2011-05-01

During infection Neisseria meningitidis (Nm) encounters multiple environments within the host, which makes rapid adaptation a crucial factor for meningococcal survival. Despite the importance of invasion into the bloodstream in the meningococcal disease process, little is known about how Nm adapts to permit survival and growth in blood. To address this, we performed a time-course transcriptome analysis using an ex vivo model of human whole blood infection. We observed that Nm alters the expression of ≈30% of ORFs of the genome and major dynamic changes were observed in the expression of transcriptional regulators, transport and binding proteins, energy metabolism, and surface-exposed virulence factors. In particular, we found that the gene encoding the regulator Fur, as well as all genes encoding iron uptake systems, were significantly up-regulated. Analysis of regulated genes encoding for surface-exposed proteins involved in Nm pathogenesis allowed us to better understand mechanisms used to circumvent host defenses. During blood infection, Nm activates genes encoding for the factor H binding proteins, fHbp and NspA, genes encoding for detoxifying enzymes such as SodC, Kat and AniA, as well as several less characterized surface-exposed proteins that might have a role in blood survival. Through mutagenesis studies of a subset of up-regulated genes we were able to identify new proteins important for survival in human blood and also to identify additional roles of previously known virulence factors in aiding survival in blood. Nm mutant strains lacking the genes encoding the hypothetical protein NMB1483 and the surface-exposed proteins NalP, Mip and NspA, the Fur regulator, the transferrin binding protein TbpB, and the L-lactate permease LctP were sensitive to killing by human blood. This increased knowledge of how Nm responds to adaptation in blood could also be helpful to develop diagnostic and therapeutic strategies to control the devastating disease cause by this microorganism.

Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival

PubMed Central

Del Tordello, Elena; Seib, Kate L.; Francois, Patrice; Rappuoli, Rino; Pizza, Mariagrazia; Serruto, Davide

2011-01-01

During infection Neisseria meningitidis (Nm) encounters multiple environments within the host, which makes rapid adaptation a crucial factor for meningococcal survival. Despite the importance of invasion into the bloodstream in the meningococcal disease process, little is known about how Nm adapts to permit survival and growth in blood. To address this, we performed a time-course transcriptome analysis using an ex vivo model of human whole blood infection. We observed that Nm alters the expression of ≈30% of ORFs of the genome and major dynamic changes were observed in the expression of transcriptional regulators, transport and binding proteins, energy metabolism, and surface-exposed virulence factors. In particular, we found that the gene encoding the regulator Fur, as well as all genes encoding iron uptake systems, were significantly up-regulated. Analysis of regulated genes encoding for surface-exposed proteins involved in Nm pathogenesis allowed us to better understand mechanisms used to circumvent host defenses. During blood infection, Nm activates genes encoding for the factor H binding proteins, fHbp and NspA, genes encoding for detoxifying enzymes such as SodC, Kat and AniA, as well as several less characterized surface-exposed proteins that might have a role in blood survival. Through mutagenesis studies of a subset of up-regulated genes we were able to identify new proteins important for survival in human blood and also to identify additional roles of previously known virulence factors in aiding survival in blood. Nm mutant strains lacking the genes encoding the hypothetical protein NMB1483 and the surface-exposed proteins NalP, Mip and NspA, the Fur regulator, the transferrin binding protein TbpB, and the L-lactate permease LctP were sensitive to killing by human blood. This increased knowledge of how Nm responds to adaptation in blood could also be helpful to develop diagnostic and therapeutic strategies to control the devastating disease cause by this microorganism. PMID:21589640

Weight and power savings shaft encoder interfacing techniques for aerospace applications

NASA Technical Reports Server (NTRS)

Breslow, Donald H.

1986-01-01

Many aerospace applications for shaft angle digitizers such as optical shaft encoders require special features that are not usually required on commercial products. Among the most important user considerations are the lowest possible weight and power consumption. A variety of mechanical and electrical interface techniques that have large potential weight and power savings are described. The principles to be presented apply to a wide variety of encoders, ranging from 16 to 22 bit resolution and with diameters from 152 to 380 mm (6 to 15 in.).

Different Topological Properties of EEG-Derived Networks Describe Working Memory Phases as Revealed by Graph Theoretical Analysis

PubMed Central

Toppi, Jlenia; Astolfi, Laura; Risetti, Monica; Anzolin, Alessandra; Kober, Silvia E.; Wood, Guilherme; Mattia, Donatella

2018-01-01

Several non-invasive imaging methods have contributed to shed light on the brain mechanisms underlying working memory (WM). The aim of the present study was to depict the topology of the relevant EEG-derived brain networks associated to distinct operations of WM function elicited by the Sternberg Item Recognition Task (SIRT) such as encoding, storage, and retrieval in healthy, middle age (46 ± 5 years) adults. High density EEG recordings were performed in 17 participants whilst attending a visual SIRT. Neural correlates of WM were assessed by means of a combination of EEG signal processing methods (i.e., time-varying connectivity estimation and graph theory), in order to extract synthetic descriptors of the complex networks underlying the encoding, storage, and retrieval phases of WM construct. The group analysis revealed that the encoding phase exhibited a significantly higher small-world topology of EEG networks with respect to storage and retrieval in all EEG frequency oscillations, thus indicating that during the encoding of items the global network organization could “optimally” promote the information flow between WM sub-networks. We also found that the magnitude of such configuration could predict subject behavioral performance when memory load increases as indicated by the negative correlation between Reaction Time and the local efficiency values estimated during the encoding in the alpha band in both 4 and 6 digits conditions. At the local scale, the values of the degree index which measures the degree of in- and out- information flow between scalp areas were found to specifically distinguish the hubs within the relevant sub-networks associated to each of the three different WM phases, according to the different role of the sub-network of regions in the different WM phases. Our findings indicate that the use of EEG-derived connectivity measures and their related topological indices might offer a reliable and yet affordable approach to monitor WM components and thus theoretically support the clinical assessment of cognitive functions in presence of WM decline/impairment, as it occurs after stroke. PMID:29379425

Transcriptional Analysis of a Whole-Body Form of Long-Term Habituation in "Aplysia Californica"

ERIC Educational Resources Information Center

Holmes, Geraldine; Herdegen, Samantha; Schuon, Jonathan; Cyriac, Ashly; Lass, Jamie; Conte, Catherine; Calin-Jageman, Irina E.; Calin-Jageman, Robert J.

2015-01-01

Habituation is the simplest form of learning, but we know little about the transcriptional mechanisms that encode long-term habituation memory. A key obstacle is that habituation is relatively stimulus-specific and is thus encoded in small sets of neurons, providing poor signal/noise ratios for transcriptional analysis. To overcome this obstacle,…

Glucose Administration Enhances fMRI Brain Activation and Connectivity Related to Episodic Memory Encoding for Neutral and Emotional Stimuli

ERIC Educational Resources Information Center

Parent, Marise B.; Krebs-Kraft, Desiree L.; Ryan, John P.; Wilson, Jennifer S.; Harenski, Carla; Hamann, Stephan

2011-01-01

Glucose enhances memory in a variety of species. In humans, glucose administration enhances episodic memory encoding, although little is known regarding the neural mechanisms underlying these effects. Here we examined whether elevating blood glucose would enhance functional MRI (fMRI) activation and connectivity in brain regions associated with…

Multidimensional analysis of the abnormal neural oscillations associated with lexical processing in schizophrenia.

PubMed

Xu, Tingting; Stephane, Massoud; Parhi, Keshab K

2013-04-01

The neural mechanisms of language abnormalities, the core symptoms in schizophrenia, remain unclear. In this study, a new experimental paradigm, combining magnetoencephalography (MEG) techniques and machine intelligence methodologies, was designed to gain knowledge about the frequency, brain location, and time of occurrence of the neural oscillations that are associated with lexical processing in schizophrenia. The 248-channel MEG recordings were obtained from 12 patients with schizophrenia and 10 healthy controls, during a lexical processing task, where the patients discriminated correct from incorrect lexical stimuli that were visually presented. Event-related desynchronization/synchronization (ERD/ERS) was computed along the frequency, time, and space dimensions combined, that resulted in a large spectral-spatial-temporal ERD/ERS feature set. Machine intelligence techniques were then applied to select a small subset of oscillation patterns that are abnormal in patients with schizophrenia, according to their discriminating power in patient and control classification. Patients with schizophrenia showed abnormal ERD/ERS patterns during both lexical encoding and post-encoding periods. The top-ranked features were located at the occipital and left frontal-temporal areas, and covered a wide frequency range, including δ (1-4 Hz), α (8-12 Hz), β (12-32 Hz), and γ (32-48 Hz) bands. These top features could discriminate the patient group from the control group with 90.91% high accuracy, which demonstrates significant brain oscillation abnormalities in patients with schizophrenia at the specific frequency, time, and brain location indicated by these top features. As neural oscillation abnormality may be due to the mechanisms of the disease, the spectral, spatial, and temporal content of the discriminating features can offer useful information for helping understand the physiological basis of the language disorder in schizophrenia, as well as the pathology of the disease itself.

Robotic Observatory System Design-Specification Considerations for Achieving Long-Term Sustainable Precision Performance

NASA Astrophysics Data System (ADS)

Wray, J. D.

2003-05-01

The robotic observatory telescope must point precisely on the target object, and then track autonomously to a fraction of the FWHM of the system PSF for durations of ten to twenty minutes or more. It must retain this precision while continuing to function at rates approaching thousands of observations per night for all its years of useful life. These stringent requirements raise new challenges unique to robotic telescope systems design. Critical design considerations are driven by the applicability of the above requirements to all systems of the robotic observatory, including telescope and instrument systems, telescope-dome enclosure systems, combined electrical and electronics systems, environmental (e.g. seeing) control systems and integrated computer control software systems. Traditional telescope design considerations include the effects of differential thermal strain, elastic flexure, plastic flexure and slack or backlash with respect to focal stability, optical alignment and angular pointing and tracking precision. Robotic observatory design must holistically encapsulate these traditional considerations within the overall objective of maximized long-term sustainable precision performance. This overall objective is accomplished through combining appropriate mechanical and dynamical system characteristics with a full-time real-time telescope mount model feedback computer control system. Important design considerations include: identifying and reducing quasi-zero-backlash; increasing size to increase precision; directly encoding axis shaft rotation; pointing and tracking operation via real-time feedback between precision mount model and axis mounted encoders; use of monolithic construction whenever appropriate for sustainable mechanical integrity; accelerating dome motion to eliminate repetitive shock; ducting internal telescope air to outside dome; and the principal design criteria: maximizing elastic repeatability while minimizing slack, plastic deformation and hysteresis to facilitate long-term repeatably precise pointing and tracking performance.

Polymyxins: Antibacterial Activity, Susceptibility Testing, and Resistance Mechanisms Encoded by Plasmids or Chromosomes

PubMed Central

Jayol, Aurélie; Nordmann, Patrice

2017-01-01

SUMMARY Polymyxins are well-established antibiotics that have recently regained significant interest as a consequence of the increasing incidence of infections due to multidrug-resistant Gram-negative bacteria. Colistin and polymyxin B are being seriously reconsidered as last-resort antibiotics in many areas where multidrug resistance is observed in clinical medicine. In parallel, the heavy use of polymyxins in veterinary medicine is currently being reconsidered due to increased reports of polymyxin-resistant bacteria. Susceptibility testing is challenging with polymyxins, and currently available techniques are presented here. Genotypic and phenotypic methods that provide relevant information for diagnostic laboratories are presented. This review also presents recent works in relation to recently identified mechanisms of polymyxin resistance, including chromosomally encoded resistance traits as well as the recently identified plasmid-encoded polymyxin resistance determinant MCR-1. Epidemiological features summarizing the current knowledge in that field are presented. PMID:28275006

AtMRP1 gene of Arabidopsis encodes a glutathione S-conjugate pump: isolation and functional definition of a plant ATP-binding cassette transporter gene.

PubMed

Lu, Y P; Li, Z S; Rea, P A

1997-07-22

Because plants produce cytotoxic compounds to which they, themselves, are susceptible and are exposed to exogenous toxins (microbial products, allelochemicals, and agrochemicals), cell survival is contingent on mechanisms for detoxifying these agents. One detoxification mechanism is the glutathione S-transferase-catalyzed glutathionation of the toxin, or an activated derivative, and transport of the conjugate out of the cytosol. We show here that a transporter responsible for the removal of glutathione S-conjugates from the cytosol, a specific Mg2+-ATPase, is encoded by the AtMRP1 gene of Arabidopsis thaliana. The sequence of AtMRP1 and the transport capabilities of membranes prepared from yeast cells transformed with plasmid-borne AtMRP1 demonstrate that this gene encodes an ATP-binding cassette transporter competent in the transport of glutathione S-conjugates of xenobiotics and endogenous substances, including herbicides and anthocyanins.

Selective scanpath repetition during memory-guided visual search.

PubMed

Wynn, Jordana S; Bone, Michael B; Dragan, Michelle C; Hoffman, Kari L; Buchsbaum, Bradley R; Ryan, Jennifer D

2016-01-02

Visual search efficiency improves with repetition of a search display, yet the mechanisms behind these processing gains remain unclear. According to Scanpath Theory, memory retrieval is mediated by repetition of the pattern of eye movements or "scanpath" elicited during stimulus encoding. Using this framework, we tested the prediction that scanpath recapitulation reflects relational memory guidance during repeated search events. Younger and older subjects were instructed to find changing targets within flickering naturalistic scenes. Search efficiency (search time, number of fixations, fixation duration) and scanpath similarity (repetition) were compared across age groups for novel (V1) and repeated (V2) search events. Younger adults outperformed older adults on all efficiency measures at both V1 and V2, while the search time benefit for repeated viewing (V1-V2) did not differ by age. Fixation-binned scanpath similarity analyses revealed repetition of initial and final (but not middle) V1 fixations at V2, with older adults repeating more initial V1 fixations than young adults. In young adults only, early scanpath similarity correlated negatively with search time at test, indicating increased efficiency, whereas the similarity of V2 fixations to middle V1 fixations predicted poor search performance. We conclude that scanpath compression mediates increased search efficiency by selectively recapitulating encoding fixations that provide goal-relevant input. Extending Scanpath Theory, results suggest that scanpath repetition varies as a function of time and memory integrity.

Continuous-variable quantum computing in optical time-frequency modes using quantum memories.

PubMed

Humphreys, Peter C; Kolthammer, W Steven; Nunn, Joshua; Barbieri, Marco; Datta, Animesh; Walmsley, Ian A

2014-09-26

We develop a scheme for time-frequency encoded continuous-variable cluster-state quantum computing using quantum memories. In particular, we propose a method to produce, manipulate, and measure two-dimensional cluster states in a single spatial mode by exploiting the intrinsic time-frequency selectivity of Raman quantum memories. Time-frequency encoding enables the scheme to be extremely compact, requiring a number of memories that are a linear function of only the number of different frequencies in which the computational state is encoded, independent of its temporal duration. We therefore show that quantum memories can be a powerful component for scalable photonic quantum information processing architectures.

MobileASL: intelligibility of sign language video over mobile phones.

PubMed

Cavender, Anna; Vanam, Rahul; Barney, Dane K; Ladner, Richard E; Riskin, Eve A

2008-01-01

For Deaf people, access to the mobile telephone network in the United States is currently limited to text messaging, forcing communication in English as opposed to American Sign Language (ASL), the preferred language. Because ASL is a visual language, mobile video phones have the potential to give Deaf people access to real-time mobile communication in their preferred language. However, even today's best video compression techniques can not yield intelligible ASL at limited cell phone network bandwidths. Motivated by this constraint, we conducted one focus group and two user studies with members of the Deaf Community to determine the intelligibility effects of video compression techniques that exploit the visual nature of sign language. Inspired by eye tracking results that show high resolution foveal vision is maintained around the face, we studied region-of-interest encodings (where the face is encoded at higher quality) as well as reduced frame rates (where fewer, better quality, frames are displayed every second). At all bit rates studied here, participants preferred moderate quality increases in the face region, sacrificing quality in other regions. They also preferred slightly lower frame rates because they yield better quality frames for a fixed bit rate. The limited processing power of cell phones is a serious concern because a real-time video encoder and decoder will be needed. Choosing less complex settings for the encoder can reduce encoding time, but will affect video quality. We studied the intelligibility effects of this tradeoff and found that we can significantly speed up encoding time without severely affecting intelligibility. These results show promise for real-time access to the current low-bandwidth cell phone network through sign-language-specific encoding techniques.

Lexical stress encoding in single word production estimated by event-related brain potentials.

PubMed

Schiller, Niels O

2006-09-27

An event-related brain potentials (ERPs) experiment was carried out to investigate the time course of lexical stress encoding in language production. Native speakers of Dutch viewed a series of pictures corresponding to bisyllabic names which were either stressed on the first or on the second syllable and made go/no-go decisions on the lexical stress location of those picture names. Behavioral results replicated a pattern that was observed earlier, i.e. faster button-press latencies to initial as compared to final stress targets. The electrophysiological results indicated that participants could make a lexical stress decision significantly earlier when picture names had initial than when they had final stress. Moreover, the present data suggest the time course of lexical stress encoding during single word form formation in language production. When word length is corrected for, the temporal interval for lexical stress encoding specified by the current ERP results falls into the time window previously identified for phonological encoding in language production.

The effects of divided attention on encoding processes under incidental and intentional learning instructions: underlying mechanisms?

PubMed

Naveh-Benjamin, Moshe; Guez, Jonathan; Hara, Yoko; Brubaker, Matthew S; Lowenschuss-Erlich, Iris

2014-01-01

Divided attention (DA) at encoding has been shown to significantly disrupt later memory for the studied information. However, what type of processing gets disrupted during DA remains unresolved. In this study, we assessed the degree to which strategic effortful processes are affected under DA by comparing the effects of DA at encoding under intentional and pure incidental learning instructions. In three experiments, participants studied list of words or word pairs under either full or divided attention. Results of three experiments, which used different methodologies, converged to show that the effects of DA at encoding reduce memory performance to the same degree under incidental and intentional learning. Secondary task performance indicated that encoding under intentional learning instructions was more effortful than under incidental learning instructions. In addition, the results indicated enhanced attention to the initial appearance of the words under both types of learning instructions. Results are interpreted to imply that other processes, rather than only strategic effortful ones, might be affected by DA at encoding.

Polymers mediate a one-pot route for functionalized quantum dot barcodes with a large encoding capacity.

PubMed

Zhang, Ding Sheng-Zi; Jiang, Yang; Wei, Dan; Wei, Xunbin; Xu, Hong; Gu, Hongchen

2018-06-21

With the increasing demands for high-throughput multiplexed bioassays, quantum dot (QD)-encoded microbeads as biocarriers for various bioreactions have attracted considerable attention. However, three key requirements for these biocarriers are still longstanding issues: a stable fluorescence intensity, a large encoding capacity and abundant surface functional groups. Here, a novel one-pot strategy is developed, generating functionalized QD-encoded microspheres with a strong fluorescence intensity and optical stability. With poly(styrene-co-maleic anhydride) (PSMA) molecules as mediators, the encapsulation of QDs and carboxylation of the bead surface are integrated together, greatly improving the preparation efficiency and guaranteeing their potential application in biodetection. Moreover, the mechanism for preparing QD-doped beads is further proposed, which helps to precisely manipulate the preparation process and accurately encode the beads. Through this approach, a single- and dual-color barcode library of QD-encoded microspheres has been successfully established, which demonstrates their great potential in suspension arrays.

Osteocyte calcium signals encode strain magnitude and loading frequency in vivo.

PubMed

Lewis, Karl J; Frikha-Benayed, Dorra; Louie, Joyce; Stephen, Samuel; Spray, David C; Thi, Mia M; Seref-Ferlengez, Zeynep; Majeska, Robert J; Weinbaum, Sheldon; Schaffler, Mitchell B

2017-10-31

Osteocytes are considered to be the major mechanosensory cells of bone, but how osteocytes in vivo process, perceive, and respond to mechanical loading remains poorly understood. Intracellular calcium (Ca 2+ ) signaling resulting from mechanical stimulation has been widely studied in osteocytes in vitro and in bone explants, but has yet to be examined in vivo. This is achieved herein by using a three-point bending device which is capable of delivering well-defined mechanical loads to metatarsal bones of living mice while simultaneously monitoring the intracellular Ca 2+ responses of individual osteocytes by using a genetically encoded fluorescent Ca 2+ indicator. Osteocyte responses are imaged by using multiphoton fluorescence microscopy. We investigated the in vivo responses of osteocytes to strains ranging from 250 to 3,000 [Formula: see text] and frequencies from 0.5 to 2 Hz, which are characteristic of physiological conditions reported for bone. At all loading frequencies examined, the number of responding osteocytes increased strongly with applied strain magnitude. However, Ca 2+ intensity within responding osteocytes did not change significantly with physiological loading magnitudes. Our studies offer a glimpse into how these critical bone cells respond to mechanical load in vivo, as well as provide a technique to determine how the cells encode magnitude and frequency of loading. Published under the PNAS license.

A MPEG-4 encoder based on TMS320C6416

NASA Astrophysics Data System (ADS)

Li, Gui-ju; Liu, Wei-ning

2013-08-01

Engineering and products need to achieve real-time video encoding by DSP, but the high computational complexity and huge amount of data requires that system has high data throughput. In this paper, a real-time MPEG-4 video encoder is designed based on TMS320C6416 platform. The kernel is the DSP of TMS320C6416T and FPGA chip f as the organization and management of video data. In order to control the flow of input and output data. Encoded stream is output using the synchronous serial port. The system has the clock frequency of 1GHz and has up to 8000 MIPS speed processing capacity when running at full speed. Due to the low coding efficiency of MPEG-4 video encoder transferred directly to DSP platform, it is needed to improve the program structure, data structures and algorithms combined with TMS320C6416T characteristics. First: Design the image storage architecture by balancing the calculation spending, storage space cost and EDMA read time factors. Open up a more buffer in memory, each buffer cache 16 lines of video data to be encoded, reconstruction image and reference image including search range. By using the variable alignment mode of the DSP, modifying the definition of structure variables and change the look-up table which occupy larger space with a direct calculation array to save memory space. After the program structure optimization, the program code, all variables, buffering buffers and the interpolation image including the search range can be placed in memory. Then, as to the time-consuming process modules and some functions which are called many times, the corresponding modules are written in parallel assembly language of TMS320C6416T which can increase the running speed. Besides, the motion estimation algorithm is improved by using a cross-hexagon search algorithm, The search speed can be increased obviously. Finally, the execution time, signal-to-noise ratio and compression ratio of a real-time image acquisition sequence is given. The experimental results show that the designed encoder in this paper can accomplish real-time encoding of a 768× 576, 25 frames per second grayscale video. The code rate is 1.5M bits per second.

Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins

PubMed Central

Soler, Nicolas; Marguet, Evelyne; Cortez, Diego; Desnoues, Nicole; Keller, Jenny; van Tilbeurgh, Herman; Sezonov, Guennadi; Forterre, Patrick

2010-01-01

Thermococcales (phylum Euryarchaeota) are model organisms for physiological and molecular studies of hyperthermophiles. Here we describe three new plasmids from Thermococcales that could provide new tools and model systems for genetic and molecular studies in Archaea. The plasmids pTN2 from Thermococcus nautilus sp. 30-1 and pP12-1 from Pyrococcus sp. 12-1 belong to the same family. They have similar size (∼12 kb) and share six genes, including homologues of genes encoded by the virus PAV1 from Pyrococcus abyssi. The plasmid pT26-2 from Thermococcus sp. 26-2 (21.5 kb), that corresponds to another plasmid family, encodes many proteins having homologues in virus-like elements integrated in several genomes of Thermococcales and Methanococcales. Our analyses confirm that viruses and plasmids are evolutionary related and co-evolve with their hosts. Whereas all plasmids previously isolated from Thermococcales replicate by the rolling circle mechanism, the three plasmids described here probably replicate by the theta mechanism. The plasmids pTN2 and pP12-1 encode a putative helicase of the SFI superfamily and a new family of DNA polymerase, whose activity was demonstrated in vitro, whereas pT26-2 encodes a putative new type of helicase. This strengthens the idea that plasmids and viruses are a reservoir of novel protein families involved in DNA replication. PMID:20403814

Reward modulation of hippocampal subfield activation during successful associative encoding and retrieval

PubMed Central

Wolosin, Sasha M.; Zeithamova, Dagmar; Preston, Alison R.

2012-01-01

Emerging evidence suggests that motivation enhances episodic memory formation through interactions between medial temporal lobe (MTL) structures and dopaminergic midbrain. In addition, recent theories propose that motivation specifically facilitates hippocampal associative binding processes, resulting in more detailed memories that are readily reinstated from partial input. Here, we used high-resolution functional magnetic resonance imaging to determine how motivation influences associative encoding and retrieval processes within human MTL subregions and dopaminergic midbrain. Participants intentionally encoded object associations under varying conditions of reward and performed a retrieval task during which studied associations were cued from partial input. Behaviorally, cued recall performance was superior for high-value relative to low-value associations; however, participants differed in the degree to which rewards influenced memory. The magnitude of behavioral reward modulation was associated with reward-related activation changes in dentate gyrus/CA2,3 during encoding and enhanced functional connectivity between dentate gyrus/CA2,3 and dopaminergic midbrain during both the encoding and retrieval phases of the task. These findings suggests that within the hippocampus, reward-based motivation specifically enhances dentate gyrus/CA2,3 associative encoding mechanisms through interactions with dopaminergic midbrain. Furthermore, within parahippocampal cortex and dopaminergic midbrain regions, activation associated with successful memory formation was modulated by reward across the group. During the retrieval phase, we also observed enhanced activation in hippocampus and dopaminergic midbrain for high-value associations that occurred in the absence of any explicit cues to reward. Collectively, these findings shed light on fundamental mechanisms through which reward impacts associative memory formation and retrieval through facilitation of MTL and VTA/SN processing. PMID:22524296

Neural Mechanisms of Context Effects on Face Recognition: Automatic Binding and Context Shift Decrements

PubMed Central

Hayes, Scott M.; Baena, Elsa; Truong, Trong-Kha; Cabeza, Roberto

2011-01-01

Although people do not normally try to remember associations between faces and physical contexts, these associations are established automatically, as indicated by the difficulty of recognizing familiar faces in different contexts (“butcher-on-the-bus” phenomenon). The present functional MRI (fMRI) study investigated the automatic binding of faces and scenes. In the Face-Face (F-F) condition, faces were presented alone during both encoding and retrieval, whereas in the Face/Scene-Face (FS-F) condition, they were presented overlaid on scenes during encoding but alone during retrieval (context change). Although participants were instructed to focus only on the faces during both encoding and retrieval, recognition performance was worse in the FS-F than the F-F condition (“context shift decrement”—CSD), confirming automatic face-scene binding during encoding. This binding was mediated by the hippocampus as indicated by greater subsequent memory effects (remembered > forgotten) in this region for the FS-F than the F-F condition. Scene memory was mediated by the right parahippocampal cortex, which was reactivated during successful retrieval when the faces were associated with a scene during encoding (FS-F condition). Analyses using the CSD as a regressor yielded a clear hemispheric asymmetry in medial temporal lobe activity during encoding: left hippocampal and parahippocampal activity was associated with a smaller CSD, indicating more flexible memory representations immune to context changes, whereas right hippocampal/rhinal activity was associated with a larger CSD, indicating less flexible representations sensitive to context change. Taken together, the results clarify the neural mechanisms of context effects on face recognition. PMID:19925208

ERP Correlates of Encoding Success and Encoding Selectivity in Attention Switching

PubMed Central

Yeung, Nick

2016-01-01

Long-term memory encoding depends critically on effective processing of incoming information. The degree to which participants engage in effective encoding can be indexed in electroencephalographic (EEG) data by studying event-related potential (ERP) subsequent memory effects. The current study investigated ERP correlates of memory success operationalised with two different measures—memory selectivity and global memory—to assess whether previously observed ERP subsequent memory effects reflect focused encoding of task-relevant information (memory selectivity), general encoding success (global memory), or both. Building on previous work, the present study combined an attention switching paradigm—in which participants were presented with compound object-word stimuli and switched between attending to the object or the word across trials—with a later recognition memory test for those stimuli, while recording their EEG. Our results provided clear evidence that subsequent memory effects resulted from selective attentional focusing and effective top-down control (memory selectivity) in contrast to more general encoding success effects (global memory). Further analyses addressed the question of whether successful encoding depended on similar control mechanisms to those involved in attention switching. Interestingly, differences in the ERP correlates of attention switching and successful encoding, particularly during the poststimulus period, indicated that variability in encoding success occurred independently of prestimulus demands for top-down cognitive control. These results suggest that while effects of selective attention and selective encoding co-occur behaviourally their ERP correlates are at least partly dissociable. PMID:27907075

L-rhamnose induction of Aspergillus nidulans α-L-rhamnosidase genes is glucose repressed via a CreA-independent mechanism acting at the level of inducer uptake.

PubMed

Tamayo-Ramos, Juan A; Flipphi, Michel; Pardo, Ester; Manzanares, Paloma; Orejas, Margarita

2012-02-21

Little is known about the structure and regulation of fungal α-L-rhamnosidase genes despite increasing interest in the biotechnological potential of the enzymes that they encode. Whilst the paradigmatic filamentous fungus Aspergillus nidulans growing on L-rhamnose produces an α-L-rhamnosidase suitable for oenological applications, at least eight genes encoding putative α-L-rhamnosidases have been found in its genome. In the current work we have identified the gene (rhaE) encoding the former activity, and characterization of its expression has revealed a novel regulatory mechanism. A shared pattern of expression has also been observed for a second α-L-rhamnosidase gene, (AN10277/rhaA). Amino acid sequence data for the oenological α-L-rhamnosidase were determined using MALDI-TOF mass spectrometry and correspond to the amino acid sequence deduced from AN7151 (rhaE). The cDNA of rhaE was expressed in Saccharomyces cerevisiae and yielded pNP-rhamnohydrolase activity. Phylogenetic analysis has revealed this eukaryotic α-L-rhamnosidase to be the first such enzyme found to be more closely related to bacterial rhamnosidases than other α-L-rhamnosidases of fungal origin. Northern analyses of diverse A. nidulans strains cultivated under different growth conditions indicate that rhaA and rhaE are induced by L-rhamnose and repressed by D-glucose as well as other carbon sources, some of which are considered to be non-repressive growth substrates. Interestingly, the transcriptional repression is independent of the wide domain carbon catabolite repressor CreA. Gene induction and glucose repression of these rha genes correlate with the uptake, or lack of it, of the inducing carbon source L-rhamnose, suggesting a prominent role for inducer exclusion in repression. The A. nidulans rhaE gene encodes an α-L-rhamnosidase phylogenetically distant to those described in filamentous fungi, and its expression is regulated by a novel CreA-independent mechanism. The identification of rhaE and the characterization of its regulation will facilitate the design of strategies to overproduce the encoded enzyme - or homologs from other fungi - for industrial applications. Moreover, A. nidulans α-L-rhamnosidase encoding genes could serve as prototypes for fungal genes coding for plant cell wall degrading enzymes regulated by a novel mechanism of CCR.

L-Rhamnose induction of Aspergillus nidulans α-L-rhamnosidase genes is glucose repressed via a CreA-independent mechanism acting at the level of inducer uptake

PubMed Central

2012-01-01

Background Little is known about the structure and regulation of fungal α-L-rhamnosidase genes despite increasing interest in the biotechnological potential of the enzymes that they encode. Whilst the paradigmatic filamentous fungus Aspergillus nidulans growing on L-rhamnose produces an α-L-rhamnosidase suitable for oenological applications, at least eight genes encoding putative α-L-rhamnosidases have been found in its genome. In the current work we have identified the gene (rhaE) encoding the former activity, and characterization of its expression has revealed a novel regulatory mechanism. A shared pattern of expression has also been observed for a second α-L-rhamnosidase gene, (AN10277/rhaA). Results Amino acid sequence data for the oenological α-L-rhamnosidase were determined using MALDI-TOF mass spectrometry and correspond to the amino acid sequence deduced from AN7151 (rhaE). The cDNA of rhaE was expressed in Saccharomyces cerevisiae and yielded pNP-rhamnohydrolase activity. Phylogenetic analysis has revealed this eukaryotic α-L-rhamnosidase to be the first such enzyme found to be more closely related to bacterial rhamnosidases than other α-L-rhamnosidases of fungal origin. Northern analyses of diverse A. nidulans strains cultivated under different growth conditions indicate that rhaA and rhaE are induced by L-rhamnose and repressed by D-glucose as well as other carbon sources, some of which are considered to be non-repressive growth substrates. Interestingly, the transcriptional repression is independent of the wide domain carbon catabolite repressor CreA. Gene induction and glucose repression of these rha genes correlate with the uptake, or lack of it, of the inducing carbon source L-rhamnose, suggesting a prominent role for inducer exclusion in repression. Conclusions The A. nidulans rhaE gene encodes an α-L-rhamnosidase phylogenetically distant to those described in filamentous fungi, and its expression is regulated by a novel CreA-independent mechanism. The identification of rhaE and the characterization of its regulation will facilitate the design of strategies to overproduce the encoded enzyme - or homologs from other fungi - for industrial applications. Moreover, A. nidulans α-L-rhamnosidase encoding genes could serve as prototypes for fungal genes coding for plant cell wall degrading enzymes regulated by a novel mechanism of CCR. PMID:22353731

Acoustic Masking Disrupts Time-Dependent Mechanisms of Memory Encoding in Word-List Recall

PubMed Central

Cousins, Katheryn A.Q.; Dar, Jonathan; Wingfield, Arthur; Miller, Paul

2013-01-01

Recall of recently heard words is affected by the clarity of presentation: even if all words are presented with sufficient clarity for successful recognition, those that are more difficult to hear are less likely to be recalled. Such a result demonstrates that memory processing depends on more than whether a word is simply “recognized” versus “not-recognized”. More surprising is that when a single item in a list of spoken words is acoustically masked, prior words that were heard with full clarity are also less likely to be recalled. To account for such a phenomenon, we developed the Linking by Active Maintenance Model (LAMM). This computational model of perception and encoding predicts that these effects are time dependent. Here we challenge our model by investigating whether and how the impact of acoustic masking on memory depends on presentation rate. We find that a slower presentation rate causes a more disruptive impact of stimulus degradation on prior, clearly heard words than does a fast rate. These results are unexpected according to prior theories of effortful listening, but we demonstrate that they can be accounted for by LAMM. PMID:24838269

Acoustic masking disrupts time-dependent mechanisms of memory encoding in word-list recall.

PubMed

Cousins, Katheryn A Q; Dar, Hayim; Wingfield, Arthur; Miller, Paul

2014-05-01

Recall of recently heard words is affected by the clarity of presentation: Even if all words are presented with sufficient clarity for successful recognition, those that are more difficult to hear are less likely to be recalled. Such a result demonstrates that memory processing depends on more than whether a word is simply "recognized" versus "not recognized." More surprising is that, when a single item in a list of spoken words is acoustically masked, prior words that were heard with full clarity are also less likely to be recalled. To account for such a phenomenon, we developed the linking-by-active-maintenance model (LAMM). This computational model of perception and encoding predicts that these effects will be time dependent. Here we challenged our model by investigating whether and how the impact of acoustic masking on memory depends on presentation rate. We found that a slower presentation rate causes a more disruptive impact of stimulus degradation on prior, clearly heard words than does a fast rate. These results are unexpected according to prior theories of effortful listening, but we demonstrated that they can be accounted for by LAMM.

Molecular defense mechanisms of Barrett's metaplasia estimated by an integrative genomics.

PubMed

Ostrowski, Jerzy; Mikula, Michal; Karczmarski, Jakub; Rubel, Tymon; Wyrwicz, Lucjan S; Bragoszewski, Piotr; Gaj, Pawel; Dadlez, Michal; Butruk, Eugeniusz; Regula, Jaroslaw

2007-07-01

Barrett's esophagus is characterized by the replacement of squamous epithelium with specialized intestinal metaplastic mucosa. The exact mechanisms of initiation and development of Barrett's metaplasia remain unknown, but a hypothesis of "successful adaptation" against noxious reflux components has been proposed. To search for the repertoire of adaptation mechanisms of Barrett's metaplasia, we employed high-throughput functional genomic and proteomic methods that defined the molecular background of metaplastic mucosa resistance to reflux. Transcriptional profiling was established for 23 pairs of esophageal squamous epithelium and Barrett's metaplasia tissue samples using Affymetrix U133A 2.0 GeneChips and validated by quantitative real-time polymerase chain reaction. Differences in protein composition were assessed by electrophoretic and mass-spectrometry-based methods. Among 2,822 genes differentially expressed between Barrett's metaplasia and squamous epithelium, we observed significantly overexpressed metaplastic mucosa genes that encode cytokines and growth factors, constituents of extracellular matrix, basement membrane and tight junctions, and proteins involved in prostaglandin and phosphoinositol metabolism, nitric oxide production, and bioenergetics. Their expression likely reflects defense and repair responses of metaplastic mucosa, whereas overexpression of genes encoding heat shock proteins and several protein kinases in squamous epithelium may reflect lower resistance of normal esophageal epithelium than Barrett's metaplasia to reflux components. Despite the methodological and interpretative difficulties in data analyses discussed in this paper, our studies confirm that Barrett's metaplasia may be regarded as a specific microevolution allowing for accumulation of mucosal morphological and physiological changes that better protect against reflux injury.

An EGFR autocrine loop encodes a slow-reacting but dominant mode of mechanotransduction in a polarized epithelium

PubMed Central

Kojic, Nikola; Chung, Euiheon; Kho, Alvin T.; Park, Jin-Ah; Huang, Austin; So, Peter T. C.; Tschumperlin, Daniel J.

2010-01-01

The mechanical landscape in biological systems can be complex and dynamic, with contrasting sustained and fluctuating loads regularly superposed within the same tissue. How resident cells discriminate between these scenarios to respond accordingly remains largely unknown. Here, we show that a step increase in compressive stress of physiological magnitude shrinks the lateral intercellular space between bronchial epithelial cells, but does so with strikingly slow exponential kinetics (time constant ∼110 s). We confirm that epidermal growth factor (EGF)-family ligands are constitutively shed into the intercellular space and demonstrate that a step increase in compressive stress enhances EGF receptor (EGFR) phosphorylation with magnitude and onset kinetics closely matching those predicted by constant-rate ligand shedding in a slowly shrinking intercellular geometry. Despite the modest degree and slow nature of EGFR activation evoked by compressive stress, we find that the majority of transcriptomic responses to sustained mechanical loading require ongoing activity of this autocrine loop, indicating a dominant role for mechanotransduction through autocrine EGFR signaling in this context. A slow deformation response to a step increase in loading, accompanied by synchronous increases in ligand concentration and EGFR activation, provides one means for cells to mount a selective and context-appropriate response to a sustained change in mechanical environment.—Kojic, N., Chung, E., Kho, A. T., Park, J.-A., Huang, A., So, P. T. C., Tschumperlin, D. J. An EGFR autocrine loop encodes a slow-reacting but dominant mode of mechanotransduction in a polarized epithelium. PMID:20056713

Stative and Stativizing Constructions in Arabic News Reports: A Corpus-Based Study

ERIC Educational Resources Information Center

Mansouri, Aous

2016-01-01

This dissertation uses a corpus of tokens retrieved from broadcast news stories and print news articles to examine the array of constructions used to encode stative predications in Modern Standard Arabic. A state is defined as a situation that includes its reference time, whether that time is encoding time or another time of orientation. A range…

Semantic and Phonological Encoding Times in Adults Who Stutter: Brain Electrophysiological Evidence

ERIC Educational Resources Information Center

Maxfield, Nathan D.

2017-01-01

Purpose: Some psycholinguistic theories of stuttering propose that language production operates along a different time course in adults who stutter (AWS) versus typically fluent adults (TFA). However, behavioral evidence for such a difference has been mixed. Here, the time course of semantic and phonological encoding in picture naming was compared…

Twistor encoding of Lienard--Wiechert fields in Minkowski space-time

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

Porter, J.R.

1985-03-01

The twistor encoding of the anti-self-dual Lienard--Wiechert field on Minkowski space-time yields a considerably richer structure than that of the Coulomb field encoding due to the presence of a nonzero radiation field. The combination of advanced and retarded transverse fields together with the longitudinal field and the individual aspects of these fields provides this structure. Higher-order longitudinal moments can be incorporated so that general longitudinal fields can be given a twistor description.

Is the encoding of Reward Prediction Error reliable during development?

PubMed

Keren, Hanna; Chen, Gang; Benson, Brenda; Ernst, Monique; Leibenluft, Ellen; Fox, Nathan A; Pine, Daniel S; Stringaris, Argyris

2018-05-16

Reward Prediction Errors (RPEs), defined as the difference between the expected and received outcomes, are integral to reinforcement learning models and play an important role in development and psychopathology. In humans, RPE encoding can be estimated using fMRI recordings, however, a basic measurement property of RPE signals, their test-retest reliability across different time scales, remains an open question. In this paper, we examine the 3-month and 3-year reliability of RPE encoding in youth (mean age at baseline = 10.6 ± 0.3 years), a period of developmental transitions in reward processing. We show that RPE encoding is differentially distributed between the positive values being encoded predominantly in the striatum and negative RPEs primarily encoded in the insula. The encoding of negative RPE values is highly reliable in the right insula, across both the long and the short time intervals. Insula reliability for RPE encoding is the most robust finding, while other regions, such as the striatum, are less consistent. Striatal reliability appeared significant as well once covarying for factors, which were possibly confounding the signal to noise ratio. By contrast, task activation during feedback in the striatum is highly reliable across both time intervals. These results demonstrate the valence-dependent differential encoding of RPE signals between the insula and striatum, and the consistency of RPE signals or lack thereof, during childhood and into adolescence. Characterizing the regions where the RPE signal in BOLD fMRI is a reliable marker is key for estimating reward-processing alterations in longitudinal designs, such as developmental or treatment studies. Copyright © 2018 Elsevier Inc. All rights reserved.

Synergistic Effect of Fluconazole and Calcium Channel Blockers against Resistant Candida albicans

PubMed Central

Liu, Shuyuan; Yue, Longtao; Gu, Wenrui; Li, Xiuyun; Zhang, Liuping; Sun, Shujuan

2016-01-01

Candidiasis has increased significantly recently that threatens patients with low immunity. However, the number of antifungal drugs on the market is limited in comparison to the number of available antibacterial drugs. This fact, coupled with the increased frequency of fungal resistance, makes it necessary to develop new therapeutic strategies. Combination drug therapy is one of the most widely used and effective strategy to alleviate this problem. In this paper, we were aimed to evaluate the combined antifungal effects of four CCBs (calcium channel blockers), amlodipine (AML), nifedipine (NIF), benidipine (BEN) and flunarizine (FNZ) with fluconazole against C. albicans by checkerboard and time-killing method. In addition, we determined gene (CCH1, MID1, CNA1, CNB1, YVC1, CDR1, CDR2 and MDR1) expression by quantitative PCR and investigated the efflux pump activity of resistant candida albicans by rhodamine 6G assay to reveal the potential mechanisms. Finally, we concluded that there was a synergy when fluconazole combined with the four tested CCBs against resistant strains, with fractional inhibitory concentration index (FICI) <0.5, but no interaction against sensitive strains (FICI = 0.56 ~ 2). The mechanism studies revealed that fluconazole plus amlodipine caused down-regulating of CNA1, CNB1 (encoding calcineurin) and YVC1 (encoding calcium channel protein in vacuole membrane). PMID:26986478

A Cooperative Downloading Method for VANET Using Distributed Fountain Code.

PubMed

Liu, Jianhang; Zhang, Wenbin; Wang, Qi; Li, Shibao; Chen, Haihua; Cui, Xuerong; Sun, Yi

2016-10-12

Cooperative downloading is one of the effective methods to improve the amount of downloaded data in vehicular ad hoc networking (VANET). However, the poor channel quality and short encounter time bring about a high packet loss rate, which decreases transmission efficiency and fails to satisfy the requirement of high quality of service (QoS) for some applications. Digital fountain code (DFC) can be utilized in the field of wireless communication to increase transmission efficiency. For cooperative forwarding, however, processing delay from frequent coding and decoding as well as single feedback mechanism using DFC cannot adapt to the environment of VANET. In this paper, a cooperative downloading method for VANET using concatenated DFC is proposed to solve the problems above. The source vehicle and cooperative vehicles encodes the raw data using hierarchical fountain code before they send to the client directly or indirectly. Although some packets may be lost, the client can recover the raw data, so long as it receives enough encoded packets. The method avoids data retransmission due to packet loss. Furthermore, the concatenated feedback mechanism in the method reduces the transmission delay effectively. Simulation results indicate the benefits of the proposed scheme in terms of increasing amount of downloaded data and data receiving rate.

Synergistic Effect of Fluconazole and Calcium Channel Blockers against Resistant Candida albicans.

PubMed

Liu, Shuyuan; Yue, Longtao; Gu, Wenrui; Li, Xiuyun; Zhang, Liuping; Sun, Shujuan

2016-01-01

Candidiasis has increased significantly recently that threatens patients with low immunity. However, the number of antifungal drugs on the market is limited in comparison to the number of available antibacterial drugs. This fact, coupled with the increased frequency of fungal resistance, makes it necessary to develop new therapeutic strategies. Combination drug therapy is one of the most widely used and effective strategy to alleviate this problem. In this paper, we were aimed to evaluate the combined antifungal effects of four CCBs (calcium channel blockers), amlodipine (AML), nifedipine (NIF), benidipine (BEN) and flunarizine (FNZ) with fluconazole against C. albicans by checkerboard and time-killing method. In addition, we determined gene (CCH1, MID1, CNA1, CNB1, YVC1, CDR1, CDR2 and MDR1) expression by quantitative PCR and investigated the efflux pump activity of resistant candida albicans by rhodamine 6G assay to reveal the potential mechanisms. Finally, we concluded that there was a synergy when fluconazole combined with the four tested CCBs against resistant strains, with fractional inhibitory concentration index (FICI) <0.5, but no interaction against sensitive strains (FICI = 0.56 ~ 2). The mechanism studies revealed that fluconazole plus amlodipine caused down-regulating of CNA1, CNB1 (encoding calcineurin) and YVC1 (encoding calcium channel protein in vacuole membrane).

Enriched Encoding: Reward Motivation Organizes Cortical Networks for Hippocampal Detection of Unexpected Events

PubMed Central

Murty, Vishnu P.; Adcock, R. Alison

2014-01-01

Learning how to obtain rewards requires learning about their contexts and likely causes. How do long-term memory mechanisms balance the need to represent potential determinants of reward outcomes with the computational burden of an over-inclusive memory? One solution would be to enhance memory for salient events that occur during reward anticipation, because all such events are potential determinants of reward. We tested whether reward motivation enhances encoding of salient events like expectancy violations. During functional magnetic resonance imaging, participants performed a reaction-time task in which goal-irrelevant expectancy violations were encountered during states of high- or low-reward motivation. Motivation amplified hippocampal activation to and declarative memory for expectancy violations. Connectivity of the ventral tegmental area (VTA) with medial prefrontal, ventrolateral prefrontal, and visual cortices preceded and predicted this increase in hippocampal sensitivity. These findings elucidate a novel mechanism whereby reward motivation can enhance hippocampus-dependent memory: anticipatory VTA-cortical–hippocampal interactions. Further, the findings integrate literatures on dopaminergic neuromodulation of prefrontal function and hippocampus-dependent memory. We conclude that during reward motivation, VTA modulation induces distributed neural changes that amplify hippocampal signals and records of expectancy violations to improve predictions—a potentially unique contribution of the hippocampus to reward learning. PMID:23529005

An operating principle of the turtle utricle to detect wide dynamic range.

PubMed

Nam, Jong-Hoon

2018-03-01

The utricle encodes both static information such as head orientation, and dynamic information such as vibrations. It is not well understood how the utricle can encode both static and dynamic information for a wide dynamic range (from <0.05 to >2 times the gravitational acceleration; from DC to > 1000 Hz vibrations). Using computational models of the hair cells in the turtle utricle, this study presents an explanation on how the turtle utricle encodes stimulations over such a wide dynamic range. Two hair bundles were modeled using the finite element method-one representing the striolar hair cell (Cell S), and the other representing the medial extrastriolar hair cell (Cell E). A mechano-transduction (MET) channel model was incorporated to compute MET current (i MET ) due to hair bundle deflection. A macro-mechanical model of the utricle was used to compute otoconial motions from head accelerations (a Head ). According to known anatomical data, Cell E has a long kinocilium that is embedded into the stiff otoconial layer. Unlike Cell E, the hair bundle of Cell S falls short of the otoconial layer. Considering such difference in the mechanical connectivity between the hair cell bundle and the otoconial layer, three cases were simulated: Cell E displacement-clamped, Cell S viscously-coupled, and Cell S displacement-clamped. Head accelerations at different amplitude levels and different frequencies were simulated for the three cases. When a realistic head motion was simulated, Cell E was responsive to head orientation, while the viscously-coupled Cell S was responsive to fast head motion imitating the feeding strike of a turtle. Copyright © 2017 Elsevier B.V. All rights reserved.

Brain and behavioral evidence for altered social learning mechanisms among women with assault-related posttraumatic stress disorder.

PubMed

Cisler, Josh M; Bush, Keith; Scott Steele, J; Lenow, Jennifer K; Smitherman, Sonet; Kilts, Clinton D

2015-04-01

Current neurocircuitry models of PTSD focus on the neural mechanisms that mediate hypervigilance for threat and fear inhibition/extinction learning. Less focus has been directed towards explaining social deficits and heightened risk of revictimization observed among individuals with PTSD related to physical or sexual assault. The purpose of the present study was to foster more comprehensive theoretical models of PTSD by testing the hypothesis that assault-related PTSD is associated with behavioral impairments in a social trust and reciprocity task and corresponding alterations in the neural encoding of social learning mechanisms. Adult women with assault-related PTSD (n = 25) and control women (n = 15) completed a multi-trial trust game outside of the MRI scanner. A subset of these participants (15 with PTSD and 14 controls) also completed a social and non-social reinforcement learning task during 3T fMRI. Brain regions that encoded the computationally modeled parameters of value expectation, prediction error, and volatility (i.e., uncertainty) were defined and compared between groups. The PTSD group demonstrated slower learning rates during the trust game and social prediction errors had a lesser impact on subsequent investment decisions. PTSD was also associated with greater encoding of negative expected social outcomes in perigenual anterior cingulate cortex and bilateral middle frontal gyri, and greater encoding of social prediction errors in the left temporoparietal junction. These data suggest mechanisms of PTSD-related deficits in social functioning and heightened risk for re-victimization in assault victims; however, comorbidity in the PTSD group and the lack of a trauma-exposed control group temper conclusions about PTSD specifically. Copyright © 2015 Elsevier Ltd. All rights reserved.

Characterising the biology of novel lytic bacteriophages infecting multidrug resistant Klebsiella pneumoniae.

PubMed

Kęsik-Szeloch, Agata; Drulis-Kawa, Zuzanna; Weber-Dąbrowska, Beata; Kassner, Jerzy; Majkowska-Skrobek, Grażyna; Augustyniak, Daria; Lusiak-Szelachowska, Marzanna; Zaczek, Maciej; Górski, Andrzej; Kropinski, Andrew M

2013-03-28

Members of the genus Klebsiella are among the leading microbial pathogens associated with nosocomial infection. The increased incidence of antimicrobial resistance in these species has propelled the need for alternate/combination therapeutic regimens to aid clinical treatment. Bacteriophage therapy forms one of these alternate strategies. Electron microscopy, burst size, host range, sensitivity of phage particles to temperature, chloroform, pH, and restriction digestion of phage DNA were used to characterize Klebsiella phages. Of the 32 isolated phages eight belonged to the family Myoviridae, eight to the Siphoviridae whilst the remaining 16 belonged to the Podoviridae. The host range of these phages was characterised against 254 clinical Enterobacteriaceae strains including multidrug resistant Klebsiella isolates producing extended-spectrum beta-lactamases (ESBLs). Based on their lytic potential, six of the phages were further characterised for burst size, physicochemical properties and sensitivity to restriction endonuclease digestion. In addition, five were fully sequenced. Multiple phage-encoded host resistance mechanisms were identified. The Siphoviridae phage genomes (KP16 and KP36) contained low numbers of host restriction sites similar to the strategy found in T7-like phages (KP32). In addition, phage KP36 encoded its own DNA adenine methyltransferase. The φKMV-like KP34 phage was sensitive to all endonucleases used in this study. Dam methylation of KP34 DNA was detected although this was in the absence of an identifiable phage encoded methyltransferase. The Myoviridae phages KP15 and KP27 both carried Dam and Dcm methyltransferase genes and other anti-restriction mechanisms elucidated in previous studies. No other anti-restriction mechanisms were found, e.g. atypical nucleotides (hmC or glucosyl hmC), although Myoviridae phage KP27 encodes an unknown anti-restriction mechanism that needs further investigation.

Anxiety Evokes Hypofrontality and Disrupts Rule-Relevant Encoding by Dorsomedial Prefrontal Cortex Neurons.

PubMed

Park, Junchol; Wood, Jesse; Bondi, Corina; Del Arco, Alberto; Moghaddam, Bita

2016-03-16

Anxiety is a debilitating symptom of most psychiatric disorders, including major depression, post-traumatic stress disorder, schizophrenia, and addiction. A detrimental aspect of anxiety is disruption of prefrontal cortex (PFC)-mediated executive functions, such as flexible decision making. Here we sought to understand how anxiety modulates PFC neuronal encoding of flexible shifting between behavioral strategies. We used a clinically substantiated anxiogenic treatment to induce sustained anxiety in rats and recorded from dorsomedial PFC (dmPFC) and orbitofrontal cortex (OFC) neurons while they were freely moving in a home cage and while they performed a PFC-dependent task that required flexible switches between rules in two distinct perceptual dimensions. Anxiety elicited a sustained background "hypofrontality" in dmPFC and OFC by reducing the firing rate of spontaneously active neuronal subpopulations. During task performance, the impact of anxiety was subtle, but, consistent with human data, behavior was selectively impaired when previously correct conditions were presented as conflicting choices. This impairment was associated with reduced recruitment of dmPFC neurons that selectively represented task rules at the time of action. OFC rule representation was not affected by anxiety. These data indicate that a neural substrate of the decision-making deficits in anxiety is diminished dmPFC neuronal encoding of task rules during conflict-related actions. Given the translational relevance of the model used here, the data provide a neuronal encoding mechanism for how anxiety biases decision making when the choice involves overcoming a conflict. They also demonstrate that PFC encoding of actions, as opposed to cues or outcome, is especially vulnerable to anxiety. A debilitating aspect of anxiety is its impact on decision making and flexible control of behavior. These cognitive constructs depend on proper functioning of the prefrontal cortex (PFC). Understanding how anxiety affects PFC encoding of cognitive events is of great clinical and evolutionary significance. Using a clinically valid experimental model, we find that, under anxiety, decision making may be skewed by salient and conflicting environmental stimuli at the expense of flexible top-down guided choices. We also find that anxiety suppresses spontaneous activity of PFC neurons, and weakens encoding of task rules by dorsomedial PFC neurons. These data provide a neuronal encoding scheme for how anxiety disengages PFC during decision making. Copyright © 2016 the authors 0270-6474/16/363322-14$15.00/0.

Externally Calibrated Parallel Imaging for 3D Multispectral Imaging Near Metallic Implants Using Broadband Ultrashort Echo Time Imaging

PubMed Central

Wiens, Curtis N.; Artz, Nathan S.; Jang, Hyungseok; McMillan, Alan B.; Reeder, Scott B.

2017-01-01

Purpose To develop an externally calibrated parallel imaging technique for three-dimensional multispectral imaging (3D-MSI) in the presence of metallic implants. Theory and Methods A fast, ultrashort echo time (UTE) calibration acquisition is proposed to enable externally calibrated parallel imaging techniques near metallic implants. The proposed calibration acquisition uses a broadband radiofrequency (RF) pulse to excite the off-resonance induced by the metallic implant, fully phase-encoded imaging to prevent in-plane distortions, and UTE to capture rapidly decaying signal. The performance of the externally calibrated parallel imaging reconstructions was assessed using phantoms and in vivo examples. Results Phantom and in vivo comparisons to self-calibrated parallel imaging acquisitions show that significant reductions in acquisition times can be achieved using externally calibrated parallel imaging with comparable image quality. Acquisition time reductions are particularly large for fully phase-encoded methods such as spectrally resolved fully phase-encoded three-dimensional (3D) fast spin-echo (SR-FPE), in which scan time reductions of up to 8 min were obtained. Conclusion A fully phase-encoded acquisition with broadband excitation and UTE enabled externally calibrated parallel imaging for 3D-MSI, eliminating the need for repeated calibration regions at each frequency offset. Significant reductions in acquisition time can be achieved, particularly for fully phase-encoded methods like SR-FPE. PMID:27403613

Recalling and forgetting dreams: theta and alpha oscillations during sleep predict subsequent dream recall.

PubMed

Marzano, Cristina; Ferrara, Michele; Mauro, Federica; Moroni, Fabio; Gorgoni, Maurizio; Tempesta, Daniela; Cipolli, Carlo; De Gennaro, Luigi

2011-05-04

Under the assumption that dream recall is a peculiar form of declarative memory, we have hypothesized that (1) the encoding of dream contents during sleep should share some electrophysiological mechanisms with the encoding of episodic memories of the awake brain and (2) recalling a dream(s) after awakening from non-rapid eye movement (NREM) and rapid eye movement (REM) sleep should be associated with different brain oscillations. Here, we report that cortical brain oscillations of human sleep are predictive of successful dream recall. In particular, after morning awakening from REM sleep, a higher frontal 5-7 Hz (theta) activity was associated with successful dream recall. This finding mirrors the increase in frontal theta activity during successful encoding of episodic memories in wakefulness. Moreover, in keeping with the different EEG background, a different predictive relationship was found after awakening from stage 2 NREM sleep. Specifically, a lower 8-12 Hz (alpha) oscillatory activity of the right temporal area was associated with a successful dream recall. These findings provide the first evidence of univocal cortical electroencephalographic correlates of dream recall, suggesting that the neurophysiological mechanisms underlying the encoding and recall of episodic memories may remain the same across different states of consciousness.

Toxin-antitoxin systems and regulatory mechanisms in Mycobacterium tuberculosis.

PubMed

Slayden, Richard A; Dawson, Clinton C; Cummings, Jason E

2018-06-01

There has been a significant reduction in annual tuberculosis incidence since the World Health Organization declared tuberculosis a global health threat. However, treatment of M. tuberculosis infections requires lengthy multidrug therapeutic regimens to achieve a durable cure. The development of new drugs that are active against resistant strains and phenotypically diverse organisms continues to present the greatest challenge in the future. Numerous phylogenomic analyses have revealed that the Mtb genome encodes a significantly expanded repertoire of toxin-antitoxin (TA) loci that makes up the Mtb TA system. A TA loci is a two-gene operon encoding a 'toxin' protein that inhibits bacterial growth and an interacting 'antitoxin' partner that neutralizes the inhibitory activity of the toxin. The presence of multiple chromosomally encoded TA loci in Mtb raises important questions in regard to expansion, regulation and function. Thus, the functional roles of TA loci in Mtb pathogenesis have received considerable attention over the last decade. The cumulative results indicate that they are involved in regulating adaptive responses to stresses associated with the host environment and drug treatment. Here we review the TA families encoded in Mtb, discuss the duplication of TA loci in Mtb, regulatory mechanism of TA loci, and phenotypic heterogeneity and pathogenesis.

Both differences in encoding processes and monitoring at retrieval reduce false alarms when distinctive information is studied.

PubMed

Hanczakowski, Maciej; Mazzoni, Giuliana

2011-04-01

A reduction in false alarms to critical lures is observed in the DRM paradigm (Roediger & McDermott, 1995) when distinctive information is presented at encoding. Two mechanisms have been proposed to account for this reduction. According to the monitoring theory (e.g., the distinctiveness heuristic), lack of diagnostic recollection serves as a basis for discarding non-presented lures. According to the encoding theory, presenting distinctive information at study leads to impoverished relational processing, which results in a reduction in memorial information elicited by critical lures. In the present study a condition was created in which the use of the distinctiveness heuristic was precluded by associating, within the same study, lures with distinctive information in a context different from the study session. Under that condition reduction in false alarms to distinctive critical lures was still observed. This result supports the predictions of the encoding theory. However, when in the same study the use of the distinctiveness heuristic was not precluded, reductions in false alarms to unrelated lures were also observed when distinctive information was presented at study, indicating that both mechanisms are likely to contribute to the rejection of false memories.

Dopaminergic influences on formation of a motor memory.

PubMed

Flöel, Agnes; Breitenstein, Caterina; Hummel, Friedhelm; Celnik, Pablo; Gingert, Christian; Sawaki, Lumy; Knecht, Stefan; Cohen, Leonardo G

2005-07-01

The ability of the central nervous system to form motor memories, a process contributing to motor learning and skill acquisition, decreases with age. Dopaminergic activity, one of the mechanisms implicated in memory formation, experiences a similar decline with aging. It is possible that restoring dopaminergic function in elderly adults could lead to improved formation of motor memories with training. We studied the influence of a single oral dose of levodopa (100mg) administered preceding training on the ability to encode an elementary motor memory in the primary motor cortex of elderly and young healthy volunteers in a randomized, double-blind, placebo-controlled design. Attention to the task and motor training kinematics were comparable across age groups and sessions. In young subjects, encoding a motor memory under placebo was more prominent than in older subjects, and the encoding process was accelerated by intake of levodopa. In the elderly group, diminished motor memory encoding under placebo was enhanced by intake of levodopa to levels present in younger subjects. Therefore, upregulation of dopaminergic activity accelerated memory formation in young subjects and restored the ability to form a motor memory in elderly subjects; possible mechanisms underlying the beneficial effects of dopaminergic agents on motor learning in neurorehabilitation.

Cytokine Diedel and a viral homologue suppress the IMD pathway in Drosophila.

PubMed

Lamiable, Olivier; Kellenberger, Christine; Kemp, Cordula; Troxler, Laurent; Pelte, Nadège; Boutros, Michael; Marques, Joao Trindade; Daeffler, Laurent; Hoffmann, Jules A; Roussel, Alain; Imler, Jean-Luc

2016-01-19

Viruses are obligatory intracellular parasites that suffer strong evolutionary pressure from the host immune system. Rapidly evolving viral genomes can adapt to this pressure by acquiring genes that counteract host defense mechanisms. For example, many vertebrate DNA viruses have hijacked cellular genes encoding cytokines or cytokine receptors to disrupt host cell communication. Insect viruses express suppressors of RNA interference or apoptosis, highlighting the importance of these cell intrinsic antiviral mechanisms in invertebrates. Here, we report the identification and characterization of a family of proteins encoded by insect DNA viruses that are homologous to a 12-kDa circulating protein encoded by the virus-induced Drosophila gene diedel (die). We show that die mutant flies have shortened lifespan and succumb more rapidly than controls when infected with Sindbis virus. This reduced viability is associated with deregulated activation of the immune deficiency (IMD) pathway of host defense and can be rescued by mutations in the genes encoding the homolog of IKKγ or IMD itself. Our results reveal an endogenous pathway that is exploited by insect viruses to modulate NF-κB signaling and promote fly survival during the antiviral response.

Item-method directed forgetting: Effects at retrieval?

PubMed

Taylor, Tracy L; Cutmore, Laura; Pries, Lotta

2018-02-01

In an item-method directed forgetting paradigm, words are presented one at a time, each followed by an instruction to Remember or Forget; a directed forgetting effect is measured as better subsequent memory for Remember words than Forget words. The dominant view is that the directed forgetting effect arises during encoding due to selective rehearsal of Remember over Forget items. In three experiments we attempted to falsify a strong view that directed forgetting effects in recognition are due only to encoding mechanisms when an item method is used. Across 3 experiments we tested for retrieval-based processes by colour-coding the recognition test items. Black colour provided no information; green colour cued a potential Remember item; and, red colour cued a potential Forget item. Recognition cues were mixed within-blocks in Experiment 1 and between-blocks in Experiments 2 and 3; Experiment 3 added explicit feedback on the accuracy of the recognition decision. Although overall recognition improved with cuing when explicit test performance feedback was added in Experiment 3, in no case was the magnitude of the directed forgetting effect influenced by recognition cueing. Our results argue against a role for retrieval-based strategies that limit recognition of Forget items at test and posit a role for encoding intentions only. Copyright © 2017 Elsevier B.V. All rights reserved.

Time dependent effects of stress prior to encoding on event-related potentials and 24 h delayed retrieval.

PubMed

Quaedflieg, Conny W E M; Schwabe, Lars; Meyer, Thomas; Smeets, Tom

2013-12-01

Stress can exert profound effects on memory encoding. Here, we investigated whether (sub)cortical information processing during encoding and memory retrieval at a 24 h delayed test are affected by the temporal proximity between stress and memory encoding. Sixty-four participants engaged in the Maastricht Acute Stress Test (MAST) or a no-stress control condition either immediately before (i.e., proximate condition) or 30 min before (i.e., distant condition) a picture encoding task. In general, stress decreased the number of freely recalled and recognized pictures and increased the number of false alarms. However, timing of stress exposure did not differentially affect picture recall, recognition or selective attention processes (i.e., LPP). Nevertheless, stress-induced cortisol responses and correctly recognized neutral pictures were positively associated within the proximate stress condition but negatively associated within the distant stress condition. These findings suggest that the time at which a stressor is applied might differentially impact the association between stress-induced cortisol elevations and memory formation and indicate the need for a finer delineation of the time window during which glucocorticoids affect memory formation processes. Copyright © 2013 Elsevier Ltd. All rights reserved.

On the Suitability of Suffix Arrays for Lempel-Ziv Data Compression

NASA Astrophysics Data System (ADS)

Ferreira, Artur J.; Oliveira, Arlindo L.; Figueiredo, Mário A. T.

Lossless compression algorithms of the Lempel-Ziv (LZ) family are widely used nowadays. Regarding time and memory requirements, LZ encoding is much more demanding than decoding. In order to speed up the encoding process, efficient data structures, like suffix trees, have been used. In this paper, we explore the use of suffix arrays to hold the dictionary of the LZ encoder, and propose an algorithm to search over it. We show that the resulting encoder attains roughly the same compression ratios as those based on suffix trees. However, the amount of memory required by the suffix array is fixed, and much lower than the variable amount of memory used by encoders based on suffix trees (which depends on the text to encode). We conclude that suffix arrays, when compared to suffix trees in terms of the trade-off among time, memory, and compression ratio, may be preferable in scenarios (e.g., embedded systems) where memory is at a premium and high speed is not critical.

Comparative transcriptome analysis to investigate the high starch accumulation of duckweed (Landoltia punctata) under nutrient starvation.

PubMed

Tao, Xiang; Fang, Yang; Xiao, Yao; Jin, Yan-Ling; Ma, Xin-Rong; Zhao, Yun; He, Kai-Ze; Zhao, Hai; Wang, Hai-Yan

2013-05-08

Duckweed can thrive on anthropogenic wastewater and produce tremendous biomass production. Due to its relatively high starch and low lignin percentage, duckweed is a good candidate for bioethanol fermentation. Previous studies have observed that water devoid of nutrients is good for starch accumulation, but its molecular mechanism remains unrevealed. This study globally analyzed the response to nutrient starvation in order to investigate the starch accumulation in duckweed (Landoltia punctata). L. punctata was transferred from nutrient-rich solution to distilled water and sampled at different time points. Physiological measurements demonstrated that the activity of ADP-glucose pyrophosphorylase, the key enzyme of starch synthesis, as well as the starch percentage in duckweed, increased continuously under nutrient starvation. Samples collected at 0 h, 2 h and 24 h time points respectively were used for comparative gene expression analysis using RNA-Seq. A comprehensive transcriptome, comprising of 74,797 contigs, was constructed by a de novo assembly of the RNA-Seq reads. Gene expression profiling results showed that the expression of some transcripts encoding key enzymes involved in starch biosynthesis was up-regulated, while the expression of transcripts encoding enzymes involved in starch consumption were down-regulated, the expression of some photosynthesis-related transcripts were down-regulated during the first 24 h, and the expression of some transporter transcripts were up-regulated within the first 2 h. Very interestingly, most transcripts encoding key enzymes involved in flavonoid biosynthesis were highly expressed regardless of starvation, while transcripts encoding laccase, the last rate-limiting enzyme of lignifications, exhibited very low expression abundance in all three samples. Our study provides a comprehensive expression profiling of L. punctata under nutrient starvation, which indicates that nutrient starvation down-regulated the global metabolic status, redirects metabolic flux of fixed CO2 into starch synthesis branch resulting in starch accumulation in L. punctata.

Comparative transcriptome analysis to investigate the high starch accumulation of duckweed (Landoltia punctata) under nutrient starvation

PubMed Central

2013-01-01

Background Duckweed can thrive on anthropogenic wastewater and produce tremendous biomass production. Due to its relatively high starch and low lignin percentage, duckweed is a good candidate for bioethanol fermentation. Previous studies have observed that water devoid of nutrients is good for starch accumulation, but its molecular mechanism remains unrevealed. Results This study globally analyzed the response to nutrient starvation in order to investigate the starch accumulation in duckweed (Landoltia punctata). L. punctata was transferred from nutrient-rich solution to distilled water and sampled at different time points. Physiological measurements demonstrated that the activity of ADP-glucose pyrophosphorylase, the key enzyme of starch synthesis, as well as the starch percentage in duckweed, increased continuously under nutrient starvation. Samples collected at 0 h, 2 h and 24 h time points respectively were used for comparative gene expression analysis using RNA-Seq. A comprehensive transcriptome, comprising of 74,797 contigs, was constructed by a de novo assembly of the RNA-Seq reads. Gene expression profiling results showed that the expression of some transcripts encoding key enzymes involved in starch biosynthesis was up-regulated, while the expression of transcripts encoding enzymes involved in starch consumption were down-regulated, the expression of some photosynthesis-related transcripts were down-regulated during the first 24 h, and the expression of some transporter transcripts were up-regulated within the first 2 h. Very interestingly, most transcripts encoding key enzymes involved in flavonoid biosynthesis were highly expressed regardless of starvation, while transcripts encoding laccase, the last rate-limiting enzyme of lignifications, exhibited very low expression abundance in all three samples. Conclusion Our study provides a comprehensive expression profiling of L. punctata under nutrient starvation, which indicates that nutrient starvation down-regulated the global metabolic status, redirects metabolic flux of fixed CO2 into starch synthesis branch resulting in starch accumulation in L. punctata. PMID:23651472

Analyzing Single-Molecule Protein Transportation Experiments via Hierarchical Hidden Markov Models

PubMed Central

Chen, Yang; Shen, Kuang

2017-01-01

To maintain proper cellular functions, over 50% of proteins encoded in the genome need to be transported to cellular membranes. The molecular mechanism behind such a process, often referred to as protein targeting, is not well understood. Single-molecule experiments are designed to unveil the detailed mechanisms and reveal the functions of different molecular machineries involved in the process. The experimental data consist of hundreds of stochastic time traces from the fluorescence recordings of the experimental system. We introduce a Bayesian hierarchical model on top of hidden Markov models (HMMs) to analyze these data and use the statistical results to answer the biological questions. In addition to resolving the biological puzzles and delineating the regulating roles of different molecular complexes, our statistical results enable us to propose a more detailed mechanism for the late stages of the protein targeting process. PMID:28943680

Improved Hardware for Higher Spatial Resolution Strain-ENCoded (SENC) Breast MRI for Strain Measurements

PubMed Central

Harouni, Ahmed A.; Hossain, Jakir; Jacobs, Michael A.; Osman, Nael F.

2012-01-01

Introduction Early detection of breast lesions using mammography has resulted in lower mortality-rates. However, some breast lesions are mammography occult and magnetic resonance imaging (MRI) is recommended, but has lower specificity. It is possible to achieve higher specificity by using Strain-ENCoded (SENC) MRI and/or magnetic resonance elastography(MRE). SENC breast MRI can measure the strain properties of breast tissue. Similarly, MRE is used to measure elasticity (i.e., shear stiffness) of different tissue compositions interrogating the tissue mechanical properties. Reports have shown that malignant tumors are 3–13 times stiffer than normal tissue and benign tumors. Methods We have developed a Strain-ENCoded (SENC) breast hardware device capable of periodically compressing the breast, thus allowing for longer scanning time and measuring the strain characteristics of breast tissue. This hardware enabled us to use SENC MRI with high spatial resolution (1×1×5mm3) instead of Fast SENC(FSENC). Simple controls and multiple safety measures were added to ensure accurate, repeatable and safe in-vivo experiments. Results Phantom experiments showed that SENC breast MRI has higher SNR and CNR than FSENC under different scanning resolutions. Finally, the SENC breast device reproducibility measurements resulted in a difference of less than one mm with a 1% strain difference. Conclusion SENC breast MR images have higher SNR and CNR than FSENC images. Thus, combining SENC breast strain measurements with diagnostic breast MRI to differentiate benign from malignant lesions could potentially increase the specificity of diagnosis in the clinical setting. PMID:21440464

Scanning mirror for infrared sensors

NASA Technical Reports Server (NTRS)

Anderson, R. H.; Bernstein, S. B.

1972-01-01

A high resolution, long life angle-encoded scanning mirror, built for application in an infrared attitude sensor, is described. The mirror uses a Moire' fringe type optical encoder and unique torsion bar suspension together with a magnetic drive to meet stringent operational and environmental requirements at a minimum weight and with minimum power consumption. Details of the specifications, design, and construction are presented with an analysis of the mirror suspension that allows accurate prediction of performance. The emphasis is on mechanical design considerations, and brief discussions are included on the encoder and magnetic drive to provide a complete view of the mirror system and its capabilities.

Exogenous attention influences visual short-term memory in infants.

PubMed

Ross-Sheehy, Shannon; Oakes, Lisa M; Luck, Steven J

2011-05-01

Two experiments examined the hypothesis that developing visual attentional mechanisms influence infants' Visual Short-Term Memory (VSTM) in the context of multiple items. Five- and 10-month-old infants (N = 76) received a change detection task in which arrays of three differently colored squares appeared and disappeared. On each trial one square changed color and one square was cued; sometimes the cued item was the changing item, and sometimes the changing item was not the cued item. Ten-month-old infants exhibited enhanced memory for the cued item when the cue was a spatial pre-cue (Experiment 1) and 5-month-old infants exhibited enhanced memory for the cued item when the cue was relative motion (Experiment 2). These results demonstrate for the first time that infants younger than 6 months can encode information in VSTM about individual items in multiple-object arrays, and that attention-directing cues influence both perceptual and VSTM encoding of stimuli in infants as in adults.

Mutations in genes encoding condensin complex proteins cause microcephaly through decatenation failure at mitosis.

PubMed

Martin, Carol-Anne; Murray, Jennie E; Carroll, Paula; Leitch, Andrea; Mackenzie, Karen J; Halachev, Mihail; Fetit, Ahmed E; Keith, Charlotte; Bicknell, Louise S; Fluteau, Adeline; Gautier, Philippe; Hall, Emma A; Joss, Shelagh; Soares, Gabriela; Silva, João; Bober, Michael B; Duker, Angela; Wise, Carol A; Quigley, Alan J; Phadke, Shubha R; Wood, Andrew J; Vagnarelli, Paola; Jackson, Andrew P

2016-10-01

Compaction of chromosomes is essential for accurate segregation of the genome during mitosis. In vertebrates, two condensin complexes ensure timely chromosome condensation, sister chromatid disentanglement, and maintenance of mitotic chromosome structure. Here, we report that biallelic mutations in NCAPD2, NCAPH, or NCAPD3, encoding subunits of these complexes, cause microcephaly. In addition, hypomorphic Ncaph2 mice have significantly reduced brain size, with frequent anaphase chromatin bridge formation observed in apical neural progenitors during neurogenesis. Such DNA bridges also arise in condensin-deficient patient cells, where they are the consequence of failed sister chromatid disentanglement during chromosome compaction. This results in chromosome segregation errors, leading to micronucleus formation and increased aneuploidy in daughter cells. These findings establish "condensinopathies" as microcephalic disorders, with decatenation failure as an additional disease mechanism for microcephaly, implicating mitotic chromosome condensation as a key process ensuring mammalian cerebral cortex size. © 2016 Martin et al.; Published by Cold Spring Harbor Laboratory Press.

Neural mechanisms of economic commitment in the human medial prefrontal cortex

PubMed Central

Tsetsos, Konstantinos; Wyart, Valentin; Shorkey, S Paul; Summerfield, Christopher

2014-01-01

Neurobiologists have studied decisions by offering successive, independent choices between goods or gambles. However, choices often have lasting consequences, as when investing in a house or choosing a partner. Here, humans decided whether to commit (by acceptance or rejection) to prospects that provided sustained financial return. BOLD signals in the rostral medial prefrontal cortex (rmPFC) encoded stimulus value only when acceptance or rejection was deferred into the future, suggesting a role in integrating value signals over time. By contrast, the dorsal anterior cingulate cortex (dACC) encoded stimulus value only when participants rejected (or deferred accepting) a prospect. dACC BOLD signals reflected two decision biases–to defer commitments to later, and to weight potential losses more heavily than gains–that (paradoxically) maximised reward in this task. These findings offer fresh insights into the pressures that shape economic decisions, and the computation of value in the medial prefrontal cortex. DOI: http://dx.doi.org/10.7554/eLife.03701.001 PMID:25333687

Determining optimal parameters of the self-referent encoding task: A large-scale examination of self-referent cognition and depression.

PubMed

Dainer-Best, Justin; Lee, Hae Yeon; Shumake, Jason D; Yeager, David S; Beevers, Christopher G

2018-06-07

Although the self-referent encoding task (SRET) is commonly used to measure self-referent cognition in depression, many different SRET metrics can be obtained. The current study used best subsets regression with cross-validation and independent test samples to identify the SRET metrics most reliably associated with depression symptoms in three large samples: a college student sample (n = 572), a sample of adults from Amazon Mechanical Turk (n = 293), and an adolescent sample from a school field study (n = 408). Across all 3 samples, SRET metrics associated most strongly with depression severity included number of words endorsed as self-descriptive and rate of accumulation of information required to decide whether adjectives were self-descriptive (i.e., drift rate). These metrics had strong intratask and split-half reliability and high test-retest reliability across a 1-week period. Recall of SRET stimuli and traditional reaction time (RT) metrics were not robustly associated with depression severity. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Design and realization of a new agorithm of calculating the absolute positon angle based on the incremental encoder

NASA Astrophysics Data System (ADS)

Liu, Peng; Yang, Yong-qing; Li, Zhi-guo; Han, Jun-feng; Wei, Yu; Jing, Feng

2018-02-01

Aiming at the shortage of the incremental encoder with simple process to change along the count "in the presence of repeatability and anti disturbance ability, combined with its application in a large project in the country, designed an electromechanical switch for generating zero, zero crossing signal. A mechanical zero electric and zero coordinate transformation model is given to meet the path optimality, single, fast and accurate requirements of adaptive fast change algorithm, the proposed algorithm can effectively solve the contradiction between the accuracy and the change of the time change. A test platform is built to verify the effectiveness and robustness of the proposed algorithm. The experimental data show that the effect of the algorithm accuracy is not influenced by the change of the speed of change, change the error of only 0.0013. Meet too fast, the change of system accuracy, and repeated experiments show that this algorithm has high robustness.

Dopaminergic inputs in the dentate gyrus direct the choice of memory encoding

DOE PAGES

Du, Huiyun; Deng, Wei; Aimone, James B.; ...

2016-09-13

Rewarding experiences are often well remembered, and such memory formation is known to be dependent on dopamine modulation of the neural substrates engaged in learning and memory; however, it is unknown how and where in the brain dopamine signals bias episodic memory toward preceding rather than subsequent events. Here we found that photostimulation of channelrhodopsin-2–expressing dopaminergic fibers in the dentate gyrus induced a long-term depression of cortical inputs, diminished theta oscillations, and impaired subsequent contextual learning. Computational modeling based on this dopamine modulation indicated an asymmetric association of events occurring before and after reward in memory tasks. In subsequent behavioralmore » experiments, preexposure to a natural reward suppressed hippocampus-dependent memory formation, with an effective time window consistent with the duration of dopamine-induced changes of dentate activity. Altogether, our results suggest a mechanism by which dopamine enables the hippocampus to encode memory with reduced interference from subsequent experience.« less

Dopaminergic inputs in the dentate gyrus direct the choice of memory encoding

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

Du, Huiyun; Deng, Wei; Aimone, James B.

Rewarding experiences are often well remembered, and such memory formation is known to be dependent on dopamine modulation of the neural substrates engaged in learning and memory; however, it is unknown how and where in the brain dopamine signals bias episodic memory toward preceding rather than subsequent events. Here we found that photostimulation of channelrhodopsin-2–expressing dopaminergic fibers in the dentate gyrus induced a long-term depression of cortical inputs, diminished theta oscillations, and impaired subsequent contextual learning. Computational modeling based on this dopamine modulation indicated an asymmetric association of events occurring before and after reward in memory tasks. In subsequent behavioralmore » experiments, preexposure to a natural reward suppressed hippocampus-dependent memory formation, with an effective time window consistent with the duration of dopamine-induced changes of dentate activity. Altogether, our results suggest a mechanism by which dopamine enables the hippocampus to encode memory with reduced interference from subsequent experience.« less

Artificial Neural Network Based Mission Planning Mechanism for Spacecraft

NASA Astrophysics Data System (ADS)

Li, Zhaoyu; Xu, Rui; Cui, Pingyuan; Zhu, Shengying

2018-04-01

The ability to plan and react fast in dynamic space environments is central to intelligent behavior of spacecraft. For space and robotic applications, many planners have been used. But it is difficult to encode the domain knowledge and directly use existing techniques such as heuristic to improve the performance of the application systems. Therefore, regarding planning as an advanced control problem, this paper first proposes an autonomous mission planning and action selection mechanism through a multiple layer perceptron neural network approach to select actions in planning process and improve efficiency. To prove the availability and effectiveness, we use autonomous mission planning problems of the spacecraft, which is a sophisticated system with complex subsystems and constraints as an example. Simulation results have shown that artificial neural networks (ANNs) are usable for planning problems. Compared with the existing planning method in EUROPA, the mechanism using ANNs is more efficient and can guarantee stable performance. Therefore, the mechanism proposed in this paper is more suitable for planning problems of spacecraft that require real time and stability.

The Influence of Music on Prefrontal Cortex during Episodic Encoding and Retrieval of Verbal Information: A Multichannel fNIRS Study

PubMed Central

Ferreri, Laura; Bigand, Emmanuel; Bard, Patrick; Bugaiska, Aurélia

2015-01-01

Music can be thought of as a complex stimulus able to enrich the encoding of an event thus boosting its subsequent retrieval. However, several findings suggest that music can also interfere with memory performance. A better understanding of the behavioral and neural processes involved can substantially improve knowledge and shed new light on the most efficient music-based interventions. Based on fNIRS studies on music, episodic encoding, and the dorsolateral prefrontal cortex (PFC), this work aims to extend previous findings by monitoring the entire lateral PFC during both encoding and retrieval of verbal material. Nineteen participants were asked to encode lists of words presented with either background music or silence and subsequently tested during a free recall task. Meanwhile, their PFC was monitored using a 48-channel fNIRS system. Behavioral results showed greater chunking of words under the music condition, suggesting the employment of associative strategies for items encoded with music. fNIRS results showed that music provided a less demanding way of modulating both episodic encoding and retrieval, with a general prefrontal decreased activity under the music versus silence condition. This suggests that music-related memory processes rely on specific neural mechanisms and that music can positively influence both episodic encoding and retrieval of verbal information. PMID:26508813

The Influence of Music on Prefrontal Cortex during Episodic Encoding and Retrieval of Verbal Information: A Multichannel fNIRS Study.

PubMed

Ferreri, Laura; Bigand, Emmanuel; Bard, Patrick; Bugaiska, Aurélia

2015-01-01

Music can be thought of as a complex stimulus able to enrich the encoding of an event thus boosting its subsequent retrieval. However, several findings suggest that music can also interfere with memory performance. A better understanding of the behavioral and neural processes involved can substantially improve knowledge and shed new light on the most efficient music-based interventions. Based on fNIRS studies on music, episodic encoding, and the dorsolateral prefrontal cortex (PFC), this work aims to extend previous findings by monitoring the entire lateral PFC during both encoding and retrieval of verbal material. Nineteen participants were asked to encode lists of words presented with either background music or silence and subsequently tested during a free recall task. Meanwhile, their PFC was monitored using a 48-channel fNIRS system. Behavioral results showed greater chunking of words under the music condition, suggesting the employment of associative strategies for items encoded with music. fNIRS results showed that music provided a less demanding way of modulating both episodic encoding and retrieval, with a general prefrontal decreased activity under the music versus silence condition. This suggests that music-related memory processes rely on specific neural mechanisms and that music can positively influence both episodic encoding and retrieval of verbal information.

Thought probes during prospective memory encoding: Evidence for perfunctory processes

PubMed Central

McDaniel, Mark A.; Dasse, Michelle N.; Lee, Ji hae; Kurinec, Courtney A.; Tami, Claudina; Krueger, Madison L.

2018-01-01

For nearly 50 years, psychologists have studied prospective memory, or the ability to execute delayed intentions. Yet, there remains a gap in understanding as to whether initial encoding of the intention must be elaborative and strategic, or whether some components of successful encoding can occur in a perfunctory, transient manner. In eight studies (N = 680), we instructed participants to remember to press the Q key if they saw words representing fruits (cue) during an ongoing lexical decision task. They then typed what they were thinking and responded whether they encoded fruits as a general category, as specific exemplars, or hardly thought about it at all. Consistent with the perfunctory view, participants often reported mind wandering (42.9%) and hardly thinking about the prospective memory task (22.5%). Even though participants were given a general category cue, many participants generated specific category exemplars (34.5%). Bayesian analyses of encoding durations indicated that specific exemplars came to mind in a perfunctory manner rather than via strategic, elaborative mechanisms. Few participants correctly guessed the research hypotheses and changing from fruit category cues to initial-letter cues eliminated reports of specific exemplar generation, thereby arguing against demand characteristics in the thought probe procedure. In a final experiment, encoding duration was unrelated to prospective memory performance; however, specific-exemplar encoders outperformed general-category encoders with no ongoing task monitoring costs. Our findings reveal substantial variability in intention encoding, and demonstrate that some components of prospective memory encoding can be done “in passing.” PMID:29874277

Thought probes during prospective memory encoding: Evidence for perfunctory processes.

PubMed

Scullin, Michael K; McDaniel, Mark A; Dasse, Michelle N; Lee, Ji Hae; Kurinec, Courtney A; Tami, Claudina; Krueger, Madison L

2018-01-01

For nearly 50 years, psychologists have studied prospective memory, or the ability to execute delayed intentions. Yet, there remains a gap in understanding as to whether initial encoding of the intention must be elaborative and strategic, or whether some components of successful encoding can occur in a perfunctory, transient manner. In eight studies (N = 680), we instructed participants to remember to press the Q key if they saw words representing fruits (cue) during an ongoing lexical decision task. They then typed what they were thinking and responded whether they encoded fruits as a general category, as specific exemplars, or hardly thought about it at all. Consistent with the perfunctory view, participants often reported mind wandering (42.9%) and hardly thinking about the prospective memory task (22.5%). Even though participants were given a general category cue, many participants generated specific category exemplars (34.5%). Bayesian analyses of encoding durations indicated that specific exemplars came to mind in a perfunctory manner rather than via strategic, elaborative mechanisms. Few participants correctly guessed the research hypotheses and changing from fruit category cues to initial-letter cues eliminated reports of specific exemplar generation, thereby arguing against demand characteristics in the thought probe procedure. In a final experiment, encoding duration was unrelated to prospective memory performance; however, specific-exemplar encoders outperformed general-category encoders with no ongoing task monitoring costs. Our findings reveal substantial variability in intention encoding, and demonstrate that some components of prospective memory encoding can be done "in passing."

Absolute Position Encoders With Vertical Image Binning

NASA Technical Reports Server (NTRS)

Leviton, Douglas B.

2005-01-01

Improved optoelectronic patternrecognition encoders that measure rotary and linear 1-dimensional positions at conversion rates (numbers of readings per unit time) exceeding 20 kHz have been invented. Heretofore, optoelectronic pattern-recognition absoluteposition encoders have been limited to conversion rates <15 Hz -- too low for emerging industrial applications in which conversion rates ranging from 1 kHz to as much as 100 kHz are required. The high conversion rates of the improved encoders are made possible, in part, by use of vertically compressible or binnable (as described below) scale patterns in combination with modified readout sequences of the image sensors [charge-coupled devices (CCDs)] used to read the scale patterns. The modified readout sequences and the processing of the images thus read out are amenable to implementation by use of modern, high-speed, ultra-compact microprocessors and digital signal processors or field-programmable gate arrays. This combination of improvements makes it possible to greatly increase conversion rates through substantial reductions in all three components of conversion time: exposure time, image-readout time, and image-processing time.

Improving the axial resolution in time-reversed ultrasonically encoded (TRUE) optical focusing with dual ultrasonic waves

NASA Astrophysics Data System (ADS)

Yang, Qiang; Xu, Xiao; Lai, Puxiang; Sang, Xinzhu; Wang, Lihong V.

2014-03-01

Focusing light inside highly scattering media beyond the ballistic regime is a challenging task in biomedical optical imaging, manipulation, and therapy. This challenge can be overcome by time reversing ultrasonically encoded (TRUE) diffuse light to the ultrasonic focus inside a turbid medium. In TRUE optical focusing, a photorefractive crystal or polymer is used as the phase conjugate mirror for optical time reversal. Accordingly, a relatively long ultrasound burst, whose duration matches the response time of the photorefractive material, is used to encode the diffuse light. With this long ultrasound burst, the resolution of the TRUE focus along the acoustic axis is poor. In this work, we used two transducers, emitting two intersecting ultrasound beams at 3.4 MHz and 3.6 MHz respectively, to modulate the diffuse light within their intersection volume at the beat frequency. We show that light encoded at the beat frequency can be time-reversed and converge to the intersection volume. Experimentally, TRUE focusing with an acoustic axial resolution of ~1.1 mm was demonstrated inside turbid media, agreeing with the theoretical estimation.

Involvement of Clostridium botulinum ATCC 3502 Sigma Factor K in Early-Stage Sporulation

PubMed Central

Kirk, David G.; Dahlsten, Elias; Zhang, Zhen; Korkeala, Hannu

2012-01-01

A key survival mechanism of Clostridium botulinum, the notorious neurotoxic food pathogen, is the ability to form heat-resistant spores. While the genetic mechanisms of sporulation are well understood in the model organism Bacillus subtilis, nothing is known about these mechanisms in C. botulinum. Using the ClosTron gene-knockout tool, sigK, encoding late-stage (stage IV) sporulation sigma factor K in B. subtilis, was disrupted in C. botulinum ATCC 3502 to produce two different mutants with distinct insertion sites and orientations. Both mutants were unable to form spores, and their elongated cell morphology suggested that the sporulation pathway was blocked at an early stage. In contrast, sigK-complemented mutants sporulated successfully. Quantitative real-time PCR analysis of sigK in the parent strain revealed expression at the late log growth phase in the parent strain. Analysis of spo0A, encoding the sporulation master switch, in the sigK mutant and the parent showed significantly reduced relative levels of spo0A expression in the sigK mutant compared to the parent strain. Similarly, sigF showed significantly lower relative transcription levels in the sigK mutant than the parent strain, suggesting that the sporulation pathway was blocked in the sigK mutant at an early stage. We conclude that σK is essential for early-stage sporulation in C. botulinum ATCC 3502, rather than being involved in late-stage sporulation, as reported for the sporulation model organism B. subtilis. Understanding the sporulation mechanism of C. botulinum provides keys to control the public health risks that the spores of this dangerous pathogen cause through foods. PMID:22544236

Involvement of Clostridium botulinum ATCC 3502 sigma factor K in early-stage sporulation.

PubMed

Kirk, David G; Dahlsten, Elias; Zhang, Zhen; Korkeala, Hannu; Lindström, Miia

2012-07-01

A key survival mechanism of Clostridium botulinum, the notorious neurotoxic food pathogen, is the ability to form heat-resistant spores. While the genetic mechanisms of sporulation are well understood in the model organism Bacillus subtilis, nothing is known about these mechanisms in C. botulinum. Using the ClosTron gene-knockout tool, sigK, encoding late-stage (stage IV) sporulation sigma factor K in B. subtilis, was disrupted in C. botulinum ATCC 3502 to produce two different mutants with distinct insertion sites and orientations. Both mutants were unable to form spores, and their elongated cell morphology suggested that the sporulation pathway was blocked at an early stage. In contrast, sigK-complemented mutants sporulated successfully. Quantitative real-time PCR analysis of sigK in the parent strain revealed expression at the late log growth phase in the parent strain. Analysis of spo0A, encoding the sporulation master switch, in the sigK mutant and the parent showed significantly reduced relative levels of spo0A expression in the sigK mutant compared to the parent strain. Similarly, sigF showed significantly lower relative transcription levels in the sigK mutant than the parent strain, suggesting that the sporulation pathway was blocked in the sigK mutant at an early stage. We conclude that σ(K) is essential for early-stage sporulation in C. botulinum ATCC 3502, rather than being involved in late-stage sporulation, as reported for the sporulation model organism B. subtilis. Understanding the sporulation mechanism of C. botulinum provides keys to control the public health risks that the spores of this dangerous pathogen cause through foods.

Dissociable effects of top-down and bottom-up attention during episodic encoding

PubMed Central

Uncapher, Melina R.; Hutchinson, J. Benjamin; Wagner, Anthony D.

2011-01-01

It is well established that the formation of memories for life’s experiences—episodic memory—is influenced by how we attend to those experiences, yet the neural mechanisms by which attention shapes episodic encoding are still unclear. We investigated how top-down and bottom-up attention contribute to memory encoding of visual objects in humans by manipulating both types of attention during functional magnetic resonance imaging (fMRI) of episodic memory formation. We show that dorsal parietal cortex—specifically, intraparietal sulcus (IPS)—was engaged during top-down attention and was also recruited during the successful formation of episodic memories. By contrast, bottom-up attention engaged ventral parietal cortex—specifically, temporoparietal junction (TPJ)—and was also more active during encoding failure. Functional connectivity analyses revealed further dissociations in how top-down and bottom-up attention influenced encoding: while both IPS and TPJ influenced activity in perceptual cortices thought to represent the information being encoded (fusiform/lateral occipital cortex), they each exerted opposite effects on memory encoding. Specifically, during a preparatory period preceding stimulus presentation, a stronger drive from IPS was associated with a higher likelihood that the subsequently attended stimulus would be encoded. By contrast, during stimulus processing, stronger connectivity with TPJ was associated with a lower likelihood the stimulus would be successfully encoded. These findings suggest that during encoding of visual objects into episodic memory, top-down and bottom-up attention can have opposite influences on perceptual areas that subserve visual object representation, suggesting that one manner in which attention modulates memory is by altering the perceptual processing of to-be-encoded stimuli. PMID:21880922

Increased Neural Activation during Picture Encoding and Retrieval in 60-Year-Olds Compared to 20-Year-Olds

ERIC Educational Resources Information Center

Burgmans, S.; van Boxtel, M. P. J.; Vuurman, E. F. P. M.; Evers, E. A. T.; Jolles, J.

2010-01-01

Brain aging has been associated with both reduced and increased neural activity during task execution. The purpose of the present study was to investigate whether increased neural activation during memory encoding and retrieval is already present at the age of 60 as well as to obtain more insight into the mechanism behind increased activity.…

Dopamine Is Differentially Encoded by D2 Receptors in Striatal Subregions.

PubMed

Engeln, Michel; Fox, Megan E; Lobo, Mary Kay

2018-05-02

Striatal dopamine signaling is differentially regulated along the dorso-ventral axis, but how these differences are encoded by dopamine receptors is unknown. In this issue of Neuron, Marcott et al. (2018) show that dopamine activates D2 receptors in regionally distinct ways and dissect the underlying mechanisms behind striatal D2 heterogeneity. Copyright © 2018 Elsevier Inc. All rights reserved.

Feasibility study of a real-time operating system for a multichannel MPEG-4 encoder

NASA Astrophysics Data System (ADS)

Lehtoranta, Olli; Hamalainen, Timo D.

2005-03-01

Feasibility of DSP/BIOS real-time operating system for a multi-channel MPEG-4 encoder is studied. Performances of two MPEG-4 encoder implementations with and without the operating system are compared in terms of encoding frame rate and memory requirements. The effects of task switching frequency and number of parallel video channels to the encoding frame rate are measured. The research is carried out on a 200 MHz TMS320C6201 fixed point DSP using QCIF (176x144 pixels) video format. Compared to a traditional DSP implementation without an operating system, inclusion of DSP/BIOS reduces total system throughput only by 1 QCIF frames/s. The operating system has 6 KB data memory overhead and program memory requirement of 15.7 KB. Hence, the overhead is considered low enough for resource critical mobile video applications.

The effect of structural design parameters on FPGA-based feed-forward space-time trellis coding-orthogonal frequency division multiplexing channel encoders

NASA Astrophysics Data System (ADS)

Passas, Georgios; Freear, Steven; Fawcett, Darren

2010-08-01

Orthogonal frequency division multiplexing (OFDM)-based feed-forward space-time trellis code (FFSTTC) encoders can be synthesised as very high speed integrated circuit hardware description language (VHDL) designs. Evaluation of their FPGA implementation can lead to conclusions that help a designer to decide the optimum implementation, given the encoder structural parameters. VLSI architectures based on 1-bit multipliers and look-up tables (LUTs) are compared in terms of FPGA slices and block RAMs (area), as well as in terms of minimum clock period (speed). Area and speed graphs versus encoder memory order are provided for quadrature phase shift keying (QPSK) and 8 phase shift keying (8-PSK) modulation and two transmit antennas, revealing best implementation under these conditions. The effect of number of modulation bits and transmit antennas on the encoder implementation complexity is also investigated.

Effects of load and maintenance duration on the time course of information encoding and retrieval in working memory: from perceptual analysis to post-categorization processes.

PubMed

Pinal, Diego; Zurrón, Montserrat; Díaz, Fernando

2014-01-01

information encoding, maintenance, and retrieval; these are supported by brain activity in a network of frontal, parietal and temporal regions. Manipulation of WM load and duration of the maintenance period can modulate this activity. Although such modulations have been widely studied using the event-related potentials (ERP) technique, a precise description of the time course of brain activity during encoding and retrieval is still required. Here, we used this technique and principal component analysis to assess the time course of brain activity during encoding and retrieval in a delayed match to sample task. We also investigated the effects of memory load and duration of the maintenance period on ERP activity. Brain activity was similar during information encoding and retrieval and comprised six temporal factors, which closely matched the latency and scalp distribution of some ERP components: P1, N1, P2, N2, P300, and a slow wave. Changes in memory load modulated task performance and yielded variations in frontal lobe activation. Moreover, the P300 amplitude was smaller in the high than in the low load condition during encoding and retrieval. Conversely, the slow wave amplitude was higher in the high than in the low load condition during encoding, and the same was true for the N2 amplitude during retrieval. Thus, during encoding, memory load appears to modulate the processing resources for context updating and post-categorization processes, and during retrieval it modulates resources for stimulus classification and context updating. Besides, despite the lack of differences in task performance related to duration of the maintenance period, larger N2 amplitude and stronger activation of the left temporal lobe after long than after short maintenance periods were found during information retrieval. Thus, results regarding the duration of maintenance period were complex, and future work is required to test the time-based decay theory predictions.

Task-selective memory effects for successfully implemented encoding strategies.

PubMed

Leshikar, Eric D; Duarte, Audrey; Hertzog, Christopher

2012-01-01

Previous behavioral evidence suggests that instructed strategy use benefits associative memory formation in paired associate tasks. Two such effective encoding strategies--visual imagery and sentence generation--facilitate memory through the production of different types of mediators (e.g., mental images and sentences). Neuroimaging evidence suggests that regions of the brain support memory reflecting the mental operations engaged at the time of study. That work, however, has not taken into account self-reported encoding task success (i.e., whether participants successfully generated a mediator). It is unknown, therefore, whether task-selective memory effects specific to each strategy might be found when encoding strategies are successfully implemented. In this experiment, participants studied pairs of abstract nouns under either visual imagery or sentence generation encoding instructions. At the time of study, participants reported their success at generating a mediator. Outside of the scanner, participants further reported the quality of the generated mediator (e.g., images, sentences) for each word pair. We observed task-selective memory effects for visual imagery in the left middle occipital gyrus, the left precuneus, and the lingual gyrus. No such task-selective effects were observed for sentence generation. Intriguingly, activity at the time of study in the left precuneus was modulated by the self-reported quality (vividness) of the generated mental images with greater activity for trials given higher ratings of quality. These data suggest that regions of the brain support memory in accord with the encoding operations engaged at the time of study.

Task-Selective Memory Effects for Successfully Implemented Encoding Strategies

PubMed Central

Leshikar, Eric D.; Duarte, Audrey; Hertzog, Christopher

2012-01-01

Previous behavioral evidence suggests that instructed strategy use benefits associative memory formation in paired associate tasks. Two such effective encoding strategies–visual imagery and sentence generation–facilitate memory through the production of different types of mediators (e.g., mental images and sentences). Neuroimaging evidence suggests that regions of the brain support memory reflecting the mental operations engaged at the time of study. That work, however, has not taken into account self-reported encoding task success (i.e., whether participants successfully generated a mediator). It is unknown, therefore, whether task-selective memory effects specific to each strategy might be found when encoding strategies are successfully implemented. In this experiment, participants studied pairs of abstract nouns under either visual imagery or sentence generation encoding instructions. At the time of study, participants reported their success at generating a mediator. Outside of the scanner, participants further reported the quality of the generated mediator (e.g., images, sentences) for each word pair. We observed task-selective memory effects for visual imagery in the left middle occipital gyrus, the left precuneus, and the lingual gyrus. No such task-selective effects were observed for sentence generation. Intriguingly, activity at the time of study in the left precuneus was modulated by the self-reported quality (vividness) of the generated mental images with greater activity for trials given higher ratings of quality. These data suggest that regions of the brain support memory in accord with the encoding operations engaged at the time of study. PMID:22693593

Encoding-related brain activity and accelerated forgetting in transient epileptic amnesia.

PubMed

Atherton, Kathryn E; Filippini, Nicola; Zeman, Adam Z J; Nobre, Anna C; Butler, Christopher R

2018-05-17

The accelerated forgetting of newly learned information is common amongst patients with epilepsy and, in particular, in the syndrome of transient epileptic amnesia (TEA). However, the neural mechanisms underlying accelerated forgetting are poorly understood. It has been hypothesised that interictal epileptiform activity during longer retention intervals disrupts normally established memory traces. Here, we tested a distinct hypothesis-that accelerated forgetting relates to the abnormal encoding of memories. We studied a group of 15 patients with TEA together with matched, healthy control subjects. Despite normal performance on standard anterograde memory tasks, patients showed accelerated forgetting of a word list over one week. We used a subsequent memory paradigm to compare encoding-related brain activity in patients and controls. Participants studied a series of visually presented scenes whilst undergoing functional MRI scanning. Recognition memory for these scenes was then probed outside the scanner after delays of 45 min and of 4 days. Patients showed poorer memory for the scenes compared with controls. In the patients but not the controls, subsequently forgotten stimuli were associated with reduced hippocampal activation at encoding. Furthermore, patients demonstrated reduced deactivation of posteromedial cortex regions upon viewing subsequently remembered stimuli as compared to subsequently forgotten ones. These data suggest that abnormal encoding-related activity in key memory areas of the brain contributes to accelerated forgetting in TEA. We propose that abnormally encoded memory traces may be particularly vulnerable to interference from subsequently encountered material and hence be forgotten more rapidly. Our results shed light on the mechanisms underlying memory impairment in epilepsy, and offer support to the proposal that accelerated forgetting may be a useful marker of subtle dysfunction in memory-related brain systems. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Bone Collagen: New Clues to its Mineralization Mechanism From Recessive Osteogenesis Imperfecta

PubMed Central

Eyre, David R.; Ann Weis, Mary

2013-01-01

Until 2006 the only mutations known to cause osteogenesis imperfecta (OI) were in the two genes coding for type I collagen chains. These dominant mutations affecting the expression or primary sequence of collagen α1(I) and α2(I) chains account for over 90% of OI cases. Since then a growing list of mutant genes causing the 5–10% of recessive cases has rapidly emerged. They include CRTAP, LEPRE1 and PPIB, which encode three proteins forming the prolyl 3-hydroxylase complex; PLOD2 and FKBP10, which encode respectively lysyl hydroxylase 2 and a foldase required for its activity in forming mature cross-links in bone collagen; SERPIN H1, which encodes the collagen chaperone HSP47; SERPIN F1, which encodes pigment epithelium-derived factor required for osteoid mineralization; and BMP1, which encodes the type I procollagen C-propeptidase. All cause fragile bone in infancy, which can include over-mineralization or under-mineralization defects as well as abnormal collagen post-translational modifications. Consistently both dominant and recessive variants lead to abnormal cross-linking chemistry in bone collagen. These recent discoveries strengthen the potential for a common pathogenic mechanism of misassembled collagen fibrils. Of the new genes identified, eight encode proteins required for collagen post-translational modification, chaperoning of newly synthesized collagen chains into native molecules or transport through the endoplasmic reticulum and Golgi for polymerization, cross-linking and mineralization. In reviewing these findings, we conclude that a common theme is emerging in the pathogenesis of brittle bone disease of mishandled collagen assembly with important insights on post-translational features of bone collagen that have evolved to optimize it as a biomineral template. PMID:23508630

Alternative intronic promoters in development and disease.

PubMed

Vacik, Tomas; Raska, Ivan

2017-05-01

Approximately 20,000 mammalian genes are estimated to encode between 250 thousand and 1 million different proteins. This enormous diversity of the mammalian proteome is caused by the ability of a single-gene locus to encode multiple protein isoforms. Protein isoforms encoded by one gene locus can be functionally distinct, and they can even have antagonistic functions. One of the mechanisms involved in creating this proteome complexity is alternative promoter usage. Alternative intronic promoters are located downstream from their canonical counterparts and drive the expression of alternative RNA isoforms that lack upstream exons. These upstream exons can encode some important functional domains, and proteins encoded by alternative mRNA isoforms can be thus functionally distinct from the full-length protein encoded by canonical mRNA isoforms. Since any misbalance of functionally distinct protein isoforms is likely to have detrimental consequences for the cell and the whole organism, their expression must be precisely regulated. Misregulation of alternative intronic promoters is frequently associated with various developmental defects and diseases including cancer, and it is becoming increasingly clear that this phenomenon deserves more attention.

Human Genomic Signatures of Brain Oscillations During Memory Encoding.

PubMed

Berto, Stefano; Wang, Guang-Zhong; Germi, James; Lega, Bradley C; Konopka, Genevieve

2018-05-01

Memory encoding is an essential step for all learning. However, the genetic and molecular mechanisms underlying human memory encoding remain poorly understood, and how this molecular framework permits the emergence of specific patterns of brain oscillations observed during mnemonic processing is unknown. Here, we directly compare intracranial electroencephalography recordings from the neocortex in individuals performing an episodic memory task with human gene expression from the same areas. We identify genes correlated with oscillatory memory effects across 6 frequency bands. These genes are enriched for autism-related genes and have preferential expression in neurons, in particular genes encoding synaptic proteins and ion channels, supporting the idea that the genes regulating voltage gradients are involved in the modulation of oscillatory patterns during successful memory encoding across brain areas. Memory-related genes are distinct from those correlated with other forms of cognitive processing and resting state fMRI. These data are the first to identify correlations between gene expression and active human brain states as well as provide a molecular window into memory encoding oscillations in the human brain.

Magnetic field shift due to mechanical vibration in functional magnetic resonance imaging.

PubMed

Foerster, Bernd U; Tomasi, Dardo; Caparelli, Elisabeth C

2005-11-01

Mechanical vibrations of the gradient coil system during readout in echo-planar imaging (EPI) can increase the temperature of the gradient system and alter the magnetic field distribution during functional magnetic resonance imaging (fMRI). This effect is enhanced by resonant modes of vibrations and results in apparent motion along the phase encoding direction in fMRI studies. The magnetic field drift was quantified during EPI by monitoring the resonance frequency interleaved with the EPI acquisition, and a novel method is proposed to correct the apparent motion. The knowledge on the frequency drift over time was used to correct the phase of the k-space EPI dataset. Since the resonance frequency changes very slowly over time, two measurements of the resonance frequency, immediately before and after the EPI acquisition, are sufficient to remove the field drift effects from fMRI time series. The frequency drift correction method was tested "in vivo" and compared to the standard image realignment method. The proposed method efficiently corrects spurious motion due to magnetic field drifts during fMRI. (c) 2005 Wiley-Liss, Inc.

The Limits of Human Stereopsis in Space and Time

PubMed Central

Kane, David; Guan, Phillip

2014-01-01

To encode binocular disparity, the visual system determines the image patches in one eye that yield the highest correlation with patches in the other eye. The computation of interocular correlation occurs after spatiotemporal filtering of monocular signals, which leads to restrictions on disparity variations that can support depth perception. We quantified those restrictions by measuring humans' ability to see disparity variation at a wide range of spatial and temporal frequencies. Lower-disparity thresholds cut off at very low spatiotemporal frequencies, which is consistent with the behavior of V1 neurons. Those thresholds are space–time separable, suggesting that the underlying neural mechanisms are separable. We also found that upper-disparity limits were characterized by a spatiotemporal, disparity-gradient limit; to be visible, disparity variation cannot exceed a fixed amount for a given interval in space–time. Our results illustrate that the disparity variations that humans can see are very restricted compared with the corresponding luminance variations. The results also provide insight into the neural mechanisms underlying depth from disparity, such as why stimuli with long interocular delays can still yield clear depth percepts. PMID:24453329

Differential Regulation and Posttranslational Processing of the Class II Hydrophobin Genes from the Biocontrol Fungus Hypocrea atroviridis▿

PubMed Central

Mikus, Marianna; Hatvani, Lóránt; Neuhof, Torsten; Komoń-Zelazowska, Monika; Dieckmann, Ralf; Schwecke, Torsten; Druzhinina, Irina S.; von Döhren, Hans; Kubicek, Christian P.

2009-01-01

Hydrophobins are small extracellular proteins, unique to and ubiquitous in filamentous fungi, which mediate interactions between the fungus and environment. The mycoparasitic fungus Hypocrea atroviridis has recently been shown to possess 10 different class II hydrophobin genes, which is a much higher number than that of any other ascomycete investigated so far. In order to learn the potential advantage of this hydrophobin multiplicity for the fungus, we have investigated their expression patterns under different physiological conditions (e.g., vegetative growth), various conditions inducing sporulation (light, carbon starvation, and mechanical injury-induced stress), and confrontation with potential hosts for mycoparasitism. The results show that the 10 hydrophobins display different patterns of response to these conditions: one hydrophobin (encoded by hfb-2b) is constitutively induced under all conditions, whereas other hydrophobins were formed only under conditions of carbon starvation (encoded by hfb-1c and hfb-6c) or light plus carbon starvation (encoded by hfb-2c, hfb-6a, and hfb-6b). The hydrophobins encoded by hfb-1b and hfb-5a were primarily formed during vegetative growth and under mechanical injury-provoked stress. hfb-22a was not expressed under any conditions and is likely a pseudogene. None of the 10 genes showed a specific expression pattern during mycoparasitic interaction. Most, but not all, of the expression patterns under the three different conditions of sporulation were dependent on one or both of the two blue-light regulator proteins BLR1 and BLR2, as shown by the use of respective loss-of-function mutants. Matrix-assisted laser desorption ionization-time of flight mass spectrometry of mycelial solvent extracts provided sets of molecular ions corresponding to HFB-1b, HFB-2a, HFB-2b, and HFB-5a in their oxidized and processed forms. These in silico-deduced sequences of the hydrophobins indicate cleavages at known signal peptide sites as well as additional N- and C-terminal processing. Mass peaks observed during confrontation with plant-pathogenic fungi indicate further proteolytic attack on the hydrophobins. Our study illustrates both divergent and redundant functions of the 10 hydrophobins of H. atroviridis. PMID:19329667

Control of information in working memory: Encoding and removal of distractors in the complex-span paradigm.

PubMed

Oberauer, Klaus; Lewandowsky, Stephan

2016-11-01

The article reports four experiments with complex-span tasks in which encoding of memory items alternates with processing of distractors. The experiments test two assumptions of a computational model of complex span, SOB-CS: (1) distractor processing impairs memory because distractors are encoded into working memory, thereby interfering with memoranda; and (2) free time following distractors is used to remove them from working memory by unbinding their representations from list context. Experiment 1 shows that distractors are erroneously chosen for recall more often than not-presented stimuli, demonstrating that distractors are encoded into memory. Distractor intrusions declined with longer free time, as predicted by distractor removal. Experiment 2 shows these effects even when distractors precede the memory list, ruling out an account based on selective rehearsal of memoranda during free time. Experiments 3 and 4 test the notion that distractors decay over time. Both experiments show that, contrary to the notion of distractor decay, the chance of a distractor intruding at test does not decline with increasing time since encoding of that distractor. Experiment 4 provides additional evidence against the prediction from distractor decay that distractor intrusions decline over an unfilled retention interval. Taken together, the results support SOB-CS and rule out alternative explanations. Data and simulation code are available on Open Science Framework: osf.io/3ewh7. Copyright © 2016 Elsevier B.V. All rights reserved.

Time-Bin-Encoded Boson Sampling with a Single-Photon Device.

PubMed

He, Yu; Ding, X; Su, Z-E; Huang, H-L; Qin, J; Wang, C; Unsleber, S; Chen, C; Wang, H; He, Y-M; Wang, X-L; Zhang, W-J; Chen, S-J; Schneider, C; Kamp, M; You, L-X; Wang, Z; Höfling, S; Lu, Chao-Yang; Pan, Jian-Wei

2017-05-12

Boson sampling is a problem strongly believed to be intractable for classical computers, but can be naturally solved on a specialized photonic quantum simulator. Here, we implement the first time-bin-encoded boson sampling using a highly indistinguishable (∼94%) single-photon source based on a single quantum-dot-micropillar device. The protocol requires only one single-photon source, two detectors, and a loop-based interferometer for an arbitrary number of photons. The single-photon pulse train is time-bin encoded and deterministically injected into an electrically programmable multimode network. The observed three- and four-photon boson sampling rates are 18.8 and 0.2 Hz, respectively, which are more than 100 times faster than previous experiments based on parametric down-conversion.

Can the hippocampus tell time? The temporo-septal engram shift model.

PubMed

Lytton, W W; Lipton, P

1999-08-02

An essential feature of episodic memory, the type of memory dependent on hippocampus, is that individual memories belong to particular moments in time. Recent PET studies suggest that memory encoding and recall occur at different locations in human hippocampus. Coupled with other attributes of hippocampus, this suggested to us that the septo-temporal hippocampal axis may play an important role in time perception. We propose a temporo-septal engram shift model of hippocampal memory. The model posits that memories gradually move along the hippocampus from a temporal encoding site to ever more septal sites from which they are recalled. We propose that the sense of time is encoded by the location of the engram along the temporo-septal axis.

Eddy current-nulled convex optimized diffusion encoding (EN-CODE) for distortion-free diffusion tensor imaging with short echo times.

PubMed

Aliotta, Eric; Moulin, Kévin; Ennis, Daniel B

2018-02-01

To design and evaluate eddy current-nulled convex optimized diffusion encoding (EN-CODE) gradient waveforms for efficient diffusion tensor imaging (DTI) that is free of eddy current-induced image distortions. The EN-CODE framework was used to generate diffusion-encoding waveforms that are eddy current-compensated. The EN-CODE DTI waveform was compared with the existing eddy current-nulled twice refocused spin echo (TRSE) sequence as well as monopolar (MONO) and non-eddy current-compensated CODE in terms of echo time (TE) and image distortions. Comparisons were made in simulations, phantom experiments, and neuro imaging in 10 healthy volunteers. The EN-CODE sequence achieved eddy current compensation with a significantly shorter TE than TRSE (78 versus 96 ms) and a slightly shorter TE than MONO (78 versus 80 ms). Intravoxel signal variance was lower in phantoms with EN-CODE than with MONO (13.6 ± 11.6 versus 37.4 ± 25.8) and not different from TRSE (15.1 ± 11.6), indicating good robustness to eddy current-induced image distortions. Mean fractional anisotropy values in brain edges were also significantly lower with EN-CODE than with MONO (0.16 ± 0.01 versus 0.24 ± 0.02, P < 1 x 10 -5 ) and not different from TRSE (0.16 ± 0.01 versus 0.16 ± 0.01, P = nonsignificant). The EN-CODE sequence eliminated eddy current-induced image distortions in DTI with a TE comparable to MONO and substantially shorter than TRSE. Magn Reson Med 79:663-672, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

False memory and importance: can we prioritize encoding without consequence?

PubMed

Bui, Dung C; Friedman, Michael C; McDonough, Ian M; Castel, Alan D

2013-10-01

Given the large amount of information that we encounter, we often must prioritize what information we attempt to remember. Although critical for everyday functioning, relatively little research has focused on how people prioritize the encoding of information. Recent research has shown that people can and do selectively remember information assigned with higher, relative to lower, importance. However, the mechanisms underlying this prioritization process and the consequences of these processes are still not well understood. In the present study, we sought to better understand these prioritization processes and whether implementing these processes comes at the cost of memory accuracy, by increasing false memories. We used a modified form of the Deese/Roediger-McDermott (DRM) paradigm, in which participants studied DRM lists, with each list paired with low, medium, or high point values. In Experiment 1, encoding higher values led to more false memories than did encoding lower values, possibly because prioritizing information enhanced relational processing among high-value words. In Experiment 2, disrupting relational processing selectively reduced false memories for high-value words. Finally, in Experiment 3, facilitating relational processing selectively increased false memories for low-value words. These findings suggest that while prioritizing information can enhance true memory, this process concomitantly increases false memories. Furthermore, the mechanism underlying these prioritization processes depends on the ability to successfully engage in relational processing. Thus, how we prioritize the encoding of incoming information can come at a cost in terms of accurate memory.

Value-based modulation of memory encoding involves strategic engagement of fronto-temporal semantic processing regions

PubMed Central

Cohen, Michael S.; Rissman, Jesse; Suthana, Nanthia A.; Castel, Alan D.; Knowlton, Barbara J.

2014-01-01

A number of prior fMRI studies have focused on the ways in which the midbrain dopaminergic reward system co-activates with hippocampus to potentiate memory for valuable items. However, another means by which people could selectively remember more valuable to-be-remembered items is to be selective in their use of effective but effortful encoding strategies. To broadly examine the neural mechanisms of value on subsequent memory, we used fMRI to examine how differences in brain activity at encoding as a function of value relate to subsequent free recall for words. Each word was preceded by an arbitrarily assigned point value, and participants went through multiple study-test cycles with feedback on their point total at the end of each list, allowing for sculpting of cognitive strategies. We examined the correlation between value-related modulation of brain activity and participants’ selectivity index, a measure of how close participants were to their optimal point total given the number of items recalled. Greater selectivity scores were associated with greater differences in activation of semantic processing regions, including left inferior frontal gyrus and left posterior lateral temporal cortex, during encoding of high-value words relative to low-value words. Although we also observed value-related modulation within midbrain and ventral striatal reward regions, our fronto-temporal findings suggest that strategic engagement of deep semantic processing may be an important mechanism for selectively encoding valuable items. PMID:24683066

Value-based modulation of memory encoding involves strategic engagement of fronto-temporal semantic processing regions.

PubMed

Cohen, Michael S; Rissman, Jesse; Suthana, Nanthia A; Castel, Alan D; Knowlton, Barbara J

2014-06-01

A number of prior fMRI studies have focused on the ways in which the midbrain dopaminergic reward system coactivates with hippocampus to potentiate memory for valuable items. However, another means by which people could selectively remember more valuable to-be-remembered items is to be selective in their use of effective but effortful encoding strategies. To broadly examine the neural mechanisms of value on subsequent memory, we used fMRI to assess how differences in brain activity at encoding as a function of value relate to subsequent free recall for words. Each word was preceded by an arbitrarily assigned point value, and participants went through multiple study-test cycles with feedback on their point total at the end of each list, allowing for sculpting of cognitive strategies. We examined the correlation between value-related modulation of brain activity and participants' selectivity index, which measures how close participants were to their optimal point total, given the number of items recalled. Greater selectivity scores were associated with greater differences in the activation of semantic processing regions, including left inferior frontal gyrus and left posterior lateral temporal cortex, during the encoding of high-value words relative to low-value words. Although we also observed value-related modulation within midbrain and ventral striatal reward regions, our fronto-temporal findings suggest that strategic engagement of deep semantic processing may be an important mechanism for selectively encoding valuable items.

Externally calibrated parallel imaging for 3D multispectral imaging near metallic implants using broadband ultrashort echo time imaging.

PubMed

Wiens, Curtis N; Artz, Nathan S; Jang, Hyungseok; McMillan, Alan B; Reeder, Scott B

2017-06-01

To develop an externally calibrated parallel imaging technique for three-dimensional multispectral imaging (3D-MSI) in the presence of metallic implants. A fast, ultrashort echo time (UTE) calibration acquisition is proposed to enable externally calibrated parallel imaging techniques near metallic implants. The proposed calibration acquisition uses a broadband radiofrequency (RF) pulse to excite the off-resonance induced by the metallic implant, fully phase-encoded imaging to prevent in-plane distortions, and UTE to capture rapidly decaying signal. The performance of the externally calibrated parallel imaging reconstructions was assessed using phantoms and in vivo examples. Phantom and in vivo comparisons to self-calibrated parallel imaging acquisitions show that significant reductions in acquisition times can be achieved using externally calibrated parallel imaging with comparable image quality. Acquisition time reductions are particularly large for fully phase-encoded methods such as spectrally resolved fully phase-encoded three-dimensional (3D) fast spin-echo (SR-FPE), in which scan time reductions of up to 8 min were obtained. A fully phase-encoded acquisition with broadband excitation and UTE enabled externally calibrated parallel imaging for 3D-MSI, eliminating the need for repeated calibration regions at each frequency offset. Significant reductions in acquisition time can be achieved, particularly for fully phase-encoded methods like SR-FPE. Magn Reson Med 77:2303-2309, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Optimal Achievable Encoding for Brain Machine Interface

DTIC Science & Technology

2017-12-22

dictionary-based encoding approach to translate a visual image into sequential patterns of electrical stimulation in real time , in a manner that...including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and...networks, and by applying linear decoding to complete recorded populations of retinal ganglion cells for the first time . Third, we developed a greedy

Self-Calibrating Wave-Encoded Variable-Density Single-Shot Fast Spin Echo Imaging.

PubMed

Chen, Feiyu; Taviani, Valentina; Tamir, Jonathan I; Cheng, Joseph Y; Zhang, Tao; Song, Qiong; Hargreaves, Brian A; Pauly, John M; Vasanawala, Shreyas S

2018-04-01

It is highly desirable in clinical abdominal MR scans to accelerate single-shot fast spin echo (SSFSE) imaging and reduce blurring due to T 2 decay and partial-Fourier acquisition. To develop and investigate the clinical feasibility of wave-encoded variable-density SSFSE imaging for improved image quality and scan time reduction. Prospective controlled clinical trial. With Institutional Review Board approval and informed consent, the proposed method was assessed on 20 consecutive adult patients (10 male, 10 female, range, 24-84 years). A wave-encoded variable-density SSFSE sequence was developed for clinical 3.0T abdominal scans to enable high acceleration (3.5×) with full-Fourier acquisitions by: 1) introducing wave encoding with self-refocusing gradient waveforms to improve acquisition efficiency; 2) developing self-calibrated estimation of wave-encoding point-spread function and coil sensitivity to improve motion robustness; and 3) incorporating a parallel imaging and compressed sensing reconstruction to reconstruct highly accelerated datasets. Image quality was compared pairwise with standard Cartesian acquisition independently and blindly by two radiologists on a scale from -2 to 2 for noise, contrast, confidence, sharpness, and artifacts. The average ratio of scan time between these two approaches was also compared. A Wilcoxon signed-rank tests with a P value under 0.05 considered statistically significant. Wave-encoded variable-density SSFSE significantly reduced the perceived noise level and improved the sharpness of the abdominal wall and the kidneys compared with standard acquisition (mean scores 0.8, 1.2, and 0.8, respectively, P < 0.003). No significant difference was observed in relation to other features (P = 0.11). An average of 21% decrease in scan time was achieved using the proposed method. Wave-encoded variable-density sampling SSFSE achieves improved image quality with clinically relevant echo time and reduced scan time, thus providing a fast and robust approach for clinical SSFSE imaging. 1 Technical Efficacy: Stage 6 J. Magn. Reson. Imaging 2018;47:954-966. © 2017 International Society for Magnetic Resonance in Medicine.

Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity island transfer.

PubMed

Bowring, Janine; Neamah, Maan M; Donderis, Jorge; Mir-Sanchis, Ignacio; Alite, Christian; Ciges-Tomas, J Rafael; Maiques, Elisa; Medmedov, Iltyar; Marina, Alberto; Penadés, José R

2017-08-08

Targeting conserved and essential processes is a successful strategy to combat enemies. Remarkably, the clinically important Staphylococcus aureus pathogenicity islands (SaPIs) use this tactic to spread in nature. SaPIs reside passively in the host chromosome, under the control of the SaPI-encoded master repressor, Stl. It has been assumed that SaPI de-repression is effected by specific phage proteins that bind to Stl, initiating the SaPI cycle. Different SaPIs encode different Stl repressors, so each targets a specific phage protein for its de-repression. Broadening this narrow vision, we report here that SaPIs ensure their promiscuous transfer by targeting conserved phage mechanisms. This is accomplished because the SaPI Stl repressors have acquired different domains to interact with unrelated proteins, encoded by different phages, but in all cases performing the same conserved function. This elegant strategy allows intra- and inter-generic SaPI transfer, highlighting these elements as one of nature's most fascinating subcellular parasites.

Circuit mechanisms encoding odors and driving aging-associated behavioral declines in Caenorhabditis elegans.

PubMed

Leinwand, Sarah G; Yang, Claire J; Bazopoulou, Daphne; Chronis, Nikos; Srinivasan, Jagan; Chalasani, Sreekanth H

2015-09-22

Chemosensory neurons extract information about chemical cues from the environment. How is the activity in these sensory neurons transformed into behavior? Using Caenorhabditis elegans, we map a novel sensory neuron circuit motif that encodes odor concentration. Primary neurons, AWC(ON) and AWA, directly detect the food odor benzaldehyde (BZ) and release insulin-like peptides and acetylcholine, respectively, which are required for odor-evoked responses in secondary neurons, ASEL and AWB. Consistently, both primary and secondary neurons are required for BZ attraction. Unexpectedly, this combinatorial code is altered in aged animals: odor-evoked activity in secondary, but not primary, olfactory neurons is reduced. Moreover, experimental manipulations increasing neurotransmission from primary neurons rescues aging-associated neuronal deficits. Finally, we correlate the odor responsiveness of aged animals with their lifespan. Together, these results show how odors are encoded by primary and secondary neurons and suggest reduced neurotransmission as a novel mechanism driving aging-associated sensory neural activity and behavioral declines.

Molecular Mechanisms of Innate Immune Inhibition by Non-Segmented Negative-Sense RNA Viruses

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

Chatterjee, Srirupa; Basler, Christopher F.; Amarasinghe, Gaya K.

The host innate immune system serves as the first line of defense against viral infections. Germline-encoded pattern recognition receptors detect molecular patterns associated with pathogens and activate innate immune responses. Of particular relevance to viral infections are those pattern recognition receptors that activate type I interferon responses, which establish an antiviral state. The order Mononegavirales is composed of viruses that possess single-stranded, non-segmented negative-sense (NNS) RNA genomes and are important human pathogens that consistently antagonize signaling related to type I interferon responses. NNS viruses have limited encoding capacity compared to many DNA viruses, and as a likely consequence, most openmore » reading frames encode multifunctional viral proteins that interact with host factors in order to evade host cell defenses while promoting viral replication. In this review, we will discuss the molecular mechanisms of innate immune evasion by select NNS viruses. A greater understanding of these interactions will be critical in facilitating the development of effective therapeutics and viral countermeasures.« less

Circuit mechanisms encoding odors and driving aging-associated behavioral declines in Caenorhabditis elegans

PubMed Central

Leinwand, Sarah G; Yang, Claire J; Bazopoulou, Daphne; Chronis, Nikos; Srinivasan, Jagan; Chalasani, Sreekanth H

2015-01-01

Chemosensory neurons extract information about chemical cues from the environment. How is the activity in these sensory neurons transformed into behavior? Using Caenorhabditis elegans, we map a novel sensory neuron circuit motif that encodes odor concentration. Primary neurons, AWCON and AWA, directly detect the food odor benzaldehyde (BZ) and release insulin-like peptides and acetylcholine, respectively, which are required for odor-evoked responses in secondary neurons, ASEL and AWB. Consistently, both primary and secondary neurons are required for BZ attraction. Unexpectedly, this combinatorial code is altered in aged animals: odor-evoked activity in secondary, but not primary, olfactory neurons is reduced. Moreover, experimental manipulations increasing neurotransmission from primary neurons rescues aging-associated neuronal deficits. Finally, we correlate the odor responsiveness of aged animals with their lifespan. Together, these results show how odors are encoded by primary and secondary neurons and suggest reduced neurotransmission as a novel mechanism driving aging-associated sensory neural activity and behavioral declines. DOI: http://dx.doi.org/10.7554/eLife.10181.001 PMID:26394000

Mechanisms for Adjusting Interaural Time Differences to Achieve Binaural Coincidence Detection

PubMed Central

Seidl, Armin H.; Rubel, Edwin W; Harris, David M.

2010-01-01

Understanding binaural perception requires detailed analyses of the neural circuitry responsible for the computation of interaural time differences (ITDs). In the avian brainstem, this circuit consists of internal axonal delay lines innervating an array of coincidence detector neurons that encode external ITDs. Nucleus magnocellularis (NM) neurons project to the dorsal dendritic field of the ipsilateral nucleus laminaris (NL) and to the ventral field of the contralateral NL. Contralateral-projecting axons form a delay line system along a band of NL neurons. Binaural acoustic signals in the form of phase-locked action potentials from NM cells arrive at NL and establish a topographic map of sound source location along the azimuth. These pathways are assumed to represent a circuit similar to the Jeffress model of sound localization, establishing a place code along an isofrequency contour of NL. Three-dimensional measurements of axon lengths reveal major discrepancies with the current model; the temporal offset based on conduction length alone makes encoding of physiological ITDs impossible. However, axon diameter and distances between Nodes of Ranvier also influence signal propagation times along an axon. Our measurements of these parameters reveal that diameter and internode distance can compensate for the temporal offset inferred from axon lengths alone. Together with other recent studies these unexpected results should inspire new thinking on the cellular biology, evolution and plasticity of the circuitry underlying low frequency sound localization in both birds and mammals. PMID:20053889

What is the function of hippocampal theta rhythm?--Linking behavioral data to phasic properties of field potential and unit recording data.

PubMed

Hasselmo, Michael E

2005-01-01

The extensive physiological data on hippocampal theta rhythm provide an opportunity to evaluate hypotheses about the role of theta rhythm for hippocampal network function. Computational models based on these hypotheses help to link behavioral data with physiological measurements of different variables during theta rhythm. This paper reviews work on network models in which theta rhythm contributes to the following functions: (1) separating the dynamics of encoding and retrieval, (2) enhancing the context-dependent retrieval of sequences, (3) buffering of novel information in entorhinal cortex (EC) for episodic encoding, and (4) timing interactions between prefrontal cortex and hippocampus for memory-guided action selection. Modeling shows how these functional mechanisms are related to physiological data from the hippocampal formation, including (1) the phase relationships of synaptic currents during theta rhythm measured by current source density analysis of electroencephalographic data from region CA1 and dentate gyrus, (2) the timing of action potentials, including the theta phase precession of single place cells during running on a linear track, the context-dependent changes in theta phase precession across trials on each day, and the context-dependent firing properties of hippocampal neurons in spatial alternation (e.g., "splitter cells"), (3) the cholinergic regulation of sustained activity in entorhinal cortical neurons, and (4) the phasic timing of prefrontal cortical neurons relative to hippocampal theta rhythm. Copyright 2005 Wiley-Liss, Inc.

The application of the HyPer fluorescent sensor in the real-time detection of H2O2 in Babesia bovis merozoites in vitro.

PubMed

Asada, Masahito; Hakimi, Hassan; Kawazu, Shin-Ichiro

2018-05-15

In recent years, genetically encoded fluorescent probes have allowed a dramatic advancement in time-lapse imaging, enabling this imaging modality to be used to investigate intracellular events in several apicomplexan parasite species. In this study, we constructed a plasmid vector to stably express a genetically encoded H 2 O 2 sensor probe called HyPer in Babesia bovis. The HyPer-transfected parasite population was successfully developed and subjected to a time-lapse imaging analysis under in vitro culture conditions. HyPer was capable of sensing an increasing H 2 O 2 concentration in the parasite cells which was induced by the administration of paraquat as a superoxide donor. HyPer fluorescence co-staining with MitoTracker Red indicated the mitochondria as the major source of reactive oxygen species (ROS) in parasite cells. The fluctuating ROS dynamics in the parasite gliding toward, attaching to, and invading the target red blood cell was visualized and monitored in real time with the HyPer expressing parasite population. This is the first report to describe the application of the HyPer probe in an imaging analysis involving Babesia parasites. Hyper-expressing parasites can be widely utilized in studies to investigate the mechanisms of emergence and the reduction of oxidative stress, as well as the signal transduction in the parasite cells during host invasion and intercellular development. Copyright © 2018 Elsevier B.V. All rights reserved.

Selective scanpath repetition during memory-guided visual search

PubMed Central

Wynn, Jordana S.; Bone, Michael B.; Dragan, Michelle C.; Hoffman, Kari L.; Buchsbaum, Bradley R.; Ryan, Jennifer D.

2016-01-01

ABSTRACT Visual search efficiency improves with repetition of a search display, yet the mechanisms behind these processing gains remain unclear. According to Scanpath Theory, memory retrieval is mediated by repetition of the pattern of eye movements or “scanpath” elicited during stimulus encoding. Using this framework, we tested the prediction that scanpath recapitulation reflects relational memory guidance during repeated search events. Younger and older subjects were instructed to find changing targets within flickering naturalistic scenes. Search efficiency (search time, number of fixations, fixation duration) and scanpath similarity (repetition) were compared across age groups for novel (V1) and repeated (V2) search events. Younger adults outperformed older adults on all efficiency measures at both V1 and V2, while the search time benefit for repeated viewing (V1–V2) did not differ by age. Fixation-binned scanpath similarity analyses revealed repetition of initial and final (but not middle) V1 fixations at V2, with older adults repeating more initial V1 fixations than young adults. In young adults only, early scanpath similarity correlated negatively with search time at test, indicating increased efficiency, whereas the similarity of V2 fixations to middle V1 fixations predicted poor search performance. We conclude that scanpath compression mediates increased search efficiency by selectively recapitulating encoding fixations that provide goal-relevant input. Extending Scanpath Theory, results suggest that scanpath repetition varies as a function of time and memory integrity. PMID:27570471

Determining the locations of the various CIRC recording format information blocks (user data blocks, C2 and C1 words and EFM frames) on a recorded compact disc

NASA Technical Reports Server (NTRS)

Howe, Dennis G.

1993-01-01

Just prior to its being EFM modulated (i.e., converted to eight-to-fourteen channel data by the EFM encoder) and written to a Compact Disc (CD), information that passes through the CIRC Block Encoder is grouped into 33-byte blocks referred to as EFM frames. Twenty four of the bytes that make up a given EFM frame are user data that was input into the CIRC encoder at various (different) times, 4 of the bytes of this same EFM frame were created by the C2 ECC encoder (each at a different time), and another 4 were created by the C1 ECC encoder (again, each at a different time). The one remaining byte of the given EFM frame, which is known as the EFM frame C&D (for Control & Display) byte, carries information that identifies which portion of the current disc program track the given EFM frame belongs to and also specifies the location of the given EFM frame on the disc (in terms of a time stamp that has a resolution of l/75th second, or 98 EFM frames). (Note: since the program track and time information is stored as a 98-byte word, a logical group consisting of 98 consecutive EFM frames must be read, and their respective C&D bytes must be catenated and decoded, before the program track identification and time position information that pertains to the entire block of 98 EFM frames can be obtained.) The C&D byte is put at the start (0th byte) of an EFM frame in real time; its placement completes the construction of the EFM frame - it is assigned just before the EFM frame enters the EFM encoder. Four distinct blocks of data are referred to: 24-byte User Input Data Blocks; 28-byte C2 words; 32-byte C1 words; and 33-byte EFM frames.

Forward Inferences: From Activation to Long-Term Memory.

ERIC Educational Resources Information Center

Klin, Celia M.; Murray, John D.; Levine, William H.; Guzman, Alexandria E.

1999-01-01

Investigates the extent to which forward inferences are activated and encoded during reading, as well as their prevalence and their time course. Finds that inferences were encoded and retained in working memory in both high- and low-predictability conditions, and that high-predictability forward inferences were encoded into long-term memory.…

Synthesizing folded band chaos.

PubMed

Corron, Ned J; Hayes, Scott T; Pethel, Shawn D; Blakely, Jonathan N

2007-04-01

A randomly driven linear filter that synthesizes Lorenz-like, reverse-time chaos is shown also to produce Rössler-like folded band wave forms when driven using a different encoding of the random source. The relationship between the topological entropy of the random source, dissipation in the linear filter, and the positive Lyapunov exponent for the reverse-time wave form is exposed. The two drive encodings are viewed as grammar restrictions on a more general encoding that produces a chaotic superset encompassing both the Lorenz butterfly and Rössler folded band paradigms of nonlinear dynamics.

Intertrial auditory neural stability supports beat synchronization in preschoolers

PubMed Central

Carr, Kali Woodruff; Tierney, Adam; White-Schwoch, Travis; Kraus, Nina

2016-01-01

The ability to synchronize motor movements along with an auditory beat places stringent demands on the temporal processing and sensorimotor integration capabilities of the nervous system. Links between millisecond-level precision of auditory processing and the consistency of sensorimotor beat synchronization implicate fine auditory neural timing as a mechanism for forming stable internal representations of, and behavioral reactions to, sound. Here, for the first time, we demonstrate a systematic relationship between consistency of beat synchronization and trial-by-trial stability of subcortical speech processing in preschoolers (ages 3 and 4 years old). We conclude that beat synchronization might provide a useful window into millisecond-level neural precision for encoding sound in early childhood, when speech processing is especially important for language acquisition and development. PMID:26760457

Spike timing precision of neuronal circuits.

PubMed

Kilinc, Deniz; Demir, Alper

2018-06-01

Spike timing is believed to be a key factor in sensory information encoding and computations performed by the neurons and neuronal circuits. However, the considerable noise and variability, arising from the inherently stochastic mechanisms that exist in the neurons and the synapses, degrade spike timing precision. Computational modeling can help decipher the mechanisms utilized by the neuronal circuits in order to regulate timing precision. In this paper, we utilize semi-analytical techniques, which were adapted from previously developed methods for electronic circuits, for the stochastic characterization of neuronal circuits. These techniques, which are orders of magnitude faster than traditional Monte Carlo type simulations, can be used to directly compute the spike timing jitter variance, power spectral densities, correlation functions, and other stochastic characterizations of neuronal circuit operation. We consider three distinct neuronal circuit motifs: Feedback inhibition, synaptic integration, and synaptic coupling. First, we show that both the spike timing precision and the energy efficiency of a spiking neuron are improved with feedback inhibition. We unveil the underlying mechanism through which this is achieved. Then, we demonstrate that a neuron can improve on the timing precision of its synaptic inputs, coming from multiple sources, via synaptic integration: The phase of the output spikes of the integrator neuron has the same variance as that of the sample average of the phases of its inputs. Finally, we reveal that weak synaptic coupling among neurons, in a fully connected network, enables them to behave like a single neuron with a larger membrane area, resulting in an improvement in the timing precision through cooperation.

Metagenomic Insights into the Fibrolytic Microbiome in Yak Rumen

PubMed Central

Song, Lei; Liu, Di; Liu, Li; Chen, Furong; Wang, Min; Li, Jiabao; Zeng, Xiaowei; Dong, Zhiyang; Hu, Songnian; Li, Lingyan; Xu, Jian; Huang, Li; Dong, Xiuzhu

2012-01-01

The rumen hosts one of the most efficient microbial systems for degrading plant cell walls, yet the predominant cellulolytic proteins and fibrolytic mechanism(s) remain elusive. Here we investigated the cellulolytic microbiome of the yak rumen by using a combination of metagenome-based and bacterial artificial chromosome (BAC)-based functional screening approaches. Totally 223 fibrolytic BAC clones were pyrosequenced and 10,070 ORFs were identified. Among them 150 were annotated as the glycoside hydrolase (GH) genes for fibrolytic proteins, and the majority (69%) of them were clustered or linked with genes encoding related functions. Among the 35 fibrolytic contigs of >10 Kb in length, 25 were derived from Bacteroidetes and four from Firmicutes. Coverage analysis indicated that the fibrolytic genes on most Bacteroidetes-contigs were abundantly represented in the metagenomic sequences, and they were frequently linked with genes encoding SusC/SusD-type outer-membrane proteins. GH5, GH9, and GH10 cellulase/hemicellulase genes were predominant, but no GH48 exocellulase gene was found. Most (85%) of the cellulase and hemicellulase proteins possessed a signal peptide; only a few carried carbohydrate-binding modules, and no cellulosomal domains were detected. These findings suggest that the SucC/SucD-involving mechanism, instead of one based on cellulosomes or the free-enzyme system, serves a major role in lignocellulose degradation in yak rumen. Genes encoding an endoglucanase of a novel GH5 subfamily occurred frequently in the metagenome, and the recombinant proteins encoded by the genes displayed moderate Avicelase in addition to endoglucanase activities, suggesting their important contribution to lignocellulose degradation in the exocellulase-scarce rumen. PMID:22808161

Genomic characterization of an extensively-drug resistance Salmonella enterica serotype Indiana strain harboring blaNDM-1 gene isolated from a chicken carcass in China.

PubMed

Wang, Wei; Peng, Zixin; Baloch, Zulqarnain; Hu, Yujie; Xu, Jin; Zhang, Wenhui; Fanning, Séamus; Li, Fengqin

2017-11-01

The objective of this study was to genetically characterize the antimicrobial resistance mechanisms of Salmonella enterica serotype Indiana C629 isolated from a chicken carcass in China in 2014. Antimicrobial susceptibility against a panel of 23 antimicrobial agents was carried out on Salmonella enterica serotype Indiana C629 and assessed according to CLSI standards. Whole-genome sequencing of this isolate was conducted to obtain the complete genome of S. Indiana. Salmonella Indiana C629 expressed an XDR phenotype being resistant to more than 20 antimicrobial agents, including imipenem and meropenem. From the analysis of the resistance mechanisms, two mutations were identified in subunit A of DNA gyrase within the quinolone resistance determining region, in addition to the acquisition of mobile efflux pumps encoding oqxA/B/R. Additionally, four beta-lactamases resistance genes (bla CTX-M-65 , bla TEM-1 , bla OXA-1 , and bla NDM-1 ), five aminoglycosides resistance genes (aac(3)-IV, aac(6')-Ib-cr, aadA2, aadA5, and aph(4)-Ia), two phenicol resistance genes (catB3 and floR), and five trimethoprim/sulfamethoxazole resistance genes (sul1/2/3 and dfrA12/17) were also identified. A total of 191 virulence genes were identified. Among them, 57 belonged to type-three secretion system (T3SS) encoding genes, 55 belonged to fimbrial adherence encoding genes, and 39 belonged to flagella-encoding genes CONCLUSIONS: This study demonstrated that multi-resistance mechanisms consistent with an XDR-phenotype, along with various virulence encoding genes of a S. Indiana strain in China These findings highlight the importance of cooperation among different sectors in order to monitor the spread of resistant pathogens among food animal, foods of animal origin and human beings that might further take measures to protect consumers' health. Copyright © 2017 Elsevier GmbH. All rights reserved.

Low-Density Parity-Check Code Design Techniques to Simplify Encoding

NASA Astrophysics Data System (ADS)

Perez, J. M.; Andrews, K.

2007-11-01

This work describes a method for encoding low-density parity-check (LDPC) codes based on the accumulate-repeat-4-jagged-accumulate (AR4JA) scheme, using the low-density parity-check matrix H instead of the dense generator matrix G. The use of the H matrix to encode allows a significant reduction in memory consumption and provides the encoder design a great flexibility. Also described are new hardware-efficient codes, based on the same kind of protographs, which require less memory storage and area, allowing at the same time a reduction in the encoding delay.

Kinetics of nif Gene Expression in a Nitrogen-Fixing Bacterium

PubMed Central

Poza-Carrión, César; Jiménez-Vicente, Emilio; Navarro-Rodríguez, Mónica; Echavarri-Erasun, Carlos

2014-01-01

Nitrogen fixation is a tightly regulated trait. Switching from N2 fixation-repressing conditions to the N2-fixing state is carefully controlled in diazotrophic bacteria mainly because of the high energy demand that it imposes. By using quantitative real-time PCR and quantitative immunoblotting, we show here how nitrogen fixation (nif) gene expression develops in Azotobacter vinelandii upon derepression. Transient expression of the transcriptional activator-encoding gene, nifA, was followed by subsequent, longer-duration waves of expression of the nitrogenase biosynthetic and structural genes. Importantly, expression timing, expression levels, and NifA dependence varied greatly among the nif operons. Moreover, the exact concentrations of Nif proteins and their changes over time were determined for the first time. Nif protein concentrations were exquisitely balanced, with FeMo cofactor biosynthetic proteins accumulating at levels 50- to 100-fold lower than those of the structural proteins. Mutants lacking nitrogenase structural genes or impaired in FeMo cofactor biosynthesis showed overenhanced responses to derepression that were proportional to the degree of nitrogenase activity impairment, consistent with the existence of at least two negative-feedback regulatory mechanisms. The first such mechanism responded to the levels of fixed nitrogen, whereas the second mechanism appeared to respond to the levels of the mature NifDK component. Altogether, these findings provide a framework to engineer N2 fixation in nondiazotrophs. PMID:24244007

Kinetics of Nif gene expression in a nitrogen-fixing bacterium.

PubMed

Poza-Carrión, César; Jiménez-Vicente, Emilio; Navarro-Rodríguez, Mónica; Echavarri-Erasun, Carlos; Rubio, Luis M

2014-02-01

Nitrogen fixation is a tightly regulated trait. Switching from N2 fixation-repressing conditions to the N2-fixing state is carefully controlled in diazotrophic bacteria mainly because of the high energy demand that it imposes. By using quantitative real-time PCR and quantitative immunoblotting, we show here how nitrogen fixation (nif) gene expression develops in Azotobacter vinelandii upon derepression. Transient expression of the transcriptional activator-encoding gene, nifA, was followed by subsequent, longer-duration waves of expression of the nitrogenase biosynthetic and structural genes. Importantly, expression timing, expression levels, and NifA dependence varied greatly among the nif operons. Moreover, the exact concentrations of Nif proteins and their changes over time were determined for the first time. Nif protein concentrations were exquisitely balanced, with FeMo cofactor biosynthetic proteins accumulating at levels 50- to 100-fold lower than those of the structural proteins. Mutants lacking nitrogenase structural genes or impaired in FeMo cofactor biosynthesis showed overenhanced responses to derepression that were proportional to the degree of nitrogenase activity impairment, consistent with the existence of at least two negative-feedback regulatory mechanisms. The first such mechanism responded to the levels of fixed nitrogen, whereas the second mechanism appeared to respond to the levels of the mature NifDK component. Altogether, these findings provide a framework to engineer N2 fixation in nondiazotrophs.

Processing of visually presented clock times.

PubMed

Goolkasian, P; Park, D C

1980-11-01

The encoding and representation of visually presented clock times was investigated in three experiments utilizing a comparative judgment task. Experiment 1 explored the effects of comparing times presented in different formats (clock face, digit, or word), and Experiment 2 examined angular distance effects created by varying positions of the hands on clock faces. In Experiment 3, encoding and processing differences between clock faces and digitally presented times were directly measured. Same/different reactions to digitally presented times were faster than to times presented on a clock face, and this format effect was found to be a result of differences in processing that occurred after encoding. Angular separation also had a limited effect on processing. The findings are interpreted within the framework of theories that refer to the importance of representational codes. The applicability to the data of Bank's semantic-coding theory, Paivio's dual-coding theory, and the levels-of-processing view of memory are discussed.

Distribution of hybrid entanglement and hyperentanglement with time-bin for secure quantum channel under noise via weak cross-Kerr nonlinearity.

PubMed

Heo, Jino; Kang, Min-Sung; Hong, Chang-Ho; Yang, Hyung-Jin; Choi, Seong-Gon; Hong, Jong-Phil

2017-08-31

We design schemes to generate and distribute hybrid entanglement and hyperentanglement correlated with degrees of freedom (polarization and time-bin) via weak cross-Kerr nonlinearities (XKNLs) and linear optical devices (including time-bin encoders). In our scheme, the multi-photon gates (which consist of XKNLs, quantum bus [qubus] beams, and photon-number-resolving [PNR] measurement) with time-bin encoders can generate hyperentanglement or hybrid entanglement. And we can also purify the entangled state (polarization) of two photons using only linear optical devices and time-bin encoders under a noisy (bit-flip) channel. Subsequently, through local operations (using a multi-photon gate via XKNLs) and classical communications, it is possible to generate a four-qubit hybrid entangled state (polarization and time-bin). Finally, we discuss how the multi-photon gate using XKNLs, qubus beams, and PNR measurement can be reliably performed under the decoherence effect.

Memory for emotional words: The role of semantic relatedness, encoding task and affective valence.

PubMed

Ferré, Pilar; Fraga, Isabel; Comesaña, Montserrat; Sánchez-Casas, Rosa

2015-01-01

Emotional stimuli have been repeatedly demonstrated to be better remembered than neutral ones. The aim of the present study was to test whether this advantage in memory is mainly produced by the affective content of the stimuli or it can be rather accounted for by factors such as semantic relatedness or type of encoding task. The valence of the stimuli (positive, negative and neutral words that could be either semantically related or unrelated) as well as the type of encoding task (focused on either familiarity or emotionality) was manipulated. The results revealed an advantage in memory for emotional words (either positive or negative) regardless of semantic relatedness. Importantly, this advantage was modulated by the encoding task, as it was reliable only in the task which focused on emotionality. These findings suggest that congruity with the dimension attended at encoding might contribute to the superiority in memory for emotional words, thus offering us a more complex picture of the underlying mechanisms behind the advantage for emotional information in memory.

'Laminopathies': A wide spectrum of human diseases

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

Worman, Howard J.; Bonne, Gisele; Universite Pierre et Marie Curie-Paris 6, Faculte de medecine, Paris F-75013

2007-06-10

Mutations in genes encoding the intermediate filament nuclear lamins and associated proteins cause a wide spectrum of diseases sometimes called 'laminopathies.' Diseases caused by mutations in LMNA encoding A-type lamins include autosomal dominant Emery-Dreifuss muscular dystrophy and related myopathies, Dunnigan-type familial partial lipodystrophy, Charcot-Marie-Tooth disease type 2B1 and developmental and accelerated aging disorders. Duplication in LMNB1 encoding lamin B1 causes autosomal dominant leukodystrophy and mutations in LMNB2 encoding lamin B2 are associated with acquired partial lipodystrophy. Disorders caused by mutations in genes encoding lamin-associated integral inner nuclear membrane proteins include X-linked Emery-Dreifuss muscular dystrophy, sclerosing bone dysplasias, HEM/Greenberg skeletal dysplasiamore » and Pelger-Huet anomaly. While mutations and clinical phenotypes of 'laminopathies' have been carefully described, data explaining pathogenic mechanisms are only emerging. Future investigations will likely identify new 'laminopathies' and a combination of basic and clinical research will lead to a better understanding of pathophysiology and the development of therapies.« less

The hippocampus and inferential reasoning: building memories to navigate future decisions

PubMed Central

Zeithamova, Dagmar; Schlichting, Margaret L.; Preston, Alison R.

2012-01-01

A critical aspect of inferential reasoning is the ability to form relationships between items or events that were not experienced together. This review considers different perspectives on the role of the hippocampus in successful inferential reasoning during both memory encoding and retrieval. Intuitively, inference can be thought of as a logical process by which elements of individual existing memories are retrieved and recombined to answer novel questions. Such flexible retrieval is sub-served by the hippocampus and is thought to require specialized hippocampal encoding mechanisms that discretely code events such that event elements are individually accessible from memory. In addition to retrieval-based inference, recent research has also focused on hippocampal processes that support the combination of information acquired across multiple experiences during encoding. This mechanism suggests that by recalling past events during new experiences, connections can be created between newly formed and existing memories. Such hippocampally mediated memory integration would thus underlie the formation of networks of related memories that extend beyond direct experience to anticipate future judgments about the relationships between items and events. We also discuss integrative encoding in the context of emerging evidence linking the hippocampus to the formation of schemas as well as prospective theories of hippocampal function that suggest memories are actively constructed to anticipate future decisions and actions. PMID:22470333

Histone Deacetylase Inhibition via RGFP966 Releases the Brakes on Sensory Cortical Plasticity and the Specificity of Memory Formation.

PubMed

Bieszczad, Kasia M; Bechay, Kiro; Rusche, James R; Jacques, Vincent; Kudugunti, Shashi; Miao, Wenyan; Weinberger, Norman M; McGaugh, James L; Wood, Marcelo A

2015-09-23

Research over the past decade indicates a novel role for epigenetic mechanisms in memory formation. Of particular interest is chromatin modification by histone deacetylases (HDACs), which, in general, negatively regulate transcription. HDAC deletion or inhibition facilitates transcription during memory consolidation and enhances long-lasting forms of synaptic plasticity and long-term memory. A key open question remains: How does blocking HDAC activity lead to memory enhancements? To address this question, we tested whether a normal function of HDACs is to gate information processing during memory formation. We used a class I HDAC inhibitor, RGFP966 (C21H19FN4O), to test the role of HDAC inhibition for information processing in an auditory memory model of learning-induced cortical plasticity. HDAC inhibition may act beyond memory enhancement per se to instead regulate information in ways that lead to encoding more vivid sensory details into memory. Indeed, we found that RGFP966 controls memory induction for acoustic details of sound-to-reward learning. Rats treated with RGFP966 while learning to associate sound with reward had stronger memory and additional information encoded into memory for highly specific features of sounds associated with reward. Moreover, behavioral effects occurred with unusually specific plasticity in primary auditory cortex (A1). Class I HDAC inhibition appears to engage A1 plasticity that enables additional acoustic features to become encoded in memory. Thus, epigenetic mechanisms act to regulate sensory cortical plasticity, which offers an information processing mechanism for gating what and how much is encoded to produce exceptionally persistent and vivid memories. Significance statement: Here we provide evidence of an epigenetic mechanism for information processing. The study reveals that a class I HDAC inhibitor (Malvaez et al., 2013; Rumbaugh et al., 2015; RGFP966, chemical formula C21H19FN4O) alters the formation of auditory memory by enabling more acoustic information to become encoded into memory. Moreover, RGFP966 appears to affect cortical plasticity: the primary auditory cortex reorganized in a manner that was unusually "tuned-in" to the specific sound cues and acoustic features that were related to reward and subsequently remembered. We propose that HDACs control "informational capture" at a systems level for what and how much information is encoded by gating sensory cortical plasticity that underlies the sensory richness of newly formed memories. Copyright © 2015 the authors 0270-6474/15/3513125-09$15.00/0.

Histone Deacetylase Inhibition via RGFP966 Releases the Brakes on Sensory Cortical Plasticity and the Specificity of Memory Formation

PubMed Central

Bechay, Kiro; Rusche, James R.; Jacques, Vincent; Kudugunti, Shashi; Miao, Wenyan; Weinberger, Norman M.; McGaugh, James L.

2015-01-01

Research over the past decade indicates a novel role for epigenetic mechanisms in memory formation. Of particular interest is chromatin modification by histone deacetylases (HDACs), which, in general, negatively regulate transcription. HDAC deletion or inhibition facilitates transcription during memory consolidation and enhances long-lasting forms of synaptic plasticity and long-term memory. A key open question remains: How does blocking HDAC activity lead to memory enhancements? To address this question, we tested whether a normal function of HDACs is to gate information processing during memory formation. We used a class I HDAC inhibitor, RGFP966 (C21H19FN4O), to test the role of HDAC inhibition for information processing in an auditory memory model of learning-induced cortical plasticity. HDAC inhibition may act beyond memory enhancement per se to instead regulate information in ways that lead to encoding more vivid sensory details into memory. Indeed, we found that RGFP966 controls memory induction for acoustic details of sound-to-reward learning. Rats treated with RGFP966 while learning to associate sound with reward had stronger memory and additional information encoded into memory for highly specific features of sounds associated with reward. Moreover, behavioral effects occurred with unusually specific plasticity in primary auditory cortex (A1). Class I HDAC inhibition appears to engage A1 plasticity that enables additional acoustic features to become encoded in memory. Thus, epigenetic mechanisms act to regulate sensory cortical plasticity, which offers an information processing mechanism for gating what and how much is encoded to produce exceptionally persistent and vivid memories. SIGNIFICANCE STATEMENT Here we provide evidence of an epigenetic mechanism for information processing. The study reveals that a class I HDAC inhibitor (Malvaez et al., 2013; Rumbaugh et al., 2015; RGFP966, chemical formula C21H19FN4O) alters the formation of auditory memory by enabling more acoustic information to become encoded into memory. Moreover, RGFP966 appears to affect cortical plasticity: the primary auditory cortex reorganized in a manner that was unusually “tuned-in” to the specific sound cues and acoustic features that were related to reward and subsequently remembered. We propose that HDACs control “informational capture” at a systems level for what and how much information is encoded by gating sensory cortical plasticity that underlies the sensory richness of newly formed memories. PMID:26400942

The role of attention in emotional memory enhancement in pathological and healthy aging.

PubMed

Sava, Alina-Alexandra; Paquet, Claire; Dumurgier, Julien; Hugon, Jacques; Chainay, Hanna

2016-01-01

After short delays between encoding and retrieval, healthy young participants have better memory performance for emotional stimuli than for neutral stimuli. Divided-attention paradigms suggest that this emotional enhancement of memory (EEM) is due to different attention mechanisms involved during encoding: automatic processing for negative stimuli, and controlled processing for positive stimuli. As far as we know, no study on the influence of these factors on EEM in Alzheimer's disease (AD) and mild cognitive impairment (MCI) patients, as compared to healthy young and older controls, has been conducted. Thus, the goal of our study was to ascertain whether the EEM in these populations depends on the attention resources available at encoding. Participants completed two encoding phases: full attention (FA) and divided attention (DA), followed by two retrieval phases (recognition tasks). There was no EEM on the discrimination accuracy, independently of group and encoding condition. Nevertheless, all participants used a more liberal response criterion for the negative and positive stimuli than for neutral ones. In AD patients, larger numbers of false recognitions for negative and positive stimuli than for neutral ones were observed after both encoding conditions. In MCI patients and in healthy older and younger controls this effect was observed only for negative stimuli, and it depended on the encoding condition. Thus, this effect was observed in young controls after both encoding conditions, in older controls after the DA encoding, and in MCI patients after the FA encoding. In conclusion, our results suggest that emotional valence does not always enhance discrimination accuracy. Nevertheless, in certain conditions related to the attention resources available at encoding, emotional valence, especially the negative one, enhances the subjective feeling of familiarity and, consequently, engenders changes in response bias. This effect seems to be sensitive to the age and the pathology of participants.

On the edge of language acquisition: inherent constraints on encoding multisyllabic sequences in the neonate brain.

PubMed

Ferry, Alissa L; Fló, Ana; Brusini, Perrine; Cattarossi, Luigi; Macagno, Francesco; Nespor, Marina; Mehler, Jacques

2016-05-01

To understand language, humans must encode information from rapid, sequential streams of syllables - tracking their order and organizing them into words, phrases, and sentences. We used Near-Infrared Spectroscopy (NIRS) to determine whether human neonates are born with the capacity to track the positions of syllables in multisyllabic sequences. After familiarization with a six-syllable sequence, the neonate brain responded to the change (as shown by an increase in oxy-hemoglobin) when the two edge syllables switched positions but not when two middle syllables switched positions (Experiment 1), indicating that they encoded the syllables at the edges of sequences better than those in the middle. Moreover, when a 25 ms pause was inserted between the middle syllables as a segmentation cue, neonates' brains were sensitive to the change (Experiment 2), indicating that subtle cues in speech can signal a boundary, with enhanced encoding of the syllables located at the edges of that boundary. These findings suggest that neonates' brains can encode information from multisyllabic sequences and that this encoding is constrained. Moreover, subtle segmentation cues in a sequence of syllables provide a mechanism with which to accurately encode positional information from longer sequences. Tracking the order of syllables is necessary to understand language and our results suggest that the foundations for this encoding are present at birth. © 2015 John Wiley & Sons Ltd.

Neural integration underlying a time-compensated sun compass in the migratory monarch butterfly

PubMed Central

Shlizerman, Eli; Phillips-Portillo, James; Reppert, Steven M.

2016-01-01

Migrating Eastern North American monarch butterflies use a time-compensated sun compass to adjust their flight to the southwest direction. While the antennal genetic circadian clock and the azimuth of the sun are instrumental for proper function of the compass, it is unclear how these signals are represented on a neuronal level and how they are integrated to produce flight control. To address these questions, we constructed a receptive field model of the compound eye that encodes the solar azimuth. We then derived a neural circuit model, which integrates azimuthal and circadian signals to correct flight direction. The model demonstrates an integration mechanism, which produces robust trajectories reaching the southwest regardless of the time of day and includes a configuration for remigration. Comparison of model simulations with flight trajectories of butterflies in a flight simulator shows analogous behaviors and affirms the prediction that midday is the optimal time for migratory flight. PMID:27149852

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

PubMed Central

Cardoso Guimarães, Romeu

2017-01-01

The proposal that the genetic code was formed on the basis of (proto)tRNA Dimer-Directed Protein Synthesis is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes—structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process—anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are stable and apt to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sink-effective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don’t accumulate to saturation, which would trigger inhibition. PMID:28383509

Phased array ghost elimination.

PubMed

Kellman, Peter; McVeigh, Elliot R

2006-05-01

Parallel imaging may be applied to cancel ghosts caused by a variety of distortion mechanisms, including distortions such as off-resonance or local flow, which are space variant. Phased array combining coefficients may be calculated that null ghost artifacts at known locations based on a constrained optimization, which optimizes SNR subject to the nulling constraint. The resultant phased array ghost elimination (PAGE) technique is similar to the method known as sensitivity encoding (SENSE) used for accelerated imaging; however, in this formulation is applied to full field-of-view (FOV) images. The phased array method for ghost elimination may result in greater flexibility in designing acquisition strategies. For example, in multi-shot EPI applications ghosts are typically mitigated by the use of an interleaved phase encode acquisition order. An alternative strategy is to use a sequential, non-interleaved phase encode order and cancel the resultant ghosts using PAGE parallel imaging. Cancellation of ghosts by means of phased array processing makes sequential, non-interleaved phase encode acquisition order practical, and permits a reduction in repetition time, TR, by eliminating the need for echo-shifting. Sequential, non-interleaved phase encode order has benefits of reduced distortion due to off-resonance, in-plane flow and EPI delay misalignment. Furthermore, the use of EPI with PAGE has inherent fat-water separation and has been used to provide off-resonance correction using a technique referred to as lipid elimination with an echo-shifting N/2-ghost acquisition (LEENA), and may further generalized using the multi-point Dixon method. Other applications of PAGE include cancelling ghosts which arise due to amplitude or phase variation during the approach to steady state. Parallel imaging requires estimates of the complex coil sensitivities. In vivo estimates may be derived by temporally varying the phase encode ordering to obtain a full k-space dataset in a scheme similar to the autocalibrating TSENSE method. This scheme is a generalization of the UNFOLD method used for removing aliasing in undersampled acquisitions. The more general scheme may be used to modulate each EPI ghost image to a separate temporal frequency as described in this paper. Copyright (c) 2006 John Wiley & Sons, Ltd.

Phased array ghost elimination

PubMed Central

Kellman, Peter; McVeigh, Elliot R.

2007-01-01

Parallel imaging may be applied to cancel ghosts caused by a variety of distortion mechanisms, including distortions such as off-resonance or local flow, which are space variant. Phased array combining coefficients may be calculated that null ghost artifacts at known locations based on a constrained optimization, which optimizes SNR subject to the nulling constraint. The resultant phased array ghost elimination (PAGE) technique is similar to the method known as sensitivity encoding (SENSE) used for accelerated imaging; however, in this formulation is applied to full field-of-view (FOV) images. The phased array method for ghost elimination may result in greater flexibility in designing acquisition strategies. For example, in multi-shot EPI applications ghosts are typically mitigated by the use of an interleaved phase encode acquisition order. An alternative strategy is to use a sequential, non-interleaved phase encode order and cancel the resultant ghosts using PAGE parallel imaging. Cancellation of ghosts by means of phased array processing makes sequential, non-interleaved phase encode acquisition order practical, and permits a reduction in repetition time, TR, by eliminating the need for echo-shifting. Sequential, non-interleaved phase encode order has benefits of reduced distortion due to off-resonance, in-plane flow and EPI delay misalignment. Furthermore, the use of EPI with PAGE has inherent fat-water separation and has been used to provide off-resonance correction using a technique referred to as lipid elimination with an echo-shifting N/2-ghost acquisition (LEENA), and may further generalized using the multi-point Dixon method. Other applications of PAGE include cancelling ghosts which arise due to amplitude or phase variation during the approach to steady state. Parallel imaging requires estimates of the complex coil sensitivities. In vivo estimates may be derived by temporally varying the phase encode ordering to obtain a full k-space dataset in a scheme similar to the autocalibrating TSENSE method. This scheme is a generalization of the UNFOLD method used for removing aliasing in undersampled acquisitions. The more general scheme may be used to modulate each EPI ghost image to a separate temporal frequency as described in this paper. PMID:16705636

Results for diffusion-weighted imaging with a fourth-channel gradient insert.

PubMed

Feldman, Rebecca E; Scholl, Timothy J; Alford, Jamu K; Handler, William B; Harris, Chad T; Chronik, Blaine A

2011-12-01

Diffusion-weighted imaging suffers from motion artifacts and relatively low signal quality due to the long echo times required to permit the diffusion encoding. We investigated the inclusion of a noncylindrical fourth gradient coil, dedicated entirely to diffusion encoding, into the imaging system. Standard three-axis whole body gradients were used during image acquisition, but we designed and constructed an insert coil to perform diffusion encodings. We imaged three phantoms on a 3-T system with a range of diffusion coefficients. Using the insert gradient, we were able to encode b values of greater than 1300 s/mm(2) with an echo time of just 83 ms. Images obtained using the insert gradient had higher signal to noise ratios than those obtained using the whole body gradient: at 500 s/mm(2) there was a 18% improvement in signal to noise ratio, at 1000 s/mm(2) there was a 39% improvement in signal to noise ratio, and at 1350 s/mm(2) there was a 56% improvement in signal to noise ratio. Using the insert gradient, we were capable of doing diffusion encoding at high b values by using relatively short echo times. Copyright © 2011 Wiley Periodicals, Inc.

Fast entrainment of human electroencephalogram to a theta-band photic flicker during successful memory encoding.

PubMed

Sato, Naoyuki

2013-01-01

Theta band power (4-8 Hz) in the scalp electroencephalogram (EEG) is thought to be stronger during memory encoding for subsequently remembered items than for forgotten items. According to simultaneous EEG-functional magnetic resonance imaging (fMRI) measurements, the memory-dependent EEG theta is associated with multiple regions of the brain. This suggests that the multiple regions cooperate with EEG theta synchronization during successful memory encoding. However, a question still remains: What kind of neural dynamic organizes such a memory-dependent global network? In this study, the modulation of the EEG theta entrainment property during successful encoding was hypothesized to lead to EEG theta synchronization among a distributed network. Then, a transient response of EEG theta to a theta-band photic flicker with a short duration was evaluated during memory encoding. In the results, flicker-induced EEG power increased and decreased with a time constant of several hundred milliseconds following the onset and the offset of the flicker, respectively. Importantly, the offset response of EEG power was found to be significantly decreased during successful encoding. Moreover, the offset response of the phase locking index was also found to associate with memory performance. According to computational simulations, the results are interpreted as a smaller time constant (i.e., faster response) of a driven harmonic oscillator rather than a change in the spontaneous oscillatory input. This suggests that the fast response of EEG theta forms a global EEG theta network among memory-related regions during successful encoding, and it contributes to a flexible formation of the network along the time course.

Re-Evaluating the Time Course of Gender and Phonological Encoding during Silent Monitoring Tasks Estimated by ERP: Serial or Parallel Processing?

ERIC Educational Resources Information Center

Camen, Christian; Morand, Stephanie; Laganaro, Marina

2010-01-01

Neurolinguistic and psycholinguistic studies suggest that grammatical (gender) and phonological information are retrieved independently and that gender can be accessed before phonological information. This study investigated the relative time courses of gender and phonological encoding using topographic evoked potentials mapping methods.…

The Challenges in Applying Magnetroesistive Sensors on the 'Curiosity' Rover

NASA Technical Reports Server (NTRS)

Johnson, Michael R.

2013-01-01

Magnetoresistive Sensors were selected for use on the motor encoders throughout the Curiosity Rover for motor position feedback devices. The Rover contains 28 acuators with a corresponding number of encoder assemblies. The environment on Mars provides opportunities for challenges to any hardware design. The encoder assemblies presented several barriers that had to be vaulted in order to say the rover was ready to fly. The environment and encoder specific design features provided challenges that had to be solved in time to fly.

Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures.

PubMed

Sankar, Punnaivanam; Aghila, Gnanasekaran

2007-01-01

The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.

X-chromosome-counting mechanisms that determine nematode sex.

PubMed

Nicoll, M; Akerib, C C; Meyer, B J

1997-07-10

Sex is determined in Caenorhabditis elegans by an X-chromosome-counting mechanism that reliably distinguishes the twofold difference in X-chromosome dose between males (1X) and hermaphrodites (2X). This small quantitative difference is translated into the 'on/off' response of the target gene, xol-1, a switch that specifies the male fate when active and the hermaphrodite fate when inactive. Specific regions of X contain counted signal elements whose combined dose sets the activity of xol-1. Here we ascribe the dose effects of one region to a discrete, protein-encoding gene, fox-1. We demonstrate that the dose-sensitive signal elements on chromosome X control xol-1 through two different molecular mechanisms. One involves the transcriptional repression of xol-1 in XX animals. The other uses the putative RNA-binding protein encoded by fox-1 to reduce the level of xol-1 protein. These two mechanisms of repression act together to ensure the fidelity of the X-chromosome counting process.

A complexity-scalable software-based MPEG-2 video encoder.

PubMed

Chen, Guo-bin; Lu, Xin-ning; Wang, Xing-guo; Liu, Ji-lin

2004-05-01

With the development of general-purpose processors (GPP) and video signal processing algorithms, it is possible to implement a software-based real-time video encoder on GPP, and its low cost and easy upgrade attract developers' interests to transfer video encoding from specialized hardware to more flexible software. In this paper, the encoding structure is set up first to support complexity scalability; then a lot of high performance algorithms are used on the key time-consuming modules in coding process; finally, at programming level, processor characteristics are considered to improve data access efficiency and processing parallelism. Other programming methods such as lookup table are adopted to reduce the computational complexity. Simulation results showed that these ideas could not only improve the global performance of video coding, but also provide great flexibility in complexity regulation.

Time-dependent effects of cortisol on the contextualization of emotional memories.

PubMed

van Ast, Vanessa A; Cornelisse, Sandra; Meeter, Martijn; Joëls, Marian; Kindt, Merel

2013-12-01

The inability to store fearful memories into their original encoding context is considered to be an important vulnerability factor for the development of anxiety disorders like posttraumatic stress disorder. Altered memory contextualization most likely involves effects of the stress hormone cortisol, acting via receptors located in the memory neurocircuitry. Cortisol via these receptors induces rapid nongenomic effects followed by slower genomic effects, which are thought to modulate cognitive function in opposite, complementary ways. Here, we targeted these time-dependent effects of cortisol during memory encoding and tested subsequent contextualization of emotional and neutral memories. In a double-blind, placebo-controlled design, 64 men were randomly assigned to one of three groups: 1) received 10 mg hydrocortisone 30 minutes (rapid cortisol effects) before a memory encoding task; 2) received 10 mg hydrocortisone 210 minutes (slow cortisol) before a memory encoding task; or 3) received placebo at both times. During encoding, participants were presented with neutral and emotional words in unique background pictures. Approximately 24 hours later, context dependency of their memories was assessed. Recognition data revealed that cortisol's rapid effects impair emotional memory contextualization, while cortisol's slow effects enhance it. Neutral memory contextualization remained unaltered by cortisol, irrespective of the timing of the drug. This study shows distinct time-dependent effects of cortisol on the contextualization of specifically emotional memories. The results suggest that rapid effects of cortisol may lead to impaired emotional memory contextualization, while slow effects of cortisol may confer protection against emotional memory generalization. © 2013 Society of Biological Psychiatry.

Enriched encoding: reward motivation organizes cortical networks for hippocampal detection of unexpected events.

PubMed

Murty, Vishnu P; Adcock, R Alison

2014-08-01

Learning how to obtain rewards requires learning about their contexts and likely causes. How do long-term memory mechanisms balance the need to represent potential determinants of reward outcomes with the computational burden of an over-inclusive memory? One solution would be to enhance memory for salient events that occur during reward anticipation, because all such events are potential determinants of reward. We tested whether reward motivation enhances encoding of salient events like expectancy violations. During functional magnetic resonance imaging, participants performed a reaction-time task in which goal-irrelevant expectancy violations were encountered during states of high- or low-reward motivation. Motivation amplified hippocampal activation to and declarative memory for expectancy violations. Connectivity of the ventral tegmental area (VTA) with medial prefrontal, ventrolateral prefrontal, and visual cortices preceded and predicted this increase in hippocampal sensitivity. These findings elucidate a novel mechanism whereby reward motivation can enhance hippocampus-dependent memory: anticipatory VTA-cortical-hippocampal interactions. Further, the findings integrate literatures on dopaminergic neuromodulation of prefrontal function and hippocampus-dependent memory. We conclude that during reward motivation, VTA modulation induces distributed neural changes that amplify hippocampal signals and records of expectancy violations to improve predictions-a potentially unique contribution of the hippocampus to reward learning. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Identifying 5-methylcytosine sites in RNA sequence using composite encoding feature into Chou's PseKNC.

PubMed

Sabooh, M Fazli; Iqbal, Nadeem; Khan, Mukhtaj; Khan, Muslim; Maqbool, H F

2018-05-01

This study examines accurate and efficient computational method for identification of 5-methylcytosine sites in RNA modification. The occurrence of 5-methylcytosine (m 5 C) plays a vital role in a number of biological processes. For better comprehension of the biological functions and mechanism it is necessary to recognize m 5 C sites in RNA precisely. The laboratory techniques and procedures are available to identify m 5 C sites in RNA, but these procedures require a lot of time and resources. This study develops a new computational method for extracting the features of RNA sequence. In this method, first the RNA sequence is encoded via composite feature vector, then, for the selection of discriminate features, the minimum-redundancy-maximum-relevance algorithm was used. Secondly, the classification method used has been based on a support vector machine by using jackknife cross validation test. The suggested method efficiently identifies m 5 C sites from non- m 5 C sites and the outcome of the suggested algorithm is 93.33% with sensitivity of 90.0 and specificity of 96.66 on bench mark datasets. The result exhibits that proposed algorithm shown significant identification performance compared to the existing computational techniques. This study extends the knowledge about the occurrence sites of RNA modification which paves the way for better comprehension of the biological uses and mechanism. Copyright © 2018 Elsevier Ltd. All rights reserved.

Individual Differences Reveal Correlates of Hidden Hearing Deficits

PubMed Central

Masud, Salwa; Mehraei, Golbarg; Verhulst, Sarah; Shinn-Cunningham, Barbara G.

2015-01-01

Clinical audiometry has long focused on determining the detection thresholds for pure tones, which depend on intact cochlear mechanics and hair cell function. Yet many listeners with normal hearing thresholds complain of communication difficulties, and the causes for such problems are not well understood. Here, we explore whether normal-hearing listeners exhibit such suprathreshold deficits, affecting the fidelity with which subcortical areas encode the temporal structure of clearly audible sound. Using an array of measures, we evaluated a cohort of young adults with thresholds in the normal range to assess both cochlear mechanical function and temporal coding of suprathreshold sounds. Listeners differed widely in both electrophysiological and behavioral measures of temporal coding fidelity. These measures correlated significantly with each other. Conversely, these differences were unrelated to the modest variation in otoacoustic emissions, cochlear tuning, or the residual differences in hearing threshold present in our cohort. Electroencephalography revealed that listeners with poor subcortical encoding had poor cortical sensitivity to changes in interaural time differences, which are critical for localizing sound sources and analyzing complex scenes. These listeners also performed poorly when asked to direct selective attention to one of two competing speech streams, a task that mimics the challenges of many everyday listening environments. Together with previous animal and computational models, our results suggest that hidden hearing deficits, likely originating at the level of the cochlear nerve, are part of “normal hearing.” PMID:25653371

OsNAC2 positively affects salt-induced cell death and binds to the OsAP37 and OsCOX11 promoters.

PubMed

Mao, Chanjuan; Ding, Jialin; Zhang, Bin; Xi, Dandan; Ming, Feng

2018-05-01

Plant development and adaptation to environmental stresses are intimately associated with programmed cell death (PCD). Although some of the mechanisms regulating PCD [e.g., accumulation of reactive oxygen species (ROS)] are common among responses to different abiotic stresses, the pathways mediating salt-induced PCD remain largely uncharacterized. Here we report that overexpression of OsNAC2, which encodes a plant-specific transcription factor, promotes salt-induced cell death accompanied by the loss of plasma membrane integrity, nuclear DNA fragmentation, and changes to caspase-like activity. In OsNAC2-knockdown lines, cell death was markedly decreased in response to severe salt stress. Additionally, OsNAC2 expression was enhanced in rice seedlings exposed to a high NaCl concentration. Moreover, the results of quantitative real-time PCR, chromatin immunoprecipitation, dual-luciferase, and yeast one-hybrid assays indicated that OsNAC2 targeted genes that encoded an ROS scavenger (OsCOX11) and a caspase-like protease (OsAP37). Furthermore, K + -efflux channels (OsGORK and OsSKOR) were clearly activated by OsNAC2. Overall, our results suggested that OsNAC2 accelerates NaCl-induced PCD and provide new insights into the mechanisms that affect ROS accumulation, plant caspase-like activity, and K + efflux. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

Uncovering the functional constraints underlying the genomic organization of the odorant-binding protein genes.

PubMed

Librado, Pablo; Rozas, Julio

2013-01-01

Animal olfactory systems have a critical role for the survival and reproduction of individuals. In insects, the odorant-binding proteins (OBPs) are encoded by a moderately sized gene family, and mediate the first steps of the olfactory processing. Most OBPs are organized in clusters of a few paralogs, which are conserved over time. Currently, the biological mechanism explaining the close physical proximity among OBPs is not yet established. Here, we conducted a comprehensive study aiming to gain insights into the mechanisms underlying the OBP genomic organization. We found that the OBP clusters are embedded within large conserved arrangements. These organizations also include other non-OBP genes, which often encode proteins integral to plasma membrane. Moreover, the conservation degree of such large clusters is related to the following: 1) the promoter architecture of the confined genes, 2) a characteristic transcriptional environment, and 3) the chromatin conformation of the chromosomal region. Our results suggest that chromatin domains may restrict the location of OBP genes to regions having the appropriate transcriptional environment, leading to the OBP cluster structure. However, the appropriate transcriptional environment for OBP and the other neighbor genes is not dominated by reduced levels of expression noise. Indeed, the stochastic fluctuations in the OBP transcript abundance may have a critical role in the combinatorial nature of the olfactory coding process.

Transcriptional analysis of sulfate reducing and chemolithoautotrophic sulfur oxidizing bacteria in the deep subseafloor.

PubMed

Orsi, William D; Barker Jørgensen, Bo; Biddle, Jennifer F

2016-08-01

Sulfate reducing bacteria (SRB) oxidize a significant proportion of subseafloor organic carbon, but their metabolic activities and subsistence mechanisms are poorly understood. Here, we report in depth phylogenetic and metabolic analyses of SRB transcripts in the Peru Margin subseafloor and interpret these results in the context of sulfate reduction activity in the sediment. Relative abundance of overall SRB gene transcripts declines strongly whereas relative abundance of ribosomal protein transcripts from sulfate reducing δ-Proteobacteria peak at 90 m below seafloor (mbsf) within a deep sulfate methane transition zone. This coincides with isotopically heavy δ(34) S values of pore water sulfate (70‰), indicating active subseafloor microbial sulfate reduction. Within the shallow sulfate reduction zone (0-5 mbsf), a transcript encoding the beta subunit of dissimilatory sulfite reductase (dsrB) was related to Desulfitobacterium dehalogenans and environmental sequences from Aarhus Bay (Denmark). At 159 mbsf we discovered a transcript encoding the reversely operating dissimilatory sulfite reductase α-subunit (rdsrA), with basal phylogenetic relation to the chemolithoautotrophic SUP05 Group II clade. A diversity of SRB transcripts involved in cellular maintenance point toward potential subsistence mechanisms under low-energy over long time periods, and provide a detailed new picture of SRB activities underlying sulfur cycling in the deep subseafloor. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Decoding and Reconstructing the Focus of Spatial Attention from the Topography of Alpha-band Oscillations.

PubMed

Samaha, Jason; Sprague, Thomas C; Postle, Bradley R

2016-08-01

Many aspects of perception and cognition are supported by activity in neural populations that are tuned to different stimulus features (e.g., orientation, spatial location, color). Goal-directed behavior, such as sustained attention, requires a mechanism for the selective prioritization of contextually appropriate representations. A candidate mechanism of sustained spatial attention is neural activity in the alpha band (8-13 Hz), whose power in the human EEG covaries with the focus of covert attention. Here, we applied an inverted encoding model to assess whether spatially selective neural responses could be recovered from the topography of alpha-band oscillations during spatial attention. Participants were cued to covertly attend to one of six spatial locations arranged concentrically around fixation while EEG was recorded. A linear classifier applied to EEG data during sustained attention demonstrated successful classification of the attended location from the topography of alpha power, although not from other frequency bands. We next sought to reconstruct the focus of spatial attention over time by applying inverted encoding models to the topography of alpha power and phase. Alpha power, but not phase, allowed for robust reconstructions of the specific attended location beginning around 450 msec postcue, an onset earlier than previous reports. These results demonstrate that posterior alpha-band oscillations can be used to track activity in feature-selective neural populations with high temporal precision during the deployment of covert spatial attention.

The inferior colliculus encodes the Franssen auditory spatial illusion

PubMed Central

Rajala, Abigail Z.; Yan, Yonghe; Dent, Micheal L.; Populin, Luis C.

2014-01-01

Illusions are effective tools for the study of the neural mechanisms underlying perception because neural responses can be correlated to the physical properties of stimuli and the subject’s perceptions. The Franssen illusion (FI) is an auditory spatial illusion evoked by presenting a transient, abrupt tone and a slowly rising, sustained tone of the same frequency simultaneously on opposite sides of the subject. Perception of the FI consists of hearing a single sound, the sustained tone, on the side that the transient was presented. Both subcortical and cortical mechanisms for the FI have been proposed, but, to date, there is no direct evidence for either. The data show that humans and rhesus monkeys perceive the FI similarly. Recordings were taken from single units of the inferior colliculus in the monkey while they indicated the perceived location of sound sources with their gaze. The results show that the transient component of the Franssen stimulus, with a shorter first spike latency and higher discharge rate than the sustained tone, encodes the perception of sound location. Furthermore, the persistent erroneous perception of the sustained stimulus location is due to continued excitation of the same neurons, first activated by the transient, by the sustained stimulus without location information. These results demonstrate for the first time, on a trial-by-trial basis, a correlation between perception of an auditory spatial illusion and a subcortical physiological substrate. PMID:23899307

Reliable Wireless Broadcast with Linear Network Coding for Multipoint-to-Multipoint Real-Time Communications

NASA Astrophysics Data System (ADS)

Kondo, Yoshihisa; Yomo, Hiroyuki; Yamaguchi, Shinji; Davis, Peter; Miura, Ryu; Obana, Sadao; Sampei, Seiichi

This paper proposes multipoint-to-multipoint (MPtoMP) real-time broadcast transmission using network coding for ad-hoc networks like video game networks. We aim to achieve highly reliable MPtoMP broadcasting using IEEE 802.11 media access control (MAC) that does not include a retransmission mechanism. When each node detects packets from the other nodes in a sequence, the correctly detected packets are network-encoded, and the encoded packet is broadcasted in the next sequence as a piggy-back for its native packet. To prevent increase of overhead in each packet due to piggy-back packet transmission, network coding vector for each node is exchanged between all nodes in the negotiation phase. Each user keeps using the same coding vector generated in the negotiation phase, and only coding information that represents which user signal is included in the network coding process is transmitted along with the piggy-back packet. Our simulation results show that the proposed method can provide higher reliability than other schemes using multi point relay (MPR) or redundant transmissions such as forward error correction (FEC). We also implement the proposed method in a wireless testbed, and show that the proposed method achieves high reliability in a real-world environment with a practical degree of complexity when installed on current wireless devices.

User Preference-Based Dual-Memory Neural Model With Memory Consolidation Approach.

PubMed

Nasir, Jauwairia; Yoo, Yong-Ho; Kim, Deok-Hwa; Kim, Jong-Hwan; Nasir, Jauwairia; Yong-Ho Yoo; Deok-Hwa Kim; Jong-Hwan Kim; Nasir, Jauwairia; Yoo, Yong-Ho; Kim, Deok-Hwa; Kim, Jong-Hwan

2018-06-01

Memory modeling has been a popular topic of research for improving the performance of autonomous agents in cognition related problems. Apart from learning distinct experiences correctly, significant or recurring experiences are expected to be learned better and be retrieved easier. In order to achieve this objective, this paper proposes a user preference-based dual-memory adaptive resonance theory network model, which makes use of a user preference to encode memories with various strengths and to learn and forget at various rates. Over a period of time, memories undergo a consolidation-like process at a rate proportional to the user preference at the time of encoding and the frequency of recall of a particular memory. Consolidated memories are easier to recall and are more stable. This dual-memory neural model generates distinct episodic memories and a flexible semantic-like memory component. This leads to an enhanced retrieval mechanism of experiences through two routes. The simulation results are presented to evaluate the proposed memory model based on various kinds of cues over a number of trials. The experimental results on Mybot are also presented. The results verify that not only are distinct experiences learned correctly but also that experiences associated with higher user preference and recall frequency are consolidated earlier. Thus, these experiences are recalled more easily relative to the unconsolidated experiences.

Multiparametric analysis of cisplatin-induced changes in cancer cells using FLIM

NASA Astrophysics Data System (ADS)

Shirmanova, Marina V.; Sergeeva, Tatiana F.; Gavrina, Alena I.; Dudenkova, Varvara V.; Lukyanov, Konstantin A.; Zagaynova, Elena V.

2018-02-01

Cisplatin is an effective anticancer drug commonly used in the treatment of solid tumors. Although DNA is considered as the primary target, the cisplatin action at the cellular level remains unknown. Advanced fluorescence microscopy techniques allow probing various physiological and physicochemical parameters in living cells and tissues with unsurpassed sensitivity in real time. This study was focused on the investigation of cellular bioenergetics and cytosolic pH in colorectal cancer cells during chemotherapy with cisplatin. Special attention was given to the changes in cisplatininduced apoptosis that was identified using genetically encoded FLIM/FRET sensor of caspase-3 activity. Metabolic measurements using FLIM of the metabolic cofactor NAD(P)H showed decreased contribution from free NAD(P)H (a1, %) in all treated cells with more pronounced alterations in the cells undergoing apoptosis. Analysis of cytosolic pH using genetically encoded fluorescent sensor SypHer1 revealed a rapid increase of the pH value upon cisplatin exposure irrespective of the induction of apoptosis. To the best of our knowledge, a simultaneous assessment of metabolic state, cytosolic pH and caspase-3 activity after treatment with cisplatin was performed for the first time. These findings improve our understanding of the cell response to chemotherapy and mechanisms of cisplatin action.

Time manages interference in visual short-term memory.

PubMed

Smith, Amy V; McKeown, Denis; Bunce, David

2017-09-01

Emerging evidence suggests that age-related declines in memory may reflect a failure in pattern separation, a process that is believed to reduce the encoding overlap between similar stimulus representations during memory encoding. Indeed, behavioural pattern separation may be indexed by a visual continuous recognition task in which items are presented in sequence and observers report for each whether it is novel, previously viewed (old), or whether it shares features with a previously viewed item (similar). In comparison to young adults, older adults show a decreased pattern separation when the number of items between "old" and "similar" items is increased. Yet the mechanisms of forgetting underpinning this type of recognition task are yet to be explored in a cognitively homogenous group, with careful control over the parameters of the task, including elapsing time (a critical variable in models of forgetting). By extending the inter-item intervals, number of intervening items and overall decay interval, we observed in a young adult sample (N = 35, M age  = 19.56 years) that the critical factor governing performance was inter-item interval. We argue that tasks using behavioural continuous recognition to index pattern separation in immediate memory will benefit from generous inter-item spacing, offering protection from inter-item interference.

High Expression of Cry1Ac Protein in Cotton (Gossypium hirsutum) by Combining Independent Transgenic Events that Target the Protein to Cytoplasm and Plastids.

PubMed

Singh, Amarjeet Kumar; Paritosh, Kumar; Kant, Uma; Burma, Pradeep Kumar; Pental, Deepak

2016-01-01

Transgenic cotton was developed using two constructs containing a truncated and codon-modified cry1Ac gene (1,848 bp), which was originally characterized from Bacillus thuringiensis subspecies kurstaki strain HD73 that encodes a toxin highly effective against many lepidopteran pests. In Construct I, the cry1Ac gene was cloned under FMVde, a strong constitutively expressing promoter, to express the encoded protein in the cytoplasm. In Construct II, the encoded protein was directed to the plastids using a transit peptide taken from the cotton rbcSIb gene. Genetic transformation experiments with Construct I resulted in a single copy insertion event in which the Cry1Ac protein expression level was 2-2.5 times greater than in the Bacillus thuringiensis cotton event Mon 531, which is currently used in varieties and hybrids grown extensively in India and elsewhere. Another high expression event was selected from transgenics developed with Construct II. The Cry protein expression resulting from this event was observed only in the green plant parts. No transgenic protein expression was observed in the non-green parts, including roots, seeds and non-green floral tissues. Thus, leucoplasts may lack the mechanism to allow entry of a protein tagged with the transit peptide from a protein that is only synthesized in tissues containing mature plastids. Combining the two events through sexual crossing led to near additive levels of the toxin at 4-5 times the level currently used in the field. The two high expression events and their combination will allow for effective resistance management against lepidopteran insect pests, particularly Helicoverpa armigera, using a high dosage strategy.

A chemokine-binding domain in the tumor necrosis factor receptor from variola (smallpox) virus

PubMed Central

Alejo, Alí; Ruiz-Argüello, M. Begoña; Ho, Yin; Smith, Vincent P.; Saraiva, Margarida; Alcami, Antonio

2006-01-01

Variola virus (VaV) is the causative agent of smallpox, one of the most devastating diseases encountered by man, that was eradicated in 1980. The deliberate release of VaV would have catastrophic consequences on global public health. However, the mechanisms that contribute to smallpox pathogenesis are poorly understood at the molecular level. The ability of viruses to evade the host defense mechanisms is an important determinant of viral pathogenesis. Here we show that the tumor necrosis factor receptor (TNFR) homologue CrmB encoded by VaV functions not only as a soluble decoy TNFR but also as a highly specific binding protein for several chemokines that mediate recruitment of immune cells to mucosal surfaces and the skin, sites of virus entry and viral replication at late stages of smallpox. CrmB binds chemokines through its C-terminal domain, which is unrelated to TNFRs, was named smallpox virus-encoded chemokine receptor (SECRET) domain and uncovers a family of poxvirus chemokine inhibitors. An active SECRET domain was found in another viral TNFR (CrmD) and three secreted proteins encoded by orthopoxviruses. These findings identify a previously undescribed chemokine-binding and inhibitory domain unrelated to host chemokine receptors and a mechanism of immune modulation in VaV that may influence smallpox pathogenesis. PMID:16581912

A chemokine-binding domain in the tumor necrosis factor receptor from variola (smallpox) virus.

PubMed

Alejo, Alí; Ruiz-Argüello, M Begoña; Ho, Yin; Smith, Vincent P; Saraiva, Margarida; Alcami, Antonio

2006-04-11

Variola virus (VaV) is the causative agent of smallpox, one of the most devastating diseases encountered by man, that was eradicated in 1980. The deliberate release of VaV would have catastrophic consequences on global public health. However, the mechanisms that contribute to smallpox pathogenesis are poorly understood at the molecular level. The ability of viruses to evade the host defense mechanisms is an important determinant of viral pathogenesis. Here we show that the tumor necrosis factor receptor (TNFR) homologue CrmB encoded by VaV functions not only as a soluble decoy TNFR but also as a highly specific binding protein for several chemokines that mediate recruitment of immune cells to mucosal surfaces and the skin, sites of virus entry and viral replication at late stages of smallpox. CrmB binds chemokines through its C-terminal domain, which is unrelated to TNFRs, was named smallpox virus-encoded chemokine receptor (SECRET) domain and uncovers a family of poxvirus chemokine inhibitors. An active SECRET domain was found in another viral TNFR (CrmD) and three secreted proteins encoded by orthopoxviruses. These findings identify a previously undescribed chemokine-binding and inhibitory domain unrelated to host chemokine receptors and a mechanism of immune modulation in VaV that may influence smallpox pathogenesis.

Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation

PubMed Central

Micali, Gabriele; Aquino, Gerardo; Richards, David M.; Endres, Robert G.

2015-01-01

Cells sense external concentrations and, via biochemical signaling, respond by regulating the expression of target proteins. Both in signaling networks and gene regulation there are two main mechanisms by which the concentration can be encoded internally: amplitude modulation (AM), where the absolute concentration of an internal signaling molecule encodes the stimulus, and frequency modulation (FM), where the period between successive bursts represents the stimulus. Although both mechanisms have been observed in biological systems, the question of when it is beneficial for cells to use either AM or FM is largely unanswered. Here, we first consider a simple model for a single receptor (or ion channel), which can either signal continuously whenever a ligand is bound, or produce a burst in signaling molecule upon receptor binding. We find that bursty signaling is more accurate than continuous signaling only for sufficiently fast dynamics. This suggests that modulation based on bursts may be more common in signaling networks than in gene regulation. We then extend our model to multiple receptors, where continuous and bursty signaling are equivalent to AM and FM respectively, finding that AM is always more accurate. This implies that the reason some cells use FM is related to factors other than accuracy, such as the ability to coordinate expression of multiple genes or to implement threshold crossing mechanisms. PMID:26030820

Optimal sparse approximation with integrate and fire neurons.

PubMed

Shapero, Samuel; Zhu, Mengchen; Hasler, Jennifer; Rozell, Christopher

2014-08-01

Sparse approximation is a hypothesized coding strategy where a population of sensory neurons (e.g. V1) encodes a stimulus using as few active neurons as possible. We present the Spiking LCA (locally competitive algorithm), a rate encoded Spiking Neural Network (SNN) of integrate and fire neurons that calculate sparse approximations. The Spiking LCA is designed to be equivalent to the nonspiking LCA, an analog dynamical system that converges on a ℓ(1)-norm sparse approximations exponentially. We show that the firing rate of the Spiking LCA converges on the same solution as the analog LCA, with an error inversely proportional to the sampling time. We simulate in NEURON a network of 128 neuron pairs that encode 8 × 8 pixel image patches, demonstrating that the network converges to nearly optimal encodings within 20 ms of biological time. We also show that when using more biophysically realistic parameters in the neurons, the gain function encourages additional ℓ(0)-norm sparsity in the encoding, relative both to ideal neurons and digital solvers.

Supervised Learning in Spiking Neural Networks for Precise Temporal Encoding

PubMed Central

Gardner, Brian; Grüning, André

2016-01-01

Precise spike timing as a means to encode information in neural networks is biologically supported, and is advantageous over frequency-based codes by processing input features on a much shorter time-scale. For these reasons, much recent attention has been focused on the development of supervised learning rules for spiking neural networks that utilise a temporal coding scheme. However, despite significant progress in this area, there still lack rules that have a theoretical basis, and yet can be considered biologically relevant. Here we examine the general conditions under which synaptic plasticity most effectively takes place to support the supervised learning of a precise temporal code. As part of our analysis we examine two spike-based learning methods: one of which relies on an instantaneous error signal to modify synaptic weights in a network (INST rule), and the other one relying on a filtered error signal for smoother synaptic weight modifications (FILT rule). We test the accuracy of the solutions provided by each rule with respect to their temporal encoding precision, and then measure the maximum number of input patterns they can learn to memorise using the precise timings of individual spikes as an indication of their storage capacity. Our results demonstrate the high performance of the FILT rule in most cases, underpinned by the rule’s error-filtering mechanism, which is predicted to provide smooth convergence towards a desired solution during learning. We also find the FILT rule to be most efficient at performing input pattern memorisations, and most noticeably when patterns are identified using spikes with sub-millisecond temporal precision. In comparison with existing work, we determine the performance of the FILT rule to be consistent with that of the highly efficient E-learning Chronotron rule, but with the distinct advantage that our FILT rule is also implementable as an online method for increased biological realism. PMID:27532262

Supervised Learning in Spiking Neural Networks for Precise Temporal Encoding.

PubMed

Gardner, Brian; Grüning, André

2016-01-01

Precise spike timing as a means to encode information in neural networks is biologically supported, and is advantageous over frequency-based codes by processing input features on a much shorter time-scale. For these reasons, much recent attention has been focused on the development of supervised learning rules for spiking neural networks that utilise a temporal coding scheme. However, despite significant progress in this area, there still lack rules that have a theoretical basis, and yet can be considered biologically relevant. Here we examine the general conditions under which synaptic plasticity most effectively takes place to support the supervised learning of a precise temporal code. As part of our analysis we examine two spike-based learning methods: one of which relies on an instantaneous error signal to modify synaptic weights in a network (INST rule), and the other one relying on a filtered error signal for smoother synaptic weight modifications (FILT rule). We test the accuracy of the solutions provided by each rule with respect to their temporal encoding precision, and then measure the maximum number of input patterns they can learn to memorise using the precise timings of individual spikes as an indication of their storage capacity. Our results demonstrate the high performance of the FILT rule in most cases, underpinned by the rule's error-filtering mechanism, which is predicted to provide smooth convergence towards a desired solution during learning. We also find the FILT rule to be most efficient at performing input pattern memorisations, and most noticeably when patterns are identified using spikes with sub-millisecond temporal precision. In comparison with existing work, we determine the performance of the FILT rule to be consistent with that of the highly efficient E-learning Chronotron rule, but with the distinct advantage that our FILT rule is also implementable as an online method for increased biological realism.

An Energy-Efficient Compressive Image Coding for Green Internet of Things (IoT).

PubMed

Li, Ran; Duan, Xiaomeng; Li, Xu; He, Wei; Li, Yanling

2018-04-17

Aimed at a low-energy consumption of Green Internet of Things (IoT), this paper presents an energy-efficient compressive image coding scheme, which provides compressive encoder and real-time decoder according to Compressive Sensing (CS) theory. The compressive encoder adaptively measures each image block based on the block-based gradient field, which models the distribution of block sparse degree, and the real-time decoder linearly reconstructs each image block through a projection matrix, which is learned by Minimum Mean Square Error (MMSE) criterion. Both the encoder and decoder have a low computational complexity, so that they only consume a small amount of energy. Experimental results show that the proposed scheme not only has a low encoding and decoding complexity when compared with traditional methods, but it also provides good objective and subjective reconstruction qualities. In particular, it presents better time-distortion performance than JPEG. Therefore, the proposed compressive image coding is a potential energy-efficient scheme for Green IoT.

SEU hardened memory cells for a CCSDS Reed Solomon encoder

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

Whitaker, S.; Canaris, J.; Liu, K.

This paper reports on design technique to harden CMOS memory circuits against Single Event Upset (SEU) in the space environment. The design technique provides a recovery mechanism which is independent of the shape of the upsetting event. A RAM cell and Flip Flop design are presented to demonstrate the method. The Flip Flop was used in the control circuitry for a Reed Solomon encoder designed for the Space Station and Explorer platforms.

Tile-Image Merging and Delivering for Virtual Camera Services on Tiled-Display for Real-Time Remote Collaboration

NASA Astrophysics Data System (ADS)

Choe, Giseok; Nang, Jongho

The tiled-display system has been used as a Computer Supported Cooperative Work (CSCW) environment, in which multiple local (and/or remote) participants cooperate using some shared applications whose outputs are displayed on a large-scale and high-resolution tiled-display, which is controlled by a cluster of PC's, one PC per display. In order to make the collaboration effective, each remote participant should be aware of all CSCW activities on the titled display system in real-time. This paper presents a capturing and delivering mechanism of all activities on titled-display system to remote participants in real-time. In the proposed mechanism, the screen images of all PC's are periodically captured and delivered to the Merging Server that maintains separate buffers to store the captured images from the PCs. The mechanism selects one tile image from each buffer, merges the images to make a screen shot of the whole tiled-display, clips a Region of Interest (ROI), compresses and streams it to remote participants in real-time. A technical challenge in the proposed mechanism is how to select a set of tile images, one from each buffer, for merging so that the tile images displayed at the same time on the tiled-display can be properly merged together. This paper presents three selection algorithms; a sequential selection algorithm, a capturing time based algorithm, and a capturing time and visual consistency based algorithm. It also proposes a mechanism of providing several virtual cameras on tiled-display system to remote participants by concurrently clipping several different ROI's from the same merged tiled-display images, and delivering them after compressing with video encoders requested by the remote participants. By interactively changing and resizing his/her own ROI, a remote participant can check the activities on the tiled-display effectively. Experiments on a 3 × 2 tiled-display system show that the proposed merging algorithm can build a tiled-display image stream synchronously, and the ROI-based clipping and delivering mechanism can provide individual views on the tiled-display system to multiple remote participants in real-time.

A new supervised learning algorithm for spiking neurons.

PubMed

Xu, Yan; Zeng, Xiaoqin; Zhong, Shuiming

2013-06-01

The purpose of supervised learning with temporal encoding for spiking neurons is to make the neurons emit a specific spike train encoded by the precise firing times of spikes. If only running time is considered, the supervised learning for a spiking neuron is equivalent to distinguishing the times of desired output spikes and the other time during the running process of the neuron through adjusting synaptic weights, which can be regarded as a classification problem. Based on this idea, this letter proposes a new supervised learning method for spiking neurons with temporal encoding; it first transforms the supervised learning into a classification problem and then solves the problem by using the perceptron learning rule. The experiment results show that the proposed method has higher learning accuracy and efficiency over the existing learning methods, so it is more powerful for solving complex and real-time problems.

Leveling the playing field: attention mitigates the effects of intelligence on memory.

PubMed

Markant, Julie; Amso, Dima

2014-05-01

Effective attention and memory skills are fundamental to typical development and essential for achievement during the formal education years. It is critical to identify the specific mechanisms linking efficiency of attentional selection of an item and the quality of its memory retention. The present study capitalized on the spatial cueing paradigm to examine the role of selection via suppression in modulating children and adolescents' memory encoding. By varying a single parameter, the spatial cueing task can elicit either a simple orienting mechanism (i.e., facilitation) or one that involves both target selection and simultaneous suppression of competing information (i.e., IOR). We modified this paradigm to include images of common items in target locations. Participants were not instructed to learn the items and were not told they would be completing a memory test later. Following the cueing task, we imposed a 7-min delay and then asked participants to complete a recognition memory test. Results indicated that selection via suppression promoted recognition memory among 7-17year-olds. Moreover, individual differences in the extent of suppression during encoding predicted recognition memory accuracy. When basic cueing facilitated orienting to target items during encoding, IQ was the best predictor of recognition memory performance for the attended items. In contrast, engaging suppression (i.e., IOR) during encoding counteracted individual differences in intelligence, effectively improving recognition memory performance among children with lower IQs. This work demonstrates that engaging selection via suppression during learning and encoding improves memory retention and has broad implications for developing effective educational techniques. Copyright © 2014 Elsevier B.V. All rights reserved.

Leveling the playing field: Attention mitigates the effects of intelligence on memory

PubMed Central

Markant, Julie; Amso, Dima

2014-01-01

Effective attention and memory skills are fundamental to typical development and essential for achievement during the formal education years. It is critical to identify the specific mechanisms linking efficiency of attentional selection of an item and the quality of its memory retention. The present study capitalized on the spatial cueing paradigm to examine the role of selection via suppression in modulating children and adolescents’ memory encoding. By varying a single parameter, the spatial cueing task can elicit either a simple orienting mechanism (i.e., facilitation) or one that involves both target selection and simultaneous suppression of competing information (i.e., IOR). We modified this paradigm to include images of common items in target locations. Participants were not instructed to learn the items and were not told they would be completing a memory test later. Following the cueing task, we imposed a seven-minute delay and then asked participants to complete a recognition memory test. Results indicated that selection via suppression promoted recognition memory among 7-17 year-olds. Moreover, individual differences in the extent of suppression during encoding predicted recognition memory accuracy. When basic cueing facilitated orienting to target items during encoding, IQ was the best predictor of recognition memory performance for the attended items. In contrast, engaging suppression (i.e, IOR) during encoding counteracted individual differences in intelligence, effectively improving recognition memory performance among children with lower IQs. This work demonstrates that engaging selection via suppression during learning and encoding improves memory retention and has broad implications for developing effective educational techniques. PMID:24549142

A Spiking Working Memory Model Based on Hebbian Short-Term Potentiation.

PubMed

Fiebig, Florian; Lansner, Anders

2017-01-04

A dominant theory of working memory (WM), referred to as the persistent activity hypothesis, holds that recurrently connected neural networks, presumably located in the prefrontal cortex, encode and maintain WM memory items through sustained elevated activity. Reexamination of experimental data has shown that prefrontal cortex activity in single units during delay periods is much more variable than predicted by such a theory and associated computational models. Alternative models of WM maintenance based on synaptic plasticity, such as short-term nonassociative (non-Hebbian) synaptic facilitation, have been suggested but cannot account for encoding of novel associations. Here we test the hypothesis that a recently identified fast-expressing form of Hebbian synaptic plasticity (associative short-term potentiation) is a possible mechanism for WM encoding and maintenance. Our simulations using a spiking neural network model of cortex reproduce a range of cognitive memory effects in the classical multi-item WM task of encoding and immediate free recall of word lists. Memory reactivation in the model occurs in discrete oscillatory bursts rather than as sustained activity. We relate dynamic network activity as well as key synaptic characteristics to electrophysiological measurements. Our findings support the hypothesis that fast Hebbian short-term potentiation is a key WM mechanism. Working memory (WM) is a key component of cognition. Hypotheses about the neural mechanism behind WM are currently under revision. Reflecting recent findings of fast Hebbian synaptic plasticity in cortex, we test whether a cortical spiking neural network model with such a mechanism can learn a multi-item WM task (word list learning). We show that our model can reproduce human cognitive phenomena and achieve comparable memory performance in both free and cued recall while being simultaneously compatible with experimental data on structure, connectivity, and neurophysiology of the underlying cortical tissue. These findings are directly relevant to the ongoing paradigm shift in the WM field. Copyright © 2017 Fiebig and Lansner.

A Spiking Working Memory Model Based on Hebbian Short-Term Potentiation

PubMed Central

Fiebig, Florian

2017-01-01

A dominant theory of working memory (WM), referred to as the persistent activity hypothesis, holds that recurrently connected neural networks, presumably located in the prefrontal cortex, encode and maintain WM memory items through sustained elevated activity. Reexamination of experimental data has shown that prefrontal cortex activity in single units during delay periods is much more variable than predicted by such a theory and associated computational models. Alternative models of WM maintenance based on synaptic plasticity, such as short-term nonassociative (non-Hebbian) synaptic facilitation, have been suggested but cannot account for encoding of novel associations. Here we test the hypothesis that a recently identified fast-expressing form of Hebbian synaptic plasticity (associative short-term potentiation) is a possible mechanism for WM encoding and maintenance. Our simulations using a spiking neural network model of cortex reproduce a range of cognitive memory effects in the classical multi-item WM task of encoding and immediate free recall of word lists. Memory reactivation in the model occurs in discrete oscillatory bursts rather than as sustained activity. We relate dynamic network activity as well as key synaptic characteristics to electrophysiological measurements. Our findings support the hypothesis that fast Hebbian short-term potentiation is a key WM mechanism. SIGNIFICANCE STATEMENT Working memory (WM) is a key component of cognition. Hypotheses about the neural mechanism behind WM are currently under revision. Reflecting recent findings of fast Hebbian synaptic plasticity in cortex, we test whether a cortical spiking neural network model with such a mechanism can learn a multi-item WM task (word list learning). We show that our model can reproduce human cognitive phenomena and achieve comparable memory performance in both free and cued recall while being simultaneously compatible with experimental data on structure, connectivity, and neurophysiology of the underlying cortical tissue. These findings are directly relevant to the ongoing paradigm shift in the WM field. PMID:28053032

High-performance reactionless scan mechanism

NASA Technical Reports Server (NTRS)

Williams, Ellen I.; Summers, Richard T.; Ostaszewski, Miroslaw A.

1995-01-01

A high-performance reactionless scan mirror mechanism was developed for space applications to provide thermal images of the Earth. The design incorporates a unique mechanical means of providing reactionless operation that also minimizes weight, mechanical resonance operation to minimize power, combined use of a single optical encoder to sense coarse and fine angular position, and a new kinematic mount of the mirror. A flex pivot hardware failure and current project status are discussed.

Comparison of compression efficiency between HEVC/H.265 and VP9 based on subjective assessments

NASA Astrophysics Data System (ADS)

Řeřábek, Martin; Ebrahimi, Touradj

2014-09-01

Current increasing effort of broadcast providers to transmit UHD (Ultra High Definition) content is likely to increase demand for ultra high definition televisions (UHDTVs). To compress UHDTV content, several alternative encoding mechanisms exist. In addition to internationally recognized standards, open access proprietary options, such as VP9 video encoding scheme, have recently appeared and are gaining popularity. One of the main goals of these encoders is to efficiently compress video sequences beyond HDTV resolution for various scenarios, such as broadcasting or internet streaming. In this paper, a broadcast scenario rate-distortion performance analysis and mutual comparison of one of the latest video coding standards H.265/HEVC with recently released proprietary video coding scheme VP9 is presented. Also, currently one of the most popular and widely spread encoder H.264/AVC has been included into the evaluation to serve as a comparison baseline. The comparison is performed by means of subjective evaluations showing actual differences between encoding algorithms in terms of perceived quality. The results indicate a general dominance of HEVC based encoding algorithm in comparison to other alternatives, while VP9 and AVC showing similar performance.

Targeted Memory Reactivation during Sleep Adaptively Promotes the Strengthening or Weakening of Overlapping Memories.

PubMed

Oyarzún, Javiera P; Morís, Joaquín; Luque, David; de Diego-Balaguer, Ruth; Fuentemilla, Lluís

2017-08-09

System memory consolidation is conceptualized as an active process whereby newly encoded memory representations are strengthened through selective memory reactivation during sleep. However, our learning experience is highly overlapping in content (i.e., shares common elements), and memories of these events are organized in an intricate network of overlapping associated events. It remains to be explored whether and how selective memory reactivation during sleep has an impact on these overlapping memories acquired during awake time. Here, we test in a group of adult women and men the prediction that selective memory reactivation during sleep entails the reactivation of associated events and that this may lead the brain to adaptively regulate whether these associated memories are strengthened or pruned from memory networks on the basis of their relative associative strength with the shared element. Our findings demonstrate the existence of efficient regulatory neural mechanisms governing how complex memory networks are shaped during sleep as a function of their associative memory strength. SIGNIFICANCE STATEMENT Numerous studies have demonstrated that system memory consolidation is an active, selective, and sleep-dependent process in which only subsets of new memories become stabilized through their reactivation. However, the learning experience is highly overlapping in content and thus events are encoded in an intricate network of related memories. It remains to be explored whether and how memory reactivation has an impact on overlapping memories acquired during awake time. Here, we show that sleep memory reactivation promotes strengthening and weakening of overlapping memories based on their associative memory strength. These results suggest the existence of an efficient regulatory neural mechanism that avoids the formation of cluttered memory representation of multiple events and promotes stabilization of complex memory networks. Copyright © 2017 the authors 0270-6474/17/377748-11$15.00/0.

Engram formation in psychiatric disorders.

PubMed

Gebicke-Haerter, Peter J

2014-01-01

Environmental factors substantially influence beginning and progression of mental illness, reinforcing or reducing the consequences of genetic vulnerability. Often initiated by early traumatic events, "engrams" or memories are formed that may give rise to a slow and subtle progression of psychiatric disorders. The large delay between beginning and time of onset (diagnosis) may be explained by efficient compensatory mechanisms observed in brain metabolism that use optional pathways in highly redundant molecular interactions. To this end, research has to deal with mechanisms of learning and long-term memory formation, which involves (a) epigenetic changes, (b) altered neuronal activities, and (c) changes in neuron-glia communication. On the epigenetic level, apparently DNA-methylations are more stable than histone modifications, although both closely interact. Neuronal activities basically deliver digital information, which clearly can serve as basis for memory formation (LTP). However, research in this respect has long time neglected the importance of glia. They are more actively involved in the control of neuronal activities than thought before. They can both reinforce and inhibit neuronal activities by transducing neuronal information from frequency-encoded to amplitude and frequency-modulated calcium wave patterns spreading in the glial syncytium by use of gap junctions. In this way, they serve integrative functions. In conclusion, we are dealing with two concepts of encoding information that mutually control each other and synergize: a digital (neuronal) and a wave-like (glial) computing, forming neuron-glia functional units with inbuilt feedback loops to maintain balance of excitation and inhibition. To better understand mental illness, we have to gain more insight into the dynamics of adverse environmental impact on those cellular and molecular systems. This report summarizes existing knowledge and draws some outline about further research in molecular psychiatry.

Engram formation in psychiatric disorders

PubMed Central

Gebicke-Haerter, Peter J.

2014-01-01

Environmental factors substantially influence beginning and progression of mental illness, reinforcing or reducing the consequences of genetic vulnerability. Often initiated by early traumatic events, “engrams” or memories are formed that may give rise to a slow and subtle progression of psychiatric disorders. The large delay between beginning and time of onset (diagnosis) may be explained by efficient compensatory mechanisms observed in brain metabolism that use optional pathways in highly redundant molecular interactions. To this end, research has to deal with mechanisms of learning and long-term memory formation, which involves (a) epigenetic changes, (b) altered neuronal activities, and (c) changes in neuron-glia communication. On the epigenetic level, apparently DNA-methylations are more stable than histone modifications, although both closely interact. Neuronal activities basically deliver digital information, which clearly can serve as basis for memory formation (LTP). However, research in this respect has long time neglected the importance of glia. They are more actively involved in the control of neuronal activities than thought before. They can both reinforce and inhibit neuronal activities by transducing neuronal information from frequency-encoded to amplitude and frequency-modulated calcium wave patterns spreading in the glial syncytium by use of gap junctions. In this way, they serve integrative functions. In conclusion, we are dealing with two concepts of encoding information that mutually control each other and synergize: a digital (neuronal) and a wave-like (glial) computing, forming neuron-glia functional units with inbuilt feedback loops to maintain balance of excitation and inhibition. To better understand mental illness, we have to gain more insight into the dynamics of adverse environmental impact on those cellular and molecular systems. This report summarizes existing knowledge and draws some outline about further research in molecular psychiatry. PMID:24904262

Levels of word processing and incidental memory: dissociable mechanisms in the temporal lobe.

PubMed

Castillo, E M; Simos, P G; Davis, R N; Breier, J; Fitzgerald, M E; Papanicolaou, A C

2001-11-16

Word recall is facilitated when deep (e.g. semantic) processing is applied during encoding. This fact raises the question of the existence of specific brain mechanisms supporting different levels of information processing that can modulate incidental memory performance. In this study we obtained spatiotemporal brain activation profiles, using magnetic source imaging, from 10 adult volunteers as they performed a shallow (phonological) processing task and a deep (semantic) processing task. When phonological analysis of the word stimuli into their constituent phonemes was required, activation was largely restricted to the posterior portion of the left superior temporal gyrus (area 22). Conversely, when access to lexical/semantic representations was required, activation was found predominantly in the left middle temporal gyrus and medial temporal cortex. The differential engagement of each mechanism during word encoding was associated with dramatic changes in subsequent incidental memory performance.

Sex determination in insects: a binary decision based on alternative splicing.

PubMed

Salz, Helen K

2011-08-01

The gene regulatory networks that control sex determination vary between species. Despite these differences, comparative studies in insects have found that alternative splicing is reiteratively used in evolution to control expression of the key sex-determining genes. Sex determination is best understood in Drosophila where activation of the RNA binding protein-encoding gene Sex-lethal is the central female-determining event. Sex-lethal serves as a genetic switch because once activated it controls its own expression by a positive feedback splicing mechanism. Sex fate choice in is also maintained by self-sustaining positive feedback splicing mechanisms in other dipteran and hymenopteran insects, although different RNA binding protein-encoding genes function as the binary switch. Studies exploring the mechanisms of sex-specific splicing have revealed the extent to which sex determination is integrated with other developmental regulatory networks. Copyright © 2011 Elsevier Ltd. All rights reserved.

Intestinal Insulin Signaling Encodes Two Different Molecular Mechanisms for the Shortened Longevity Induced by Graphene Oxide in Caenorhabditis elegans

NASA Astrophysics Data System (ADS)

Zhao, Yunli; Yang, Ruilong; Rui, Qi; Wang, Dayong

2016-04-01

Graphene oxide (GO) has been shown to cause multiple toxicities in various organisms. However, the underlying molecular mechanisms for GO-induced shortened longevity are still unclear. We employed Caenorhabditis elegans to investigate the possible involvement of insulin signaling pathway in the control of GO toxicity and its underlying molecular mechanisms. Mutation of daf-2, age-1, akt-1, or akt-2 gene induced a resistant property of nematodes to GO toxicity, while mutation of daf-16 gene led to a susceptible property of nematodes to GO toxicity, suggesting that GO may dysregulate the functions of DAF-2/IGF-1 receptor, AGE-1, AKT-1 and AKT-2-mediated kinase cascade, and DAF-16/FOXO transcription factor. Genetic interaction analysis suggested the involvement of signaling cascade of DAF-2-AGE-1-AKT-1/2-DAF-16 in the control of GO toxicity on longevity. Moreover, intestinal RNA interference (RNAi) analysis demonstrated that GO reduced longevity by affecting the functions of signaling cascade of DAF-2-AGE-1-AKT-1/2-DAF-16 in the intestine. DAF-16 could also regulate GO toxicity on longevity by functioning upstream of SOD-3, which encodes an antioxidation system that prevents the accumulation of oxidative stress. Therefore, intestinal insulin signaling may encode two different molecular mechanisms responsible for the GO toxicity in inducing the shortened longevity. Our results highlight the key role of insulin signaling pathway in the control of GO toxicity in organisms.

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

Liphardt, Jan

In April 1953, Watson and Crick largely defined the program of 20th century biology: obtaining the blueprint of life encoded in the DNA. Fifty years later, in 2003, the sequencing of the human genome was completed. Like any major scientific breakthrough, the sequencing of the human genome raised many more questions than it answered. I'll brief you on some of the big open problems in cell and developmental biology, and I'll explain why approaches, tools, and ideas from the physical sciences are currently reshaping biological research. Super-resolution light microscopies are revealing the intricate spatial organization of cells, single-molecule methods showmore » how molecular machines function, and new probes are clarifying the role of mechanical forces in cell and tissue function. At the same time, Physics stands to gain beautiful new problems in soft condensed matter, quantum mechanics, and non-equilibrium thermodynamics.« less

Unraveling hadron structure with generalized parton distributions

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

Andrei Belitsky; Anatoly Radyushkin

2004-10-01

The recently introduced generalized parton distributions have emerged as a universal tool to describe hadrons in terms of quark and gluonic degrees of freedom. They combine the features of form factors, parton densities and distribution amplitudes - the functions used for a long time in studies of hadronic structure. Generalized parton distributions are analogous to the phase-space Wigner quasi-probability function of non-relativistic quantum mechanics which encodes full information on a quantum-mechanical system. We give an extensive review of main achievements in the development of this formalism. We discuss physical interpretation and basic properties of generalized parton distributions, their modeling andmore » QCD evolution in the leading and next-to-leading orders. We describe how these functions enter a wide class of exclusive reactions, such as electro- and photo-production of photons, lepton pairs, or mesons.« less

The Intersection of Physics and Biology

ScienceCinema

Liphardt, Jan

2017-12-22

In April 1953, Watson and Crick largely defined the program of 20th century biology: obtaining the blueprint of life encoded in the DNA. Fifty years later, in 2003, the sequencing of the human genome was completed. Like any major scientific breakthrough, the sequencing of the human genome raised many more questions than it answered. I'll brief you on some of the big open problems in cell and developmental biology, and I'll explain why approaches, tools, and ideas from the physical sciences are currently reshaping biological research. Super-resolution light microscopies are revealing the intricate spatial organization of cells, single-molecule methods show how molecular machines function, and new probes are clarifying the role of mechanical forces in cell and tissue function. At the same time, Physics stands to gain beautiful new problems in soft condensed matter, quantum mechanics, and non-equilibrium thermodynamics.

Selective attention to phonology dynamically modulates initial encoding of auditory words within the left hemisphere.

PubMed

Yoncheva, Yuliya; Maurer, Urs; Zevin, Jason D; McCandliss, Bruce D

2014-08-15

Selective attention to phonology, i.e., the ability to attend to sub-syllabic units within spoken words, is a critical precursor to literacy acquisition. Recent functional magnetic resonance imaging evidence has demonstrated that a left-lateralized network of frontal, temporal, and posterior language regions, including the visual word form area, supports this skill. The current event-related potential (ERP) study investigated the temporal dynamics of selective attention to phonology during spoken word perception. We tested the hypothesis that selective attention to phonology dynamically modulates stimulus encoding by recruiting left-lateralized processes specifically while the information critical for performance is unfolding. Selective attention to phonology was captured by manipulating listening goals: skilled adult readers attended to either rhyme or melody within auditory stimulus pairs. Each pair superimposed rhyming and melodic information ensuring identical sensory stimulation. Selective attention to phonology produced distinct early and late topographic ERP effects during stimulus encoding. Data-driven source localization analyses revealed that selective attention to phonology led to significantly greater recruitment of left-lateralized posterior and extensive temporal regions, which was notably concurrent with the rhyme-relevant information within the word. Furthermore, selective attention effects were specific to auditory stimulus encoding and not observed in response to cues, arguing against the notion that they reflect sustained task setting. Collectively, these results demonstrate that selective attention to phonology dynamically engages a left-lateralized network during the critical time-period of perception for achieving phonological analysis goals. These findings suggest a key role for selective attention in on-line phonological computations. Furthermore, these findings motivate future research on the role that neural mechanisms of attention may play in phonological awareness impairments thought to underlie developmental reading disabilities. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Test-Retest Reliability of fMRI Brain Activity during Memory Encoding

PubMed Central

Brandt, David J.; Sommer, Jens; Krach, Sören; Bedenbender, Johannes; Kircher, Tilo; Paulus, Frieder M.; Jansen, Andreas

2013-01-01

The mechanisms underlying hemispheric specialization of memory are not completely understood. Functional magnetic resonance imaging (fMRI) can be used to develop and test models of hemispheric specialization. In particular for memory tasks however, the interpretation of fMRI results is often hampered by the low reliability of the data. In the present study we therefore analyzed the test-retest reliability of fMRI brain activation related to an implicit memory encoding task, with a particular focus on brain activity of the medial temporal lobe (MTL). Fifteen healthy subjects were scanned with fMRI on two sessions (average retest interval 35 days) using a commonly applied novelty encoding paradigm contrasting known and unknown stimuli. To assess brain lateralization, we used three different stimuli classes that differed in their verbalizability (words, scenes, fractals). Test-retest reliability of fMRI brain activation was assessed by an intraclass-correlation coefficient (ICC), describing the stability of inter-individual differences in the brain activation magnitude over time. We found as expected a left-lateralized brain activation network for the words paradigm, a bilateral network for the scenes paradigm, and predominantly right-hemispheric brain activation for the fractals paradigm. Although these networks were consistently activated in both sessions on the group level, across-subject reliabilities were only poor to fair (ICCs ≤ 0.45). Overall, the highest ICC values were obtained for the scenes paradigm, but only in strongly activated brain regions. In particular the reliability of brain activity of the MTL was poor for all paradigms. In conclusion, for novelty encoding paradigms the interpretation of fMRI results on a single subject level is hampered by its low reliability. More studies are needed to optimize the retest reliability of fMRI activation for memory tasks. PMID:24367338

Apoptotic role of TGF-β mediated by Smad4 mitochondria translocation and cytochrome c oxidase subunit II interaction.

PubMed

Pang, Lijuan; Qiu, Tao; Cao, Xu; Wan, Mei

2011-07-01

Smad4, originally isolated from the human chromosome 18q21, is a key factor in transducing the signals of the TGF-β superfamily of growth hormones and plays a pivotal role in mediating antimitogenic and proapoptotic effects of TGF-β, but the mechanisms by which Smad4 induces apoptosis are elusive. Here we report that Smad4 directly translocates to the mitochondria of apoptotic cells. Smad4 gene silencing by siRNA inhibits TGF-β-induced apoptosis in Hep3B cells and UV-induced apoptosis in PANC-1 cells. Cell fractionation assays demonstrated that a fraction of Smad4 translocates to mitochondria after long time TGF-β treatment or UV exposure, during which the cells were under apoptosis. Smad4 mitochondria translocation during apoptosis was also confirmed by fluorescence observation of Smad4 colocalization with MitoTracker Red. We searched for mitochondria proteins that have physical interactions with Smad4 using yeast two-hybrid screening approach. DNA sequence analysis identified 34 positive clones, five of which encoded subunits in mitochondria complex IV, i.e., one clone encoded cytochrome c oxidase COXII, three clones encoded COXIII and one clone encoded COXVb. Strong interaction between Smad4 with COXII, an important apoptosis regulator, was verified in yeast by β-gal activity assays and in mammalian cells by immunoprecipitation assays. Further, mitochondrial portion of cells was isolated and the interaction between COXII and Smad4 in mitochondria upon TGF-β treatment or UV exposure was confirmed. Importantly, targeting Smad4 to mitochondria using import leader fusions enhanced TGF-β-induced apoptosis. Collectively, the results suggest that Smad4 promote apoptosis of the cells through its mitochondrial translocation and association with mitochondria protein COXII. Copyright © 2011 Elsevier Inc. All rights reserved.

Event Boundaries Trigger Rapid Memory Reinstatement of the Prior Events to Promote Their Representation in Long-Term Memory.

PubMed

Sols, Ignasi; DuBrow, Sarah; Davachi, Lila; Fuentemilla, Lluís

2017-11-20

Although everyday experiences unfold continuously over time, shifts in context, or event boundaries, can influence how those events come to be represented in memory [1-4]. Specifically, mnemonic binding across sequential representations is more challenging at context shifts, such that successful temporal associations are more likely to be formed within than across contexts [1, 2, 5-9]. However, in order to preserve a subjective sense of continuity, it is important that the memory system bridge temporally adjacent events, even if they occur in seemingly distinct contexts. Here, we used pattern similarity analysis to scalp electroencephalographic (EEG) recordings during a sequential learning task [2, 3] in humans and showed that the detection of event boundaries triggered a rapid memory reinstatement of the just-encoded sequence episode. Memory reactivation was detected rapidly (∼200-800 ms from the onset of the event boundary) and was specific to context shifts that were preceded by an event sequence with episodic content. Memory reinstatement was not observed during the sequential encoding of events within an episode, indicating that memory reactivation was induced specifically upon context shifts. Finally, the degree of neural similarity between neural responses elicited during sequence encoding and at event boundaries correlated positively with participants' ability to later link across sequences of events, suggesting a critical role in binding temporally adjacent events in long-term memory. Current results shed light onto the neural mechanisms that promote episodic encoding not only for information within the event, but also, importantly, in the ability to link across events to create a memory representation of continuous experience. Copyright © 2017 Elsevier Ltd. All rights reserved.

Differentiation and Response Bias in Episodic Memory: Evidence from Reaction Time Distributions

ERIC Educational Resources Information Center

Criss, Amy H.

2010-01-01

In differentiation models, the processes of encoding and retrieval produce an increase in the distribution of memory strength for targets and a decrease in the distribution of memory strength for foils as the amount of encoding increases. This produces an increase in the hit rate and decrease in the false-alarm rate for a strongly encoded compared…

Implementation of MPEG-2 encoder to multiprocessor system using multiple MVPs (TMS320C80)

NASA Astrophysics Data System (ADS)

Kim, HyungSun; Boo, Kenny; Chung, SeokWoo; Choi, Geon Y.; Lee, YongJin; Jeon, JaeHo; Park, Hyun Wook

1997-05-01

This paper presents the efficient algorithm mapping for the real-time MPEG-2 encoding on the KAIST image computing system (KICS), which has a parallel architecture using five multimedia video processors (MVPs). The MVP is a general purpose digital signal processor (DSP) of Texas Instrument. It combines one floating-point processor and four fixed- point DSPs on a single chip. The KICS uses the MVP as a primary processing element (PE). Two PEs form a cluster, and there are two processing clusters in the KICS. Real-time MPEG-2 encoder is implemented through the spatial and the functional partitioning strategies. Encoding process of spatially partitioned half of the video input frame is assigned to ne processing cluster. Two PEs perform the functionally partitioned MPEG-2 encoding tasks in the pipelined operation mode. One PE of a cluster carries out the transform coding part and the other performs the predictive coding part of the MPEG-2 encoding algorithm. One MVP among five MVPs is used for system control and interface with host computer. This paper introduces an implementation of the MPEG-2 algorithm with a parallel processing architecture.

Memory network plasticity after temporal lobe resection: a longitudinal functional imaging study

PubMed Central

Sidhu, Meneka K.; Stretton, Jason; Winston, Gavin P.; McEvoy, Andrew W.; Symms, Mark; Thompson, Pamela J.; Koepp, Matthias J.

2016-01-01

Abstract Anterior temporal lobe resection can control seizures in up to 80% of patients with temporal lobe epilepsy. Memory decrements are the main neurocognitive complication. Preoperative functional reorganization has been described in memory networks, but less is known of postoperative reorganization. We investigated reorganization of memory-encoding networks preoperatively and 3 and 12 months after surgery. We studied 36 patients with unilateral medial temporal lobe epilepsy (19 right) before and 3 and 12 months after anterior temporal lobe resection. Fifteen healthy control subjects were studied at three equivalent time points. All subjects had neuropsychological testing at each of the three time points. A functional magnetic resonance imaging memory-encoding paradigm of words and faces was performed with subsequent out-of-scanner recognition assessments. Changes in activations across the time points in each patient group were compared to changes in the control group in a single flexible factorial analysis. Postoperative change in memory across the time points was correlated with postoperative activations to investigate the efficiency of reorganized networks. Left temporal lobe epilepsy patients showed increased right anterior hippocampal and frontal activation at both 3 and 12 months after surgery relative to preoperatively, for word and face encoding, with a concomitant reduction in left frontal activation 12 months postoperatively. Right anterior hippocampal activation 12 months postoperatively correlated significantly with improved verbal learning in patients with left temporal lobe epilepsy from preoperatively to 12 months postoperatively. Preoperatively, there was significant left posterior hippocampal activation that was sustained 3 months postoperatively at word encoding, and increased at face encoding. For both word and face encoding this was significantly reduced from 3 to 12 months postoperatively. Patients with right temporal lobe epilepsy showed increased left anterior hippocampal activation on word encoding from 3 to 12 months postoperatively compared to preoperatively. On face encoding, left anterior hippocampal activations were present preoperatively and 12 months postoperatively. Left anterior hippocampal and orbitofrontal cortex activations correlated with improvements in both design and verbal learning 12 months postoperatively. On face encoding, there were significantly increased left posterior hippocampal activations that reduced significantly from 3 to 12 months postoperatively. Postoperative changes occur in the memory-encoding network in both left and right temporal lobe epilepsy patients across both verbal and visual domains. Three months after surgery, compensatory posterior hippocampal reorganization that occurs is transient and inefficient. Engagement of the contralateral hippocampus 12 months after surgery represented efficient reorganization in both patient groups, suggesting that the contralateral hippocampus contributes to memory outcome 12 months after surgery. PMID:26754787

Biophysical Regulation of Chromatin Architecture Instills a Mechanical Memory in Mesenchymal Stem Cells

PubMed Central

Heo, Su-Jin; Thorpe, Stephen D.; Driscoll, Tristan P.; Duncan, Randall L.; Lee, David A.; Mauck, Robert L.

2015-01-01

Mechanical cues direct the lineage commitment of mesenchymal stem cells (MSCs). In this study, we identified the operative molecular mechanisms through which dynamic tensile loading (DL) regulates changes in chromatin organization and nuclear mechanics in MSCs. Our data show that, in the absence of exogenous differentiation factors, short term DL elicits a rapid increase in chromatin condensation, mediated by acto-myosin based cellular contractility and the activity of the histone-lysine N-methyltransferase EZH2. The resulting change in chromatin condensation stiffened the MSC nucleus, making it less deformable when stretch was applied to the cell. We also identified stretch induced ATP release and purinergic calcium signaling as a central mediator of this chromatin condensation process. Further, we showed that DL, through differential stabilization of the condensed chromatin state, established a ‘mechanical memory’ in these cells. That is, increasing strain levels and number of loading events led to a greater degree of chromatin condensation that persisted for longer periods of time after the cessation of loading. These data indicate that, with mechanical perturbation, MSCs develop a mechanical memory encoded in structural changes in the nucleus which may sensitize them to future mechanical loading events and define the trajectory and persistence of their lineage specification. PMID:26592929

Jr-ZFP2, encoding a Cys2/His2-type transcription factor, is involved in the early stages of the mechano-perception pathway and specifically expressed in mechanically stimulated tissues in woody plants.

PubMed

Leblanc-Fournier, Nathalie; Coutand, Catherine; Crouzet, Jerome; Brunel, Nicole; Lenne, Catherine; Moulia, Bruno; Julien, Jean-Louis

2008-06-01

Plants respond to environmental mechanical stimulation, such as wind, by modifying their growth and development. To study the molecular effects of stem bending on 3-week-old walnut trees, a cDNA-AFLP approach was developed. This study allowed the identification of a cDNA, known as Jr-ZFP2, encoding a Cys2/His2-type two-zinc-fingered transcription factor. Reverse transcriptase-polymerase chain reaction analysis confirmed that Jr-ZFP2 mRNA accumulation is rapidly and transiently induced after mechanical stimulation. After bending, Jr-ZFP2 transcript increase was restricted to the stem, the organ where the mechanical solicitation was applied. Furthermore, other abiotic factors, such as cold or salt, did not modify Jr-ZFP2 mRNA accumulation in walnut stems under our experimental conditions, whereas growth studies demonstrated that salt stress was actually perceived by the plants. These results suggest that the regulation of Jr-ZFP2 expression is more sensitive to mechanical stimulus. This gene will be a good marker for studying the early stages of mechanical perception in woody plants.

Solution NMR studies of the plant peptide hormone CEP inform function.

PubMed

Bobay, Benjamin G; DiGennaro, Peter; Scholl, Elizabeth; Imin, Nijat; Djordjevic, Michael A; Mck Bird, David

2013-12-11

The C-terminally Encoded Peptide (CEP) family of regulatory peptides controls root development in vascular plants. Here, we present the first NMR structures of CEP. We show that root-knot nematode (RKN: Meloidogyne spp.) also encodes CEP, presumably to mimic plant CEP as part of their stereotypic, parasitic interaction with vascular plants. Molecular dynamics simulations of plant- and nematode-encoded CEP displaying known posttranslational modifications (PTM) provided insight into the structural effects of PTM and the conformational plasticity and rigidity of CEP. Potential mechanisms of action are discussed with respect to the structure and sampling of conformational space. © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Area, speed and power measurements of FPGA-based complex orthogonal space-time block code channel encoders

NASA Astrophysics Data System (ADS)

Passas, Georgios; Freear, Steven; Fawcett, Darren

2010-01-01

Space-time coding (STC) is an important milestone in modern wireless communications. In this technique, more copies of the same signal are transmitted through different antennas (space) and different symbol periods (time), to improve the robustness of a wireless system by increasing its diversity gain. STCs are channel coding algorithms that can be readily implemented on a field programmable gate array (FPGA) device. This work provides some figures for the amount of required FPGA hardware resources, the speed that the algorithms can operate and the power consumption requirements of a space-time block code (STBC) encoder. Seven encoder very high-speed integrated circuit hardware description language (VHDL) designs have been coded, synthesised and tested. Each design realises a complex orthogonal space-time block code with a different transmission matrix. All VHDL designs are parameterisable in terms of sample precision. Precisions ranging from 4 bits to 32 bits have been synthesised. Alamouti's STBC encoder design [Alamouti, S.M. (1998), 'A Simple Transmit Diversity Technique for Wireless Communications', IEEE Journal on Selected Areas in Communications, 16:55-108.] proved to be the best trade-off, since it is on average 3.2 times smaller, 1.5 times faster and requires slightly less power than the next best trade-off in the comparison, which is a 3/4-rate full-diversity 3Tx-antenna STBC.

Semantic Encoding Enhances the Pictorial Superiority Effect in the Oldest-Old

PubMed Central

Cherry, Katie E.; Brown, Jennifer Silva; Walker, Erin Jackson; Smitherman, Emily A.; Boudreaux, Emily O.; Volaufova, Julia; Jazwinski, S. Michal

2011-01-01

We examined the effect of a semantic orienting task during encoding on free recall and recognition of simple line drawings and matching words in middle-aged (44 to 59 years), older (60 to 89 years), and oldest-old (90 + years) adults. Participants studied line drawings and matching words presented in blocked order. Half of the participants were given a semantic orienting task and the other half received standard intentional learning instructions. Results confirmed that the pictorial superiority effect was greater in magnitude following semantic encoding compared to the control condition. Analyses of clustering in free recall revealed that oldest-old adults’ encoding and retrieval strategies were generally similar to the two younger groups. Self-reported strategy use was less frequent among the oldest-old adults. These data strongly suggest that semantic elaboration is an effective compensatory mechanism underlying preserved episodic memory performance that persists well into the ninth decade of life. PMID:22053814

An Electrophysiological Signature of Unconscious Recognition Memory

PubMed Central

Voss, Joel L.; Paller, Ken A.

2009-01-01

Contradicting the common assumption that accurate recognition reflects explicit-memory processing, we describe evidence for recognition lacking two hallmark explicit-memory features: awareness of memory retrieval and facilitation by attentive encoding. Kaleidoscope images were encoded in conjunction with an attentional diversion and subsequently recognized more accurately than those encoded without diversion. Confidence in recognition was superior following attentive encoding, though recognition was remarkably accurate when people claimed to be unaware of memory retrieval. This “implicit recognition” was associated with frontal-occipital negative brain potentials at 200-400 ms post-stimulus-onset, which were spatially and temporally distinct from positive brain potentials corresponding to explicit recollection and familiarity. This dissociation between behavioral and electrophysiological characteristics of “implicit recognition” versus explicit recognition indicates that a neurocognitive mechanism with properties similar to those that produce implicit memory can be operative in standard recognition tests. People can accurately discriminate repeat stimuli from new stimuli without necessarily knowing it. PMID:19198606

Epigenetics, chromatin and genome organization: recent advances from the ENCODE project.

PubMed

Siggens, L; Ekwall, K

2014-09-01

The organization of the genome into functional units, such as enhancers and active or repressed promoters, is associated with distinct patterns of DNA and histone modifications. The Encyclopedia of DNA Elements (ENCODE) project has advanced our understanding of the principles of genome, epigenome and chromatin organization, identifying hundreds of thousands of potential regulatory regions and transcription factor binding sites. Part of the ENCODE consortium, GENCODE, has annotated the human genome with novel transcripts including new noncoding RNAs and pseudogenes, highlighting transcriptional complexity. Many disease variants identified in genome-wide association studies are located within putative enhancer regions defined by the ENCODE project. Understanding the principles of chromatin and epigenome organization will help to identify new disease mechanisms, biomarkers and drug targets, particularly as ongoing epigenome mapping projects generate data for primary human cell types that play important roles in disease. © 2014 The Association for the Publication of the Journal of Internal Medicine.

The impact of path crossing on visuo-spatial serial memory: encoding or rehearsal effect?

PubMed

Parmentier, Fabrice B R; Andrés, Pilar

2006-11-01

The determinants of visuo-spatial serial memory have been the object of little research, despite early evidence that not all sequences are equally remembered. Recently, empirical evidence was reported indicating that the complexity of the path formed by the to-be-remembered locations impacted on recall performance, defined for example by the presence of crossings in the path formed by successive locations (Parmentier, Elford, & Maybery, 2005). In this study, we examined whether this effect reflects rehearsal or encoding processes. We examined the effect of a retention interval and spatial interference on the ordered recall of spatial sequences with and without path crossings. Path crossings decreased recall performance, as did a retention interval. In line with the encoding hypothesis, but in contrast with the rehearsal hypothesis, the effect of crossing was not affected by the retention interval nor by tapping. The possible nature of the impact of path crossing on encoding mechanisms is discussed.

Females scan more than males: a potential mechanism for sex differences in recognition memory.

PubMed

Heisz, Jennifer J; Pottruff, Molly M; Shore, David I

2013-07-01

Recognition-memory tests reveal individual differences in episodic memory; however, by themselves, these tests provide little information regarding the stage (or stages) in memory processing at which differences are manifested. We used eye-tracking technology, together with a recognition paradigm, to achieve a more detailed analysis of visual processing during encoding and retrieval. Although this approach may be useful for assessing differences in memory across many different populations, we focused on sex differences in face memory. Females outperformed males on recognition-memory tests, and this advantage was directly related to females' scanning behavior at encoding. Moreover, additional exposures to the faces reduced sex differences in face recognition, which suggests that males may be able to improve their recognition memory by extracting more information at encoding through increased scanning. A strategy of increased scanning at encoding may prove to be a simple way to enhance memory performance in other populations with memory impairment.

An Information Theoretic Characterisation of Auditory Encoding

PubMed Central

Overath, Tobias; Cusack, Rhodri; Kumar, Sukhbinder; von Kriegstein, Katharina; Warren, Jason D; Grube, Manon; Carlyon, Robert P; Griffiths, Timothy D

2007-01-01

The entropy metric derived from information theory provides a means to quantify the amount of information transmitted in acoustic streams like speech or music. By systematically varying the entropy of pitch sequences, we sought brain areas where neural activity and energetic demands increase as a function of entropy. Such a relationship is predicted to occur in an efficient encoding mechanism that uses less computational resource when less information is present in the signal: we specifically tested the hypothesis that such a relationship is present in the planum temporale (PT). In two convergent functional MRI studies, we demonstrated this relationship in PT for encoding, while furthermore showing that a distributed fronto-parietal network for retrieval of acoustic information is independent of entropy. The results establish PT as an efficient neural engine that demands less computational resource to encode redundant signals than those with high information content. PMID:17958472

Eye coding mechanisms in early human face event-related potentials.

PubMed

Rousselet, Guillaume A; Ince, Robin A A; van Rijsbergen, Nicola J; Schyns, Philippe G

2014-11-10

In humans, the N170 event-related potential (ERP) is an integrated measure of cortical activity that varies in amplitude and latency across trials. Researchers often conjecture that N170 variations reflect cortical mechanisms of stimulus coding for recognition. Here, to settle the conjecture and understand cortical information processing mechanisms, we unraveled the coding function of N170 latency and amplitude variations in possibly the simplest socially important natural visual task: face detection. On each experimental trial, 16 observers saw face and noise pictures sparsely sampled with small Gaussian apertures. Reverse-correlation methods coupled with information theory revealed that the presence of the eye specifically covaries with behavioral and neural measurements: the left eye strongly modulates reaction times and lateral electrodes represent mainly the presence of the contralateral eye during the rising part of the N170, with maximum sensitivity before the N170 peak. Furthermore, single-trial N170 latencies code more about the presence of the contralateral eye than N170 amplitudes and early latencies are associated with faster reaction times. The absence of these effects in control images that did not contain a face refutes alternative accounts based on retinal biases or allocation of attention to the eye location on the face. We conclude that the rising part of the N170, roughly 120-170 ms post-stimulus, is a critical time-window in human face processing mechanisms, reflecting predominantly, in a face detection task, the encoding of a single feature: the contralateral eye. © 2014 ARVO.

Lateral and medial prefrontal contributions to emotion generation by semantic elaboration during episodic encoding.

PubMed

Kaneda, Takumi; Shigemune, Yayoi; Tsukiura, Takashi

2017-02-01

Memories for emotion-laden stimuli are remembered more accurately than those for neutral stimuli. Although this enhancement reflects stimulus-driven modulation of memory by emotions, functional neuroimaging evidence of the interacting mechanisms between emotions generated by intentional processes, such as semantic elaboration, and memory is scarce. The present fMRI study investigated how encoding-related activation is modulated by emotions generated during the process of semantic elaboration. During encoding with fMRI, healthy young adults viewed neutral (target) pictures either passively or with semantic elaboration. In semantic elaboration, participants imagined background stories related to the pictures. Encoding trials with semantic elaboration were subdivided into conditions in which participants imagined negative, positive, or neutral stories. One week later, memories for target pictures were tested. In behavioral results, memories for target pictures were significantly enhanced by semantic elaboration, compared to passive viewing, and the memory enhancement was more remarkable when negative or positive stories were imagined. fMRI results demonstrated that activations in the left inferior frontal gyrus and dorsal medial prefrontal cortex (dmPFC) were greater during the encoding of target pictures with semantic elaboration than those with passive viewing, and that these activations further increased during encoding with semantic elaboration of emotional stories than of neutral stories. Functional connectivity between the left inferior frontal gyrus and dmPFC/hippocampus during encoding significantly predicted retrieval accuracies of memories encoded with self-generated emotional stories. These findings suggest that networks including the left inferior frontal region, dmPFC, and hippocampus could contribute to the modulation of memories encoded with the emotion generation.

Interneurons in the Honeybee Primary Auditory Center Responding to Waggle Dance-Like Vibration Pulses.

PubMed

Ai, Hiroyuki; Kai, Kazuki; Kumaraswamy, Ajayrama; Ikeno, Hidetoshi; Wachtler, Thomas

2017-11-01

Female honeybees use the "waggle dance" to communicate the location of nectar sources to their hive mates. Distance information is encoded in the duration of the waggle phase (von Frisch, 1967). During the waggle phase, the dancer produces trains of vibration pulses, which are detected by the follower bees via Johnston's organ located on the antennae. To uncover the neural mechanisms underlying the encoding of distance information in the waggle dance follower, we investigated morphology, physiology, and immunohistochemistry of interneurons arborizing in the primary auditory center of the honeybee ( Apis mellifera ). We identified major interneuron types, named DL-Int-1, DL-Int-2, and bilateral DL-dSEG-LP, that responded with different spiking patterns to vibration pulses applied to the antennae. Experimental and computational analyses suggest that inhibitory connection plays a role in encoding and processing the duration of vibration pulse trains in the primary auditory center of the honeybee. SIGNIFICANCE STATEMENT The waggle dance represents a form of symbolic communication used by honeybees to convey the location of food sources via species-specific sound. The brain mechanisms used to decipher this symbolic information are unknown. We examined interneurons in the honeybee primary auditory center and identified different neuron types with specific properties. The results of our computational analyses suggest that inhibitory connection plays a role in encoding waggle dance signals. Our results are critical for understanding how the honeybee deciphers information from the sound produced by the waggle dance and provide new insights regarding how common neural mechanisms are used by different species to achieve communication. Copyright © 2017 the authors 0270-6474/17/3710624-12$15.00/0.

Achieving unequal error protection with convolutional codes

NASA Technical Reports Server (NTRS)

Mills, D. G.; Costello, D. J., Jr.; Palazzo, R., Jr.

1994-01-01

This paper examines the unequal error protection capabilities of convolutional codes. Both time-invariant and periodically time-varying convolutional encoders are examined. The effective free distance vector is defined and is shown to be useful in determining the unequal error protection (UEP) capabilities of convolutional codes. A modified transfer function is used to determine an upper bound on the bit error probabilities for individual input bit positions in a convolutional encoder. The bound is heavily dependent on the individual effective free distance of the input bit position. A bound relating two individual effective free distances is presented. The bound is a useful tool in determining the maximum possible disparity in individual effective free distances of encoders of specified rate and memory distribution. The unequal error protection capabilities of convolutional encoders of several rates and memory distributions are determined and discussed.

A neural theory of visual attention and short-term memory (NTVA).

PubMed

Bundesen, Claus; Habekost, Thomas; Kyllingsbæk, Søren

2011-05-01

The neural theory of visual attention and short-term memory (NTVA) proposed by Bundesen, Habekost, and Kyllingsbæk (2005) is reviewed. In NTVA, filtering (selection of objects) changes the number of cortical neurons in which an object is represented so that this number increases with the behavioural importance of the object. Another mechanism of selection, pigeonholing (selection of features), scales the level of activation in neurons coding for a particular feature. By these mechanisms, behaviourally important objects and features are likely to win the competition to become encoded into visual short-term memory (VSTM). The VSTM system is conceived as a feedback mechanism that sustains activity in the neurons that have won the attentional competition. NTVA accounts both for a wide range of attentional effects in human performance (reaction times and error rates) and a wide range of effects observed in firing rates of single cells in the primate visual system. Copyright © 2010 Elsevier Ltd. All rights reserved.

Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia.

PubMed

Janes, Daniel E; Organ, Christopher L; Stiglec, Rami; O'Meally, Denis; Sarre, Stephen D; Georges, Arthur; Graves, Jennifer A M; Valenzuela, Nicole; Literman, Robert A; Rutherford, Kim; Gemmell, Neil; Iverson, John B; Tamplin, Jeffrey W; Edwards, Scott V; Ezaz, Tariq

2014-12-01

In reptiles, sex-determining mechanisms have evolved repeatedly and reversibly between genotypic and temperature-dependent sex determination. The gene Dmrt1 directs male determination in chicken (and presumably other birds), and regulates sex differentiation in animals as distantly related as fruit flies, nematodes and humans. Here, we show a consistent molecular difference in Dmrt1 between reptiles with genotypic and temperature-dependent sex determination. Among 34 non-avian reptiles, a convergently evolved pair of amino acids encoded by sequence within exon 2 near the DM-binding domain of Dmrt1 distinguishes species with either type of sex determination. We suggest that this amino acid shift accompanied the evolution of genotypic sex determination from an ancestral condition of temperature-dependent sex determination at least three times among reptiles, as evident in turtles, birds and squamates. This novel hypothesis describes the evolution of sex-determining mechanisms as turnover events accompanied by one or two small mutations. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks

PubMed Central

Behar, Marcelo; Dohlman, Henrik G.; Elston, Timothy C.

2007-01-01

Intracellular signaling pathways that share common components often elicit distinct physiological responses. In most cases, the biochemical mechanisms responsible for this signal specificity remain poorly understood. Protein scaffolds and cross-inhibition have been proposed as strategies to prevent unwanted cross-talk. Here, we report a mechanism for signal specificity termed “kinetic insulation.” In this approach signals are selectively transmitted through the appropriate pathway based on their temporal profile. In particular, we demonstrate how pathway architectures downstream of a common component can be designed to efficiently separate transient signals from signals that increase slowly over time. Furthermore, we demonstrate that upstream signaling proteins can generate the appropriate input to the common pathway component regardless of the temporal profile of the external stimulus. Our results suggest that multilevel signaling cascades may have evolved to modulate the temporal profile of pathway activity so that stimulus information can be efficiently encoded and transmitted while ensuring signal specificity. PMID:17913886

Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia

PubMed Central

Janes, Daniel E.; Organ, Christopher L.; Stiglec, Rami; O'Meally, Denis; Sarre, Stephen D.; Georges, Arthur; Graves, Jennifer A. M.; Valenzuela, Nicole; Literman, Robert A.; Rutherford, Kim; Gemmell, Neil; Iverson, John B.; Tamplin, Jeffrey W.; Edwards, Scott V.; Ezaz, Tariq

2014-01-01

In reptiles, sex-determining mechanisms have evolved repeatedly and reversibly between genotypic and temperature-dependent sex determination. The gene Dmrt1 directs male determination in chicken (and presumably other birds), and regulates sex differentiation in animals as distantly related as fruit flies, nematodes and humans. Here, we show a consistent molecular difference in Dmrt1 between reptiles with genotypic and temperature-dependent sex determination. Among 34 non-avian reptiles, a convergently evolved pair of amino acids encoded by sequence within exon 2 near the DM-binding domain of Dmrt1 distinguishes species with either type of sex determination. We suggest that this amino acid shift accompanied the evolution of genotypic sex determination from an ancestral condition of temperature-dependent sex determination at least three times among reptiles, as evident in turtles, birds and squamates. This novel hypothesis describes the evolution of sex-determining mechanisms as turnover events accompanied by one or two small mutations. PMID:25540158

Molecular and physiological mechanisms of plant tolerance to toxic metals

USDA-ARS?s Scientific Manuscript database

Plants have evolved a myriad of adaptive mechanisms based on a number of genes to deal with the different toxic metals they encounter in the soils worldwide. These genes encode a range of different metal and organic compound transporters and enzyme pathways for the synthesis of metal detoxifying lig...

Free Recall Test Experience Potentiates Strategy-Driven Effects of Value on Memory

ERIC Educational Resources Information Center

Cohen, Michael S.; Rissman, Jesse; Hovhannisyan, Mariam; Castel, Alan D.; Knowlton, Barbara J.

2017-01-01

People tend to show better memory for information that is deemed valuable or important. By one mechanism, individuals selectively engage deeper, semantic encoding strategies for high value items (Cohen, Rissman, Suthana, Castel, & Knowlton, 2014). By another mechanism, information paired with value or reward is automatically strengthened in…

The Coding Question.

PubMed

Gallistel, C R

2017-07-01

Recent electrophysiological results imply that the duration of the stimulus onset asynchrony in eyeblink conditioning is encoded by a mechanism intrinsic to the cerebellar Purkinje cell. This raises the general question - how is quantitative information (durations, distances, rates, probabilities, amounts, etc.) transmitted by spike trains and encoded into engrams? The usual assumption is that information is transmitted by firing rates. However, rate codes are energetically inefficient and computationally awkward. A combinatorial code is more plausible. If the engram consists of altered synaptic conductances (the usual assumption), then we must ask how numbers may be written to synapses. It is much easier to formulate a coding hypothesis if the engram is realized by a cell-intrinsic molecular mechanism. Copyright © 2017 Elsevier Ltd. All rights reserved.

Time course of word production in fast and slow speakers: a high density ERP topographic study.

PubMed

Laganaro, Marina; Valente, Andrea; Perret, Cyril

2012-02-15

The transformation of an abstract concept into an articulated word is achieved through a series of encoding processes, which time course has been repeatedly investigated in the psycholinguistic and neuroimaging literature on single word production. The estimates of the time course issued from previous investigations represent the timing of process duration for mean processing speed: as production speed varies significantly across speakers, a crucial question is how the timing of encoding processing varies with speed. Here we investigated whether between-subjects variability in the speed of speech production is distributed along all encoding processes or if it is accounted for by a specific processing stage. We analysed event-related electroencephalographical (ERP) correlates during overt picture naming in 45 subjects divided into three speed subgroups according to their production latencies. Production speed modulated waveform amplitudes in the time window ranging from about 200 to 350 ms after picture presentation and the duration of a stable electrophysiological spatial configuration in the same time period. The remaining time windows from picture onset to 200 ms before articulation were unaffected by speed. By contrast, the manipulation of a psycholinguistic variable, word age-of-acquisition, modulated ERPs in all speed subgroups in a different and later time period, starting at around 400 ms after picture presentation, associated with phonological encoding processes. These results indicate that the between-subject variability in the speed of single word production is principally accounted for by the timing of a stable electrophysiological activity in the 200-350 ms time period, presumably associated with lexical selection. Copyright © 2011 Elsevier Inc. All rights reserved.

Applicability of the Compensatory Encoding Model in Foreign Language Reading: An Investigation with Chinese College English Language Learners

PubMed Central

Han, Feifei

2017-01-01

While some first language (L1) reading models suggest that inefficient word recognition and small working memory tend to inhibit higher-level comprehension processes; the Compensatory Encoding Model maintains that slow word recognition and small working memory do not normally hinder reading comprehension, as readers are able to operate metacognitive strategies to compensate for inefficient word recognition and working memory limitation as long as readers process a reading task without time constraint. Although empirical evidence is accumulated for support of the Compensatory Encoding Model in L1 reading, there is lack of research for testing of the Compensatory Encoding Model in foreign language (FL) reading. This research empirically tested the Compensatory Encoding Model in English reading among Chinese college English language learners (ELLs). Two studies were conducted. Study one focused on testing whether reading condition varying time affects the relationship between word recognition, working memory, and reading comprehension. Students were tested on a computerized English word recognition test, a computerized Operation Span task, and reading comprehension in time constraint and non-time constraint reading. The correlation and regression analyses showed that the strength of association was much stronger between word recognition, working memory, and reading comprehension in time constraint than that in non-time constraint reading condition. Study two examined whether FL readers were able to operate metacognitive reading strategies as a compensatory way of reading comprehension for inefficient word recognition and working memory limitation in non-time constraint reading. The participants were tested on the same computerized English word recognition test and Operation Span test. They were required to think aloud while reading and to complete the comprehension questions. The think-aloud protocols were coded for concurrent use of reading strategies, classified into language-oriented strategies, content-oriented strategies, re-reading, pausing, and meta-comment. The correlation analyses showed that while word recognition and working memory were only significantly related to frequency of language-oriented strategies, re-reading, and pausing, but not with reading comprehension. Jointly viewed, the results of the two studies, complimenting each other, supported the applicability of the Compensatory Encoding Model in FL reading with Chinese college ELLs. PMID:28522984

Applicability of the Compensatory Encoding Model in Foreign Language Reading: An Investigation with Chinese College English Language Learners.

PubMed

Han, Feifei

2017-01-01

While some first language (L1) reading models suggest that inefficient word recognition and small working memory tend to inhibit higher-level comprehension processes; the Compensatory Encoding Model maintains that slow word recognition and small working memory do not normally hinder reading comprehension, as readers are able to operate metacognitive strategies to compensate for inefficient word recognition and working memory limitation as long as readers process a reading task without time constraint. Although empirical evidence is accumulated for support of the Compensatory Encoding Model in L1 reading, there is lack of research for testing of the Compensatory Encoding Model in foreign language (FL) reading. This research empirically tested the Compensatory Encoding Model in English reading among Chinese college English language learners (ELLs). Two studies were conducted. Study one focused on testing whether reading condition varying time affects the relationship between word recognition, working memory, and reading comprehension. Students were tested on a computerized English word recognition test, a computerized Operation Span task, and reading comprehension in time constraint and non-time constraint reading. The correlation and regression analyses showed that the strength of association was much stronger between word recognition, working memory, and reading comprehension in time constraint than that in non-time constraint reading condition. Study two examined whether FL readers were able to operate metacognitive reading strategies as a compensatory way of reading comprehension for inefficient word recognition and working memory limitation in non-time constraint reading. The participants were tested on the same computerized English word recognition test and Operation Span test. They were required to think aloud while reading and to complete the comprehension questions. The think-aloud protocols were coded for concurrent use of reading strategies, classified into language-oriented strategies, content-oriented strategies, re-reading, pausing, and meta-comment. The correlation analyses showed that while word recognition and working memory were only significantly related to frequency of language-oriented strategies, re-reading, and pausing, but not with reading comprehension. Jointly viewed, the results of the two studies, complimenting each other, supported the applicability of the Compensatory Encoding Model in FL reading with Chinese college ELLs.

Data encoding based on the shape of the ferroelectric domains produced by a scanning probe microscopy tip

DOE PAGES

Ievlev, Anton; Kalinin, Sergei V.

2015-05-28

Ferroelectric materials are broadly considered for information storage due to extremely high storage and information processing densities they enable. To date, ferroelectric based data storage has invariably relied on formation of cylindrical domains, allowing for binary information encoding. Here we demonstrate and explore the potential of high-density encoding based on domain morphology. We explore the domain morphogenesis during the tip-induced polarization switching by sequences of positive and negative pulses in a lithium niobate single-crystal and demonstrate the principal of information coding by shape and size of the domains. We applied cross-correlation and neural network approaches for recognition of the switchingmore » sequence by the shape of the resulting domains and establish optimal parameters for domain shape recognition. These studies both provide insight into the highly non-trivial mechanism of domain switching and potentially establish a new paradigm for multilevel information storage and content retrieval memories. Furthermore, this approach opens a pathway to exploration of domain switching mechanisms via shape analysis.« less

Microelectronics Instrument Products Shock and Vibration Electro-optics: C-Qualification Test Report

NASA Technical Reports Server (NTRS)

1994-01-01

In this test report all measurements made during testing are recorded in ATP 20049 DS data sheets and are included in the log. The motor/encoder (henceforth referred to as the UUT) test sequence began with a baseline functional evaluation, which demonstrated that the motor satisfied the operating torque, cogging torque, winding resistance, and mechanical requirements of SOW. In addition, the encoder electrical requirements were verified, as well as the alignment of the encoder outputs relative tc, the motor shaft position. There were no discrepancies observed in this portion of the test. The UUT was then exposed to a number of environments, including thermal vacuum, thermal cycling, random and sine vibration, and mechanical shock. During the thermal environments, the performance of the UUT under load was verified at specified points in the cycles, as described in ATP 20049. In addition, the UUT was bench tested between the two thermal environments. No anomalies were observed during the thermal tests. The load attachment method was subsequently corrected, and vibration of S/N 0002 began while 0003 was being repaired.

Evaluation of GOES encoder lamps

NASA Technical Reports Server (NTRS)

Viehmann, W.; Helmold, N.

1983-01-01

Aging characteristics and life expectancies of flight quality, tungsten filament, encoder lamps are similar to those of 'commercial' grade gas filled lamps of similar construction, filament material and filament temperature. The aging and final failure by filament burnout are caused by single crystal growth over large portions of the filament with the concomitant development of facets and notches resulting in reduction of cross section and mechanical weakening of the filament. The life expectancy of presently produced lamps is about one year at their nominal operating voltage of five volts dc. At 4.5 volts, it is about two years. These life times are considerably shorter, and the degradation rates of lamp current and light flux are considerably higher, than were observed in the laboratory and in orbit on lamps of the same type manufactured more than a decade ago. It is speculated that the filaments of these earlier lamps contained a crystallization retarding dopant, possibly thorium oxide. To obtain the desired life expectancy of or = to four years in present lamps, operating voltages of or = to four volts dc would be required.

Kid cleaves specific mRNAs at UUACU sites to rescue the copy number of plasmid R1

PubMed Central

Pimentel, Belén; Madine, Mark A; de la Cueva-Méndez, Guillermo

2005-01-01

Stability and copy number of extra-chromosomal elements are tightly regulated in prokaryotes and eukaryotes. Toxin Kid and antitoxin Kis are the components of the parD stability system of prokaryotic plasmid R1 and they can also function in eukaryotes. In bacteria, Kid was thought to become active only in cells that lose plasmid R1 and to cleave exclusively host mRNAs at UA(A/C/U) trinucleotide sites to eliminate plasmid-free cells. Instead, we demonstrate here that Kid becomes active in plasmid-containing cells when plasmid copy number decreases, cleaving not only host- but also a specific plasmid-encoded mRNA at the longer and more specific target sequence UUACU. This specific cleavage by Kid inhibits bacterial growth and, at the same time, helps to restore the plasmid copy number. Kid targets a plasmid RNA that encodes a repressor of the synthesis of an R1 replication protein, resulting in increased plasmid DNA replication. This mechanism resembles that employed by some human herpesviruses to regulate viral amplification during infection. PMID:16163387

Mutations in ORC1, encoding the largest subunit of the origin recognition complex, cause microcephalic primordial dwarfism resembling Meier-Gorlin syndrome.

PubMed

Bicknell, Louise S; Walker, Sarah; Klingseisen, Anna; Stiff, Tom; Leitch, Andrea; Kerzendorfer, Claudia; Martin, Carol-Anne; Yeyati, Patricia; Al Sanna, Nouriya; Bober, Michael; Johnson, Diana; Wise, Carol; Jackson, Andrew P; O'Driscoll, Mark; Jeggo, Penny A

2011-02-27

Studies into disorders of extreme growth failure (for example, Seckel syndrome and Majewski osteodysplastic primordial dwarfism type II) have implicated fundamental cellular processes of DNA damage response signaling and centrosome function in the regulation of human growth. Here we report that mutations in ORC1, encoding a subunit of the origin recognition complex, cause microcephalic primordial dwarfism resembling Meier-Gorlin syndrome. We establish that these mutations disrupt known ORC1 functions including pre-replicative complex formation and origin activation. ORC1 deficiency perturbs S-phase entry and S-phase progression. Additionally, we show that Orc1 depletion in zebrafish is sufficient to markedly reduce body size during rapid embryonic growth. Our data suggest a model in which ORC1 mutations impair replication licensing, slowing cell cycle progression and consequently impeding growth during development, particularly at times of rapid proliferation. These findings establish a novel mechanism for the pathogenesis of microcephalic dwarfism and show a surprising but important developmental impact of impaired origin licensing.

Genetic code mutations: the breaking of a three billion year invariance.

PubMed

Mat, Wai-Kin; Xue, Hong; Wong, J Tze-Fei

2010-08-20

The genetic code has been unchanging for some three billion years in its canonical ensemble of encoded amino acids, as indicated by the universal adoption of this ensemble by all known organisms. Code mutations beginning with the encoding of 4-fluoro-Trp by Bacillus subtilis, initially replacing and eventually displacing Trp from the ensemble, first revealed the intrinsic mutability of the code. This has since been confirmed by a spectrum of other experimental code alterations in both prokaryotes and eukaryotes. To shed light on the experimental conversion of a rigidly invariant code to a mutating code, the present study examined code mutations determining the propagation of Bacillus subtilis on Trp and 4-, 5- and 6-fluoro-tryptophans. The results obtained with the mutants with respect to cross-inhibitions between the different indole amino acids, and the growth effects of individual nutrient withdrawals rendering essential their biosynthetic pathways, suggested that oligogenic barriers comprising sensitive proteins which malfunction with amino acid analogues provide effective mechanisms for preserving the invariance of the code through immemorial time, and mutations of these barriers open up the code to continuous change.

Tomographic Aperture-Encoded Particle Tracking Velocimetry: A New Approach to Volumetric PIV

NASA Astrophysics Data System (ADS)

Troolin, Dan; Boomsma, Aaron; Lai, Wing; Pothos, Stamatios; Fluid Mechanics Research Instruments Team

2016-11-01

Volumetric velocity fields are useful in a wide variety of fluid mechanics applications. Several types of three-dimensional imaging methods have been used in the past to varying degrees of success, for example, 3D PTV (Maas et al., 1993), DDPIV (Peireira et al., 2006), Tomographic PIV (Elsinga, 2006), and V3V (Troolin and Longmire, 2009), among others. Each of these techniques has shown advantages and disadvantages in different areas. With the advent of higher resolution and lower noise cameras with higher stability levels, new techniques are emerging that combine the advantages of the existing techniques. This talk describes a new technique called Tomographic Aperture-Encoded Particle Tracking Velocimetry (TAPTV), in which segmented triangulation and diameter tolerance are used to achieve three-dimensional particle tracking with extremely high particle densities (on the order of ppp = 0.2 or higher) without the drawbacks normally associated with ghost particles (for example in TomoPIV). The results are highly spatially-resolved data with very fast processing times. A detailed explanation of the technique as well as plots, movies, and experimental considerations will be discussed.

Spatial organization shapes the turnover of a bacterial transcriptome

PubMed Central

Moffitt, Jeffrey R; Pandey, Shristi; Boettiger, Alistair N; Wang, Siyuan; Zhuang, Xiaowei

2016-01-01

Spatial organization of the transcriptome has emerged as a powerful means for regulating the post-transcriptional fate of RNA in eukaryotes; however, whether prokaryotes use RNA spatial organization as a mechanism for post-transcriptional regulation remains unclear. Here we used super-resolution microscopy to image the E. coli transcriptome and observed a genome-wide spatial organization of RNA: mRNAs encoding inner-membrane proteins are enriched at the membrane, whereas mRNAs encoding outer-membrane, cytoplasmic and periplasmic proteins are distributed throughout the cytoplasm. Membrane enrichment is caused by co-translational insertion of signal peptides recognized by the signal-recognition particle. Time-resolved RNA-sequencing revealed that degradation rates of inner-membrane-protein mRNAs are on average greater that those of the other mRNAs and that this selective destabilization of inner-membrane-protein mRNAs is abolished by dissociating the RNA degradosome from the membrane. Together, these results demonstrate that the bacterial transcriptome is spatially organized and suggest that this organization shapes the post-transcriptional dynamics of mRNAs. DOI: http://dx.doi.org/10.7554/eLife.13065.001 PMID:27198188

Neural activity in the hippocampus and perirhinal cortex during encoding is associated with the durability of episodic memory.

PubMed

Carr, Valerie A; Viskontas, Indre V; Engel, Stephen A; Knowlton, Barbara J

2010-11-01

Studies examining medial temporal lobe (MTL) involvement in memory formation typically assess memory performance after a single, short delay. Thus, the relationship between MTL encoding activity and memory durability over time remains poorly characterized. To explore this relationship, we scanned participants using high-resolution functional imaging of the MTL as they encoded object pairs; using the remember/know paradigm, we then assessed memory performance for studied items both 10 min and 1 week later. Encoding trials were classified as either subsequently recollected across both delays, transiently recollected (i.e., recollected at 10 min but not after 1 week), consistently familiar, or consistently forgotten. Activity in perirhinal cortex (PRC) and a hippocampal subfield comprising the dentate gyrus and CA fields 2 and 3 reflected successful encoding only when items were recollected consistently across both delays. Furthermore, in PRC, encoding activity for items that later were consistently recollected was significantly greater than that for transiently recollected and consistently familiar items. Parahippocampal cortex, in contrast, showed a subsequent memory effect during encoding of items that were recollected after 10 min, regardless of whether they also were recollected after 1 week. These data suggest that MTL subfields contribute uniquely to the formation of memories that endure over time, and highlight a role for PRC in supporting subsequent durable episodic recollection.

A tolerance gene for prenylated flavonoid encodes a 26S proteasome regulatory subunit in Sophora flavescens.

PubMed

Shitan, Nobukazu; Kamimoto, Yoshihisa; Minami, Shota; Kubo, Mizuki; Ito, Kozue; Moriyasu, Masataka; Yazaki, Kazufumi

2011-01-01

Yeast functional screening with a Sophora flavescens cDNA library was performed to identify the genes involved in the tolerant mechanism to the self-producing prenylated flavonoid sophoraflavanone G (SFG). One cDNA, which conferred SFG tolerance, encoded a regulatory particle triple-A ATPase 2 (SfRPT2), a member of the 26S proteasome subunit. The yeast transformant of SfRPT2 showed reduced SFG accumulation in the cells.

Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments.

PubMed

Scott, Kathleen M; Williams, John; Porter, Cody M B; Russel, Sydney; Harmer, Tara L; Paul, John H; Antonen, Kirsten M; Bridges, Megan K; Camper, Gary J; Campla, Christie K; Casella, Leila G; Chase, Eva; Conrad, James W; Cruz, Mercedez C; Dunlap, Darren S; Duran, Laura; Fahsbender, Elizabeth M; Goldsmith, Dawn B; Keeley, Ryan F; Kondoff, Matthew R; Kussy, Breanna I; Lane, Marannda K; Lawler, Stephanie; Leigh, Brittany A; Lewis, Courtney; Lostal, Lygia M; Marking, Devon; Mancera, Paola A; McClenthan, Evan C; McIntyre, Emily A; Mine, Jessica A; Modi, Swapnil; Moore, Brittney D; Morgan, William A; Nelson, Kaleigh M; Nguyen, Kimmy N; Ogburn, Nicholas; Parrino, David G; Pedapudi, Anangamanjari D; Pelham, Rebecca P; Preece, Amanda M; Rampersad, Elizabeth A; Richardson, Jason C; Rodgers, Christina M; Schaffer, Brent L; Sheridan, Nancy E; Solone, Michael R; Staley, Zachery R; Tabuchi, Maki; Waide, Ramond J; Wanjugi, Pauline W; Young, Suzanne; Clum, Alicia; Daum, Chris; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos; Mikhailova, Natalia; Palaniappan, Krishnaveni; Pillay, Manoj; Reddy, T B K; Shapiro, Nicole; Stamatis, Dimitrios; Varghese, Neha; Woyke, Tanja; Boden, Rich; Freyermuth, Sharyn K; Kerfeld, Cheryl A

2018-03-09

Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1-3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb 3 cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba 3 -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO 2 concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Integration of light and circadian signals that regulate chloroplast transcription by a nuclear-encoded sigma factor.

PubMed

Belbin, Fiona E; Noordally, Zeenat B; Wetherill, Sarah J; Atkins, Kelly A; Franklin, Keara A; Dodd, Antony N

2017-01-01

We investigated the signalling pathways that regulate chloroplast transcription in response to environmental signals. One mechanism controlling plastid transcription involves nuclear-encoded sigma subunits of plastid-encoded plastid RNA polymerase. Transcripts encoding the sigma factor SIG5 are regulated by light and the circadian clock. However, the extent to which a chloroplast target of SIG5 is regulated by light-induced changes in SIG5 expression is unknown. Moreover, the photoreceptor signalling pathways underlying the circadian regulation of chloroplast transcription by SIG5 are unidentified. We monitored the regulation of chloroplast transcription in photoreceptor and sigma factor mutants under controlled light regimes in Arabidopsis thaliana. We established that a chloroplast transcriptional response to light intensity was mediated by SIG5; a chloroplast transcriptional response to the relative proportions of red and far red light was regulated by SIG5 through phytochrome and photosynthetic signals; and the circadian regulation of chloroplast transcription by SIG5 was predominantly dependent on blue light and cryptochrome. Our experiments reveal the extensive integration of signals concerning the light environment by a single sigma factor to regulate chloroplast transcription. This may originate from an evolutionarily ancient mechanism that protects photosynthetic bacteria from high light stress, which subsequently became integrated with higher plant phototransduction networks. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Watching a Black Hole Feed: Sgr A* in the X-ray and Infrared

NASA Astrophysics Data System (ADS)

Fazio, Giovanni

2017-09-01

Black hole accretion drives extreme astrophysical phenomena in the universe. Sgr A*, the nearest supermassive black hole, is highly variable, but sparse data and short observations preclude determination of its emission physics. Despite enormous advances in accretion models in recent years, even the radiation mechanisms of Sgr A* are still unknown. Because the needed information is encoded in the time-dependent relationship between X-ray and IR emission, we propose four new epochs of Chandra monitoring with Spitzer at 4.5 microns. This will double the exposure time for X-ray flares where the NIR state is known, moving us out of the realm of small-number statistics and enabling diagnostics of the true X-ray/IR relationship. This will be the final chance for Chandra+Spitzer observations.

Disruption of the psbA gene by the copy correction mechanism reveals that the expression of plastid-encoded genes is regulated by photosynthesis activity.

PubMed

Khan, Muhammad Sarwar; Hameed, Waqar; Nozoe, Mikio; Shiina, Takashi

2007-05-01

The functional analysis of genes encoded by the chloroplast genome of tobacco by reverse genetics is routine. Nevertheless, for a small number of genes their deletion generates heteroplasmic genotypes, complicating their analysis. There is thus the need for additional strategies to develop deletion mutants for these genes. We have developed a homologous copy correction-based strategy for deleting/mutating genes encoded on the chloroplast genome. This system was used to produce psbA knockouts. The resulting plants are homoplasmic and lack photosystem II (PSII) activity. Further, the deletion mutants exhibit a distinct phenotype; young leaves are green, whereas older leaves are bleached, irrespective of light conditions. This suggests that senescence is promoted by the absence of psbA. Analysis of the transcript levels indicates that NEP (nuclear-encoded plastid RNA polymerase)-dependent plastid genes are up regulated in the psbA deletion mutants, whereas the bleached leaves retain plastid-encoded plastid RNA polymerase activity. Hence, the expression of NEP-dependent plastid genes may be regulated by photosynthesis, either directly or indirectly.

Ultrashort Phenomena in Biochemistry and Biological Signaling

NASA Astrophysics Data System (ADS)

Splinter, Robert

2014-11-01

In biological phenomena there are indications that within the long pulse-length of the action potential on millisecond scale, there is additional ultrashort perturbation encoding that provides the brain with detailed information about the origin (location) and physiological characteristics. The objective is to identify the mechanism-of-action providing the potential for encoding in biological signal propagation. The actual molecular processes involved in the initiation of the action potential have been identified to be in the femtosecond and pico-second scale. The depolarization process of the cellular membrane itself, leading to the onset of the actionpotential that is transmitted to the brain, however is in the millisecond timeframe. One example of the femtosecond chemical interaction is the photoresponse of bacteriorhodopsin. No clear indication for the spatial encoding has so far been verified. Further research will be required on a cellular signal analysis level to confirm or deny the spatial and physiological encoding in the signal wave-trains of intercellular communications and sensory stimuli. The pathological encoding process for cardiac depolarization is however very pronounced and validated, however this electro-chemical process is in the millisecond amplitude and frequency modulation spectrum.

Categorization and decision-making in a neurobiologically plausible spiking network using a STDP-like learning rule.

PubMed

Beyeler, Michael; Dutt, Nikil D; Krichmar, Jeffrey L

2013-12-01

Understanding how the human brain is able to efficiently perceive and understand a visual scene is still a field of ongoing research. Although many studies have focused on the design and optimization of neural networks to solve visual recognition tasks, most of them either lack neurobiologically plausible learning rules or decision-making processes. Here we present a large-scale model of a hierarchical spiking neural network (SNN) that integrates a low-level memory encoding mechanism with a higher-level decision process to perform a visual classification task in real-time. The model consists of Izhikevich neurons and conductance-based synapses for realistic approximation of neuronal dynamics, a spike-timing-dependent plasticity (STDP) synaptic learning rule with additional synaptic dynamics for memory encoding, and an accumulator model for memory retrieval and categorization. The full network, which comprised 71,026 neurons and approximately 133 million synapses, ran in real-time on a single off-the-shelf graphics processing unit (GPU). The network was constructed on a publicly available SNN simulator that supports general-purpose neuromorphic computer chips. The network achieved 92% correct classifications on MNIST in 100 rounds of random sub-sampling, which is comparable to other SNN approaches and provides a conservative and reliable performance metric. Additionally, the model correctly predicted reaction times from psychophysical experiments. Because of the scalability of the approach and its neurobiological fidelity, the current model can be extended to an efficient neuromorphic implementation that supports more generalized object recognition and decision-making architectures found in the brain. Copyright © 2013 Elsevier Ltd. All rights reserved.

Minimal Increase Network Coding for Dynamic Networks.

PubMed

Zhang, Guoyin; Fan, Xu; Wu, Yanxia

2016-01-01

Because of the mobility, computing power and changeable topology of dynamic networks, it is difficult for random linear network coding (RLNC) in static networks to satisfy the requirements of dynamic networks. To alleviate this problem, a minimal increase network coding (MINC) algorithm is proposed. By identifying the nonzero elements of an encoding vector, it selects blocks to be encoded on the basis of relationship between the nonzero elements that the controls changes in the degrees of the blocks; then, the encoding time is shortened in a dynamic network. The results of simulations show that, compared with existing encoding algorithms, the MINC algorithm provides reduced computational complexity of encoding and an increased probability of delivery.

Minimal Increase Network Coding for Dynamic Networks

PubMed Central

Wu, Yanxia

2016-01-01

Because of the mobility, computing power and changeable topology of dynamic networks, it is difficult for random linear network coding (RLNC) in static networks to satisfy the requirements of dynamic networks. To alleviate this problem, a minimal increase network coding (MINC) algorithm is proposed. By identifying the nonzero elements of an encoding vector, it selects blocks to be encoded on the basis of relationship between the nonzero elements that the controls changes in the degrees of the blocks; then, the encoding time is shortened in a dynamic network. The results of simulations show that, compared with existing encoding algorithms, the MINC algorithm provides reduced computational complexity of encoding and an increased probability of delivery. PMID:26867211

Where to start? Bottom-up attention improves working memory by determining encoding order.

PubMed

Ravizza, Susan M; Uitvlugt, Mitchell G; Hazeltine, Eliot

2016-12-01

The present study aimed to characterize the mechanism by which working memory is enhanced for items that capture attention because of their novelty or saliency-that is, via bottom-up attention. The first experiment replicated previous research by corroborating that bottom-up attention directed to an item is sufficient for enhancing working memory and, moreover, generalized the effect to the domain of verbal working memory. The subsequent 3 experiments sought to determine how bottom-up attention affects working memory. We considered 2 hypotheses: (1) Bottom-up attention enhances the encoded representation of the stimulus, similar to how voluntary attention functions, or (2) It affects the order of encoding by shifting priority onto the attended stimulus. By manipulating how stimuli were presented (simultaneous/sequential display) and whether the cue predicted the tested items, we found evidence that bottom-up attention improves working memory performance via the order of encoding hypothesis. This finding was observed across change detection and free recall paradigms. In contrast, voluntary attention improved working memory regardless of encoding order and showed greater effects on working memory. We conclude that when multiple information sources compete, bottom-up attention prioritizes the location at which encoding should begin. When encoding order is set, bottom-up attention has little or no benefit to working memory. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Power-rate-distortion analysis for wireless video communication under energy constraint

NASA Astrophysics Data System (ADS)

He, Zhihai; Liang, Yongfang; Ahmad, Ishfaq

2004-01-01

In video coding and streaming over wireless communication network, the power-demanding video encoding operates on the mobile devices with limited energy supply. To analyze, control, and optimize the rate-distortion (R-D) behavior of the wireless video communication system under the energy constraint, we need to develop a power-rate-distortion (P-R-D) analysis framework, which extends the traditional R-D analysis by including another dimension, the power consumption. Specifically, in this paper, we analyze the encoding mechanism of typical video encoding systems and develop a parametric video encoding architecture which is fully scalable in computational complexity. Using dynamic voltage scaling (DVS), a hardware technology recently developed in CMOS circuits design, the complexity scalability can be translated into the power consumption scalability of the video encoder. We investigate the rate-distortion behaviors of the complexity control parameters and establish an analytic framework to explore the P-R-D behavior of the video encoding system. Both theoretically and experimentally, we show that, using this P-R-D model, the encoding system is able to automatically adjust its complexity control parameters to match the available energy supply of the mobile device while maximizing the picture quality. The P-R-D model provides a theoretical guideline for system design and performance optimization in wireless video communication under energy constraint, especially over the wireless video sensor network.

A contourlet transform based algorithm for real-time video encoding

NASA Astrophysics Data System (ADS)

Katsigiannis, Stamos; Papaioannou, Georgios; Maroulis, Dimitris

2012-06-01

In recent years, real-time video communication over the internet has been widely utilized for applications like video conferencing. Streaming live video over heterogeneous IP networks, including wireless networks, requires video coding algorithms that can support various levels of quality in order to adapt to the network end-to-end bandwidth and transmitter/receiver resources. In this work, a scalable video coding and compression algorithm based on the Contourlet Transform is proposed. The algorithm allows for multiple levels of detail, without re-encoding the video frames, by just dropping the encoded information referring to higher resolution than needed. Compression is achieved by means of lossy and lossless methods, as well as variable bit rate encoding schemes. Furthermore, due to the transformation utilized, it does not suffer from blocking artifacts that occur with many widely adopted compression algorithms. Another highly advantageous characteristic of the algorithm is the suppression of noise induced by low-quality sensors usually encountered in web-cameras, due to the manipulation of the transform coefficients at the compression stage. The proposed algorithm is designed to introduce minimal coding delay, thus achieving real-time performance. Performance is enhanced by utilizing the vast computational capabilities of modern GPUs, providing satisfactory encoding and decoding times at relatively low cost. These characteristics make this method suitable for applications like video-conferencing that demand real-time performance, along with the highest visual quality possible for each user. Through the presented performance and quality evaluation of the algorithm, experimental results show that the proposed algorithm achieves better or comparable visual quality relative to other compression and encoding methods tested, while maintaining a satisfactory compression ratio. Especially at low bitrates, it provides more human-eye friendly images compared to algorithms utilizing block-based coding, like the MPEG family, as it introduces fuzziness and blurring instead of artificial block artifacts.

Transcription patterns of genes encoding four metallothionein homologs in Daphnia pulex exposed to copper and cadmium are time- and homolog- dependent

PubMed Central

Asselman, Jana; Shaw, Joseph R.; Glaholt, Stephen P.; Colbourne, John K.; De Schamphelaere, Karel AC.

2013-01-01

Metallothioneins are proteins that play an essential role in metal homeostasis and detoxification in nearly all organisms studied to date. Yet discrepancies between outcomes of chronic and acute exposure experiments hamper the understanding of the regulatory mechanisms of their isoforms following metal exposure. Here, we investigated transcriptional differences among four identified homologs (mt1–mt4) in Daphnia pulex exposed across time to copper and cadmium relative to a control. Transcriptional upregulation of mt1 and mt3 was detected on day four following exposure to cadmium, whereas that of mt2 and mt4 was detected on day two and day eight following exposure to copper. These results confirm temporal and metal-specific differences in the transcriptional induction of genes encoding metallothionein homologs upon metal exposure which should be considered in ecotoxicological monitoring programs of metal-contaminated water bodies. Indeed, the mRNA expression patterns observed here illustrate the complex regulatory system associated with metallothioneins, as these patterns are not only dependent on the metal, but also on exposure time and the homolog studied. Further phylogenetic analysis and analysis of regulatory elements in upstream promoter regions revealed a high degree of similarity between metallothionein genes of Daphnia pulex and Daphnia magna, a species belonging to the same genus. These findings, combined with a limited amount of available expression data for D. magna metallothionein genes, tentatively suggest a potential generalization of the metallothionein response system between these Daphnia species. PMID:24113165

Total sleep deprivation does not significantly degrade semantic encoding.

PubMed

Honn, K A; Grant, D A; Hinson, J M; Whitney, P; Van Dongen, Hpa

2018-01-17

Sleep deprivation impairs performance on cognitive tasks, but it is unclear which cognitive processes it degrades. We administered a semantic matching task with variable stimulus onset asynchrony (SOA) and both speeded and self-paced trial blocks. The task was administered at the baseline and 24 hours later after 30.8 hours of total sleep deprivation (TSD) or matching well-rested control. After sleep deprivation, the 20% slowest response times (RTs) were significantly increased. However, the semantic encoding time component of the RTs remained at baseline level. Thus, the performance impairment induced by sleep deprivation on this task occurred in cognitive processes downstream of semantic encoding.

Regulative feedback in pattern formation: towards a general relativistic theory of positional information.

PubMed

Jaeger, Johannes; Irons, David; Monk, Nick

2008-10-01

Positional specification by morphogen gradients is traditionally viewed as a two-step process. A gradient is formed and then interpreted, providing a spatial metric independent of the target tissue, similar to the concept of space in classical mechanics. However, the formation and interpretation of gradients are coupled, dynamic processes. We introduce a conceptual framework for positional specification in which cellular activity feeds back on positional information encoded by gradients, analogous to the feedback between mass-energy distribution and the geometry of space-time in Einstein's general theory of relativity. We discuss how such general relativistic positional information (GRPI) can guide systems-level approaches to pattern formation.

A neural mechanism for detecting the distance of a selected target by modulating the FM sweep rate of biosonar in echolocation of bat.

PubMed

Kamata, Eigo; Inoue, Satoru; Zheng, MeiHong; Kashimori, Yoshiki; Kambara, Takeshi

2004-01-01

Most species of bats making echolocation use frequency modulated (FM) ultrasonic pulses to measure the distance to targets. These bats detect with a high accuracy the arrival time differences between emitted pulses and their echoes generated by targets. In order to clarify the neural mechanism for echolocation, we present neural model of inferior colliculus (IC), medial geniculate body (MGB) and auditory cortex (AC) along which information of echo delay times is processed. The bats increase the downward frequency sweep rate of emitted FM pulse as they approach the target. The functional role of this modulation of sweep rate is not yet clear. In order to investigate the role, we calculated the response properties of our models of IC, MGB, and AC changing the target distance and the sweep rate. We found based on the simulations that the distance of a target in various ranges may be encoded the most clearly into the activity pattern of delay time map network in AC, when the sweep rate of FM pulse used is coincided with the observed value which the bats adopt for each range of target distance.

Characterization, adaptive traffic shaping, and multiplexing of real-time MPEG II video

NASA Astrophysics Data System (ADS)

Agrawal, Sanjay; Barry, Charles F.; Binnai, Vinay; Kazovsky, Leonid G.

1997-01-01

We obtain network traffic model for real-time MPEG-II encoded digital video by analyzing video stream samples from real-time encoders from NUKO Information Systems. MPEG-II sample streams include a resolution intensive movie, City of Joy, an action intensive movie, Aliens, a luminance intensive (black and white) movie, Road To Utopia, and a chrominance intensive (color) movie, Dick Tracy. From our analysis we obtain a heuristic model for the encoded video traffic which uses a 15-stage Markov process to model the I,B,P frame sequences within a group of pictures (GOP). A jointly-correlated Gaussian process is used to model the individual frame sizes. Scene change arrivals are modeled according to a gamma process. Simulations show that our MPEG-II traffic model generates, I,B,P frame sequences and frame sizes that closely match the sample MPEG-II stream traffic characteristics as they relate to latency and buffer occupancy in network queues. To achieve high multiplexing efficiency we propose a traffic shaping scheme which sets preferred 1-frame generation times among a group of encoders so as to minimize the overall variation in total offered traffic while still allowing the individual encoders to react to scene changes. Simulations show that our scheme results in multiplexing gains of up to 10% enabling us to multiplex twenty 6 Mbps MPEG-II video streams instead of 18 streams over an ATM/SONET OC3 link without latency or cell loss penalty. This scheme is due for a patent.

Design of a CAN bus interface for photoelectric encoder in the spaceflight camera

NASA Astrophysics Data System (ADS)

Sun, Ying; Wan, Qiu-hua; She, Rong-hong; Zhao, Chang-hai; Jiang, Yong

2009-05-01

In order to make photoelectric encoder usable in a spaceflight camera which adopts CAN bus as the communication method, CAN bus interface of the photoelectric encoder is designed in this paper. CAN bus interface hardware circuit of photoelectric encoder consists of CAN bus controller SJA 1000, CAN bus transceiver TJA1050 and singlechip. CAN bus interface controlling software program is completed in C language. A ten-meter shield twisted pair line is used as the transmission medium in the spaceflight camera, and speed rate is 600kbps.The experiments show that: the photoelectric encoder with CAN bus interface which has the advantages of more reliability, real-time, transfer rate and transfer distance overcomes communication line's shortcomings of classical photoelectric encoder system. The system works well in automatic measuring and controlling system.

Pathological mechanisms underlying single large‐scale mitochondrial DNA deletions

PubMed Central

Rocha, Mariana C.; Rosa, Hannah S.; Grady, John P.; Blakely, Emma L.; He, Langping; Romain, Nadine; Haller, Ronald G.; Newman, Jane; McFarland, Robert; Ng, Yi Shiau; Gorman, Grainne S.; Schaefer, Andrew M.; Tuppen, Helen A.; Taylor, Robert W.

2018-01-01

Objective Single, large‐scale deletions in mitochondrial DNA (mtDNA) are a common cause of mitochondrial disease. This study aimed to investigate the relationship between the genetic defect and molecular phenotype to improve understanding of pathogenic mechanisms associated with single, large‐scale mtDNA deletions in skeletal muscle. Methods We investigated 23 muscle biopsies taken from adult patients (6 males/17 females with a mean age of 43 years) with characterized single, large‐scale mtDNA deletions. Mitochondrial respiratory chain deficiency in skeletal muscle biopsies was quantified by immunoreactivity levels for complex I and complex IV proteins. Single muscle fibers with varying degrees of deficiency were selected from 6 patient biopsies for determination of mtDNA deletion level and copy number by quantitative polymerase chain reaction. Results We have defined 3 “classes” of single, large‐scale deletion with distinct patterns of mitochondrial deficiency, determined by the size and location of the deletion. Single fiber analyses showed that fibers with greater respiratory chain deficiency harbored higher levels of mtDNA deletion with an increase in total mtDNA copy number. For the first time, we have demonstrated that threshold levels for complex I and complex IV deficiency differ based on deletion class. Interpretation Combining genetic and immunofluorescent assays, we conclude that thresholds for complex I and complex IV deficiency are modulated by the deletion of complex‐specific protein‐encoding genes. Furthermore, removal of mt‐tRNA genes impacts specific complexes only at high deletion levels, when complex‐specific protein‐encoding genes remain. These novel findings provide valuable insight into the pathogenic mechanisms associated with these mutations. Ann Neurol 2018;83:115–130 PMID:29283441

Neuronal representation of individual heroin choices in the orbitofrontal cortex.

PubMed

Guillem, Karine; Brenot, Viridiana; Durand, Audrey; Ahmed, Serge H

2018-05-01

Drug addiction is a harmful preference for drug use over and at the expense of other non-drug-related activities. We previously identified in the rat orbitofrontal cortex (OFC) a mechanism that influences individual preferences between cocaine use and an alternative action rewarded by a non-drug reward (i.e. sweet water). Here, we sought to test the generality of this mechanism to a different addictive drug, heroin. OFC neuronal activity was recorded while rats responded for heroin or the alternative non-drug reward separately or while they chose between the two. First, we found that heroin-rewarded and sweet water-rewarded actions were encoded by two non-overlapping OFC neuronal populations and that the relative size of the heroin population represented individual drug choices. Second, OFC neurons encoding the preferred action-which was the non-drug action in the large majority of individuals-progressively fired more than non-preferred action-coding neurons 1 second after the onset of choice trials and around 1 second before the preferred action was actually chosen, suggesting a pre-choice neuronal competition for action selection. Together with a previous study on cocaine choice, the present study on heroin choice reveals important commonalities in how OFC neurons encode individual drug choices and preferences across different classes of drugs. It also reveals some drug-specific differences in OFC encoding activity. Notably, the proportion of neurons that non-selectively encode both the drug and the non-drug reward was higher when the drug was heroin (present study) than when it was cocaine (previous study). We will discuss the potential functional significance of these commonalities and differences in OFC neuronal activity across different drugs for understanding drug choice. © 2017 Society for the Study of Addiction.

The pupil as an indicator of unconscious memory: Introducing the pupil priming effect.

PubMed

Gomes, Carlos Alexandre; Montaldi, Daniela; Mayes, Andrew

2015-06-01

We explored whether object behavioral priming and pupil changes occur in the absence of recognition memory. Experiment 1 found behavioral priming for unrecognized objects (Ms) regardless of whether they had been encoded perceptually or conceptually. Using the same perceptual encoding task, Experiment 2 showed greater pupil dilation for Ms than for correct rejections of unstudied objects (CRs) when reaction times were matched. In Experiment 3, there was relatively less pupil dilation for Ms than for similarly matched CRs when objects had been encoded conceptually. Mean/peak pupil dilation for CRs, but not Ms, increased in Experiment 3, in which novelty expectation was also reduced, and the pupillary time course for both Ms and CRs was distinct in the two experiments. These findings indicate that both behavioral and pupil memory occur for studied, but unrecognized stimuli, and suggest that encoding and novelty expectation modulate pupillary memory responses. © 2015 Society for Psychophysiological Research.

The Coat Protein and NIa Protease of Two Potyviridae Family Members Independently Confer Superinfection Exclusion

PubMed Central

French, Roy

2016-01-01

ABSTRACT Superinfection exclusion (SIE) is an antagonistic virus-virus interaction whereby initial infection by one virus prevents subsequent infection by closely related viruses. Although SIE has been described in diverse viruses infecting plants, humans, and animals, its mechanisms, including involvement of specific viral determinants, are just beginning to be elucidated. In this study, SIE determinants encoded by two economically important wheat viruses, Wheat streak mosaic virus (WSMV; genus Tritimovirus, family Potyviridae) and Triticum mosaic virus (TriMV; genus Poacevirus, family Potyviridae), were identified in gain-of-function experiments that used heterologous viruses to express individual virus-encoded proteins in wheat. Wheat plants infected with TriMV expressing WSMV P1, HC-Pro, P3, 6K1, CI, 6K2, NIa-VPg, or NIb cistrons permitted efficient superinfection by WSMV expressing green fluorescent protein (WSMV-GFP). In contrast, wheat infected with TriMV expressing WSMV NIa-Pro or coat protein (CP) substantially excluded superinfection by WSMV-GFP, suggesting that both of these cistrons are SIE effectors encoded by WSMV. Importantly, SIE is due to functional WSMV NIa-Pro or CP rather than their encoding RNAs, as altering the coded protein products by minimally changing RNA sequences led to abolishment of SIE. Deletion mutagenesis further revealed that elicitation of SIE by NIa-Pro requires the entire protein while CP requires only a 200-amino-acid (aa) middle fragment (aa 101 to 300) of the 349 aa. Strikingly, reciprocal experiments with WSMV-mediated expression of TriMV proteins showed that TriMV CP, and TriMV NIa-Pro to a lesser extent, likewise excluded superinfection by TriMV-GFP. Collectively, these data demonstrate that WSMV- and TriMV-encoded CP and NIa-Pro proteins are effectors of SIE and that these two proteins trigger SIE independently of each other. IMPORTANCE Superinfection exclusion (SIE) is an antagonistic virus-virus interaction that prevents secondary invasions by identical or closely related viruses in the same host cells. Although known to occur in diverse viruses, SIE remains an enigma in terms of key molecular determinants and action mechanisms. In this study, we found that Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) encode two independently functioning cistrons that serve as effectors of SIE at the protein but not the RNA level. The coat protein and NIa-Pro encoded by these two viruses, when expressed from a heterologous virus, exerted SIE to the cognate viruses. The identification of virus-encoded effectors of SIE and their transgenic expression could potentially facilitate the development of virus-resistant crop plants. Additionally, functional conservation of SIE in diverse virus groups suggests that a better understanding of the underlying mechanisms of SIE could facilitate the development of novel antiviral therapies against viral diseases. PMID:27681136

Efficient biprediction decision scheme for fast high efficiency video coding encoding

NASA Astrophysics Data System (ADS)

Park, Sang-hyo; Lee, Seung-ho; Jang, Euee S.; Jun, Dongsan; Kang, Jung-Won

2016-11-01

An efficient biprediction decision scheme of high efficiency video coding (HEVC) is proposed for fast-encoding applications. For low-delay video applications, bidirectional prediction can be used to increase compression performance efficiently with previous reference frames. However, at the same time, the computational complexity of the HEVC encoder is significantly increased due to the additional biprediction search. Although a some research has attempted to reduce this complexity, whether the prediction is strongly related to both motion complexity and prediction modes in a coding unit has not yet been investigated. A method that avoids most compression-inefficient search points is proposed so that the computational complexity of the motion estimation process can be dramatically decreased. To determine if biprediction is critical, the proposed method exploits the stochastic correlation of the context of prediction units (PUs): the direction of a PU and the accuracy of a motion vector. Through experimental results, the proposed method showed that the time complexity of biprediction can be reduced to 30% on average, outperforming existing methods in view of encoding time, number of function calls, and memory access.

Regression-Based Identification of Behavior-Encoding Neurons During Large-Scale Optical Imaging of Neural Activity at Cellular Resolution

PubMed Central

Miri, Andrew; Daie, Kayvon; Burdine, Rebecca D.; Aksay, Emre

2011-01-01

The advent of methods for optical imaging of large-scale neural activity at cellular resolution in behaving animals presents the problem of identifying behavior-encoding cells within the resulting image time series. Rapid and precise identification of cells with particular neural encoding would facilitate targeted activity measurements and perturbations useful in characterizing the operating principles of neural circuits. Here we report a regression-based approach to semiautomatically identify neurons that is based on the correlation of fluorescence time series with quantitative measurements of behavior. The approach is illustrated with a novel preparation allowing synchronous eye tracking and two-photon laser scanning fluorescence imaging of calcium changes in populations of hindbrain neurons during spontaneous eye movement in the larval zebrafish. Putative velocity-to-position oculomotor integrator neurons were identified that showed a broad spatial distribution and diversity of encoding. Optical identification of integrator neurons was confirmed with targeted loose-patch electrical recording and laser ablation. The general regression-based approach we demonstrate should be widely applicable to calcium imaging time series in behaving animals. PMID:21084686

Generative Representations for Evolving Families of Designs

NASA Technical Reports Server (NTRS)

Hornby, Gregory S.

2003-01-01

Since typical evolutionary design systems encode only a single artifact with each individual, each time the objective changes a new set of individuals must be evolved. When this objective varies in a way that can be parameterized, a more general method is to use a representation in which a single individual encodes an entire class of artifacts. In addition to saving time by preventing the need for multiple evolutionary runs, the evolution of parameter-controlled designs can create families of artifacts with the same style and a reuse of parts between members of the family. In this paper an evolutionary design system is described which uses a generative representation to encode families of designs. Because a generative representation is an algorithmic encoding of a design, its input parameters are a way to control aspects of the design it generates. By evaluating individuals multiple times with different input parameters the evolutionary design system creates individuals in which the input parameter controls specific aspects of a design. This system is demonstrated on two design substrates: neural-networks which solve the 3/5/7-parity problem and three-dimensional tables of varying heights.

Distinct Patterns of Neural Activity during Memory Formation of Nonwords versus Words

PubMed Central

Otten, Leun J.; Sveen, Josefin; Quayle, Angela H.

2008-01-01

Research into the neural underpinnings of memory formation has focused on the encoding of familiar verbal information. Here, we address how the brain supports the encoding of novel information that does not have meaning. Electrical brain activity was recorded from the scalps of healthy young adults while they performed an incidental encoding task (syllable judgments) on separate series of words and ‘nonwords’ (nonsense letter strings that are orthographically legal and pronounceable). Memory for the items was then probed with a recognition memory test. For words as well as nonwords, event-related potentials differed depending on whether an item would subsequently be remembered or forgotten. However, the polarity and timing of the effect varied across item type. For words, subsequently remembered items showed the usually observed positive-going, frontally-distributed modulation from around 600 ms after word onset. For nonwords, by contrast, a negative-going, spatially widespread modulation predicted encoding success from 1000 ms onwards. Nonwords also showed a modulation shortly after item onset. These findings imply that the brain supports the encoding of familiar and unfamiliar letter strings in qualitatively different ways, including the engagement of distinct neural activity at different points in time. The processing of semantic attributes plays an important role in the encoding of words and the associated positive frontal modulation. PMID:17958481

Auditory stimulation of sleep slow oscillations modulates subsequent memory encoding through altered hippocampal function

PubMed Central

Ong, Ju Lynn; Chee, Nicholas I Y N; Lee, Xuan Kai; Poh, Jia-Hou; Chee, Michael W L

2018-01-01

Abstract Study Objectives Slow oscillations (SO) during sleep contribute to the consolidation of learned material. How the encoding of declarative memories during subsequent wakefulness might benefit from their enhancement during sleep is less clear. In this study, we investigated the impact of acoustically enhanced SO during a nap on subsequent encoding of declarative material. Methods Thirty-seven healthy young adults were studied under two conditions: stimulation (STIM) and no stimulation (SHAM), in counter-balanced order following a night of sleep restriction (4 hr time-in-bed [TIB]). In the STIM condition, auditory tones were phase-locked to the SO up-state during a 90 min nap opportunity. In the SHAM condition, corresponding time points were marked but tones were not presented. Thirty minutes after awakening, participants encoded pictures while undergoing fMRI. Picture recognition was tested 60 min later. Results Acoustic stimulation augmented SO across the group, but there was no group level benefit on memory. However, the magnitude of SO enhancement correlated with greater recollection. SO enhancement was also positively correlated with hippocampal activation at encoding. Although spindle activity increased, this did not correlate with memory benefit or shift in hippocampal signal. Conclusions Acoustic stimulation during a nap can benefit encoding of declarative memories. Hippocampal activation positively correlated with SO augmentation. PMID:29425369

Auditory stimulation of sleep slow oscillations modulates subsequent memory encoding through altered hippocampal function.

PubMed

Ong, Ju Lynn; Patanaik, Amiya; Chee, Nicholas I Y N; Lee, Xuan Kai; Poh, Jia-Hou; Chee, Michael W L

2018-05-01

Slow oscillations (SO) during sleep contribute to the consolidation of learned material. How the encoding of declarative memories during subsequent wakefulness might benefit from their enhancement during sleep is less clear. In this study, we investigated the impact of acoustically enhanced SO during a nap on subsequent encoding of declarative material. Thirty-seven healthy young adults were studied under two conditions: stimulation (STIM) and no stimulation (SHAM), in counter-balanced order following a night of sleep restriction (4 hr time-in-bed [TIB]). In the STIM condition, auditory tones were phase-locked to the SO up-state during a 90 min nap opportunity. In the SHAM condition, corresponding time points were marked but tones were not presented. Thirty minutes after awakening, participants encoded pictures while undergoing fMRI. Picture recognition was tested 60 min later. Acoustic stimulation augmented SO across the group, but there was no group level benefit on memory. However, the magnitude of SO enhancement correlated with greater recollection. SO enhancement was also positively correlated with hippocampal activation at encoding. Although spindle activity increased, this did not correlate with memory benefit or shift in hippocampal signal. Acoustic stimulation during a nap can benefit encoding of declarative memories. Hippocampal activation positively correlated with SO augmentation.

Cell transformation by human adenoviruses.

PubMed

Endter, C; Dobner, T

2004-01-01

The last 40 years of molecular biological investigations into human adenoviruses have contributed enormously to our understanding of the basic principles of normal and malignant cell growth. Much of this knowledge stems from analyses of their productive infection cycle in permissive host cells. Also, initial observations concerning the carcinogenic potential of human adenoviruses subsequently revealed decisive insights into the molecular mechanisms of the origins of cancer, and established adenoviruses as a model system for explaining virus-mediated transformation processes. Today it is well established that cell transformation by human adenoviruses is a multistep process involving several gene products encoded in early transcription units 1A (E1A) and 1B (E1B). Moreover, a large body of evidence now indicates that alternative or additional mechanisms are engaged in adenovirus-mediated oncogenic transformation involving gene products encoded in early region 4 (E4) as well as epigenetic changes resulting from viral DNA integration. In particular, detailed studies on the tumorigenic potential of subgroup D adenovirus type 9 (Ad9) E4 have now revealed a new pathway that points to a novel, general mechanism of virus-mediated oncogenesis. In this chapter, we summarize the current state of knowledge about the oncogenes and oncogene products of human adenoviruses, focusing particularly on recent findings concerning the transforming and oncogenic properties of viral proteins encoded in the E1B and E4 transcription units.

Gene duplication and fragment recombination drive functional diversification of a superfamily of cytoplasmic effectors in Phytophthora sojae.

PubMed

Shen, Danyu; Liu, Tingli; Ye, Wenwu; Liu, Li; Liu, Peihan; Wu, Yuren; Wang, Yuanchao; Dou, Daolong

2013-01-01

Phytophthora and other oomycetes secrete a large number of putative host cytoplasmic effectors with conserved FLAK motifs following signal peptides, termed crinkling and necrosis inducing proteins (CRN), or Crinkler. Here, we first investigated the evolutionary patterns and mechanisms of CRN effectors in Phytophthora sojae and compared them to two other Phytophthora species. The genes encoding CRN effectors could be divided into 45 orthologous gene groups (OGG), and most OGGs unequally distributed in the three species, in which each underwent large number of gene gains or losses, indicating that the CRN genes expanded after species evolution in Phytophthora and evolved through pathoadaptation. The 134 expanded genes in P. sojae encoded family proteins including 82 functional genes and expressed at higher levels while the other 68 genes encoding orphan proteins were less expressed and contained 50 pseudogenes. Furthermore, we demonstrated that most expanded genes underwent gene duplication or/and fragment recombination. Three different mechanisms that drove gene duplication or recombination were identified. Finally, the expanded CRN effectors exhibited varying pathogenic functions, including induction of programmed cell death (PCD) and suppression of PCD through PAMP-triggered immunity or/and effector-triggered immunity. Overall, these results suggest that gene duplication and fragment recombination may be two mechanisms that drive the expansion and neofunctionalization of the CRN family in P. sojae, which aids in understanding the roles of CRN effectors within each oomycete pathogen.

Forced to remember: when memory is biased by salient information.

PubMed

Santangelo, Valerio

2015-04-15

The last decades have seen a rapid growing in the attempt to understand the key factors involved in the internal memory representation of the external world. Visual salience have been found to provide a major contribution in predicting the probability for an item/object embedded in a complex setting (i.e., a natural scene) to be encoded and then remembered later on. Here I review the existing literature highlighting the impact of perceptual- (based on low-level sensory features) and semantics-related salience (based on high-level knowledge) on short-term memory representation, along with the neural mechanisms underpinning the interplay between these factors. The available evidence reveal that both perceptual- and semantics-related factors affect attention selection mechanisms during the encoding of natural scenes. Biasing internal memory representation, both perceptual and semantics factors increase the probability to remember high- to the detriment of low-saliency items. The available evidence also highlight an interplay between these factors, with a reduced impact of perceptual-related salience in biasing memory representation as a function of the increasing availability of semantics-related salient information. The neural mechanisms underpinning this interplay involve the activation of different portions of the frontoparietal attention control network. Ventral regions support the assignment of selection/encoding priorities based on high-level semantics, while the involvement of dorsal regions reflects priorities assignment based on low-level sensory features. Copyright © 2015 Elsevier B.V. All rights reserved.

The Role of Nonlinear Gradients in Parallel Imaging: A k-Space Based Analysis.

PubMed

Galiana, Gigi; Stockmann, Jason P; Tam, Leo; Peters, Dana; Tagare, Hemant; Constable, R Todd

2012-09-01

Sequences that encode the spatial information of an object using nonlinear gradient fields are a new frontier in MRI, with potential to provide lower peripheral nerve stimulation, windowed fields of view, tailored spatially-varying resolution, curved slices that mirror physiological geometry, and, most importantly, very fast parallel imaging with multichannel coils. The acceleration for multichannel images is generally explained by the fact that curvilinear gradient isocontours better complement the azimuthal spatial encoding provided by typical receiver arrays. However, the details of this complementarity have been more difficult to specify. We present a simple and intuitive framework for describing the mechanics of image formation with nonlinear gradients, and we use this framework to review some the main classes of nonlinear encoding schemes.

A linear-encoding model explains the variability of the target morphology in regeneration

PubMed Central

Lobo, Daniel; Solano, Mauricio; Bubenik, George A.; Levin, Michael

2014-01-01

A fundamental assumption of today's molecular genetics paradigm is that complex morphology emerges from the combined activity of low-level processes involving proteins and nucleic acids. An inherent characteristic of such nonlinear encodings is the difficulty of creating the genetic and epigenetic information that will produce a given self-assembling complex morphology. This ‘inverse problem’ is vital not only for understanding the evolution, development and regeneration of bodyplans, but also for synthetic biology efforts that seek to engineer biological shapes. Importantly, the regenerative mechanisms in deer antlers, planarian worms and fiddler crabs can solve an inverse problem: their target morphology can be altered specifically and stably by injuries in particular locations. Here, we discuss the class of models that use pre-specified morphological goal states and propose the existence of a linear encoding of the target morphology, making the inverse problem easy for these organisms to solve. Indeed, many model organisms such as Drosophila, hydra and Xenopus also develop according to nonlinear encodings producing linear encodings of their final morphologies. We propose the development of testable models of regeneration regulation that combine emergence with a top-down specification of shape by linear encodings of target morphology, driving transformative applications in biomedicine and synthetic bioengineering. PMID:24402915

Brain computer interface to enhance episodic memory in human participants

PubMed Central

Burke, John F.; Merkow, Maxwell B.; Jacobs, Joshua; Kahana, Michael J.

2015-01-01

Recent research has revealed that neural oscillations in the theta (4–8 Hz) and alpha (9–14 Hz) bands are predictive of future success in memory encoding. Because these signals occur before the presentation of an upcoming stimulus, they are considered stimulus-independent in that they correlate with enhanced memory encoding independent of the item being encoded. Thus, such stimulus-independent activity has important implications for the neural mechanisms underlying episodic memory as well as the development of cognitive neural prosthetics. Here, we developed a brain computer interface (BCI) to test the ability of such pre-stimulus activity to modulate subsequent memory encoding. We recorded intracranial electroencephalography (iEEG) in neurosurgical patients as they performed a free recall memory task, and detected iEEG theta and alpha oscillations that correlated with optimal memory encoding. We then used these detected oscillatory changes to trigger the presentation of items in the free recall task. We found that item presentation contingent upon the presence of pre-stimulus theta and alpha oscillations modulated memory performance in more sessions than expected by chance. Our results suggest that an electrophysiological signal may be causally linked to a specific behavioral condition, and contingent stimulus presentation has the potential to modulate human memory encoding. PMID:25653605

Remembering with gains and losses: effects of monetary reward and punishment on successful encoding activation of source memories.

PubMed

Shigemune, Yayoi; Tsukiura, Takashi; Kambara, Toshimune; Kawashima, Ryuta

2014-05-01

The motivation of getting rewards or avoiding punishments reinforces learning behaviors. Although the neural mechanisms underlying the effect of rewards on episodic memory have been demonstrated, there is little evidence of the effect of punishments on this memory. Our functional magnetic resonance imaging (fMRI) study investigated the effects of monetary rewards and punishments on activation during the encoding of source memories. During encoding, participants memorized words (item) and locations of presented words (source) under 3 conditions (Reward, Punishment, and Control). During retrieval, participants retrieved item and source memories of the words and were rewarded or penalized according to their performance. Source memories encoded with rewards or punishments were remembered better than those without such encoding. fMRI data demonstrated that the ventral tegmental area and substantia nigra and nucleus accumbens activations reflected both the processes of reward and punishment, whereas insular activation increased as a linear function of punishment. Activation in the hippocampus and parahippocampal cortex predicted subsequent retrieval success of source memories. Additionally, correlations between these reward/punishment-related regions and the hippocampus were significant. The successful encoding of source memories could be enhanced by punishments and rewards, and interactions between reward/punishment-related regions and memory-related regions could contribute to memory enhancement by reward and/or punishment.

Detecting weak position fluctuations from encoder signal using singular spectrum analysis.

PubMed

Xu, Xiaoqiang; Zhao, Ming; Lin, Jing

2017-11-01

Mechanical fault or defect will cause some weak fluctuations to the position signal. Detection of such fluctuations via encoders can help determine the health condition and performance of the machine, and offer a promising alternative to the vibration-based monitoring scheme. However, besides the interested fluctuations, encoder signal also contains a large trend and some measurement noise. In applications, the trend is normally several orders larger than the concerned fluctuations in magnitude, which makes it difficult to detect the weak fluctuations without signal distortion. In addition, the fluctuations can be complicated and amplitude modulated under non-stationary working condition. To overcome this issue, singular spectrum analysis (SSA) is proposed for detecting weak position fluctuations from encoder signal in this paper. It enables complicated encode signal to be reduced into several interpretable components including a trend, a set of periodic fluctuations and noise. A numerical simulation is given to demonstrate the performance of the method, it shows that SSA outperforms empirical mode decomposition (EMD) in terms of capability and accuracy. Moreover, linear encoder signals from a CNC machine tool are analyzed to determine the magnitudes and sources of fluctuations during feed motion. The proposed method is proven to be feasible and reliable for machinery condition monitoring. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

Remembering with Gains and Losses: Effects of Monetary Reward and Punishment on Successful Encoding Activation of Source Memories

PubMed Central

Shigemune, Yayoi; Tsukiura, Takashi; Kambara, Toshimune; Kawashima, Ryuta

2014-01-01

The motivation of getting rewards or avoiding punishments reinforces learning behaviors. Although the neural mechanisms underlying the effect of rewards on episodic memory have been demonstrated, there is little evidence of the effect of punishments on this memory. Our functional magnetic resonance imaging (fMRI) study investigated the effects of monetary rewards and punishments on activation during the encoding of source memories. During encoding, participants memorized words (item) and locations of presented words (source) under 3 conditions (Reward, Punishment, and Control). During retrieval, participants retrieved item and source memories of the words and were rewarded or penalized according to their performance. Source memories encoded with rewards or punishments were remembered better than those without such encoding. fMRI data demonstrated that the ventral tegmental area and substantia nigra and nucleus accumbens activations reflected both the processes of reward and punishment, whereas insular activation increased as a linear function of punishment. Activation in the hippocampus and parahippocampal cortex predicted subsequent retrieval success of source memories. Additionally, correlations between these reward/punishment-related regions and the hippocampus were significant. The successful encoding of source memories could be enhanced by punishments and rewards, and interactions between reward/punishment-related regions and memory-related regions could contribute to memory enhancement by reward and/or punishment. PMID:23314939

Action and language mechanisms in the brain: data, models and neuroinformatics.

PubMed

Arbib, Michael A; Bonaiuto, James J; Bornkessel-Schlesewsky, Ina; Kemmerer, David; MacWhinney, Brian; Nielsen, Finn Årup; Oztop, Erhan

2014-01-01

We assess the challenges of studying action and language mechanisms in the brain, both singly and in relation to each other to provide a novel perspective on neuroinformatics, integrating the development of databases for encoding – separately or together – neurocomputational models and empirical data that serve systems and cognitive neuroscience.

Oxalic acid biosynthesis is encoded by an operon in Burkholderia glumae

USDA-ARS?s Scientific Manuscript database

Although the biosynthesis of oxalic acid is known to occur in a number of bacteria, the mechanism(s) regulating its production remains largely unknown. To date, there is no report on the identification of an oxalic acid biosynthetic pathway gene from bacteria. In an attempt to identify such a gene...

Results from field tests of the one-dimensional Time-Encoded Imaging System.

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

Marleau, Peter; Brennan, James S.; Brubaker, Erik

2014-09-01

A series of field experiments were undertaken to evaluate the performance of the one dimensional time encoded imaging system. The significant detection of a Cf252 fission radiation source was demonstrated at a stand-off of 100 meters. Extrapolations to different quantities of plutonium equivalent at different distances are made. Hardware modifications to the system for follow on work are suggested.

Innate immune response during Yersinia infection: critical modulation of cell death mechanisms through phagocyte activation.

PubMed

Bergsbaken, Tessa; Cookson, Brad T

2009-11-01

Yersinia pestis, the etiological agent of plague, is one of the most deadly pathogens on our planet. This organism shares important attributes with its ancestral progenitor, Yersinia pseudotuberculosis, including a 70-kb virulence plasmid, lymphotropism during growth in the mammalian host, and killing of host macrophages. Infections with both organisms are biphasic, where bacterial replication occurs initially with little inflammation, followed by phagocyte influx, inflammatory cytokine production, and tissue necrosis. During infection, plasmid-encoded attributes facilitate bacterial-induced macrophage death, which results from two distinct processes and corresponds to the inflammatory crescendo observed in vivo: Naïve cells die by apoptosis (noninflammatory), and later in infection, activated macrophages die by pyroptosis (inflammatory). The significance of this redirected cell death for the host is underscored by the importance of phagocyte activation for immunity to Yersinia and the protective role of pyroptosis during host responses to anthrax lethal toxin and infections with Francisella, Legionella, Pseudomonas, and Salmonella. The similarities of Y. pestis and Y. pseudotuberculosis, including conserved, plasmid-encoded functions inducing at least two distinct mechanisms of cell death, indicate that comparative studies are revealing about their critical pathogenic mechanism(s) and host innate immune responses during infection. Validation of this idea and evidence of similar interactions with the host immune system are provided by Y. pseudotuberculosis-priming, cross-protective immunity against Y. pestis. Despite these insights, additional studies indicate much remains to be understood concerning effective host responses against Yersinia, including chromosomally encoded attributes that also contribute to bacterial evasion and modulation of innate and adaptive immune responses.

Metaplasticity contributes to memory formation in the hippocampus.

PubMed

Crestani, Ana P; Krueger, Jamie N; Barragan, Eden V; Nakazawa, Yuki; Nemes, Sonya E; Quillfeldt, Jorge A; Gray, John A; Wiltgen, Brian J

2018-05-16

Prior learning can modify the plasticity mechanisms that are used to encode new information. For example, NMDA receptor (NMDAR) activation is typically required for new spatial and contextual learning in the hippocampus. However, once animals have acquired this information, they can learn new tasks even if NMDARs are blocked. This finding suggests that behavioral training alters cellular plasticity mechanisms such that NMDARs are not required for subsequent learning. The mechanisms that mediate this change are currently unknown. To address this issue, we tested the idea that changes in intrinsic excitability (induced by learning) facilitate the encoding of new memories via metabotropic glutamate receptor (mGluR) activation. Consistent with this hypothesis, hippocampal neurons exhibited increases in intrinsic excitability after learning that lasted for several days. This increase was selective and only observed in neurons that were activated by the learning event. When animals were trained on a new task during this period, excitable neurons were reactivated and memory formation required the activation of mGluRs instead of NMDARs. These data suggest that increases in intrinsic excitability may serve as a metaplastic mechanism for memory formation.

Faithful conversion of propagating quantum information to mechanical motion

NASA Astrophysics Data System (ADS)

Reed, A. P.; Mayer, K. H.; Teufel, J. D.; Burkhart, L. D.; Pfaff, W.; Reagor, M.; Sletten, L.; Ma, X.; Schoelkopf, R. J.; Knill, E.; Lehnert, K. W.

2017-12-01

The motion of micrometre-sized mechanical resonators can now be controlled and measured at the fundamental limits imposed by quantum mechanics. These resonators have been prepared in their motional ground state or in squeezed states, measured with quantum-limited precision, and even entangled with microwave fields. Such advances make it possible to process quantum information using the motion of a macroscopic object. In particular, recent experiments have combined mechanical resonators with superconducting quantum circuits to frequency-convert, store and amplify propagating microwave fields. But these systems have not been used to manipulate states that encode quantum bits (qubits), which are required for quantum communication and modular quantum computation. Here we demonstrate the conversion of propagating qubits encoded as superpositions of zero and one photons to the motion of a micromechanical resonator with a fidelity in excess of the classical bound. This ability is necessary for mechanical resonators to convert quantum information between the microwave and optical domains or to act as storage elements in a modular quantum information processor. Additionally, these results are an important step towards testing speculative notions that quantum theory may not be valid for sufficiently massive systems.

A Novel Connectionist Network for Solving Long Time-Lag Prediction Tasks

NASA Astrophysics Data System (ADS)

Johnson, Keith; MacNish, Cara

Traditional Recurrent Neural Networks (RNNs) perform poorly on learning tasks involving long time-lag dependencies. More recent approaches such as LSTM and its variants significantly improve on RNNs ability to learn this type of problem. We present an alternative approach to encoding temporal dependencies that associates temporal features with nodes rather than state values, where the nodes explicitly encode dependencies over variable time delays. We show promising results comparing the network's performance to LSTM variants on an extended Reber grammar task.

Exploring the Caste-Specific Multi-Layer Defense Mechanism of Formosan Subterranean Termites, Coptotermes formosanus Shiraki.

PubMed

Hussain, Abid; Tian, Ming-Yi; Wen, Shuo-Yang

2017-12-12

The survival and foraging of Coptotermes formosanus Shiraki in a microbe-rich environment reflect the adaptation of an extraordinary, sophisticated defense mechanism by the nest-mates. We aimed to explore the host pathogen interaction by studying caste-specific volatile chemistry and genes encoding the antioxidant defense of winged imagoes, nymphs, soldiers and workers of Formosan subterranean termites. Qualitative analyses of C. formosanus Shiraki performed by HS-SPME/GC-MS showed considerable variations in the chemical composition of volatile organic compounds (VOCs) and their proportions among all the castes. Winged imagoes produced the most important compounds such as naphthalene and n- hexanoic acid. The antifungal activity of these compounds along with nonanal, n -pentadecane, n- tetradecane, n -heptadecane and methyl octanoate against the conidial suspensions of Metarhizium anisopliae and Beauveria bassiana isolates enable us to suggest that the failure of natural fungal infection in the nest is due to the antiseptic environment of the nest, which is mainly controlled by the VOCs of nest-mates. In addition, conidial germination of M. anisopliae and B. bassiana isolates evaluated on the cuticle of each caste showed significant variations among isolates and different castes. Our results showed that the conidia of M. anisopliae 02049 exhibited the highest germination on the cuticle of all the inoculated castes. Moreover, we recorded the lowest germination of the conidia of B. bassiana 200436. Caste-specific germination variations enabled us to report for the first time that the cuticle of winged imagoes was found to be the most resistant cuticle. The analysis of the transcriptome of C. formosanus Shiraki revealed the identification of 17 genes directly involved in antioxidant defense. Expression patterns of the identified antioxidant genes by quantitative real-time PCR (qPCR) revealed the significantly highest upregulation of CAT , GST , PRXSL , Cu/Zn-SOD2 , TXN1 , TXN2 , TXNL1 , TXNL2 , TXNL4A and TPx genes among winged imagoes upon infection with the most virulent isolate, M. anisopliae 02049. Furthermore, soldiers showed the least expression of genes encoding antioxidant defense. Our findings indicated that the volatile chemistry of nest-mates and genes encoding antioxidant defense greatly contribute to the survival and foraging of Formosan subterranean termites in a microbe-rich habitat.

Insights into Mechanisms of Chronic Neurodegeneration

PubMed Central

Diack, Abigail B.; Alibhai, James D.; Barron, Rona; Bradford, Barry; Piccardo, Pedro; Manson, Jean C.

2016-01-01

Chronic neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), and prion diseases are characterised by the accumulation of abnormal conformers of a host encoded protein in the central nervous system. The process leading to neurodegeneration is still poorly defined and thus development of early intervention strategies is challenging. Unique amongst these diseases are Transmissible Spongiform Encephalopathies (TSEs) or prion diseases, which have the ability to transmit between individuals. The infectious nature of these diseases has permitted in vivo and in vitro modelling of the time course of the disease process in a highly reproducible manner, thus early events can be defined. Recent evidence has demonstrated that the cell-to-cell spread of protein aggregates by a “prion-like mechanism” is common among the protein misfolding diseases. Thus, the TSE models may provide insights into disease mechanisms and testable hypotheses for disease intervention, applicable to a number of these chronic neurodegenerative diseases. PMID:26771599

Acousto-optic modulation and opto-acoustic gating in piezo-optomechanical circuits

PubMed Central

Balram, Krishna C.; Davanço, Marcelo I.; Ilic, B. Robert; Kyhm, Ji-Hoon; Song, Jin Dong; Srinivasan, Kartik

2017-01-01

Acoustic wave devices provide a promising chip-scale platform for efficiently coupling radio frequency (RF) and optical fields. Here, we use an integrated piezo-optomechanical circuit platform that exploits both the piezoelectric and photoelastic coupling mechanisms to link 2.4 GHz RF waves to 194 THz (1550 nm) optical waves, through coupling to propagating and localized 2.4 GHz acoustic waves. We demonstrate acousto-optic modulation, resonant in both the optical and mechanical domains, in which waveforms encoded on the RF carrier are mapped to the optical field. We also show opto-acoustic gating, in which the application of modulated optical pulses interferometrically gates the transmission of propagating acoustic pulses. The time-domain characteristics of this system under both pulsed RF and pulsed optical excitation are considered in the context of the different physical pathways involved in driving the acoustic waves, and modelled through the coupled mode equations of cavity optomechanics. PMID:28580373

The genomic landscape of human cellular circadian variation points to a novel role for the signalosome

PubMed Central

Gaspar, Ludmila; Howald, Cedric; Popadin, Konstantin; Maier, Bert; Mauvoisin, Daniel; Moriggi, Ermanno; Gutierrez-Arcelus, Maria; Falconnet, Emilie; Borel, Christelle; Kunz, Dieter; Kramer, Achim; Gachon, Frederic; Dermitzakis, Emmanouil T; Antonarakis, Stylianos E

2017-01-01

The importance of natural gene expression variation for human behavior is undisputed, but its impact on circadian physiology remains mostly unexplored. Using umbilical cord fibroblasts, we have determined by genome-wide association how common genetic variation impacts upon cellular circadian function. Gene set enrichment points to differences in protein catabolism as one major source of clock variation in humans. The two most significant alleles regulated expression of COPS7B, a subunit of the COP9 signalosome. We further show that the signalosome complex is imported into the nucleus in timed fashion to stabilize the essential circadian protein BMAL1, a novel mechanism to oppose its proteasome-mediated degradation. Thus, circadian clock properties depend in part upon a genetically-encoded competition between stabilizing and destabilizing forces, and genetic alterations in these mechanisms provide one explanation for human chronotype. PMID:28869038

Generalisation benefits of output gating in a model of prefrontal cortex

NASA Astrophysics Data System (ADS)

Kriete, Trent; Noelle, David C.

2011-06-01

The prefrontal cortex (PFC) plays a central role in flexible cognitive control, including the suppression of habitual responding in favour of situation-appropriate behaviours that can be quite novel. PFC provides a kind of working memory, maintaining the rules, goals, and/or actions that are to control behaviour in the current context. For flexible control, these PFC representations must be sufficiently componential to support systematic generalisation to novel situations. The anatomical structure of PFC can be seen as implementing a componential 'slot-filler' structure, with different components encoded over isolated pools of neurons. Previous PFC models have highlighted the importance of a dynamic gating mechanism to selectively update individual 'slot' contents. In this article, we present simulation results that suggest that systematic generalisation also requires an 'output gating' mechanism that limits the influence of PFC on more posterior brain areas to reflect a small number of representational components at any one time.

Achieving a golden mean: mechanisms by which coronaviruses ensure synthesis of the correct stoichiometric ratios of viral proteins.

PubMed

Plant, Ewan P; Rakauskaite, Rasa; Taylor, Deborah R; Dinman, Jonathan D

2010-05-01

In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed -1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the -1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a "golden mean" model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins.

Multicore-based 3D-DWT video encoder

NASA Astrophysics Data System (ADS)

Galiano, Vicente; López-Granado, Otoniel; Malumbres, Manuel P.; Migallón, Hector

2013-12-01

Three-dimensional wavelet transform (3D-DWT) encoders are good candidates for applications like professional video editing, video surveillance, multi-spectral satellite imaging, etc. where a frame must be reconstructed as quickly as possible. In this paper, we present a new 3D-DWT video encoder based on a fast run-length coding engine. Furthermore, we present several multicore optimizations to speed-up the 3D-DWT computation. An exhaustive evaluation of the proposed encoder (3D-GOP-RL) has been performed, and we have compared the evaluation results with other video encoders in terms of rate/distortion (R/D), coding/decoding delay, and memory consumption. Results show that the proposed encoder obtains good R/D results for high-resolution video sequences with nearly in-place computation using only the memory needed to store a group of pictures. After applying the multicore optimization strategies over the 3D DWT, the proposed encoder is able to compress a full high-definition video sequence in real-time.

A novel optical rotary encoder with eccentricity self-detection ability.

PubMed

Li, Xuan; Ye, Guoyong; Liu, Hongzhong; Ban, Yaowen; Shi, Yongsheng; Yin, Lei; Lu, Bingheng

2017-11-01

Eccentricity error is the main error source of optical rotary encoders. Real-time detection and compensation of the eccentricity error is an effective way of improving the accuracy of rotary optical encoders. In this paper, a novel rotary optical encoder is presented to realize eccentricity self-detection. The proposed encoder adopts a spider-web-patterned scale grating as a measuring standard which is scanned by a dual-head scanning unit. Two scanning heads of the dual-head scanning unit, which are arranged orthogonally, have the function of scanning the periodic pattern of the scale grating along the angular and radial directions, respectively. By this means, synchronous measurement of angular and radial displacements of the scale grating is realized. This paper gives the details of the operating principle of the rotary optical encoder, developing and testing work of a prototype. The eccentricity self-detection result agrees well with the result measured by an optical microscope. The experimental result preliminarily proves the feasibility and effectiveness of the proposed optical encoder.

A novel optical rotary encoder with eccentricity self-detection ability

NASA Astrophysics Data System (ADS)

Li, Xuan; Ye, Guoyong; Liu, Hongzhong; Ban, Yaowen; Shi, Yongsheng; Yin, Lei; Lu, Bingheng

2017-11-01

Eccentricity error is the main error source of optical rotary encoders. Real-time detection and compensation of the eccentricity error is an effective way of improving the accuracy of rotary optical encoders. In this paper, a novel rotary optical encoder is presented to realize eccentricity self-detection. The proposed encoder adopts a spider-web-patterned scale grating as a measuring standard which is scanned by a dual-head scanning unit. Two scanning heads of the dual-head scanning unit, which are arranged orthogonally, have the function of scanning the periodic pattern of the scale grating along the angular and radial directions, respectively. By this means, synchronous measurement of angular and radial displacements of the scale grating is realized. This paper gives the details of the operating principle of the rotary optical encoder, developing and testing work of a prototype. The eccentricity self-detection result agrees well with the result measured by an optical microscope. The experimental result preliminarily proves the feasibility and effectiveness of the proposed optical encoder.

Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters.

PubMed

de Lima-Morales, Daiana; Chaves-Moreno, Diego; Wos-Oxley, Melissa L; Jáuregui, Ruy; Vilchez-Vargas, Ramiro; Pieper, Dietmar H

2016-01-01

Pseudomonas veronii 1YdBTEX2, a benzene and toluene degrader, and Pseudomonas veronii 1YB2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. These strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. Extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydroxymuconic semialdehyde dehydrogenase necessary for benzene degradation but typically absent from isopropylbenzene dioxygenase-encoding gene clusters. The benzene dihydrodiol dehydrogenase-encoding gene was not clustered with any other aromatic degradation genes, and the encoded protein was only distantly related to dehydrogenases of aromatic degradation pathways. The involvement of the different gene clusters in the degradation pathways was suggested by real-time quantitative reverse transcription PCR. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Research on application of photoelectric rotary encoder in space optical remote sensor

NASA Astrophysics Data System (ADS)

Zheng, Jun; Qi, Shao-fan; Wang, Yuan-yuan; Zhang, Zhan-dong

2016-11-01

For space optical remote sensor, especially wide swath detecting sensor, the focusing control system for the focal plane should be well designed to obtain the best image quality. The crucial part of this system is the measuring instrument. For previous implements, the potentiometer, which is essentially a voltage divider, is usually introduced to conduct the position in feedback closed-loop control process system. However, the performances of both electro-mechanical and digital potentiometers is limited in accuracy, temperature coefficients, and scale range. To have a better performance of focal plane moving detection, this article presents a new measuring implement with photoelectric rotary encoder, which consists of the photoelectric conversion system and the signal process system. In this novel focusing control system, the photoelectric conversion system is fixed on main axis, which can transform the angle information into a certain analog signal. Through the signal process system, after analog-to-digital converting and data format processing of the certain analog signal, the focusing control system can receive the digital precision angle position which can be used to deduct the current moving position of the focal plane. For utilization of space optical remote sensor in aerospace areas, the reliability design of photoelectric rotary encoder system should be considered with highest priority. As mentioned above, this photoelectric digital precision angle measurement device is well designed for this real-time control and dynamic measurement system, because its characters of high resolution, high accuracy, long endurance, and easy to maintain.

The impact of napping on memory for future-relevant stimuli: Prioritization among multiple salience cues.

PubMed

Bennion, Kelly A; Payne, Jessica D; Kensinger, Elizabeth A

2016-06-01

Prior research has demonstrated that sleep enhances memory for future-relevant information, including memory for information that is salient due to emotion, reward, or knowledge of a later memory test. Although sleep has been shown to prioritize information with any of these characteristics, the present study investigates the novel question of how sleep prioritizes information when multiple salience cues exist. Participants encoded scenes that were future-relevant based on emotion (emotional vs. neutral), reward (rewarded vs. unrewarded), and instructed learning (intentionally vs. incidentally encoded), preceding a delay consisting of a nap, an equivalent time period spent awake, or a nap followed by wakefulness (to control for effects of interference). Recognition testing revealed that when multiple dimensions of future relevance co-occur, sleep prioritizes top-down, goal-directed cues (instructed learning, and to a lesser degree, reward) over bottom-up, stimulus-driven characteristics (emotion). Further, results showed that these factors interact; the effect of a nap on intentionally encoded information was especially strong for neutral (relative to emotional) information, suggesting that once one cue for future relevance is present, there are diminishing returns with additional cues. Sleep may binarize information based on whether it is future-relevant or not, preferentially consolidating memory for the former category. Potential neural mechanisms underlying these selective effects and the implications of this research for educational and vocational domains are discussed. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Rank Order Coding: a Retinal Information Decoding Strategy Revealed by Large-Scale Multielectrode Array Retinal Recordings.

PubMed

Portelli, Geoffrey; Barrett, John M; Hilgen, Gerrit; Masquelier, Timothée; Maccione, Alessandro; Di Marco, Stefano; Berdondini, Luca; Kornprobst, Pierre; Sernagor, Evelyne

2016-01-01

How a population of retinal ganglion cells (RGCs) encodes the visual scene remains an open question. Going beyond individual RGC coding strategies, results in salamander suggest that the relative latencies of a RGC pair encode spatial information. Thus, a population code based on this concerted spiking could be a powerful mechanism to transmit visual information rapidly and efficiently. Here, we tested this hypothesis in mouse by recording simultaneous light-evoked responses from hundreds of RGCs, at pan-retinal level, using a new generation of large-scale, high-density multielectrode array consisting of 4096 electrodes. Interestingly, we did not find any RGCs exhibiting a clear latency tuning to the stimuli, suggesting that in mouse, individual RGC pairs may not provide sufficient information. We show that a significant amount of information is encoded synergistically in the concerted spiking of large RGC populations. Thus, the RGC population response described with relative activities, or ranks, provides more relevant information than classical independent spike count- or latency- based codes. In particular, we report for the first time that when considering the relative activities across the whole population, the wave of first stimulus-evoked spikes is an accurate indicator of stimulus content. We show that this coding strategy coexists with classical neural codes, and that it is more efficient and faster. Overall, these novel observations suggest that already at the level of the retina, concerted spiking provides a reliable and fast strategy to rapidly transmit new visual scenes.

A neural coding scheme reproducing foraging trajectories

NASA Astrophysics Data System (ADS)

Gutiérrez, Esther D.; Cabrera, Juan Luis

2015-12-01

The movement of many animals may follow Lévy patterns. The underlying generating neuronal dynamics of such a behavior is unknown. In this paper we show that a novel discovery of multifractality in winnerless competition (WLC) systems reveals a potential encoding mechanism that is translatable into two dimensional superdiffusive Lévy movements. The validity of our approach is tested on a conductance based neuronal model showing WLC and through the extraction of Lévy flights inducing fractals from recordings of rat hippocampus during open field foraging. Further insights are gained analyzing mice motor cortex neurons and non motor cell signals. The proposed mechanism provides a plausible explanation for the neuro-dynamical fundamentals of spatial searching patterns observed in animals (including humans) and illustrates an until now unknown way to encode information in neuronal temporal series.

Does long-term object priming depend on the explicit detection of object identity at encoding?

PubMed Central

Gomes, Carlos A.; Mayes, Andrew

2015-01-01

It is currently unclear whether objects have to be explicitly identified at encoding for reliable behavioral long-term object priming to occur. We conducted two experiments that investigated long-term object and non-object priming using a selective-attention encoding manipulation that reduces explicit object identification. In Experiment 1, participants either counted dots flashed within an object picture (shallow encoding) or engaged in an animacy task (deep encoding) at study, whereas, at test, they performed an object-decision task. Priming, as measured by reaction times (RTs), was observed for both types of encoding, and was of equivalent magnitude. In Experiment 2, non-object priming (faster RTs for studied relative to unstudied non-objects) was also obtained under the same selective-attention encoding manipulation as in Experiment 1, and the magnitude of the priming effect was equivalent between experiments. In contrast, we observed a linear decrement in recognition memory accuracy across conditions (deep encoding of Experiment 1 > shallow encoding Experiment 1 > shallow encoding of Experiment 2), suggesting that priming was not contaminated by explicit memory strategies. We argue that our results are more consistent with the identification/production framework than the perceptual/conceptual distinction, and we conclude that priming of pictures largely ignored at encoding can be subserved by the automatic retrieval of two types of instances: one at the motor level and another at an object-decision level. PMID:25852594

Individual differences reveal correlates of hidden hearing deficits.

PubMed

Bharadwaj, Hari M; Masud, Salwa; Mehraei, Golbarg; Verhulst, Sarah; Shinn-Cunningham, Barbara G

2015-02-04

Clinical audiometry has long focused on determining the detection thresholds for pure tones, which depend on intact cochlear mechanics and hair cell function. Yet many listeners with normal hearing thresholds complain of communication difficulties, and the causes for such problems are not well understood. Here, we explore whether normal-hearing listeners exhibit such suprathreshold deficits, affecting the fidelity with which subcortical areas encode the temporal structure of clearly audible sound. Using an array of measures, we evaluated a cohort of young adults with thresholds in the normal range to assess both cochlear mechanical function and temporal coding of suprathreshold sounds. Listeners differed widely in both electrophysiological and behavioral measures of temporal coding fidelity. These measures correlated significantly with each other. Conversely, these differences were unrelated to the modest variation in otoacoustic emissions, cochlear tuning, or the residual differences in hearing threshold present in our cohort. Electroencephalography revealed that listeners with poor subcortical encoding had poor cortical sensitivity to changes in interaural time differences, which are critical for localizing sound sources and analyzing complex scenes. These listeners also performed poorly when asked to direct selective attention to one of two competing speech streams, a task that mimics the challenges of many everyday listening environments. Together with previous animal and computational models, our results suggest that hidden hearing deficits, likely originating at the level of the cochlear nerve, are part of "normal hearing." Copyright © 2015 the authors 0270-6474/15/352161-12$15.00/0.

Short-term memory in networks of dissociated cortical neurons.

PubMed

Dranias, Mark R; Ju, Han; Rajaram, Ezhilarasan; VanDongen, Antonius M J

2013-01-30

Short-term memory refers to the ability to store small amounts of stimulus-specific information for a short period of time. It is supported by both fading and hidden memory processes. Fading memory relies on recurrent activity patterns in a neuronal network, whereas hidden memory is encoded using synaptic mechanisms, such as facilitation, which persist even when neurons fall silent. We have used a novel computational and optogenetic approach to investigate whether these same memory processes hypothesized to support pattern recognition and short-term memory in vivo, exist in vitro. Electrophysiological activity was recorded from primary cultures of dissociated rat cortical neurons plated on multielectrode arrays. Cultures were transfected with ChannelRhodopsin-2 and optically stimulated using random dot stimuli. The pattern of neuronal activity resulting from this stimulation was analyzed using classification algorithms that enabled the identification of stimulus-specific memories. Fading memories for different stimuli, encoded in ongoing neural activity, persisted and could be distinguished from each other for as long as 1 s after stimulation was terminated. Hidden memories were detected by altered responses of neurons to additional stimulation, and this effect persisted longer than 1 s. Interestingly, network bursts seem to eliminate hidden memories. These results are similar to those that have been reported from similar experiments in vivo and demonstrate that mechanisms of information processing and short-term memory can be studied using cultured neuronal networks, thereby setting the stage for therapeutic applications using this platform.

SUI-family genes encode phosphatidylserine synthases and regulate stem development in rice.

PubMed

Yin, Hengfu; Gao, Peng; Liu, Chengwu; Yang, Jun; Liu, Zhongchi; Luo, Da

2013-01-01

In vascular plants, the regulation of stem cell niche determines development of aerial shoot which consists of stems and lateral organs. Intercalary meristem (IM) controls internode elongation in rice and other grasses, however little attention has been paid to the underlying mechanism of stem cell maintenance. Here, we investigated the stem development in rice and showed that the Shortened Uppermost Internode 1 (SUI1) family of genes are pivotal for development of rice stems. We demonstrated that SUI-family genes regulate the development of IM for internode elongation and also the cell expansion of the panicle stem rachis in rice. The SUI-family genes encoded base-exchange types of phosphatidylserine synthases (PSSs), which possessed enzymatic activity in a yeast complementary assay. Overexpression of SUI1 and SUI2 caused outgrowths of internodes during vegetative development, and we showed that expression patterns of Oryza Sativa Homeobox 15 (OSH15) and Histone4 were impaired. Furthermore, genome-wide gene expression analysis revealed that overexpression and RNA knockdown of SUI-family genes affected downstream gene expression related to phospholipid metabolic pathways. Moreover, using Ultra-performance liquid chromatography-quadrupole time of flight-mass spectrometry, we analyzed PS contents in different genetic backgrounds of rice and showed that the quantity of very long chain fatty acids PS is affected by transgene of SUI-family genes. Our study reveals a new mechanism conveyed by the SUI1 pathway and provides evidence to link lipid metabolism with plant stem cell maintenance.

Fluctuating observation time ensembles in the thermodynamics of trajectories

NASA Astrophysics Data System (ADS)

Budini, Adrián A.; Turner, Robert M.; Garrahan, Juan P.

2014-03-01

The dynamics of stochastic systems, both classical and quantum, can be studied by analysing the statistical properties of dynamical trajectories. The properties of ensembles of such trajectories for long, but fixed, times are described by large-deviation (LD) rate functions. These LD functions play the role of dynamical free energies: they are cumulant generating functions for time-integrated observables, and their analytic structure encodes dynamical phase behaviour. This ‘thermodynamics of trajectories’ approach is to trajectories and dynamics what the equilibrium ensemble method of statistical mechanics is to configurations and statics. Here we show that, just like in the static case, there are a variety of alternative ensembles of trajectories, each defined by their global constraints, with that of trajectories of fixed total time being just one of these. We show how the LD functions that describe an ensemble of trajectories where some time-extensive quantity is constant (and large) but where total observation time fluctuates can be mapped to those of the fixed-time ensemble. We discuss how the correspondence between generalized ensembles can be exploited in path sampling schemes for generating rare dynamical trajectories.

Memory processing in great apes: the effect of time and sleep

PubMed Central

Martin-Ordas, Gema; Call, Josep

2011-01-01

Following encoding, memory remains temporarily vulnerable to disruption. Consolidation refers to offline time-dependent processes that continue after encoding and stabilize, transform or enhance the memory trace. Memory consolidation resulting from sleep has been reported for declarative and non-declarative memories in humans. We first investigated the temporal course of memory retrieval in chimpanzees, bonobos and orangutans. We found that the amount of retrieved information was time dependent: apes' performance degraded after 1 and 2 h, stabilized after 4 h, started to increase after 8 and 12 h and fully recovered after 24 h. Second, we show that although memories during wakefulness were highly vulnerable to interference from events similar to those witnessed during the original encoding event, an intervening period of sleep not only stabilized apes' memories into more permanent ones but also protected them against interference. PMID:21632621

Memory processing in great apes: the effect of time and sleep.

PubMed

Martin-Ordas, Gema; Call, Josep

2011-12-23

Following encoding, memory remains temporarily vulnerable to disruption. Consolidation refers to offline time-dependent processes that continue after encoding and stabilize, transform or enhance the memory trace. Memory consolidation resulting from sleep has been reported for declarative and non-declarative memories in humans. We first investigated the temporal course of memory retrieval in chimpanzees, bonobos and orangutans. We found that the amount of retrieved information was time dependent: apes' performance degraded after 1 and 2 h, stabilized after 4 h, started to increase after 8 and 12 h and fully recovered after 24 h. Second, we show that although memories during wakefulness were highly vulnerable to interference from events similar to those witnessed during the original encoding event, an intervening period of sleep not only stabilized apes' memories into more permanent ones but also protected them against interference.

Divided attention reduces resistance to distraction at encoding but not retrieval.

PubMed

Weeks, Jennifer C; Hasher, Lynn

2017-08-01

Older adults show implicit memory for previously seen distraction, an effect attributed to poor attentional control. It is unclear whether this effect results from lack of control over encoding during the distraction task, lack of retrieval constraint during the test task, or both. In the present study, we simulated poor distraction control in young adults using divided attention at encoding, at retrieval, at both times, or not at all. The encoding task was a 1-back task on pictures with distracting superimposed letter strings, some of which were words. The retrieval task was a word fragment completion task testing implicit memory for the distracting words. Attention was divided using an auditory odd digit detection task. Dividing attention at encoding, but not at retrieval, resulted in significant priming for distraction, which suggests that control over encoding processes is a primary determinant of distraction transfer in populations with low inhibitory control (e.g. older adults).