The Influence of Closeness Centrality on Lexical Processing.
Ontology highlight
ABSTRACT:
SUBMITTER: Goldstein R
PROVIDER: S-EPMC5622968 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BackgroundWe examine the accuracy of enzyme catalytic residue predictions from a network representation of protein structure. In this model, amino acid alpha-carbons specify vertices within a graph and edges connect vertices that are proximal in structure. Closeness centrality, which has shown promise in previous investigations, is used to identify important positions within the network. Closeness centrality, a global measure of network centrality, is calculated as the reciprocal of the average distance between vertex i and all other vertices.ResultsWe benchmark the approach against 283 structurally unique proteins within the Catalytic Site Atlas. Our results, which are inline with previous investigations of smaller datasets, indicate closeness centrality predictions are statistically significant. However, unlike previous approaches, we specifically focus on residues with the very best scores. Over the top five closeness centrality scores, we observe an average true to false positive rate ratio of 6.8 to 1. As demonstrated previously, adding a solvent accessibility filter significantly improves predictive power; the average ratio is increased to 15.3 to 1. We also demonstrate (for the first time) that filtering the predictions by residue identity improves the results even more than accessibility filtering. Here, we simply eliminate residues with physiochemical properties unlikely to be compatible with catalytic requirements from consideration. Residue identity filtering improves the average true to false positive rate ratio to 26.3 to 1. Combining the two filters together has little affect on the results. Calculated p-values for the three prediction schemes range from 2.7E-9 to less than 8.8E-134. Finally, the sensitivity of the predictions to structure choice and slight perturbations is examined.ConclusionOur results resolutely confirm that closeness centrality is a viable prediction scheme whose predictions are statistically significant. Simple filtering schemes substantially improve the method's predicted power. Moreover, no clear effect on performance is observed when comparing ligated and unligated structures. Similarly, the CC prediction results are robust to slight structural perturbations from molecular dynamics simulation.
| S-EPMC1876251 | biostudies-literature
Project description:In spite of the reduced visual acuity, parafoveal information plays an important role in natural reading. However, competing models on reading disagree on whether words are previewed parafoveally at the lexical level. We find neural evidence for lexical parafoveal processing by combining a rapid invisible frequency tagging (RIFT) approach with magnetoencephalography (MEG) and eye-tracking. In a silent reading task, target words are tagged (flickered) subliminally at 60 Hz. The tagging responses measured when fixating on the pre-target word reflect parafoveal processing of the target word. We observe stronger tagging responses during pre-target fixations when followed by low compared with high lexical frequency targets. Moreover, this lexical parafoveal processing is associated with individual reading speed. Our findings suggest that reading unfolds in the fovea and parafovea simultaneously to support fluent reading.
| S-EPMC8413448 | biostudies-literature
Project description:Cooperation played a significant role in the self-organization and evolution of living organisms. Both network topology and the initial position of cooperators heavily affect the cooperation of social dilemma games. We developed a novel simulation program package, called 'NetworGame', which is able to simulate any type of social dilemma games on any model, or real world networks with any assignment of initial cooperation or defection strategies to network nodes. The ability of initially defecting single nodes to break overall cooperation was called as 'game centrality'. The efficiency of this measure was verified on well-known social networks, and was extended to 'protein games', i.e. the simulation of cooperation between proteins, or their amino acids. Hubs and in particular, party hubs of yeast protein-protein interaction networks had a large influence to convert the cooperation of other nodes to defection. Simulations on methionyl-tRNA synthetase protein structure network indicated an increased influence of nodes belonging to intra-protein signaling pathways on breaking cooperation. The efficiency of single, initially defecting nodes to convert the cooperation of other nodes to defection in social dilemma games may be an important measure to predict the importance of nodes in the integration and regulation of complex systems. Game centrality may help to design more efficient interventions to cellular networks (in forms of drugs), to ecosystems and social networks.
| S-EPMC3696096 | biostudies-literature
Project description:Visual reaction times to target pictures after naming events are an informative measurement in language acquisition research, because gaze shifts measured in looking-while-listening paradigms are an indicator of infants' lexical speed of processing. This measure is very useful, as it can be applied from a young age onwards and has been linked to later language development. However, to obtain valid reaction times, the infant is required to switch the fixation of their eyes from a distractor to a target object. This means that usually at least half the trials have to be discarded-those where the participant is already fixating the target at the onset of the target word-so that no reaction time can be measured. With few trials, reliability suffers, which is especially problematic when studying individual differences. In order to solve this problem, we developed a gaze-triggered looking-while-listening paradigm. The trials do not differ from the original paradigm apart from the fact that the target object is chosen depending on the infant's eye fixation before naming. The object the infant is looking at becomes the distractor and the other object is used as the target, requiring a fixation switch, and thus providing a reaction time. We tested our paradigm with forty-three 18-month-old infants, comparing the results to those from the original paradigm. The Gaze-triggered paradigm yielded more valid reaction time trials, as anticipated. The results of a ranked correlation between the conditions confirmed that the manipulated paradigm measures the same concept as the original paradigm.
| S-EPMC7575460 | biostudies-literature
Project description:It has been proposed that poor reading abilities in deaf readers might be related to weak connections between the orthographic and lexical-semantic levels of processing. Here we used event related potentials (ERPs), known for their excellent time resolution, to examine whether lexical feedback modulates early orthographic processing. Twenty congenitally deaf readers made lexical decisions to target words and pseudowords. Each of those target stimuli could be preceded by a briefly presented matched-case or mismatched-case identity prime (e.g., ALTAR-ALTAR vs. altar- ALTAR). Results showed an early effect of case overlap at the N/P150 for all targets. Critically, this effect disappeared for words but not for pseudowords, at the N250-an ERP component sensitive to orthographic processing. This dissociation in the effect of case for word and pseudowords targets provides strong evidence of early automatic lexical-semantic feedback modulating orthographic processing in deaf readers. Interestingly, despite the dissociation found in the ERP data, behavioural responses to words still benefited from the physical overlap between prime and target, particularly in less skilled readers and those with less experience with words. Overall, our results support the idea that skilled deaf readers have a stronger connection between the orthographic and the lexical-semantic levels of processing.
| S-EPMC6707270 | biostudies-literature
Project description:There is extensive evidence that the segmental (i.e., phonemic) layer of phonology is routinely activated during reading, but little is known about whether phonological activation extends beyond phonemes to subsegmental layers (which include articulatory information, such as voicing) and suprasegmental layers (which include prosodic information, such as lexical stress). In three proofreading experiments, we show that spelling errors are detected more reliably in syllables that are stressed than in syllables that are unstressed if comprehension is a goal of the reader, indicating that suprasegmental phonology is both active during silent reading and can influence orthographic processes. In Experiment 1, participants received instructions to read for both errors and comprehension, and we found that the effect of lexical stress interacted with linguistic predictability, such that detection of errors in more predictable words was aided by stress but detection of errors in less predictable words was not. This finding suggests that lexical stress patterns can be accessed prelexically if an upcoming word is sufficiently predictable from context. Participants with stronger vocabularies showed decreased effects of stress on task performance, which is consistent with previous findings that more skilled readers are less swayed by phonological information in decisions about orthographic form. In two subsequent experiments, participants were instructed to read only for errors (Experiment 2) or only for comprehension (Experiment 3); the effect of stress disappeared when participants read for errors and reappeared when participants read for comprehension, reconfirming our hypothesis that predictability is a driver of lexical stress effects. In all experiments, errors were detected more reliably in words that were difficult to predict from context than in words that were highly predictable. Taken together, this series of experiments contributes two important findings to the field of reading and cognition: (1) The prosodic property of lexical stress can influence orthographic processing, and (2) Predictability inhibits the detection of errors in written language processing.
| S-EPMC4746312 | biostudies-literature
Project description:Language comprehension involves both sub-lexical (e.g., phonological) and lexical-semantic processing. We conducted a task using functional magnetic resonance imaging (fMRI) to compare the processing of verbs in these two domains. Additionally, we examined the representation of concrete-motor and abstract-non-motor concepts by including two semantic categories of verbs: motor and mental. The findings indicate that sub-lexical processing during the reading of pseudo-verbs primarily involves the left dorsal stream of the perisylvian network, while lexical-semantic representation during the reading of verbs predominantly engages the ventral stream. According to the embodied or grounded cognition approach, modality-specific mechanisms (such as sensory-motor systems) and the well-established multimodal left perisylvian network contribute to the semantic representation of both concrete and abstract verbs. Our study identified the visual system as a preferential modality-specific system for abstract-mental verbs, which exhibited functional connectivity with the right crus I/lobule VI of the cerebellum. Taken together, these results confirm the dissociation between sub-lexical and lexical-semantic processing and provide neurobiological evidence of functional coupling between specific visual modality regions and the right cerebellum, forming a network that supports the semantic representation of abstract concepts. Further, the results shed light on the underlying mechanisms of semantic processing and contribute to our understanding of how the brain processes abstract concepts.
| S-EPMC10501569 | biostudies-literature
Project description:Reciprocated trust plays a critical role in forming and maintaining relationships, and has consistently been shown to implicate neural circuits involved in reward-related processing and social cognition. Less is known about neural network connectivity during social interactions involving trust, however, particularly as a function of closeness between an investor and a trustee. We examined network reactivity and connectivity in participants who played an economic trust game with close friends, strangers and a computer. Network reactivity analyses showed enhanced activation of the default-mode network (DMN) to social relative to non-social outcomes. A novel network psychophysiological interaction (nPPI) analysis revealed enhanced connectivity between the DMN and the superior frontal gyrus and superior parietal lobule when experiencing reciprocated vs violated trust from friends relative to strangers. Such connectivity tracked with differences in self-reported social closeness with these partners. Interestingly, reactivity of the executive control network (ECN), involved in decision processes, demonstrated no social vs non-social preference, and ECN-ventral striatum connectivity did not track social closeness. Taken together, these novel findings suggest that DMN interacts with components of attention and control networks to signal the relative importance of positive experiences with close others vs strangers.
| S-EPMC7235957 | biostudies-literature
Project description:Some early studies of people with aphasia reported strikingly better performance on lexical than on sublexical speech perception tasks. These findings challenged the claim that lexical processing depends on sublexical processing and suggested that acoustic information could be mapped directly to lexical representations. However, Dial and Martin (Neuropsychologia 96: 192-212, 2017) argued that these studies failed to match the discriminability of targets and distractors for the sublexical and lexical stimuli and showed that when using closely matched tasks with natural speech tokens, no patient performed substantially better at the lexical than at the sublexical processing task. In the current study, we sought to provide converging evidence for the dependence of lexical on sublexical processing by examining the perception of synthetic speech stimuli varied on a voice-onset time continuum using eye-tracking methodology, which is sensitive to online speech perception processes. Eight individuals with aphasia and ten age-matched controls completed two visual world paradigm tasks: phoneme (sublexical) and word (lexical) identification. For both identification and eye-movement data, strong correlations were observed between the sublexical and lexical tasks. Critically, no patient within the control range on the lexical task was impaired on the sublexical task. Overall, the current study supports the claim that lexical processing depends on sublexical processing. Implications for inferring deficits in people with aphasia and the use of sublexical tasks to assess sublexical processing are also discussed.
| S-EPMC6615952 | biostudies-literature
Project description:In tonal languages such as Chinese, lexical tone with varying pitch contours serves as a key feature to provide contrast in word meaning. Similar to phoneme processing, behavioral studies have suggested that Chinese tone is categorically perceived. However, its underlying neural mechanism remains poorly understood. By conducting cortical surface recordings in surgical patients, we revealed a cooperative cortical network along with its dynamics responsible for this categorical perception. Based on an oddball paradigm, we found amplified neural dissimilarity between cross-category tone pairs, rather than between within-category tone pairs, over cortical sites covering both the ventral and dorsal streams of speech processing. The bilateral superior temporal gyrus (STG) and the middle temporal gyrus (MTG) exhibited increased response latencies and enlarged neural dissimilarity, suggesting a ventral hierarchy that gradually differentiates the acoustic features of lexical tones. In addition, the bilateral motor cortices were also found to be involved in categorical processing, interacting with both the STG and the MTG and exhibiting a response latency in between. Moreover, the motor cortex received enhanced Granger causal influence from the semantic hub, the anterior temporal lobe, in the right hemisphere. These unique data suggest that there exists a distributed cooperative cortical network supporting the categorical processing of lexical tone in tonal language speakers, not only encompassing a bilateral temporal hierarchy that is shared by categorical processing of phonemes but also involving intensive speech-motor interactions over the right hemisphere, which might be the unique machinery responsible for the reliable discrimination of tone identities.
| S-EPMC5699060 | biostudies-literature