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PubMed2006

Norwegian norms and factor-structure of phonemic and semantic word list generation.

Word list generation (WLG) tasks are used world wide as measures of executive function, although the tests are sensitive also to deficits in other cognitive functions. Norms derived from English-speaking samples are often used in Norway, even though the consequences of language differences are not yet been assessed. The reliability of WLG testing in Norway is increased by the norms presented in the first part of the study. The validity of WLG tests as measures of executive function is addressed in the second part, by performing a factor-analysis of neuropsychological performance in a mixed psychiatric sample. Education contributed most to performance. There were no sex-differences in overall performance. Factor analysis indicated that phonemic WLG is a more specific measure of executive function than semantic WLG. Semantic WLG correlated higher with basal processing speed, thus being more sensitive to aging. In conclusion the clinical neuropsychologist is advised to control for reduction in basal processing speed before interpreting WLG scores as specific deficits in executive function. The Norwegian norms correspond well with most comparable studies in other languages, thus failing to show any language specific effects.

Adolescent↗

PubMed2006

Primacy of functional knowledge in semantic representations: the case of living and nonliving things.

In 3 experiments, participants decided whether sensory and functional features were true of living and nonliving concepts. In Experiments 1 and 2, concepts were presented twice: test phase followed study phase after either 3 min (Experiment 1) or 3 s (Experiment 2). At test, concepts were paired with the same feature as that at study, or a different feature from either the same modality (within-modality priming) or another modality (cross-modality priming). In both experiments functional decisions were faster than sensory decisions for living and nonliving concepts. Whilst no semantic priming occurred between study and test in Experiment 1, the shorter study-test interval of Experiment 2 did lead to test phase semantic priming. Here there was greater within- than cross-modality priming for sensory decisions, but equivalent within- and cross-modality priming for functional decisions owing to significantly greater facilitation of functional decisions from prior sensory decisions than vice versa. Experiment 3 involved a single verification phase: For half the participants the feature name preceded the concept name, and for half the concept name preceded the feature name. The functional processing advantage persisted irrespective of presentation order. Results suggest that functional information is central to the representation of all concepts: Function is processed faster than sensory information and is activated obligatorily.

Adolescent↗

PubMed1996

Spatial orienting controlled without awareness: a semantically based implicit learning effect.

Three experiments tested whether spatial attention can be influenced by a predictive relation between incidental information and the location of target events. Subjects performed a simple dot detection task; 600 msec prior to each target a word was presented briefly 5 degrees to the left or right of fixation. There was a predictive relationship between the semantic category (living or non-living) of the words and target location. However, subjects were instructed to ignore the words, and a post-experiment questionnaire confirmed that they remained unaware of the word-target relationship. In all three experiments, given some practice on the task, response times were faster when target appeared at likely ( p = 0.8 ), compared to unlikely ( p = 0.2 ) locations, in relation to lateral word category. Experiments 2 and 3 confirmed that this effect was driven by semantic encoding of the irrelevant words, and not by repetition of individual stimuli. Theoretical implications of this finding are discussed.

Adult↗

PubMed2025

Accurate prediction of toxicity peptide and its function using multi-view tensor learning and latent semantic learning framework.

MOTIVATION: Therapeutic peptide is an important ingredient in the treatment of various diseases and drug discovery. The toxicity of peptides is one of the major challenges in peptide drug therapy. With the abundance of therapeutic peptides generated in the post-genomics era, it is a challenge to promptly identify toxicity peptides using computational methods. Although several efforts have been made, few algorithms are designed to identify whether a query peptide exhibits toxicity. Considering the varied levels of biological activities, the toxicity peptides should be further classified into multi-functional peptides. RESULTS: This study introduces a two-level predictor, ToxPre-2L, developed using the multi-view tensor learning and latent semantic learning framework. The proposed method utilized multi-label learning with feature induced labels to avoid the redundancy of information from each view. Then the multi-view tensor learning was employed to establish the latent semantic information among different views, while low-rank constraint learning was leveraged to exploit the correlation information among multi-labels. Finally, we constructed an updated toxicity peptide benchmark dataset to assess the effectiveness of the proposed method. Experimental results demonstrated that ToxPre-2L achieves a better performance than alternative computational methods in the prediction of toxicity peptides and their multi-functional types. AVAILABILITY AND IMPLEMENTATION: The source code and data of ToxPre-2L can be accessed at http://bliulab.net/ToxPre-2L.

Peptides↗

PubMed2025

ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation.

MOTIVATION: Hypothesis generation is a fundamental problem in biomedical text mining that aims to generate ideas that are new, interesting, and plausible by discovering unexplored links between biomedical concepts. Despite significant advances made by existing approaches, they do not fully leverage the evolutionary properties of biomedical concepts. This is limiting because scientific knowledge continually evolves over time, with new facts being added and old ones becoming obsolete. Thus, it is crucial to capture the evolutionary properties of biomedical concepts from multiple perspectives (e.g. spatial, temporal, and semantic) to generate hypotheses that reflect the up-to-date information landscape of the biomedical domain. RESULTS: We introduce a novel framework, ConceptDrift, that models the hypothesis generation task as a sequence of temporal graphlets and simultaneously encodes spatial, temporal, and semantic change. Unlike existing approaches that treat these dimensions independently, ConceptDrift is the first to provide a holistic understanding of concept evolution by integrating them into a unified framework. Grounded in the theories of the Distributional Hypothesis and Conceptual Change, our method adapts these principles to the unique challenges of large-scale biomedical literature. We conduct extensive experiments across multiple datasets and demonstrate that ConceptDrift consistently outperforms state-of-the-art baselines in generating accurate and meaningful hypotheses. Our framework shows immediate practical benefits for web-based literature mining tools in life sciences and biomedicine, offering more robust and predictive feature representations. AVAILABILITY AND IMPLEMENTATION: https://github.com/amir-hassan25/ConceptDrift (DOI: 10.6084/m9.figshare.29975476).

Semantics↗

PubMed2005

A semantic analysis of the annotations of the human genome.

The correct interpretation of any biological experiment depends in an essential way on the accuracy and consistency of the existing annotation databases. Such databases are ubiquitous and used by all life scientists in most experiments. However, it is well known that such databases are incomplete and many annotations may also be incorrect. In this paper we describe a technique that can be used to analyze the semantic content of such annotation databases. Our approach is able to extract implicit semantic relationships between genes and functions. This ability allows us to discover novel functions for known genes. This approach is able to identify missing and inaccurate annotations in existing annotation databases, and thus help improve their accuracy. We used our technique to analyze the current annotations of the human genome. From this body of annotations, we were able to predict 212 additional gene-function assignments. A subsequent literature search found that 138 of these gene-functions assignments are supported by existing peer-reviewed papers. An additional 23 assignments have been confirmed in the meantime by the addition of the respective annotations in later releases of the Gene Ontology database. Overall, the 161 confirmed assignments represent 75.95% of the proposed gene-function assignments. Only one of our predictions (0.4%) was contradicted by the existing literature. We could not find any relevant articles for 50 of our predictions (23.58%). The method is independent of the organism and can be used to analyze and improve the quality of the data of any public or private annotation database.

Chromosome Mapping↗

PubMed1977

Perceptual, semantic and phonetic aspects of elementary language processes in split-brain patients.

Patients with total forebrain commissurotomy were examined on three tests of elementary linguistic ability. We found that the right hemisphere was dominant for the visual recognition of words when no semantic or phonetic decoding was required. The left hemisphere assumed control of behaviour when written words had to be matched semantically to pictures, though the right hemisphere was also competent at this task. On a test of rhyming, the left hemisphere was not only dominant, but was vastly superior to the right which displayed little, if any, ability. We suggest that the two hemispheres are basically differentiated with respect to their generative, constructive capacities in language, as in other functions of intelligence.

Adolescent↗

PubMed1998

Acquisition of post-morbid vocabulary and semantic facts in the absence of episodic memory.

Disagreement exists in the literature over whether it is possible for new semantic (factual) information to be learned in the absence of episodic (event) memory. We report the case of R.S., a 49-year-old amnesic man, who we found to have acquired information about famous people, public events and new vocabulary during the 13-year period since he became amnesic, despite having no measurable anterograde episodic memory function and a profound loss of autobiographical memory. These data suggest that at least some severe amnesics are able to acquire new semantic knowledge, provided that critical temporal neocortical regions are spared. We discuss these findings in the context of recent connectionist models of memory.

Amnesia↗

PubMed2000

Semantic dementia with ubiquitin-positive tau-negative inclusion bodies.

Three cases are reported with dementia and ubiquitin-positive but tau-negative inclusion bodies. All patients had a semantic dementia and the clinical details of two of these have been published as the first description of a selective semantic memory impairment. The original diagnosis had been of Pick's disease based on frontotemporal atrophy, but re-examination has revealed ubiquitin-positive but tau-negative inclusions as well as neurites in the frontotemporal cortices and ubiquitin-positive, intracytoplasmic inclusions in the granule cells of the dentate fascia. These inclusions are identical to those reported in association with amyotrophic lateral sclerosis (motor neuron disease), but none were seen in brainstem or spinal cord motor neurons.

Dementia↗

PubMed2003

Spatial coding of semantic information: knowledge of country and city names depends on their geographical proximity.

We report the case of a patient, A.Z., with a refractory disorder of semantic processing. Using a number of spoken word-written word matching paradigms, her comprehension of the broad proper nouns category of place names was investigated. In addition to being sensitive to temporal factors, A.Z.'s ability to identify country or city names accurately was significantly worse when selecting a target from an array of geographically close rather than distant places. The influence of geographical proximity and location was observed even when identifying proximal and distal English towns, but not with less well-known American states. These close and distant effects are attributed to the build-up of refractoriness in representations with shared neural circuitry. Our findings reveal a previously undocumented level of fine-grain organization in this domain of semantic space. It is argued that information about geographical proximity cannot be encoded in purely verbal or visual terms. Consequently, we propose the existence of a separate module of spatially encoded information within conceptual knowledge.

Acoustic Stimulation↗

PubMed2006

Mood states modulate activity in semantic brain areas during emotional word encoding.

It is controversially discussed whether or not mood-congruent recall (i.e., superior recall for mood-congruent material) reflects memory encoding processes or reduces to processes during retrieval. We therefore investigated the neurophysiological correlates of mood-dependent memory during emotional word encoding. Event-related potentials (ERPs) were recorded while participants in good or bad mood states encoded words of positive and negative valence. Words were either complete or had to be generated from fragments. Participants had to memorize words for subsequent recall. Mood-congruent recall tended to be largest in good mood for generated words. Starting at 200 ms, mood-congruent ERP effects of word valence were obtained in good, but not in bad mood. Only for good mood, source analysis revealed valence-related activity in ventral temporal cortex and for generated words also in prefrontal cortex. These areas are known to be involved in semantic processing. Our findings are consistent with the view that mood-congruent recall depends on the activation of mood-congruent semantic knowledge during encoding. Incoming stimuli are more readily transformed according to stored knowledge structures in good mood particularly during generative encoding tasks. The present results therefore show that mood-congruent memory originates already during encoding and cannot be reduced to strategic processes during retrieval.

Adult↗

PubMed2000

Evidence for separate perceptive and semantic memories for odours: a priming experiment.

Sixty-four subjects participated in an olfactory priming experiment comprising separate study and test phases. Priming was measured within the olfactory modality (intramodal condition) and from the visual modality to the olfactory modality (intermodal condition). In the study phase of the intramodal condition, subjects were exposed twice to a series of odours: once performing a semantic orientation task (deciding which of seven categories odour stimuli belonged to) and once performing a perceptual orientation task (judging the intensity, the hedonicity and the familiarity of odour stimuli). Half of the odour stimuli corresponded to edible products, the other half did not. The study phase of the intermodal condition was similar, with the exception that the names of the odours (instead of the odours themselves) were presented. In the test phase, subjects were presented with primed and non-primed odour targets and had to decide as fast as possible whether the target corresponded to an edible product or not. Response times and types were recorded by a computer. The analysis of response times revealed a priming effect in the intramodal condition only. Results are discussed in terms of separate perceptual and semantic subsystems that store odour representations.

Adolescent↗

PubMed2006

Identification of latent variables in a semantic odor profile database using principal component analysis.

Many classifications of odors have been proposed, but none of them have yet gained wide acceptance. Odor sensation is usually described by means of odor character descriptors. If these semantic profiles are obtained for a large diversity of compounds, the resulting database can be considered representative of odor perception space. Few of these comprehensive databases are publicly available, being a valuable source of information for fragrance research. Their statistical analysis has revealed that the underlying structure of odor space is high dimensional and not governed by a few primary odors. In a new effort to study the underlying sensory dimensions of the multivariate olfactory perception space, we have applied principal component analysis to a database of 881 perfume materials with semantic profiles comprising 82 odor descriptors. The relationships identified between the descriptors are consistent with those reported in similar studies and have allowed their classification into 17 odor classes.

Cluster Analysis↗

PubMed2001

Verb comprehension in frontotemporal degeneration: the role of grammatical, semantic and executive components.

Verb comprehension has been associated with the left frontal cortex, but assessments of verb comprehension in frontotemporal degeneration (FTD) have been rare. This study assessed word-picture matching for verbs and nouns under two conditions: alone (baseline) and during concurrent performance of a secondary task. In addition, we correlated FTD patients' verb comprehension with their performance on measures of executive resources and language. We found that FTD patients were significantly less accurate and required significantly longer to make word-picture matching decisions about verbs compared with nouns at baseline. During concurrent performance of a secondary task, accuracy decreased and response latencies became prolonged for nouns to the point that these measures equaled the performance with verbs at baseline. Verb comprehension accuracy was significantly correlated with the performance on executive measures such as category naming fluency, the Stroop test, and the Trail Making Test Part B (Trails B test). Assessment of FTD patient subgroups revealed distinct profiles of performance, suggesting that several factors contribute to verb comprehension in FTD. Verb comprehension in FTD patients with a dysexecutive syndrome (EXEC, n = 10) was sensitive to concurrent performance of a secondary task, and their verb comprehension accuracy correlated with the time required to complete executive measures such as the Stroop test and the Trails B test. This suggested a relationship between impaired verb comprehension and limited information-processing speed in EXEC patients. Verb comprehension in patients with a progressive non-fluent aphasia (PNFA, n = 7) was not selectively influenced by executive resources. Instead, verb comprehension accuracy in PNFA was significantly correlated with sentence comprehension accuracy, suggesting that grammatical aspects of verbs play a crucial role in their verb comprehension difficulty. Although we studied only a small number of patients with semantic dementia (SD, n = 4), we observed significant verb comprehension difficulty that was minimally influenced by executive resources and was unrelated to sentence comprehension. It is possible that impaired verb comprehension in SD is related in part to the degradation of semantic feature knowledge.

Adult↗

PubMed1998

Is there semantic specificity in overlapping-figures agnosia?

A case of apperceptive visual agnosia, revealing difficulties only in the performance on a standard overlapping-figures test, has been studied. Unusually, the patient demonstrated difficulties only with two semantic categories of the overlapped figures (clothes and school accessories); preserving, however, the knowledge of the same figures when presented isolated. We propose that the underlying deficit is only of a pseudo-semantic nature and is actually due to certain similarities of the two overlapping combinations, creating difficulties still on the apperception level only.

Agnosia↗

PubMed1998

Upper limb movement differentiation according to taxonomic semantic category.

The size or shape of an object, its perceptual features, determine the patterning of an arm and hand action involving that object. Little is known about the role played by the taxonomic semantic attributes of an object for perceptuomotor processing. In this study we investigated whether the semantic relationship between two target stimuli influences the kinematics of a bilateral reach-to-grasp action. The results showed that reach-to-grasp movements preceding the action of putting living-thing pairs together were faster, and showed earlier settings of reach and grasp temporal parameters, than movements involving pairs of non-living things. It is hypothesized that this reflects the recruitment of different categorical perceptuomotor pathways.

Adult↗

PubMed2001

Judging semantic and episodic incongruity: a magnetoencephalographic study.

Evoked magnetic fields over the entire head were measured during a semantic judgment task, in which conditions of the pre-test learning session were manipulated. Subjects learnt related and unrelated category-noun pairs, and were then asked to judge the relationship between category and noun. Unrelated pairs evoked activation around 400 ms in the left temporal area. In addition, newly presented related pairs, of which the categories were used to learn unrelated pairs, also evoked similar activities. Our findings suggest that these activities are not only related to the semantic incongruity between a pair of words as in previous studies, but also to the episodic incongruity between the learning and measurement sessions.

Adult↗

PubMed2005

A functional magnetic resonance imaging study of the tradeoff between semantics and phonology in reading aloud.

Using functional magnetic resonance imaging, we explored the role of semantics in mediating orthographic-to-phonological processing in reading aloud, focusing on the interaction of imageability with spelling-to-sound consistency for low-frequency words. Behaviorally, high-imageable words attenuate the standard latency and accuracy disadvantage for low-frequency inconsistent words relative to their consistent counterparts. Neurobiologically, high-imageable words reduced consistency-related activation in the inferior frontal gyrus but increased posterior activation in the angular and middle temporal gyri, representing a possible neural signature of the tradeoff between semantics and phonology in reading aloud. We discuss implications for neurobiological models of reading in terms of understanding the interplay among areas associated with component processes and suggest that the results constitute an important step toward integrating neurobiological and computational models of reading.

Brain Mapping↗