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PubMed1997

Adding semantics to genome databases: towards an ontology for molecular biology.

Molecular biology has a communication problem. There are many databases using their own labels and categories for storing data objects and some using identical labels and categories but with a different meaning. Conversely, one concept is often found under different names. Prominent examples are the concepts "gene" and "protein sequence" which are used with different semantics by major international genomic and protein databases thereby making database integration difficult and strenuous. This situation can only be improved by either defining individual semantic interfaces between each pair of databases (complexity of order n2) or by implementing one agreeable, transparent and computationally tractable semantic repository and linking each database to it (complexity of order n). Ontologies are one means to provide such semantic repository by explicitly specifying the meaning of and relation between the fundamental concepts in an application domain. Here, heuristics for building an ontology and the upper level and a database branch of a prospective Ontology for Molecular Biology are presented and compared to other ontologies with respect to suitability for molecular biology (http:/(/)igd.rz-berlin.mpg.de/www/oe/mbo.html).

Computational Biology↗

PubMed1998

Creative, paranormal, and delusional thought: a consequence of right hemisphere semantic activation?

OBJECTIVE: There is a rapidly growing body of evidence for an association between schizophrenic syndromes and the absence of a clear pattern of hemispheric dominance for language. Independent work with healthy subjects suggests that one feature of right hemispheric (RH) linguistic processing is a coarse as opposed to a focused semantic activation. We provide a comprehensive review of the literature to these hitherto unrelated fields of research and present an experiment assessing functional hemispheric asymmetries for language processing in healthy volunteers, differing in the susceptibility to schizophrenia-like experiences and thoughts. BACKGROUND: Forty right-handed men were administered a lateralized tachistoscopic lexical decision task. They also completed the Magical Ideation (MI) scale, which examines a variety of paranormal experiences and beliefs. RESULTS: Although the 20 subjects with MI scores below the median displayed the expected right visual field/left hemisphere (RVF/LH) superiority in lexical decision accuracy, the 20 high scorers were equally proficient in both visual fields. Compared to the low scorers, they made significantly more correct decisions in the left visual field/right hemisphere (LVF/RH). CONCLUSIONS: These results corroborate previous findings of a reduced LH language dominance for subjects scoring high on scales measuring proneness to schizophrenic behavior and thought ("schizotypy"). We propose that this dominance failure, which is commonly observed in patients with acute signs of psychosis, facilitates the emergence of paranormal and delusional ideas by way of RH associative processing characteristics, that is, coarse rather than focused semantic activation. As unfocused semantic processing is also characteristic of creative thinking, the use of the RH semantic system may constitute a selective evolutionary advantage allowing the genes predisposing to schizophrenia to proliferate despite the obvious disadvantages of this devastating disease.

Adolescent↗

PubMed1998

[Cerebral evoked potentials and semantic categorization].

INTRODUCTION: Cerebral evoked potentials represent variations in the electrical activity of the nervous system, excited by a sensory stimulus and which are recorded on the surface. They may be classified as endogenous or exogenous. Amongst the late endogenous evoked potentials (EEP) we may emphasize N400 which seems to represent the linguistic management wave, particularly for semantics. OBJECTIVE: To observe the EEP recorded throughout the process of carrying out a task involving sequential semantic categorization. PATIENTS AND METHODS: Nine healthy subjects carried out a task based on a paradigm of sequential reaction time (RT), similar to that designed by us in 1994. The data recorded were the RT and EEP at the level of the electrodes Fz, Cz and Pz in five lots of stimuli (in the first four lots the same list of words were repeated and in the fifth and final lot a different, new list appeared). CONCLUSIONS: It was seen that only N400 varied during the procedure. This variation was related to familiarity with the task. That is to say that the amplitude of N400 was reduced when the same words were repeated and increased when new words appeared for semantic classification. The reduction in parallel, although not significant for RT, allowed the reduction in N400 alone to be followed whilst the task was carried out. It may be the electrophysiological marker of the process of learning semantic categorization.

Adult↗

PubMed2001

Semantic Domains of Rational Numbers and the Acquisition of Fraction Equivalence.

This study examined how the semantic meanings of rational numbers embodied in graphical representations pose a constraint on children's construction of the concept of fraction equivalence. A test consisting of graphical representations representing the part-whole and measuring semantic meaning was given to 205 fifth-graders and 208 sixth-graders from China. Results showed that the fifth-graders' overall performance on equivalent fraction items was poor across the semantic domains of rational numbers. The sixth-graders showed significantly improved performance on the equivalent fraction items representing the part-whole relation but not on those representing the measure aspect of rational number. The results provide evidence that semantic meanings of fractional numbers in different relevant contexts also constitute a source of difficulty in children's constructing the concept of fraction equivalence, in addition to the multiplicative nature of the concept. Copyright 2001 Academic Press.

Journal Article↗

PubMed2003

Benzodiazepines and semantic memory: effects of lorazepam on the Moses illusion.

RATIONALE: When asked "How many animals of each kind did Moses take on the ark?", people fail to notice the distortion introduced by the impostor "Moses" and respond "two". It has been argued that the effect must be due to the existence of a partial-match process. In most situations, the form of a question is not likely to closely match the memory representation it queries. Thus, for the partial match hypothesis people ignore some semantic distortions. In the same vein, it has been shown that the benzodiazepine lorazepam drug induces some impairments of semantic memory as participants under lorazepam provide more incorrect recalls than placebo do with general information questions. OBJECTIVES: The aim of this study was to investigate the effects of the benzodiazepine lorazepam on the Moses illusion paradigm. METHOD: The effects of lorazepam (0.038 mg/kg) and of a placebo were investigated in 28 healthy volunteers. Twenty-two illusory questions were presented along with 72 normal general information questions. RESULTS: Lorazepam impaired the ability to detect the Moses illusion. Moreover, lorazepam participants appeared less biased to consider a question distorted than placebo participants. CONCLUSIONS: The temporary and reversible semantic memory impairments experienced by participants when falling into the Moses illusion are more frequent under lorazepam. The amnesic drug lorazepam may impair semantic processing as well as the strategic control of memory.

Adult↗

PubMed2004

Semantic congruence is a critical factor in multisensory behavioral performance.

It has repeatedly been demonstrated that the presence of multiple cues in different sensory modalities can enhance behavioral performance by speeding responses, increasing accuracy, and/or improving stimulus detection. Despite an extensive knowledge base as to how the spatial, temporal, and physical (eg., intensity) characteristics of multisensory stimuli influence such enhancements, little is known about the role of semantic or contextual congruence. Our hypothesis was that semantically congruent multisensory stimuli would result in enhanced behavioral performance, and that semantically incongruent multisensory stimuli would result in either no enhancement or a decrement in behavioral performance. The results from a redundant cue feature discrimination task clearly demonstrate that congruent cross-modal stimulation improves behavioral performance. This effect is specific to the multisensory stimuli, as no improvements are seen in the presence of redundant unimodal stimulus pairs. In contrast, incongruent stimulus pairs result in behavioral decrements for both multisensory and paired unimodal stimuli. These results highlight that in addition to such simple stimulus features as space, time and relative effectiveness, the semantic content of a multisensory stimulus plays a critical role in determining how it is processed by the nervous system.

Acoustic Stimulation↗

PubMed2001

Modulation of reach-to-grasp parameters: semantic category, volumetric properties and distractor interference?

In the two experiments of this study, we assessed the influence of target size and semantic category on the expression of reach-to-grasp kinematic parameters. Moreover, we investigated the influence of size and semantic category of distractors on reaches to the target. The experimental objects represented living and non-living categories and wide and narrow grasp sizes. Participants reached for and picked up mid-sagittally placed targets, which were either alone or flanked by distractors congruent or incongruent to semantic category and size of the target. In experiment 1, movement duration was faster to living objects. We could not replicate this, however, in experiment 2. Conversely, significant and reliable Category x Size interactions for grasp were obtained in experiment 1 and replicated in experiment 2. The pattern of the means in these interactions coincided with the absolute volumetric properties of the stimuli, indicating that the size of the stimuli was the main determinant of the expression of kinematic parameters. We conclude that volumetric properties such as size, rather than semantic category, are the crucial features in the programming and execution of movement to targets. As regards the category and size of the distractor, interference effects were evident: both category and size exerted a comparable influence on reaches to the target. The direction of interference, however, was not systematic. The interference effects are discussed in the context of visual search models of attention.

Adolescent↗

PubMed2002

Apraxia, mechanical problem solving and semantic knowledge: contributions to object usage in corticobasal degeneration.

To investigate the nature of the apraxia in corticobasal degeneration (CBD) five patients with CBD and five matched controls were compared on tests of: i) meaningless and symbolic gesture production, ii) a battery of semantic tasks based on 20 everyday items (involving naming and picture-picture matching according to semantic attributes, matching gestures-to-objects, object usage from name and with the real object) and iii) a novel tool test of mechanical problem solving. All five patients showed severe impairment in the production of meaningless and symbolic gestures from command, and by imitation, and were also impaired when using real objects. Deficits were not, however, restricted to action production: four were unable to match gestures to objects and all five showed impairment in the selection and usage of novel tools in the mechanical problem solving task. Surprising was the finding of an additional semantic knowledge breakdown in three cases, two of whom were markedly anomic. The apraxia in CBD is, therefore, multifactorial. There is profound breakdown in the organisation and co-ordination of motor programming. In addition, patients show central deficits in action knowledge and mechanical problem solving, which has been linked to parietal lobe pathology. General semantic memory may also be affected in CBD in some cases and this may then contribute to impaired object usage. This combination of more than one deficit relevant for object use may explain why CBD patients are far more disabled by their dyspraxia in everyday life than any other patient group.

Aged↗

PubMed1991

Episodic and semantic memory in early versus late onset Alzheimer's disease.

The aim of this study was to replicate and extend previous work demonstrating selective impairment of semantic, but not episodic, memory in late versus early onset Alzheimer's disease (AD). Measures of episodic and semantic memory were administered to 12 pairs of patients; early (less than or equal to 62) and late (greater than or equal to 68) onset pairs were matched on dementia severity and education. As hypothesized, the groups did not differ on the three episodic memory measures but did on two of three semantic memory measures. In conjunction with prior research, these findings indicate that late onset AD is characterized by more profound impairment on measures of semantic processing.

Age Factors↗

PubMedDate not supplied

Topographic analysis of auditory event-related potentials associated with acoustic and semantic processing.

The topography of auditory event-related potentials (ERPs) was examined during 3 kinds of tasks: selection of a specified real word or nonsense syllable from a list; simple detection of each of the same stimuli without discrimination; and classification of a set of words according to a specified semantic category. The potentials that were associated with the additional processing required by the discriminative tasks were disclosed by subtracting the wave forms obtained in the detection condition from those obtained during discriminative performance. Difference wave forms were also derived between the semantic classification and verbal discriminative ERP to delineate the changes associated with the extraction of word meaning. The topography of the ERP associated with stimulus detection was comparable to that found in previous studies of evoked potentials to non-speech stimuli. This distribution was consistent with 2 cortical generators, one within the supratemporal plane and the other on the lateral surface of the superior temporal gyrus. When discriminative performance was required on the basis of acoustic stimulus properties, the topography of the difference wave form that reflected this discriminative processing extended more posteriorly over temporal cortex. Semantic processing elicited a further posterior extension of ERP components by 330 msec after stimulus onset, as well as longer latency potentials that were not present in the verbal selection task. These differences imply that a more extensive portion of language cortex is engaged in semantic classification than in verbal identification.

Adolescent↗

PubMed2005

Semantic priming after ketamine acutely in healthy volunteers and following chronic self-administration in substance users.

BACKGROUND: Ketamine is used acutely as a model of schizophrenia. It has been suggested that chronic ketamine may also mimic aspects of this disorder, in particular impaired cognitive function. As semantic processing deficits are considered central to cognitive impairments in schizophrenia, this study aimed to characterize semantic impairments following both acute and chronic ketamine. METHODS: We examined the acute effects of two doses of ketamine (Experiment 1) using a double-blind, placebo-controlled, independent group design with 48 volunteers. Ketamine's chronic effects (Experiment 2) were explored in 16 ketamine users and 16 poly-drug controls. A semantic priming task with a frequency (high and low) and stimulus onset asynchrony (SOA: short-200 msec, long-750 msec) manipulation was used. RESULTS: In Experiment 1, acute ketamine produced inverse priming at the long SOA. In Experiment 2, ketamine users showed inverse priming for low-frequency words at the long SOA compared to poly-drug controls. CONCLUSIONS: The inverse priming effect at the long SOA induced by acute ketamine was indicative of controlled processing impairments. In ketamine users, there was also an indication of controlled processing impairments. Decreased priming for low-frequency words suggested that long-term ketamine abuse results in damage to the semantic store.

Adult↗

PubMed2006

Ubiquitin-positive frontotemporal lobar degeneration presenting with progressive Gogi (word-meaning) aphasia. A neuropsychological, radiological and pathological evaluation of a Japanese semantic dementia patient.

A patient with progressive anomia and alexia with agraphia for kanji (Japanese morphograms) is described. The patient showed a deficit in single-word comprehension and on-reading (a type of reading that conveys phonetic value) dominance in kanji reading, i.e. on-preceding (pronouncing first with on-reading, irrespective of its preferred reading) and kun-deletion (inability to recall and recognize kun-reading [another type of reading that conveys meaning]) when reading a single-character kanji. These features were due to loss of lexico-semantic information and thus the patient was regarded as having progressive Gogi (word-meaning) aphasia by Imura, a Japanese manifestation of semantic dementia. Macroscopically, neuropathological examination disclosed atrophy of the left frontotemporal lobe with accentuation in the anterior portion of the temporal lobe. Histologically, there was neuronal loss in the cerebral cortex, hippocampus, parahippocampal gyrus, amygdala, caudate nucleus, and putamen. Ubiquitin-immunoreactive neuronal inclusions were present in the hippocampal dentate granular cells. This case demonstrates that progressive Gogi aphasia is semiologically identical to semantic dementia, and our patient clinicopathologically resembled those of Rossor et al. [Rossor, M.N., Revesz, T., Lantos, P.L., Warrington, E.K. Semantic dementia with ubiquitin-positive tau-negative inclusion bodies. Brain 2000; 123: 267-76.] and Hodges et al. [Hodges, J.R., Davies, R.R., Xuereb, J.H., Casey, B., Broe, M., Bak, T.H., et al. Clinicopathological correlates in frontotemporal dementia. Ann Neurol 2004; 56: 399-406.].

Aged↗

PubMed2001

Abnormal semantic network for "animals" but not "tools" in patients with Alzheimer's disease.

The effects of Alzheimer's disease (AD) on the organization of semantic knowledge (i.e., the semantic network) for living (e.g., animals) and non-living (e.g., tools) categories was examined. Multidimensional scaling and Pathfinder analyses of data from triadic comparison tasks showed that the semantic network for "animals", but not the network for "tools", was abnormal in patients with AD. Specifically, patients with AD tended to use a different primary dimension than control subjects for categorizing animals and their network was characterized by atypical associations between concepts. The differences in the integrity of the AD patients' networks for "animals" and "tools" was not likely to be an artifact of differences in the difficulty in identifying the stimuli in the two categories as all stimuli were identified on simple naming or matching tasks. These findings support the results of previous studies that have shown the presence of category-specific semantic deficits in patients with AD.

Aged↗

PubMed1988

Concreteness/abstractness of stimulus-words and semantic clustering in right brain-damaged patients.

Fifteen right brain-damaged patients and 15 normal controls were tested for learning, delayed recall and semantic clustering abilities using two lists of two/three-syllable words. The first list consisted of 12 familiar, concrete, high-imageability nouns belonging to three semantic categories and the second of 12 abstract, low-imageability, familiar nouns also belonging to three semantic categories. The right brain-damaged patients proved to have a learning and semantic clustering deficit for concrete but not for abstract words. This was interpreted as evidence for a selective right hemisphere capability for processing concrete, high-imageability words.

Aged↗

PubMed1998

A reversal of the temporal gradient for famous person knowledge in semantic dementia: implications for the neural organisation of long-term memory.

On tests of autobiographical memory, patients with semantic dementia demonstrate significantly better retrieval of episodic events from the recent past compared with the distant past. This reversal of the Ribot effect has been attributed to the relative sparing of the hippocampal complex in the disorder. Current computational models of long-term memory predict a similar time-dependent pattern of impairment on tests of remote semantic memory. Five patients with semantic dementia were tested on recognition (familiarity) and identification (knowledge) of famous names selected from four different time-periods: 1950's, 1980's, 1990-1993 (early 1990's) and 19941996 (current). As expected, it was found that one patient DM (who had focal left temporal lobe atrophy) showed no significant impairment on recognition of famous names, but was significantly better at producing information about people who were currently famous compared to people famous in the other three time-periods. The other four patients (who had bilateral temporal lobe damage) showed better recognition of famous names from the current time-period (and to a lesser extent the 1950's), yet were profoundly impaired on the identification component, producing very little information across all four time-periods. The results are discussed with respect to current views of the neural organisation of person-specific and general semantic memory.

Aphasia, Wernicke↗

PubMed2000

Acquisition of novel semantic information in amnesia: effects of lesion location.

Two patients with severe global amnesia are described who differ in the extent to which they have acquired new semantic information. Patient SS, who has extensive medial temporal lobe damage including the hippocampus as well as surrounding cortical areas, has failed to acquire virtually any new information regarding vocabulary or famous faces that entered the public domain since the onset of his amnesia. In contrast, patient PS, who has a selective lesion of the hippocampus proper, has gained a sense of familiarity of novel vocabulary and famous people, even though her effortful retrieval of this new semantic knowledge remains impaired. These findings extend to amnesia of adult onset, the proposal of Vargha-Khadem and colleagues that in patients with selective hippocampal injury, cortical areas surrounding the hippocampus may play an important role in new semantic learning [Vargha-Khadem, F., Gadian, D.G., Watkins, K. E., Connelly, A., Van Paesschen, W. and Mishkin, M., regarding the importance of the subhippocampal cortices in the mediation of new semantic learning in children with hippocampal lesions, Science, 1997, 277, 376-380].

Amnesia↗

PubMed2002

Medial temporal lobe activity during semantic classification using a flexible fMRI design.

In this study, we evaluated the use of a self-paced fMRI design, to allow a flexible speed of responding with only four alternating stimulus blocks to minimize the influence of task switching on a group of young subjects. This was done in view of our intention to use such a design on groups of elderly and demented subjects in the near future. In addition, the hypothesis was tested that the medial temporal lobe is involved in semantic memory similar to episodic memory using a semantic retrieval task. In line with previous imaging studies that compared a semantic (living/nonliving) to a perceptual (alphabetically ascending/descending) classification condition, activity was seen in lateral temporal and inferior frontal regions, indicating the applicability of our design. Additional activity was seen in the right, and, at a slightly lower threshold, also in the left MTL, providing support for the involvement of the MTL in retrieval from semantic memory.

Adolescent↗

PubMed2003

Semantic memory and the human hippocampus.

It has been unclear whether the hippocampus is uniquely important for episodic memory (memory for events that are specific to time and place) or whether the hippocampus is also important for learning and remembering facts (semantic memory). In two studies, we assessed the capacity for semantic memory in patients with bilateral damage thought to be restricted primarily to the hippocampal region who developed memory impairment at a known time. Since the onset of their memory impairment, the patients have acquired less factual knowledge than controls. The patients also exhibit temporally limited retrograde amnesia for factual information from the several years preceding the onset of memory impairment. Remote memory for factual knowledge (from 11-30 years before amnesia) is intact. The results show that the hippocampal region supports semantic memory as well as episodic memory and that its role in the acquisition and storage of semantic knowledge is time limited.

Adult↗