Encoding information in synthetic metabolomes.
Ontology highlight
ABSTRACT:
SUBMITTER: Kennedy E
PROVIDER: S-EPMC6608926 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:A new approach to controlling the flow of a plasmatic electron packet at the interface between metallic and dielectric layers is described. The proposed metamaterial structure operates in the optical frequency range and can be used as a digital processing filter. It exhibits two double negative resonances and one special passband region, while the existence of a metal-dielectric nano-tunnel enhances electromagnetic wave-metal interactions. The structural arrangement of this metamaterial coupled with the tunnel layer can effectively control the electric field and allows digital encoding of electron packets.
| S-EPMC7039869 | biostudies-literature
Project description:Synthetic DNA is a growing alternative to electronic-based technologies in fields such as data storage, product tagging, or signal processing. Its value lies in its characteristic attributes, namely Watson-Crick base pairing, array synthesis, sequencing, toehold displacement and polymerase chain reaction (PCR) capabilities. In this review, we provide an overview of the most prevalent applications of synthetic DNA that could shape the future of information technology. We emphasize the reasons why the biomolecule can be a valuable alternative for conventional electronic-based media, and give insights on where the DNA-analog technology stands with respect to its electronic counterparts.
| S-EPMC8763860 | biostudies-literature
Project description: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.
| S-EPMC2039771 | biostudies-literature
Project description:In a dynamic world, accurate beliefs about the environment are vital for survival, and individuals should therefore regularly seek out new information with which to update their beliefs. This aspect of behaviour is not well captured by standard theories of decision making, and the neural mechanisms of information seeking remain unclear. One recent theory posits that valuation of information results from representation of informative stimuli within canonical neural reward-processing circuits, even if that information lacks instrumental use. We investigated this question by recording EEG from twenty-three human participants performing a non-instrumental information-seeking task. In this task, participants could pay a monetary cost to receive advance information about the likelihood of receiving reward in a lottery at the end of each trial. Behavioural results showed that participants were willing to incur considerable monetary costs to acquire early but non-instrumental information. Analysis of the event-related potential elicited by informative cues revealed that the feedback-related negativity independently encoded both an information prediction error and a reward prediction error. These findings are consistent with the hypothesis that information seeking results from processing of information within neural reward circuits, and suggests that information may represent a distinct dimension of valuation in decision making under uncertainty.
| S-EPMC5904167 | biostudies-literature
Project description:Brain decoding can predict visual perception from non-invasive electrophysiological data by combining information across multiple channels. However, decoding methods typically conflate the composite and distributed neural processes underlying perception that are together present in the signal, making it unclear what specific aspects of the neural computations involved in perception are reflected in this type of macroscale data. Using MEG data recorded while participants viewed a large number of naturalistic images, we analytically decomposed the brain signal into its oscillatory and non-oscillatory components, and used this decomposition to show that there are at least three dissociable stimulus-specific aspects to the brain data: a slow, non-oscillatory component, reflecting the temporally stable aspect of the stimulus representation; a global phase shift of the oscillation, reflecting the overall speed of processing of specific stimuli; and differential patterns of phase across channels, likely reflecting stimulus-specific computations. Further, we show that common cognitive interpretations of decoding analysis, in particular about how representations generalize across time, can benefit from acknowledging the multicomponent nature of the signal in the study of perception.
| S-EPMC8568005 | biostudies-literature
Project description:In most animals, natural stimuli are characterized by a high degree of redundancy, limiting the ensemble of ecologically valid stimuli to a significantly reduced subspace of the representation space. Neural encodings can exploit this redundancy and increase sensing efficiency by generating low-dimensional representations that retain all information essential to support behavior. In this study, we investigate whether such an efficient encoding can be found to support a broad range of echolocation tasks in bats. Starting from an ensemble of echo signals collected with a biomimetic sonar system in natural indoor and outdoor environments, we use independent component analysis to derive a low-dimensional encoding of the output of a cochlear model. We show that this compressive encoding retains all essential information. To this end, we simulate a range of psycho-acoustic experiments with bats. In these simulations, we train a set of neural networks to use the encoded echoes as input while performing the experiments. The results show that the neural networks' performance is at least as good as that of the bats. We conclude that our results indicate that efficient encoding of echo information is feasible and, given its many advantages, very likely to be employed by bats. Previous studies have demonstrated that low-dimensional encodings allow for task resolution at a relatively high level. In contrast to previous work in this area, we show that high performance can also be achieved when low-dimensional filters are derived from a data set of realistic echo signals, not tailored to specific experimental conditions.
| S-EPMC8270447 | biostudies-literature
Project description:Humans and other species continually perform microscopic eye movements, even when attending to a single point. These movements, which include drifts and microsaccades, are under oculomotor control, elicit strong neural responses, and have been thought to serve important functions. The influence of these fixational eye movements on the acquisition and neural processing of visual information remains unclear. Here, we show that during viewing of natural scenes, microscopic eye movements carry out a crucial information-processing step: they remove predictable correlations in natural scenes by equalizing the spatial power of the retinal image within the frequency range of ganglion cells' peak sensitivity. This transformation, which had been attributed to center-surround receptive field organization, occurs prior to any neural processing and reveals a form of matching between the statistics of natural images and those of normal eye movements. We further show that the combined effect of microscopic eye movements and retinal receptive field organization is to convert spatial luminance discontinuities into synchronous firing events, beginning the process of edge detection. Thus, microscopic eye movements are fundamental to two goals of early visual processing: redundancy reduction and feature extraction.
| S-EPMC3332095 | biostudies-literature
Project description:Information that is encoded in relation to the self has been shown to be better remembered, yet reports have disagreed on whether the memory benefit from self-referential encoding extends to source memory (the context in which information was learned). In this study, we investigated the self-referential effect on source memory in recollection and familiarity-based memory. Using a Remember/Know paradigm, we compared source memory accuracy under self-referential encoding and semantic encoding. Two types of source information were included, a "peripheral" source which was not inherent to the encoding activity, and a source information about the encoding context. We observed the facilitation in item memory from self-referential encoding compared to semantic encoding in recollection but not in familiarity-based memory. The self-referential benefit to source accuracy was observed in recollection memory, with source memory for the encoding context being stronger in the self-referential condition. No significant self-referential effect was observed with regards to peripheral source information (information not required for the participant to focus on), suggesting not all source information benefit from self-referential encoding. Self-referential encoding also resulted in a higher ratio of "Remember/Know" responses rate than semantically encoded items, denoting stronger recollection. These results suggest self-referential encoding creates a richer, more detailed memory trace which can be recollected later on.
| S-EPMC8049320 | biostudies-literature
Project description:High-throughput in vitro methods have been extensively applied to identify linear information that encodes peptide recognition. However, these methods are limited in number of peptides, sequence variation, and length of peptides that can be explored, and often produce solutions that are not found in the cell. Despite the large number of methods developed to attempt addressing these issues, the exhaustive search of linear information encoding protein-peptide recognition has been so far physically unfeasible. Here, we describe a strategy, called DALEL, for the exhaustive search of linear sequence information encoded in proteins that bind to a common partner. We applied DALEL to explore binding specificity of SH3 domains in the budding yeast Saccharomyces cerevisiae. Using only the polypeptide sequences of SH3 domain binding proteins, we succeeded in identifying the majority of known SH3 binding sites previously discovered either in vitro or in vivo. Moreover, we discovered a number of sites with both non-canonical sequences and distinct properties that may serve ancillary roles in peptide recognition. We compared DALEL to a variety of state-of-the-art algorithms in the blind identification of known binding sites of the human Grb2 SH3 domain. We also benchmarked DALEL on curated biological motifs derived from the ELM database to evaluate the effect of increasing/decreasing the enrichment of the motifs. Our strategy can be applied in conjunction with experimental data of proteins interacting with a common partner to identify binding sites among them. Yet, our strategy can also be applied to any group of proteins of interest to identify enriched linear motifs or to exhaustively explore the space of linear information encoded in a polypeptide sequence. Finally, we have developed a webserver located at http://michnick.bcm.umontreal.ca/dalel, offering user-friendly interface and providing different scenarios utilizing DALEL.
| S-EPMC5417721 | biostudies-literature
Project description:Urodynamic status must interact with arousal and attentional processes so that voiding occurs under appropriate conditions. To elucidate the central encoding of this visceral demand, multisite recordings were made within a putative pontine-cortical micturition circuit from the pontine micturition center (PMC), locus coeruleus (LC) and medial prefrontal cortex (mPFC) during cystometry in unanesthetized rats. PMC neurons had homogeneous firing patterns, characterized by tonic activity and phasic bursts that were temporally associated with distinct phases of the micturition cycle. LC and cortical activation became synchronized 20-30 s prior to micturition. During this pre-micturition interval, a theta oscillation developed in the LC, the mPFC desynchronized and LC-mPFC coherence increased in the theta frequency range. The temporal offset between the shift in LC-mPFC network activity and micturition may allow time to disengage from ongoing behaviors unrelated to micturition and initiate specific voiding behaviors so that micturition occurs in environmentally and socially appropriate conditions.
| S-EPMC5714501 | biostudies-literature