julilili42/papers huggingface dataset:
Impact of the COVID-19 pandemic on cardiac magnetic resonance imaging practices: insights from the MRCT registry
2025-02-19

Abstract Purpose To assess the relationship between the COVID-19 pandemic and the spectrum of indications for cardiac magnetic resonance imaging (MRI) with a focus on myocarditis. Materials and methods This was a retrospective analysis of data from the MRCT registry of the European Society of Cardiovascular Radiology (ESCR). Data regarding indications and diagnoses of myocarditis between January 1, 2018, and April 30, 2024, were extracted. Data was analyzed for the periods before and after the beginning (i.e., March 11, 2020) of the COVID-19 pandemic. Results Data from 112,361 cardiac MRI examinations was analyzed (63.5% male, median age 58 [IQR 44–69]). Over the entire period, assessment of myocarditis was the most common indication for cardiac MRI (31%, n = 34,906/112,361). Before the pandemic, this indication comprised 28% of examinations and increased to a maximum of 41% in 2022 after the onset of the pandemic. Simultaneously, the positivity rate of these examinations decreased from 21% before the pandemic to 14% in 2022. Male patients had a higher positivity rate than female patients both before and during the pandemic, with mirroring trends between sexes. The proportion of cardiac MRI examinations performed for suspected and known coronary artery disease showed an inverse relationship with those performed for myocarditis and decreased from 24% and 17% pre-pandemic to a minimum of 21% and 13% during the pandemic. Conclusion The COVID-19 pandemic considerably influenced the pattern of referrals for cardiac MRI examinations in Europe, leading to a higher proportion of examinations for suspected myocarditis but a reduced positivity rate, suggesting a lower referral threshold for this indication. At the same time, proportionally fewer examinations were performed for suspected and known coronary artery disease. Key Points Question The COVID-19 pandemic may have influenced the spectrum and positivity rates of indications for cardiac MRI, especially examinations for myocarditis . Findings The COVID-19 pandemic led to a higher proportion of cardiac MRI examinations for suspected myocarditis but a reduced positivity rate . Clinical relevance The spectrum and proportions of indications for cardiac MRI give important information on the historical and current trends in cardiac imaging and provide insight into resource deployment .
Cortisol in schizophrenia spectrum disorders: A comprehensive meta-analysis
2025-02-20

Schizophrenia spectrum disorders (SSD) are characterized by alterations in cortisol levels across various parameters, including stress reactivity, hair cortisol, and baseline levels, which may be influenced by antipsychotic treatment. To provide a comprehensive overview of cortisol dysregulation in SSD, we conducted meta-analyses assessing (1) the effects of antipsychotic treatment in SSD patients, and additionally comparing cortisol in SSD patients versus healthy controls (HC) (2) following stress induction (metabolic, physiological, psychological stressors), (3) in hair and (4) baseline levels. Systematic literature searches in PubMed, Web of Science, and PsycINFO (November 2024) identified 121 studies (9049 SSD patients) for inclusion. Meta-analytic results revealed that antipsychotic treatment significantly reduced cortisol levels in SSD (k = 16, g = -0.480, 95 % CI [-0.818, -0.142], p = 0.005). Additionally, compared to HC, SSD was associated with reduced cortisol suppression following dexamethasone exposure (k = 9, g = 0.299, 95 % CI [0.091, 0.507], p = 0.005) and with elevated baseline cortisol levels in the morning (k = 71, g = 0.38, 95 % CI [0.210, 0.546], p < 0.001) and evening (k = 11, g = 0.368, 95 % CI [0.076, 0.661], p = 0.014). However, there were no significant group differences in afternoon baseline cortisol, hair cortisol or cortisol reactivity to stress (p > 0.05). These findings offer a detailed understanding of cortisol alterations in SSD and improve our understanding of HPA axis dysregulation in SSD.
AI Model for Predicting Anti-PD1 Response in Melanoma Using Multi-Omics Biomarkers
2025-02-20

Background: Immune checkpoint inhibitors (ICIs) have demonstrated significantly improved clinical efficacy in a minority of patients with advanced melanoma, whereas non-responders potentially suffer from severe side effects and delays in other treatment options. Predicting the response to anti-PD1 treatment in melanoma remains a challenge because the current FDA-approved gold standard, the nonsynonymous tumor mutation burden (nsTMB), offers limited accuracy. Methods: In this study, we developed a multi-omics-based machine learning model that integrates genomic and transcriptomic biomarkers to predict the response to anti-PD1 treatment in patients with advanced melanoma. We employed least absolute shrinkage and selection operator (LASSO) regression with 49 biomarkers extracted from tumor–normal whole-exome and RNA sequencing as input features. The performance of the multi-omics AI model was thoroughly compared to that of nsTMB alone and to models that use only genomic or transcriptomic biomarkers. Results: We used publicly available DNA and RNA-seq datasets of melanoma patients for the training and validation of our model, forming a meta-cohort of 449 patients for which the outcome was recorded as a RECIST score. The model substantially improved the prediction of anti-PD1 outcomes compared to nsTMB alone, with an ROC AUC of 0.7 in the training set and an ROC AUC of 0.64 in the test set. Using SHAP values, we demonstrated the explainability of the model’s predictions on a per-sample basis. Conclusions: We demonstrated that models using only RNA-seq or multi-omics biomarkers outperformed nsTMB in predicting the response of melanoma patients to ICI. Furthermore, our machine learning approach improves clinical usability by providing explanations of its predictions on a per-patient basis. Our findings underscore the utility of multi-omics data for selecting patients for treatment with anti-PD1 drugs. However, to train clinical-grade AI models for routine applications, prospective studies collecting larger melanoma cohorts with consistent application of exome and RNA sequencing are required.
True colors SNARC: Semantic number processing is highly automatic.
2025-02-20

Numbers are highly relevant in our everyday lives. Besides intentionally processing number magnitude when necessary, we often automatically process it even when not required. The SNARC (Spatial-Numerical Association of Response Codes; Dehaene et al., 1993) effect, describing faster left-/right-sided responses to smaller/larger numbers, respectively, provides evidence for this automaticity. It arises in semantic number-processing tasks both, when number magnitude is task-relevant (e.g., magnitude classification) and task-irrelevant (e.g., parity judgment). However, findings on the SNARC effect in tasks requiring the processing of nonsemantic number features are mixed: While it has been observed in orientation judgment tasks, it was mostly absent in color judgment tasks. Importantly, previous studies were underpowered or did not control for confounding variables. In two highly powered online experiments, we found a small but significant SNARC effect in both nominal color judgment (cyan vs. yellow; slope = -1.71 ms) and color intensity judgment (light cyan vs. dark cyan; slope = -1.13 ms) of Arabic digits from 1 to 9 excluding 5, which did not significantly differ in size. Further, we found little evidence for the Linguistic Markedness of Response Codes (i.e., faster left-/right-sided responses to odd/even numbers, respectively; Nuerk et al., 2004) effect. Moreover, the odd effect (i.e., faster responses to even than to odd numbers; Hines, 1990) was detected. Taken together, both magnitude and parity are processed automatically even if participants respond to physical nonsemantic and nonspatial number features, but the spatial mapping seems more automatic for magnitude than for parity. (PsycInfo Database Record (c) 2025 APA, all rights reserved).
Visual Discourses of Identity-Making
2025-02-20

Abstract NATO’s identity-making is best understood through a discourse approach that investigates the Alliance’s articulation of textual and visual sites. Such an understanding helps uncover the ways in which NATO’s collective identity is made and projected. Visual discourse analysis is applied to NATO’s 2022 Strategic Concept and the accompanying themes of ‘NATO 2030’. Two nodal points are identified in that discourse: seeing NATO as a gender-equalizing alliance and as a perpetual and affective community of people, not only states. A closer look at the textual and visual discourses that establish self-ascribed meanings and truths is key to understanding both change and persistence in NATO.
Candidate Key Proteins in Tinnitus—A Bioinformatic Study of Synaptic Transmission in the Inferior Colliculus
2025-02-20

Proteins involved in synaptic transmission in normal hearing, acoustic stimulation, and tinnitus were identified using protein–protein interaction (PPI) networks. The gene list for tinnitus was compiled from the GeneCards database using the keywords “synaptic transmission” AND “inferior colliculus” AND “tinnitus” (Tin). For comparison, two gene lists were built using the keywords “auditory perception” (AP) and “acoustic stimulation” (AS). The STRING and the Cytoscape data analyzer were used to identify the top two high-degree proteins (HDPs) and the corresponding high-score interaction proteins (HSIP). The top1 key proteins of the AP and AS processes are BDNF and the receptor NTRK2; the top2 key proteins in the AP process are PVALB, together with GAD1, CALB1, and CALB2, which are important for the balance of excitation and inhibition. In the AS process, the top2 key proteins are FOS, CREB1, EGR1, and MAPK1, reflecting an activated state. The top1 key proteins of the Tin process are BDNF, NTRK3, and NTF3; these proteins are associated with the proliferation and differentiation of neurons and indicate the remodeling of synaptic transmission in IC. The top2 key proteins are GFAP and S100B, indicating a role for astrocytes in the modulation of synaptic transmission.
Stochastic cell-intrinsic stem cell decisions control colony growth in planarians
2025-02-20

Abstract Stem cells contribute to organismal homeostasis by balancing division, self-renewal and differentiation. Elucidating the strategies by which stem cells achieve this balance is critical for understanding homeostasis, and for addressing pathogenesis associated with the disruption of this balance (e.g., cancer). Planarians, highly regenerative flatworms, use pluripotent stem cells called neoblasts to maintain and regrow organs. A single neoblast can rescue an entire animal depleted from stem cells and regenerate all cell lineages. How neoblast differentiation and clonal expansion are governed to produce all the required cell types is unclear. Here, we integrated experimental and computational approaches to develop a quantitative model revealing basic principles of clonal growth of individual neoblasts. By experimentally suppressing differentiation to major lineages, we elucidated the interplay between colony growth and lineage decisions. Our findings suggest that neoblasts select their progenitor lineage based on a cell-intrinsic fate distribution. Arresting differentiation into specific lineages disrupts neoblast proliferative capacity without inducing compensatory expression of other lineages. Our analysis of neoblast colonies is consistent with a cell-intrinsic decision model that can operate without memory or communication between neoblasts. This simple cell fate decision process breaks down in homeostasis, likely because of the activity of feedback mechanisms. Our findings uncover essential principles of stem cell regulation in planarians, which are distinct from those observed in many vertebrate models. These mechanisms enable robust production of diverse cell types and facilitate regeneration of missing tissues.
Chromatic imaging properties of myopia-control spectacle lenses
2025-02-20

Myopia progression in children can lead to ocular morbidity during adulthood. Spectacle lenses have been developed and commercialized for myopia control (MC), but their imaging properties have only been assessed under monochromatic illumination. In this study, we quantified the chromatic imaging properties (wavelengths, 450, 532 and 635 nm) of four MC lenses and a single vision lens at three retinal eccentricities (0°, 20° and 30°) along the horizontal meridian using spatial light modulation technology. Our results suggest that the design of myopia-control lenses based on simultaneous competing blurring should enhance the quality of images projected in front of the peripheral retina at long wavelengths.
Can AI grade your essays? A comparative analysis of large language models and teacher ratings in multidimensional essay scoring
2025-02-21

The manual assessment and grading of student writing is a time-consuming yet critical task for teachers. Recent developments in generative AI offer potential solutions to facilitate essay-scoring tasks for teachers. In our study, we evaluate the performance (e.g. alignment and reliability) of both open-source and closed-source LLMs in assessing German student essays, comparing their evaluations to those of 37 teachers across 10 pre-defined criteria (i.e., plot logic, expression). A corpus of 20 real-world essays from Year 7 and 8 students was analyzed using five LLMs: GPT-3.5, GPT-4, o1-preview, LLaMA 3-70B, and Mixtral 8x7B, aiming to provide in-depth insights into LLMs’ scoring capabilities. Closed-source GPT models outperform open-source models in both internal consistency and alignment with human ratings, particularly excelling in language-related criteria. The o1 model outperforms all other LLMs, achieving Spearman’s = .74 with human assessments in the Overall score, and an internal consistency of = .80, though biased towards higher scores. These findings indicate that LLM-based assessment can be a useful tool to reduce teacher workload by supporting the evaluation of essays, especially with regard to language-related criteria. However, due to their tendency to overrate and their remaining issues to capture the content quality, the models require further refinement.
Deciphering the Genetic Architecture of Parkinson’s Disease in India
2025-02-21

Abstract The genomic landscape of the Indian population, particularly for age-related disorders like Parkinson’s disease (PD) remains underrepresented in global research. Genetic variability in PD has been studied predominantly in European populations, offering limited insights into its role within the Indian population. To address this gap, we conducted the first pan-India genomic survey of PD involving 4,806 cases and 6,364 controls, complemented by a meta-analysis integrating summary statistics from a multi-ancestry PD meta-analysis (N=611,485). We further leveraged RNA-sequencing data from lymphoblastoid cell lines of 731 individuals from the 1000 Genomes project to evaluate the expression of key loci across global populations. Our findings reveal a higher genetic burden of PD in the Indian population compared to Europeans, accounting for ∼30% of the previously unexplained heritability. Thirteen genome-wide significant loci were identified, including two novel loci, with an additional three loci uncovered through meta-analysis. Polygenic risk score analysis showed moderate transferability from European populations. Our results highlight the importance of genetic loci in immune function, lipid metabolism and SNCA aggregation in PD pathogenesis, with gene expression variability emphasizing population-specific differences. We also established South Asia’s largest PD biobank, providing a foundation for patient-centric approaches to PD research and treatment in India.
Pulsed inhibition of corticospinal excitability by the thalamocortical sleep spindle
2025-02-21

Thalamocortical sleep spindles, i.e., oscillatory bursts at ∼12-15 Hz of waxing and waning amplitude, are a hallmark feature of non-rapid eye movement (NREM) sleep and believed to play a key role in memory reactivation and consolidation. Generated in the thalamus and projecting to neocortex and hippocampus, they are phasically modulated by neocortical slow oscillations (<1 Hz) and in turn phasically modulate hippocampal sharp-wave ripples (>80 Hz). This hierarchical cross-frequency nesting, where slower oscillations group faster ones into certain excitability phases, may enable phase-dependent plasticity in the neocortex, and spindles have thus been considered windows of plasticity in the sleeping brain. However, the assumed phasic excitability modulation had not yet been demonstrated for spindles. Utilizing a recently developed real-time spindle detection algorithm, we applied spindle phase-triggered transcranial magnetic stimulation (TMS) to the primary motor cortex (M1) hand area to characterize the corticospinal excitability profile of spindles via motor evoked potentials (MEP). MEPs showed net suppression during spindles, driven by a "pulse of inhibition" during its falling flank with no inhibition or facilitation during its peak, rising flank, or trough. This unidirectional ("asymmetric") modulation occurred on top of the general sleep-related inhibition during spindle-free NREM sleep and did not extend into the refractory post-spindle periods. We conclude that spindles exert "asymmetric pulsed inhibition" on corticospinal excitability. These findings and the developed real-time spindle targeting methods enable future studies to investigate the causal role of spindles in phase-dependent synaptic plasticity and systems memory consolidation during sleep by repetitively targeting relevant spindle phases.
Mechanosensing alters platelet migration
2025-02-21

Platelets have long been established as a safeguard of our vascular system. Recently, haptotactic platelet migration has been discovered as a part of the immune response. In addition, platelets exhibit mechanosensing properties, changing their behavior in response to the stiffness of the underlying substrate. However, the influence of substrate stiffness on platelet migration behavior remains elusive. Here, we investigated the migration of platelets on fibrinogen-coated polydimethylsiloxane (PDMS) substrates with different stiffnesses. Using phase-contrast and fluorescence microscopy as well as a deep-learning neural network, we tracked single migrating platelets and measured their migration distance and velocity. We found that platelets migrated on stiff PDMS substrates (E = 2 MPa), while they did not migrate on soft PDMS substrates (E = 5 kPa). Platelets migrated also on PDMS substrates with intermediate stiffness (E = 100 kPa), but their velocity and the fraction of migrating platelets were diminished compared to platelets on stiff PDMS substrates. The straightness of platelet migration, however, was not significantly influenced by substrate stiffness. We used scanning ion conductance microscopy (SICM) to image the three-dimensional shape of migrating platelets, finding that platelets on soft substrates did not show the polarization and shape change associated with migration. Furthermore, the fibrinogen density gradient, which is generated by migrating platelets, was reduced for platelets on soft substrates. Our work demonstrates that substrate stiffness, and thus platelet mechanosensing, influences platelet migration. Substrate stiffness for optimal platelet migration is quite high (>100 kPa) in comparison to other cell types, with possible implications on platelet behavior in inflammatory and injured tissue. STATEMENT OF SIGNIFICANCE: Platelets can feel and react to the stiffness of their surroundings - a process called mechanosensation. Additionally, platelets migrate via substrate-bound fibrinogen as part of the innate immune response during injury or inflammation. It has been shown that the migration of immune cells is influenced by the stiffness of the underlying substrate, but the effect of substrate stiffness on the migration of platelets has not yet been investigated. Using differently stiff substrates made from PDMS, we show that substrate stiffness affects platelet migration. Stiff substrates facilitate fast and frequent platelet migration with a strong platelet shape anisotropy and a strong fibrinogen removal while soft substrates inhibit platelet migration. These findings highlight the influence of the stiffness of the surrounding tissue on the platelet immune response, possibly enhancing platelet migration in inflamed tissue.
International Consortium to Classify Ageing-related Pathologies (ICCARP) senescence definitions: achieving international consensus
2025-02-21

With the global increase in ageing populations, a clear understanding of the physiological and pathological changes associated with ageing is vital for advancing research and clinical practice. Following the World Health Organization’s decision to classify age-related aetiologies, the International Consortium to Classify Ageing-Related Pathologies (ICCARP) was established in 2023, led by Cardiff Metropolitan University.<br>The aim of the ICCARP is to develop a systematic and comprehensive classification system for ageing-related changes including pathologies, diseases, and syndromes. Currently, the ICCARP is in the process of identifying all phenomena that meet the criteria for ageing-related pathologies, to develop proposals for grouping and naming them within a comprehensive classification system. However, during the course of this project, it became evident that certain terms, specifically relating to ‘senescence’, were interpreted and understood in multiple ways, often dependent upon the professional background of an expert and the context in which the term was being used. To achieve our goals, it is vital that we use a universal language when naming and proposing ageing-related changes to provide a clear, unambiguous understanding of the changes and their underlying contribution to maintaining or degrading organismal integrity (physiology versus pathology). Furthermore, establishing clear nomenclature will be advantageous in the wider efforts to unify the study of ageing, and to better align research and clinical practice.<br>The purpose of this letter is to explicitly state the definitions primarily relating to ‘senescence’ that will be used by the ICCARP, as agreed by ICCARP members through consensus meetings in 2024. The terms that will be defined are:<br>1. Normative ageing 2. Senescence3. Cellular senescence, including acute and chronic senescence4. Physiological senescence5. Pathological senescence6. Tissue senescence7. Organ senescence8. Systems senescence9. Organismal senescence<br>