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Computers in Biology and Medicine Feb 2023Annotation of biomedical entities with ontology classes provides for formal semantic analysis and mobilisation of background knowledge in determining their...
Annotation of biomedical entities with ontology classes provides for formal semantic analysis and mobilisation of background knowledge in determining their relationships. To date, enrichment analysis has been routinely employed to identify classes that are over-represented in annotations across sets of groups, such as biosample gene expression profiles or patient phenotypes, and is useful for a range of tasks including differential diagnosis and causative variant prioritisation. These approaches, however, usually consider only univariate relationships, make limited use of the semantic features of ontologies, and provide limited information and evaluation of the explanatory power of both singular and grouped candidate classes. Moreover, they are not designed to solve the problem of deriving cohesive, characteristic, and discriminatory sets of classes for entity groups. We have developed a new tool, called Klarigi, which introduces multiple scoring heuristics for identification of classes that are both compositional and discriminatory for groups of entities annotated with ontology classes. The tool includes a novel algorithm for derivation of multivariable semantic explanations for entity groups, makes use of semantic inference through live use of an ontology reasoner, and includes a classification method for identifying the discriminatory power of candidate sets, in addition to significance testing apposite to traditional enrichment approaches. We describe the design and implementation of Klarigi, including its scoring and explanation determination methods, and evaluate its use in application to two test cases with clinical significance, comparing and contrasting methods and results with literature-based and enrichment analysis methods. We demonstrate that Klarigi produces characteristic and discriminatory explanations for groups of biomedical entities in two settings. We also show that these explanations recapitulate and extend the knowledge held in existing biomedical databases and literature for several diseases. We conclude that Klarigi provides a distinct and valuable perspective on biomedical datasets when compared with traditional enrichment methods, and therefore constitutes a new method by which biomedical datasets can be explored, contributing to improved insight into semantic data.
Topics: Biological Ontologies; Semantics; Algorithms; Phenotype; Databases, Factual
PubMed: 36638616
DOI: 10.1016/j.compbiomed.2022.106425 -
Frontiers in Psychiatry 2020Although there is ample evidence from cross-sectional studies indicating cognitive deficits in high schizotypal individuals that resemble the cognitive profile of...
Although there is ample evidence from cross-sectional studies indicating cognitive deficits in high schizotypal individuals that resemble the cognitive profile of schizophrenia-spectrum patients, there is still lack of evidence by longitudinal/follow-up studies. The present study included assessments of schizotypal traits and a wide range of cognitive functions at two time points (baseline and 4-years assessments) in order to examine (a) their stability over time, (b) the predictive value of baseline schizotypy on cognition at follow-up and (c) differences in cognition between the two time points in high negative schizotypal and control individuals. Only high negative schizotypal individuals were compared with controls due to the limited number of participants falling in the other schizotypal groups at follow-up. Seventy participants (mean age: 36.17; 70% females) were assessed at baseline and follow-up. Schizotypal traits were evaluated with the Schizotypal Personality Questionnaire. We found that schizotypal traits decreased over time, except in a sub-group of participants ("schizotypy congruent") that includes individuals who consistently meet normative criteria of inclusion in either a schizotypal or control group. In these individuals, negative schizotypy and aspects of cognitive-perceptual and disorganized schizotypy remained stable. The stability of cognitive functioning also varied over time: response inhibition, aspects of cued attention switching, set-shifting and phonemic/semantic verbal fluency improved at follow-up. High negative schizotypy at baseline predicted poorer response inhibition and semantic switching at follow-up while high disorganized schizotypy predicted poorer semantic processing and complex processing speed/set-shifting. The between-group analyses revealed that response inhibition, set-shifting and complex processing speed/set-shifting were poorer in negative schizotypals compared with controls at both time points, while maintaining set and semantic switching were poorer only at follow-up. Taken together, the findings show differential stability of the schizotypal traits over time and indicate that different aspects of schizotypy predict a different pattern of neuropsychological task performance during a 4-years time window. These results are of significant use in the formulation of targeted early-intervention strategies for high-risk populations.
PubMed: 33488431
DOI: 10.3389/fpsyt.2020.613015 -
Wiley Interdisciplinary Reviews.... Jul 2022The three human at-rest postures of sitting, standing, and lying are basic, recurring features of human behavior and may reasonably be called primary postures. The three... (Review)
Review
The three human at-rest postures of sitting, standing, and lying are basic, recurring features of human behavior and may reasonably be called primary postures. The three postures share the property of being stable through time, but they are also differentiated in terms of their overall shape, their physiological properties, and typical associated behaviors such as the association of sitting with social interaction, and lying with sleeping. The experiential realities of the three postures underlie and motivate a range of cross-linguistic phenomena involving morphemes with meanings of "sit", "stand," and "lie". The relevant linguistic phenomena include higher frequencies of occurrence compared with other kinds of posture verbs and differential behavior with respect to some morphosyntactic patterns involving notions such as agentivity. The posture morphemes can also be the source for a variety of semantic extensions reflecting experiential realities of the postures, such as the extension of "lie" to mean "sleep" in some languages. Extensions also include grammaticalizations of the posture morphemes to locative and aspectual markers which reflect the temporal stability and spatial fixedness of the postures themselves. This article is categorized under: Linguistics > Cognitive Linguistics Linguistics > Language in Mind and Brain.
Topics: Brain; Humans; Linguistics; Motivation; Posture; Sleep
PubMed: 35106947
DOI: 10.1002/wcs.1592 -
Cerebral Cortex (New York, N.Y. : 1991) Aug 2022Neurodegeneration has multiscalar impacts, including behavioral, neuroanatomical, and neurofunctional disruptions. Can disease-differential alterations be captured...
Neurodegeneration has multiscalar impacts, including behavioral, neuroanatomical, and neurofunctional disruptions. Can disease-differential alterations be captured across such dimensions using naturalistic stimuli? To address this question, we assessed comprehension of four naturalistic stories, highlighting action, nonaction, social, and nonsocial events, in Parkinson's disease (PD) and behavioral variant frontotemporal dementia (bvFTD) relative to Alzheimer's disease patients and healthy controls. Text-specific correlates were evaluated via voxel-based morphometry, spatial (fMRI), and temporal (hd-EEG) functional connectivity. PD patients presented action-text deficits related to the volume of action-observation regions, connectivity across motor-related and multimodal-semantic hubs, and frontal hd-EEG hypoconnectivity. BvFTD patients exhibited social-text deficits, associated with atrophy and spatial connectivity patterns along social-network hubs, alongside right frontotemporal hd-EEG hypoconnectivity. Alzheimer's disease patients showed impairments in all stories, widespread atrophy and spatial connectivity patterns, and heightened occipitotemporal hd-EEG connectivity. Our framework revealed disease-specific signatures across behavioral, neuroanatomical, and neurofunctional dimensions, highlighting the sensitivity and specificity of a single naturalistic task. This investigation opens a translational agenda combining ecological approaches and multimodal cognitive neuroscience for the study of neurodegeneration.
Topics: Alzheimer Disease; Atrophy; Biomarkers; Brain; Frontotemporal Dementia; Humans; Magnetic Resonance Imaging; Neurodegenerative Diseases; Neuropsychological Tests
PubMed: 34875690
DOI: 10.1093/cercor/bhab421 -
Sensors (Basel, Switzerland) Feb 2023With the rapid development of intelligent mobile terminals and communication technologies, location-based services (LBSs) have become an essential part of users' lives....
With the rapid development of intelligent mobile terminals and communication technologies, location-based services (LBSs) have become an essential part of users' lives. LBS providers upload and share the collected users' location data. The more commonly used methods for location privacy protection are differential privacy and its extensions. However, the semantic information about location, which is an integral part of the location data, often contains sensitive user information. Most existing research methods have failed to pay enough attention to protecting the semantic information in the location data. To remedy this problem, two different scenarios for location semantic privacy protection methods are proposed in this paper to address single-point and continuous location queries. Simulation experiments on real social location check-in datasets, and comparison of three different privacy protection mechanisms, show that our solution demonstrates good service quality and privacy protection considering location semantics.
PubMed: 36850715
DOI: 10.3390/s23042121 -
Frontiers in Psychology 2021The paper presents the results of a study on the analysis of the perception of coronavirus disease 2019 (COVID-19) by Spanish-, German- and Russian-speaking social media...
The paper presents the results of a study on the analysis of the perception of coronavirus disease 2019 (COVID-19) by Spanish-, German- and Russian-speaking social media actors after the emergence of vaccines and attitudes toward vaccination. The empirical base of the study was corpus data, materials from online media, social networks, microblogging, blogs, instant messengers, forums, reviews, and video hosting data. The Spanish-language database included 6,640,912 tokens and 43,251,900 characters; the German-language database included 16,322,042 tokens and 109,139,405 characters; and the Russian-language database included 16,310,307 tokens and 109,060,935 characters. With a neural network approach, a multilingual analysis was performed, which made it possible to analyze the topic structure and the semantic network with the allocation of the semantic core and the associative network. Differential and integral features of the identified structures based on the material of these three databases made it possible to determine the general and different characteristics of the perception by Spanish-, German-, and Russian-speaking users of the development of the pandemic, a number of social problems, attitudes toward various types of vaccines, observance of preventive measures, and readiness for vaccination.
PubMed: 35178008
DOI: 10.3389/fpsyg.2021.792042 -
BMC Medical Informatics and Decision... Feb 2022Semantic similarity is a valuable tool for analysis in biomedicine. When applied to phenotype profiles derived from clinical text, they have the capacity to enable and...
BACKGROUND
Semantic similarity is a valuable tool for analysis in biomedicine. When applied to phenotype profiles derived from clinical text, they have the capacity to enable and enhance 'patient-like me' analyses, automated coding, differential diagnosis, and outcome prediction. While a large body of work exists exploring the use of semantic similarity for multiple tasks, including protein interaction prediction, and rare disease differential diagnosis, there is less work exploring comparison of patient phenotype profiles for clinical tasks. Moreover, there are no experimental explorations of optimal parameters or better methods in the area.
METHODS
We develop a platform for reproducible benchmarking and comparison of experimental conditions for patient phentoype similarity. Using the platform, we evaluate the task of ranking shared primary diagnosis from uncurated phenotype profiles derived from all text narrative associated with admissions in the medical information mart for intensive care (MIMIC-III).
RESULTS
300 semantic similarity configurations were evaluated, as well as one embedding-based approach. On average, measures that did not make use of an external information content measure performed slightly better, however the best-performing configurations when measured by area under receiver operating characteristic curve and Top Ten Accuracy used term-specificity and annotation-frequency measures.
CONCLUSION
We identified and interpreted the performance of a large number of semantic similarity configurations for the task of classifying diagnosis from text-derived phenotype profiles in one setting. We also provided a basis for further research on other settings and related tasks in the area.
Topics: Humans; Phenotype; ROC Curve; Rare Diseases; Semantics
PubMed: 35123470
DOI: 10.1186/s12911-022-01770-4 -
Neurotherapeutics : the Journal of the... Apr 2021Frontotemporal dementia encompasses a group of clinical syndromes defined pathologically by degeneration of the frontal and temporal lobes. Historically, these syndromes... (Review)
Review
Frontotemporal dementia encompasses a group of clinical syndromes defined pathologically by degeneration of the frontal and temporal lobes. Historically, these syndromes have been challenging to diagnose, with an average of about three years between the time of symptom onset and the initial evaluation and diagnosis. Research in the field of neuroimaging has revealed numerous biomarkers of the various frontotemporal dementia syndromes, which has provided clinicians with a method of narrowing the differential diagnosis and improving diagnostic accuracy. As such, neuroimaging is considered a core investigative tool in the evaluation of neurodegenerative disorders. Furthermore, patterns of neurodegeneration correlate with the underlying neuropathological substrates of the frontotemporal dementia syndromes, which can aid clinicians in determining the underlying etiology and improve prognostication. This review explores the advancements in neuroimaging and discusses the phenotypic and pathologic features of behavioral variant frontotemporal dementia, semantic variant primary progressive aphasia, and nonfluent variant primary progressive aphasia, as seen on structural magnetic resonance imaging and positron emission tomography.
Topics: Biomarkers; Brain; Frontotemporal Dementia; Genetic Variation; Humans; Magnetic Resonance Imaging; Neuroimaging; Positron-Emission Tomography; tau Proteins
PubMed: 34389969
DOI: 10.1007/s13311-021-01101-x -
Journal of Alzheimer's Disease Reports 2023The differentiation of semantic variant primary progressive aphasia from dementia and Alzheimer's disease can be difficult, particularly when the semantic anomia is...
The differentiation of semantic variant primary progressive aphasia from dementia and Alzheimer's disease can be difficult, particularly when the semantic anomia is pronounced. This report describes a patient who presented with complaints of memory loss and proved to have prominent semantic loss of all types of nouns, common and proper, concrete and abstract, yet continued to live independently and maintain his activities of daily living. The evaluation was consistent for semantic variant primary progressive aphasia with degradation of semantic knowledge and focal anterior temporal atrophy and hypometabolism. This report summarizes the literature and discusses the differential diagnosis of this disorder from Alzheimer's disease and related dementias.
PubMed: 37090957
DOI: 10.3233/ADR-230010 -
Frontiers in Psychology 2023Virtual reality (VR) has become a popular tool for investigating human behavior and brain functions. Nevertheless, it is unclear whether VR constitutes an actual form of...
Virtual reality (VR) has become a popular tool for investigating human behavior and brain functions. Nevertheless, it is unclear whether VR constitutes an actual form of reality or is more like an advanced simulation. Determining the nature of VR has been mostly achieved by self-reported presence measurements, defined as the feeling of being submerged in the experience. However, subjective measurements might be prone to bias and, most importantly, do not allow for a comparison with real-life experiences. Here, we show that real-life and VR height exposures using 3D-360° videos are mostly indistinguishable on a psychophysiological level (EEG and HRV), while both differ from a conventional 2D laboratory setting. Using a fire truck, three groups of participants experienced a real-life ( = 25), a virtual ( = 24), or a 2D laboratory ( = 25) height exposure. Behavioral and psychophysiological results suggest that identical exogenous and endogenous cognitive as well as emotional mechanisms are deployed to process the real-life and virtual experience. Specifically, alpha- and theta-band oscillations in line with heart rate variability, indexing vigilance, and anxiety were barely indistinguishable between those two conditions, while they differed significantly from the laboratory setup. Sensory processing, as reflected by beta-band oscillations, exhibits a different pattern for all conditions, indicating further room for improving VR on a haptic level. In conclusion, the study shows that contemporary photorealistic VR setups are technologically capable of mimicking reality, thus paving the way for the investigation of real-world cognitive and emotional processes under controlled laboratory conditions. For a video summary, see https://youtu.be/fPIrIajpfiA.
PubMed: 36874824
DOI: 10.3389/fpsyg.2023.1093014