-
Nucleic Acids Research Jan 2020We present the Small RNA Expression Atlas (SEAweb), a web application that allows for the interactive querying, visualization and analysis of known and novel small RNAs...
We present the Small RNA Expression Atlas (SEAweb), a web application that allows for the interactive querying, visualization and analysis of known and novel small RNAs across 10 organisms. It contains sRNA and pathogen expression information for over 4200 published samples with standardized search terms and ontologies. In addition, SEAweb allows for the interactive visualization and re-analysis of 879 differential expression and 514 classification comparisons. SEAweb's user model enables sRNA researchers to compare and re-analyze user-specific and published datasets, highlighting common and distinct sRNA expression patterns. We provide evidence for SEAweb's fidelity by (i) generating a set of 591 tissue specific miRNAs across 29 tissues, (ii) finding known and novel bacterial and viral infections across diseases and (iii) determining a Parkinson's disease-specific blood biomarker signature using novel data. We believe that SEAweb's simple semantic search interface, the flexible interactive reports and the user model with rich analysis capabilities will enable researchers to better understand the potential function and diagnostic value of sRNAs or pathogens across tissues, diseases and organisms.
Topics: Animals; Bacterial Infections; Cattle; Databases, Nucleic Acid; Humans; Internet; Mice; Organ Specificity; Parkinson Disease; RNA, Bacterial; RNA, Small Untranslated; RNA, Viral; Rats; Virus Diseases
PubMed: 31598718
DOI: 10.1093/nar/gkz869 -
Psychiatria Danubina 2022It is known that an interactive design and good participants' involvement strengthens the motivation to engage in learning processes. Previous research suggests... (Observational Study)
Observational Study
BACKGROUND
It is known that an interactive design and good participants' involvement strengthens the motivation to engage in learning processes. Previous research suggests attitude-behaviour consistency with relevance of subjective meaning and interest in learning. This observational study aims to measure the attitude of medical students.
METHODS
The connotative meaning and perception of e-learning were explored. A semantic differential scale was given to all students (N=328) of a case-based blended-learning (CBBL) course, 296 medical students were included in this study.
RESULTS
The online-survey completion rate was 100%. An exploratory principal components analysis with varimax rotation was performed. Five components could be extracted that explained 47.21% of the total variance. The five components are best described by the following adjectives taken from the item pool: "soft, emotional, playful", "clear and organised", "vigorous and serious", "vivid and outgoing", "economical and introverted". An additional qualitative analysis revealed relevant positive connotations ascribed to e-learning by the students: freedom in time and space for learning, interdisciplinary approach and communication, playfulness and clear, structured procedure.
CONCLUSION
Our study demonstrated that a specific set of aspects is essential for students to feel comfortable and affect-cognitively engaged to learn and gain the best exam grades.
Topics: Communication; Humans; Language; Learning; Motivation; Students, Medical
PubMed: 35772130
DOI: 10.24869/psyd.2022.209 -
Current Issues in Personality Psychology 2022From 2014 to the present, Ukrainian military personnel have been fighting in Eastern Ukraine against illegal armed formations of separatists. The resulting combat stress...
BACKGROUND
From 2014 to the present, Ukrainian military personnel have been fighting in Eastern Ukraine against illegal armed formations of separatists. The resulting combat stress negatively affects servicemen's mental health status. This study aimed to examine the factor structure of a scale to assess the psychological safety of a soldier's personality (PSSP), taking into account changes in the conditions of military service to improve the professional and psychological training of military personnel.
PARTICIPANTS AND PROCEDURE
The study involved 118 officers of the National Guard of Ukraine. The semantic differential method, expert judgment, and exploratory factor analysis were used to determine the factor structure of the PSSP.
RESULTS
The PSSP model to maintain combat readiness in daily activities includes four components: "Moral and communicative", "Motivational and volitional", "Value and meaning of life" and "Inner comfort". For activities in extreme conditions (during combat deployment), the personality potential of four structural components is used: "Moral and volitional regulation", "Coping strategies", "Value and meaning of life" and "Post-traumatic growth/regression".
CONCLUSIONS
The PSSP model consists of four components that have different content depending on the conditions for performance of professional tasks by military personnel. It is advisable to use the obtained results of the content of the PSSP model in the development of professional and psychological training programs for the purposeful formation of the resilience of military personnel, taking into account the conditions of their activities.
PubMed: 38013921
DOI: 10.5114/cipp.2021.108684 -
Scientific Reports Jun 2022The role of evolutionarily conserved homeobox-containing HOX genes as transcriptional regulators in the developmental specification of organisms is well known. The...
The role of evolutionarily conserved homeobox-containing HOX genes as transcriptional regulators in the developmental specification of organisms is well known. The contribution of HOX genes involvement in oral cancer phenotype has yet to be fully ascertained. TCGA-HNSC HTSeq-counts and clinical data were retrieved from the GDC portal for oral cavity neoplasms. GEO datasets (GSE72627, GSE30784, GSE37991) were accessed and analyzed using GEO2R. Differential HOX gene expression was profiled using the DESeq2 R package with a log2 fold change cut-off (- 1 and + 1) and Benjamini-Hochberg p-adjusted value at ≤ 0.01. Gene set over-representation analysis and semantic analysis associated with the disease ontology was performed using the ClusterProfiler R package, and pathway over-representation analysis was performed using IMPaLa. HOX protein interaction network was constructed using the Pathfind R package. HOX phenotype associations were performed using Mammalian Phenotype Ontology, Human Phenotype Ontology, PhenGenI associations, Jensen tissues, and OMIM entries. Drug connectivity mapping was carried out with Dr. Insight R package. HOXA2 was upregulated in oral dysplasia but silenced during tumor progression. Loss of HOXB2 expression was consistent in the potentially malignant oral lesions as well as in the primary tumor. HOXA7, HOXA10, HOXB7, HOXC6, HOXC10, HOXD10, and HOXD11 were consistently upregulated from premalignancy to malignancy and were notably associated with risk factors. Overrepresentation analysis suggested HOXA10 was involved in the transcriptional misregulation contributing to the oral cancer phenotype. HOX genes subnetwork analysis showed crucial interactions with cell cycle regulators, growth responsive elements, and proto-oncogenes. Phenotype associations specific to the oral region involving HOX genes provide intrinsic cues to tumor development. The 5' HOX genes were aberrantly upregulated during oral carcinogenesis reflecting their posterior prevalence.
Topics: Animals; Genes, Homeobox; Homeodomain Proteins; Mammals; Mouth Neoplasms; Phenotype; Transcription Factors
PubMed: 35710803
DOI: 10.1038/s41598-022-14412-6 -
Medicina (Kaunas, Lithuania) Oct 2021: It is widely agreed that patients suffering from Alzheimer's disease (AD) and patients suffering from semantic dementia (SD) might fail clinically administered...
: It is widely agreed that patients suffering from Alzheimer's disease (AD) and patients suffering from semantic dementia (SD) might fail clinically administered semantic tasks due to a different combination of underlying cognitive deficits: namely, degraded semantic representations in SD and degraded representations plus executive control deficit in AD. However, no easy administrable test or test battery for differentiating the semantic impairment profile in these populations has been devised yet. : In this study, we propose a new easy administrable task based on a free association procedure (F-Assoc) to be used in conjunction with category fluency (Cat-Fl) and letter fluency (Lett-Fl) for quantifying pure representational and pure control deficits, thus teasing apart the semantic profile of SD and AD patients. : In a sample of 10 AD and 10 SD subjects, matched for disease severity, we show that indices of asymmetric performance contrasting F-Assoc and each of the two verbal fluency tasks yield a clearly distinguishable discrepancy pattern across SD and AD. We also provide empirical support for the validity of an asymmetry measure contrasting F-Assoc and Cat-FL as an index of control impairment. : The present study suggests that the free association procedure provides a pure measure of degradation of semantic representations avoiding the confound of possible concomitant executive deficits.
Topics: Alzheimer Disease; Free Association; Frontotemporal Dementia; Humans; Neuropsychological Tests; Semantics
PubMed: 34833389
DOI: 10.3390/medicina57111171 -
Neurorehabilitation and Neural Repair Apr 2022Contralesional 1-Hz repetitive transcranial magnetic stimulation (rTMS) over the right pars triangularis combined with speech-language therapy (SLT) has shown positive... (Randomized Controlled Trial)
Randomized Controlled Trial
BACKGROUND & OBJECTIVE
Contralesional 1-Hz repetitive transcranial magnetic stimulation (rTMS) over the right pars triangularis combined with speech-language therapy (SLT) has shown positive results on the recovery of naming in subacute (5-45 days) post-stroke aphasia. NORTHSTAR-CA is an extension of the previously reported NORTHSTAR trial to chronic aphasia (>6 months post-stroke) designed to compare the effectiveness of the same rTMS protocol in both phases.
METHODS
Sixty-seven patients with left middle cerebral artery infarcts (28 chronic, 39 subacute) were recruited (01-2014 to 07-2019) and randomized to receive rTMS (N = 34) or sham stimulation (N = 33) with SLT for 10 days. Primary outcome variables were Z-score changes in naming, semantic fluency and comprehension tests and adverse event frequency. Intention-to-treat analyses tested between-group effects at days 1 and 30 post-treatment. Chronic and subacute results were compared.
RESULTS
Adverse events were rare, mild, and did not differ between groups. Language outcomes improved significantly in all groups irrespective of treatment and recovery phase. At 30-day follow-up, there was a significant interaction of stimulation and recovery phase on naming recovery ( <.001). Naming recovery with rTMS was larger in subacute (Mdn = 1.91/IQR = .77) than chronic patients (Mdn = .15/IQR = 1.68/ = .015). There was no significant rTMS effect in the chronic aphasia group.
CONCLUSIONS
The addition of rTMS to SLT led to significant supplemental gains in naming recovery in the subacute phase only. While this needs confirmation in larger studies, our results clarify neuromodulatory vs training-induced effects and indicate a possible window of opportunity for contralesional inhibitory stimulation interventions in post-stroke aphasia.
NORTHSTAR TRIAL REGISTRATION
https://clinicaltrials.gov/ct2/show/NCT02020421.
Topics: Aphasia; Humans; Language Therapy; Speech; Speech Therapy; Transcranial Magnetic Stimulation; Treatment Outcome
PubMed: 35337223
DOI: 10.1177/15459683211065448 -
Journal of Biomedical Informatics Mar 2023Many important clinical decisions require causal knowledge (CK) to take action. Although many causal knowledge bases for medicine have been constructed, a comprehensive...
BACKGROUND
Many important clinical decisions require causal knowledge (CK) to take action. Although many causal knowledge bases for medicine have been constructed, a comprehensive evaluation based on real-world data and methods for handling potential knowledge noise are still lacking.
OBJECTIVE
The objectives of our study are threefold: (1) propose a framework for the construction of a large-scale and high-quality causal knowledge graph (CKG); (2) design the methods for knowledge noise reduction to improve the quality of the CKG; (3) evaluate the knowledge completeness and accuracy of the CKG using real-world data.
MATERIAL AND METHODS
We extracted causal triples from three knowledge sources (SemMedDB, UpToDate and Churchill's Pocketbook of Differential Diagnosis) based on rule methods and language models, performed ontological encoding, and then designed semantic modeling between electronic health record (EHR) data and the CKG to complete knowledge instantiation. We proposed two graph pruning strategies (co-occurrence ratio and causality ratio) to reduce the potential noise introduced by SemMedDB. Finally, the evaluation was carried out by taking the diagnostic decision support (DDS) of diabetic nephropathy (DN) as a real-world case. The data originated from a Chinese hospital EHR system from October 2010 to October 2020. The knowledge completeness and accuracy of the CKG were evaluated based on three state-of-the-art embedding methods (R-GCN, MHGRN and MedPath), the annotated clinical text and the expert review, respectively.
RESULTS
This graph included 153,289 concepts and 1,719,968 causal triples. A total of 1427 inpatient data were used for evaluation. Better results were achieved by combining three knowledge sources than using only SemMedDB (three models: area under the receiver operating characteristic curve (AUC): p < 0.01, F1: p < 0.01), and the graph covered 93.9 % of the causal relations between diseases and diagnostic evidence recorded in clinical text. Causal relations played a vital role in all relations related to disease progression for DDS of DN (three models: AUC: p > 0.05, F1: p > 0.05), and after pruning, the knowledge accuracy of the CKG was significantly improved (three models: AUC: p < 0.01, F1: p < 0.01; expert review: average accuracy: + 5.5 %).
CONCLUSIONS
The results demonstrated that our proposed CKG could completely and accurately capture the abstract CK under the concrete EHR data, and the pruning strategies could improve the knowledge accuracy of our CKG. The CKG has the potential to be applied to the DDS of diseases.
Topics: Humans; Decision Support Systems, Clinical; Diabetic Nephropathies; Pattern Recognition, Automated; Semantics; Language; Diabetes Mellitus
PubMed: 36731730
DOI: 10.1016/j.jbi.2023.104298 -
NeuroImage Oct 2022Our ability to understand and interact with our environment relies upon conceptual knowledge of the meaning of objects. This process is supported by a distributed...
Our ability to understand and interact with our environment relies upon conceptual knowledge of the meaning of objects. This process is supported by a distributed network of frontal, parietal, and temporal brain regions. Insight into the differential roles of various elements of this system can be inferred from the timing of activation, and here we use similarity-based fMRI-MEG fusion to understand when the representational spaces in different elements of the semantic system converge with representational spaces in the evolving MEG signal. Participants performed a semantic-typicality judgement of written words drawn from nine different semantic categories in separate fMRI and MEG sessions. Results indicate an initial period of congruence between MEG and fMRI informational spaces dominated by the posterior inferior temporal gyrus and the ventral temporal cortex between 350 and 450 msec. This is followed by a second period of convergence between 450 and 795 msec where MEG and fMRI representational spaces conform in left angular gyrus and precuneus in addition to ventral temporal cortex. Results are consistent with the multistage recruitment of the semantic system, initially involving automatic aspects of the representational system and later extending to broader elements of the semantic system more strongly associated with internalised cognition.
Topics: Brain; Brain Mapping; Humans; Magnetic Resonance Imaging; Semantics; Temporal Lobe
PubMed: 35752412
DOI: 10.1016/j.neuroimage.2022.119405 -
Current Issues in Personality Psychology 2021The main research question of the article is how the perception of help and the style of interpersonal relations are connected. In a broad sense, the question refers to...
BACKGROUND
The main research question of the article is how the perception of help and the style of interpersonal relations are connected. In a broad sense, the question refers to the problem of constant and situational variables of prosocial activity. The main methodological framework is Vygotsky's cultural-historical psychology, in particular, the mechanism of interiorization and the interaction of interpsychological and intrapsychological processes.
PARTICIPANTS AND PROCEDURE
Over 215 participants (students attending school and university, living in Ukraine, aged from 12 to 22 years) took part in our experiment, but because not all of them completed all the necessary forms correctly, only 193 participants' answers were further analyzed. Our two research techniques were Leary's Interpersonal Behavior Circle Personal Inventory and the semantic differential ( = 193).
RESULTS
Each disposition from Leary's questionnaire had at least one significant correlation with the way Ukrainian adolescents perceive help. The semantic aspects of perceiving help were investigated with the help of ranking the qualities of the semantic differential for the words "help the other".
CONCLUSIONS
The identified correlations contribute to the psychological analysis of the detailed characteristics of perceiving help concerning personal dispositions. Personal, communicational and semantic aspects of help are interconnected and their further research can bring rich insights.
PubMed: 38013700
DOI: 10.5114/cipp.2021.104594 -
Neuropsychology Feb 2020The present study investigates whether associations between telomere length (TL) and cognitive performance across multiple domains are moderated by poverty status and...
OBJECTIVE
The present study investigates whether associations between telomere length (TL) and cognitive performance across multiple domains are moderated by poverty status and race.
METHOD
Participants were 325 African American and White urban-dwelling adults (M age = 47.9 years; 49.5% African American; 50.2% female; 48.9% living in poverty) from the Healthy Aging in Neighborhoods of Diversity across the Life Span study. TL was assayed from peripheral blood mononuclear cells using quantitative polymerase chain reactions. Multivariable regression analyses examined interactions of TL, poverty status, and race with performance on the following cognitive tests: Trail-Making Test Parts A and B, Digit Span Forward and Backward, semantic verbal fluency, Brief Test of Attention, Benton Visual Retention Test (BVRT), and California Verbal Learning Test-II total learning, short-delay free recall, and long-delay free recall scores. Analyses adjusted for age, sex, and high school-or-greater educational attainment.
RESULTS
Significant three-way interactions of TL × Poverty Status × Race revealed that, among White participants living in poverty, shorter TL was associated with worse performance on Digit Span Forward and Backward (ps<.05). Additionally, significant two-way interactions of TL × Poverty Status revealed that, among all participants living in poverty, shorter TL was associated with worse performance on the Trail-Making Test Part B and the BVRT (ps<.05).
CONCLUSIONS
TL may be differentially associated with aspects of attention, executive functioning, and memory among individuals living in poverty, who may be uniquely vulnerable to adverse effects of shorter telomeres. Replication of these findings is needed to determine their generalizability. (PsycINFO Database Record (c) 2020 APA, all rights reserved).
Topics: Adult; Black or African American; Attention; Cognition; Executive Function; Female; Humans; Leukocytes, Mononuclear; Male; Memory; Mental Recall; Middle Aged; Neuropsychological Tests; Poverty; Telomere; Trail Making Test; White People
PubMed: 31613132
DOI: 10.1037/neu0000601