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Results for “Large Language Models”

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PubMed2001

Comparison of Hilbert transform and wavelet methods for the analysis of neuronal synchrony.

The quantification of phase synchrony between neuronal signals is of crucial importance for the study of large-scale interactions in the brain. Two methods have been used to date in neuroscience, based on two distinct approaches which permit a direct estimation of the instantaneous phase of a signal [Phys. Rev. Lett. 81 (1998) 3291; Human Brain Mapping 8 (1999) 194]. The phase is either estimated by using the analytic concept of Hilbert transform or, alternatively, by convolution with a complex wavelet. In both methods the stability of the instantaneous phase over a window of time requires quantification by means of various statistical dependence parameters (standard deviation, Shannon entropy or mutual information). The purpose of this paper is to conduct a direct comparison between these two methods on three signal sets: (1) neural models; (2) intracranial signals from epileptic patients; and (3) scalp EEG recordings. Levels of synchrony that can be considered as reliable are estimated by using the technique of surrogate data. Our results demonstrate that the differences between the methods are minor, and we conclude that they are fundamentally equivalent for the study of neuroelectrical signals. This offers a common language and framework that can be used for future research in the area of synchronization.

Brain↗

PubMed2004

Assessment of mutual understanding of physician patient encounters: development and validation of a Mutual Understanding Scale (MUS) in a multicultural general practice setting.

Mutual understanding between physician and patient is essential for good quality of care; however, both parties have different views on health complaints and treatment. This study aimed to develop and validate a measure of mutual understanding (MU) in a multicultural setting. The study included 986 patients from 38 general practices. GPs completed a questionnaire and patients were interviewed after the consultation. To assess mutual understanding the answers from GP and patient to questions about different consultation aspects were compared. An expert panel, using nominal group technique, developed criteria for mutual understanding on consultation aspects and secondly, established a ranking to combine all aspects into an overall consultation judgement. Regarding construct validity, patients' ethnicity, age and language proficiency were the most important predictors for MU. Regarding criterion validity, all GP-related criteria (the GPs perception of his ability to explain to the patient, the patient's ability to explain to the GP, and the patient's understanding of consultation aspects), were well-related to MU. The same can be said of patient's consultation satisfaction and feeling that the GP was considerate. We conclude that the Mutual Understanding Scale is regarded a reliable and valid measure to be used in large-scale quantitative studies.

Adolescent↗

PubMed2005

An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets.

With the recent exponential increase in protein phosphorylation sites identified by mass spectrometry, a unique opportunity has arisen to understand the motifs surrounding such sites. Here we present an algorithm designed to extract motifs from large data sets of naturally occurring phosphorylation sites. The methodology relies on the intrinsic alignment of phospho-residues and the extraction of motifs through iterative comparison to a dynamic statistical background. Results show the identification of dozens of novel and known phosphorylation motifs from recently published serine, threonine and tyrosine phosphorylation studies. When applied to a linguistic data set to test the versatility of the approach, the algorithm successfully extracted hundreds of language motifs. This method, in addition to shedding light on the consensus sequences of identified and as yet unidentified kinases and modular protein domains, may also eventually be used as a tool to determine potential phosphorylation sites in proteins of interest.

Algorithms↗

PubMed1998

Towards knowledge-based retrieval of medical images. The role of semantic indexing, image content representation and knowledge-based retrieval.

Medicine is increasingly image-intensive. The central importance of imaging technologies such as computerized tomography and magnetic resonance imaging in clinical decision making, combined with the trend to store many "traditional" clinical images such as conventional radiographs, microscopic pathology and dermatology images in digital format present both challenges and an opportunities for the designers of clinical information systems. The emergence of Multimedia Electronic Medical Record Systems (MEMRS), architectures that integrate medical images with text-based clinical data, will further hasten this trend. The development of these systems, storing a large and diverse set of medical images, suggests that in the future MEMRS will become important digital libraries supporting patient care, research and education. The representation and retrieval of clinical images within these systems is problematic as conventional database architectures and information retrieval models have, until recently, focused largely on text-based data. Medical imaging data differs in many ways from text-based medical data but perhaps the most important difference is that the information contained within imaging data is fundamentally knowledge-based. New representational and retrieval models for clinical images will be required to address this issue. Within the Image Engine multimedia medical record system project at the University of Pittsburgh we are evolving an approach to representation and retrieval of medical images which combines semantic indexing using the UMLS Metathesuarus, image content-based representation and knowledge-based image analysis.

Abstracting and Indexing↗

PubMed1999

A methodology for partitioning a vocabulary hierarchy into trees.

Controlled medical vocabularies are useful in application areas such as medical information systems and decision-support systems. However, such vocabularies are large and complex, and working with them can be daunting. It is important to provide a means for orienting vocabulary designers and users to the vocabulary's contents. We describe a methodology for partitioning a vocabulary based on an IS-A hierarchy into small meaningful pieces. The methodology uses our disciplined modeling framework to refine the IS-A hierarchy according to prescribed rules in a process carried out by a user in conjunction with the computer. The partitioning of the hierarchy implies a partitioning of the vocabulary. We demonstrate the methodology with respect to a complex sample of the MED, an existing medical vocabulary.

Models, Theoretical↗

PubMed2005

Factor structure and reliability of the Hungarian version of the Illness Intrusiveness Scale: invariance across North American and Hungarian dialysis patients.

OBJECTIVES: The objectives of this study were to compare the factor structure and to assess the reliability of the Hungarian version of the Illness Intrusiveness Rating Scale (IIRS), testing internal validity and employing simultaneous confirmatory factor analysis (SCFA) in two large samples of North American versus Hungarian patients with end-stage renal disease (ESRD). METHODS: Translation was conducted according to current recommendations. Following pilot testing, 365 maintenance haemodialysis patients completed the scale. Hungarian data were compared with IIRS data from North American ESRD patients undergoing maintenance hemodialysis to evaluate item bias (Group x Item ANOVA). RESULTS: Confirmatory factor analyses indicated a good fit between the previously hypothesized three-factor model ("relationships and personal development", "intimacy", and "instrumental" life domains) of the original English version and the Hungarian translation. Although statistically significant (P<.05), the effect size for the Groups x Items interaction was not substantial. Internal consistency was very good (Cronbach's alpha=.80) for the total score, and, although somewhat lower than ideal, it was still in the acceptable range for the subscales (.64-.67). These numbers are similar to values reported for the original English version. Test-retest reliability was also acceptable. CONCLUSION: The Hungarian translation of the IIRS has the same three-dimensional factor structure as the original English-language version does. Furthermore, it is sufficiently reliable for research applications. These features satisfy important requirements of cultural equivalence.

Cost of Illness↗

PubMedDate not supplied

Understanding emergency medical dispatch in terms of distributed cognition: a case study.

Emergency medical dispatch (EMD) is typically a team activity, requiring fluid coordination and communication between team members. Such working situations have often been described in terms of distributed cognition (DC), a framework for understanding team working. DC takes account of factors such as shared representations and artefacts to support reasoning about team working. Although the language of DC has been developed over several years, little attention has been paid to developing a methodology or reusable representation which supports reasoning about an interactive system from a DC perspective. We present a case study in which we developed a method for constructing a DC account of team working in the domain of EMD, focusing on the use of the method for describing an existing EMD work system, identifying sources of weakness in that system, and reasoning about the likely consequences of redesign of the system. The resulting DC descriptions have yielded new insights into the design of EMD work and of tools to support that work within a large EMD centre.

Ambulances↗

PubMed1997

Psychometric considerations when measuring cognitive decline in Alzheimer's disease.

Measuring cognitive decline is important for both clinical and basic research purposes, but to do so is a complicated methodologic and statistical exercise. Some promising predictive measures have been identified, such as baseline severity of disease, early language deterioration, other early behavioral disturbance and extrapyramidal signs. Nevertheless, investigations of demographic, cognitive and biologic variables have not consistently identified factors affecting differences in the course or rate of decline. Moreover, contradictory results using similar measures are common. Such contradictory results may be attributed, in part, to differences among samples, cognitive tests selected, research design, and methods of statistical analysis. Large samples of patients with dementia examined repeatedly for long time periods are needed. However, tests developed for initial screening, diagnosing and categorizing Alzheimer's disease are not necessarily the most appropriate for longitudinal studies of disease course. New instruments with a broader range of item difficulty, and less susceptibility to floor and ceiling effects must be developed. Also, standardized ways of defining cognitive decline are needed which are more sophisticated than simple change scores. Standardization will improve the ability to compare investigations and perhaps reconcile apparent differences in results.

Alzheimer Disease↗

PubMed2004

Efficient combination of multiple word models for improved sequence comparison.

MOTIVATION: Studies of efficient and sensitive sequence comparison methods are driven by a need to find homologous regions of weak similarity between large genomes. RESULTS: We describe an improved method for finding similar regions between two sets of DNA sequences. The new method generalizes existing methods by locating word matches between sequences under two or more word models and extending word matches into high-scoring segment pairs (HSPs). The method is implemented as a computer program named DDS2. Experimental results show that DDS2 can find more HSPs by using several word models than by using one word model. AVAILABILITY: The DDS2 program is freely available for academic use in binary code form at http://bioinformatics.iastate.edu/aat/align/align.html and in source code form from the corresponding author.

Algorithms↗

PubMed2004

An adaptive high-order neural tree for pattern recognition.

A new neural tree model, called adaptive high-order neural tree (AHNT), is proposed for classifying large sets of multidimensional patterns. The AHNT is built by recursively dividing the training set into subsets and by assigning each subset to a different child node. Each node is composed of a high-order perceptron (HOP) whose order is automatically tuned taking into account the complexity of the pattern set reaching that node. First-order nodes divide the input space with hyperplanes, while HOPs divide the input space arbitrarily, but at the expense of increased complexity. Experimental results demonstrate that the AHNT generalizes better than trees with homogeneous nodes, produces small trees and avoids the use of complex comparative statistical tests and/or a priori selection of large parameter sets.

Algorithms↗

PubMed1996

Biomechanical epidemiology: a new approach to injury control research.

Injury control studies, from inception and design to dissemination of results, tend to remain within individual discipline. This is largely because each of the disciplines has a unique language and approach to research. Collaborative research is often performed serially with one discipline presenting the results of that discipline's studies to another discipline. Epidemiologists and clinicians tell engineers to design a safety technology to prevent a specific injury. Engineers tell lawyers what is feasible to include in standards. As a result, epidemiological studies lack mechanical data needed by the engineers and engineering studies lack generalizability. The procedure for incorporating the best of multiple disciplines throughout the performance of injury control studies has not existed until recently and is presented conceptually in this manuscript. This new approach, Biomechanical Epidemiology, is an exciting enhancement to current injury control research.

Biomechanical Phenomena↗

PubMed2001

Racial and ethnic differences in parents' assessments of pediatric care in Medicaid managed care.

OBJECTIVE: This study examines whether parents' reports and ratings of pediatric health care vary by race/ethnicity and language in Medicaid managed care. DATA SOURCES: The data analyzed are from the National Consumer Assessment of Health Plans (CAHPS) Benchmarking Database 1.0 and consist of 9,540 children enrolled in Medicaid managed care plans in Arkansas, Kansas, Minnesota, Oklahoma, Vermont, and Washington state from 1997 to 1998. DATA COLLECTION: The data were collected by telephone and mail, and surveys were administered in Spanish and English. The mean response rate for all plans was 42.1 percent. STUDY DESIGN: Data were analyzed using multiple regression models. The dependent variables are CAHPS 1.0 ratings (personal doctor, specialist, health care, health plan) and reports of care (getting needed care, timeliness of care, provider communication, staff helpfulness, plan service). The independent variables are race/ethnicity (white, African American, American Indian, Asian, and Hispanic), Hispanic language (English or Spanish), and Asian language (English or other), controlling for gender, age, education, and health status. PRINCIPAL FINDINGS: Racial/ethnic minorities had worse reports of care than whites. Among Hispanics and Asians language barriers had a larger negative effect on reports of care than race/ethnicity. For example, while Asian non-English-speakers had lower scores than whites for staff helpfulness (beta = -20.10), timeliness of care (beta = -18.65), provider communication (beta = -17.19), plan service (beta = -10.95), and getting needed care (beta = -8.11), Asian English speakers did not differ significantly from whites on any of the reports of care. However, lower reports of care for racial/ethnic groups did not translate necessarily into lower ratings of care. CONCLUSIONS: Health plans need to pay increased attention to racial/ethnic differences in assessments of care. This study's finding that language barriers are largely responsible for racial/ethnic disparities in care suggests that linguistically appropriate health care services are needed to address these gaps.

Adolescent↗

PubMed1999

Chlamydia pneumoniae and atherosclerosis.

OBJECTIVE: To review the literature for evidence that chronic infection with Chlamydia pneumoniae is associated with atherosclerosis and acute coronary syndromes. DATA SOURCES: MEDLINE and Institute of Science and Information bibliographic databases were searched at the end of September 1998. Indexing terms used were chlamydi*, heart, coronary, and atherosclerosis. Serological and pathological studies published as papers in any language since 1988 or abstracts since 1997 were selected. DATA EXTRACTION: It was assumed that chronic C pneumoniae infection is characterised by the presence of both specific IgG and IgA, and serological studies were examined for associations that fulfilled these criteria. Pathological studies were also reviewed for evidence that the presence of C pneumoniae in diseased vessels is associated with the severity and extent of atherosclerosis. DATA SYNTHESIS: The majority of serological studies have shown an association between C pneumoniae and atherosclerosis. However, the number of cases in studies that have reported a positive association when using strict criteria for chronic infection is similar to the number of cases in studies which found no association. Nevertheless, the organism is widely found in atherosclerotic vessels, although it may not be at all diseased sites and is not confined to the most severe lesions. Rabbit models and preliminary antibiotic trials suggest that the organism might exacerbate atherosclerosis. CONCLUSION: More evidence is required before C pneumoniae can be accepted as playing a role in atherosclerosis. Although use of antibiotics in routine practice is not justified, large scale trials in progress will help to elucidate the role of C pneumoniae.

Acute Disease↗

PubMed2004

Hemispheric specialization for language.

Hemispheric specialization for language is one of the most robust findings of cognitive neuroscience. In this review, we first present the main hypotheses about the origins of this important aspect of brain organization. These theories are based in part on the main approaches to hemispheric specialization: studies of aphasia, anatomical asymmetries and, nowadays, neuroimaging. All these approaches uncovered a large inter-individual variability which became the bulk of research on hemispheric specialization. This is why, in a second part of the review, we present the main facts about inter-individual variability, trying to relate findings to the theories presented in the first part. This review focuses on neuroimaging as it has recently given important results, thanks to investigations of both anatomical and functional asymmetries in healthy subjects. Such investigations have confirmed that left-handers, especially "familial left-handers", are more likely to have an atypical pattern of hemispheric specialization for language. Differences between men and women seem less evident although a less marked hemispheric specialization for language was depicted in women. As for the supposed relationship between anatomical and functional asymmetries, it has been shown that the size of the left (not the right) planum temporale could explain part of the variability of left hemispheric specialization for language comprehension. Taken as a whole, findings seem to vary with language tasks and brain regions, therefore showing that hemispheric specialization for language is multi-dimensional. This is not accounted for in the existing models of hemispheric specialization.

Animals↗

PubMed2005

Beyond verbal fluency: investigating the long-term effects of bilateral subthalamic (STN) deep brain stimulation (DBS) on language function in two cases.

Cognitive functioning has been described as largely impervious to chronic STN-DBS administered over 12-month periods. In relation to the domain of language, however, the effects of STN-DBS are yet to be thoroughly delineated. Verbal fluency tasks represent an almost exclusively applied index of linguistic proficiency relative to neuropsychological research within this population. Comprehensive investigations of the impact of STN-DBS on language function, however, have never been undertaken. The more precise elucidation of the role of the STN in the mediation of language processes, by way of assessments which probe language comprehension and production mechanisms, served as the primary focus of this research. Longitudinal analysis also afforded consideration of the way in which cognitive-linguistic circuits respond to STN-DBS over time. Bilateral STN-DBS primarily effected clinically reliable fluctuations (i.e., both improvements and declines) in performance in both subjects on tasks demanding cognitive-linguistic flexibility in the formulation and comprehension of complex language. Of particular note, both subjects demonstrated a cumulative increase in the proportion of reliable post-operative improvements achieved over time. The findings of this research lend support to models of subcortical participation in language which endorse a role for the STN, and suggest that bilateral STN-DBS may serve to enhance the proficiency of basal ganglia-thalamocortical linguistic circuits over time.

Aged↗

PubMed1987

Sign acquisition and use following traumatic brain injury: case report.

A case report is presented of an aphasic patient whose oral communication skills remained nonfunctional eight months after a traumatic head injury. After several unsuccessful attempts at using a variety of augmentative communication devices, manual signing was attempted. Several signs believed to be useful for communicating the patient's needs and wants were selected. The signs were introduced in a three-stage training procedure: imitation of a sign model, pointing to a picture of the concept signed, and producing the sign when presented with the pictured concept. A sign item was considered to be acquired when the patient had progressed through all three of the training stages. The patient acquired 47 signs over a five-month period, but was unable to use these signs in spontaneous, self-initiated communication. These findings illustrate the vast gap that exists between learning to produce a sign in response to a stimulus and using those signs for functional communication. The distinction between sign acquisition and sign use has largely been ignored in previous investigations of sign training with aphasic patients. Programming for generalization of acquired signs is a logical next step for future research on this topic.

Adult↗

PubMed2026

CancerOmicsStudio (CoS): a web server for integrative and interpretable analysis of multi-omics cancer data.

MOTIVATION: Large-scale omics resources, including The Cancer Genome Atlas, Genomics of Drug Sensitivity in Cancer, and the Cancer Dependency Map, have become essential for cancer research. However, these datasets are distributed across different platforms, formats and analysis frameworks, which limits their practical use by researchers without extensive computational expertise. RESULTS: We developed CancerOmicsStudio (CoS), a web server for integrative and interpretable analysis of multi-omics cancer data across 33 cancer types. CoS provides five major modules: CosAI, Traditional Analysis, Drug Sensitivity, CRISPR Dependency and Single-Cell Tumor Microenvironment. The Traditional Analysis module supports expression comparison, diagnostic evaluation, survival analysis, enrichment analysis and gene correlation. The Drug Sensitivity and CRISPR Dependency modules enable systematic evaluation of gene-drug response associations and gene essentiality in cancer cell lines. The Single-Cell Tumor Microenvironment module supports tumor microenvironment analysis at single-cell resolution. In total, approximately 1.23 million results have been precomputed to enable rapid retrieval. CosAI further allows users to submit natural-language queries and obtain results through a Real-time Analysis as Retrieval framework, with responses summarized by a lightweight language model. AVAILABILITY AND IMPLEMENTATION: CancerOmicsStudio is freely available at Zenodo (doi: 10.5281/zenodo.18744990) and https://cos.wanglab.bio.

Humans↗

PubMed2001

Rethinking the word frequency effect: the neglected role of distributional information in lexical processing.

Attempts to quantify lexical variation have produced a large number of theoretical and empirical constructs, such as Word Frequency, Concreteness, and Ambiguity, which have been claimed to predict between-word differences in lexical processing behavior. Models of word recognition that have been developed to account for the effects of these variables have typically lacked adequate semantic representations, and have dealt with words as if they exist in isolation from their environment. We present a new dimension of lexical variation that is addressed to this concern. Contextual Distinctiveness (CD), a corpus-derived summary measure of the frequency distribution of the contexts in which a word occurs, is naturally compatible with contextual theories of semantic representation and meaning. Experiment 1 demonstrates that CD is a significantly better predictor of lexical decision latencies than occurrence frequency, suggesting that CD is the more psychologically relevant variable. We additionally explore the relationship between CD and six subjectively-defined measures: Concreteness, Context Availability, Number of Contexts, Ambiguity, Age of Acquisition and Familiarity and find CD to be reliably related to Ambiguity only. We argue for the priority of immediate context in determining the representation and processing of language.

Databases, Factual↗