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10 pages, 1191 KiB  
Article
RNA Sequencing on Muscle Biopsies from Exertional Rhabdomyolysis Patients Revealed Down-Regulation of Mitochondrial Function and Enhancement of Extracellular Matrix Composition
by Mingqiang Ren, Luke P. Michaelson, Ognoon Mungunsukh, Peter Bedocs, Liam Friel, Kristen Cofer, Carolyn E. Dartt, Nyamkhishig Sambuughin and Francis G. O’Connor
Genes 2025, 16(8), 930; https://doi.org/10.3390/genes16080930 (registering DOI) - 2 Aug 2025
Viewed by 139
Abstract
Background/Objective: Exertional rhabdomyolysis (ER) is primarily driven by mechanical stress on muscles during strenuous or unaccustomed exercise, often exacerbated by environmental factors like heat and dehydration. While the general cellular pathway involving energy depletion and calcium overload is understood in horse ER models, [...] Read more.
Background/Objective: Exertional rhabdomyolysis (ER) is primarily driven by mechanical stress on muscles during strenuous or unaccustomed exercise, often exacerbated by environmental factors like heat and dehydration. While the general cellular pathway involving energy depletion and calcium overload is understood in horse ER models, the underlying mechanisms specific to the ER are not universally known within humans. This study aimed to evaluate whether patients with ER exhibited transcriptional signatures that were significantly different from those of healthy individuals. Methods: This study utilized RNA sequencing on skeletal muscle samples from 19 human patients with ER history, collected at a minimum of six months after the most recent ER event, and eight healthy controls to investigate the transcriptomic landscape of ER. To identify any alterations in biological processes between the case and control groups, functional pathway analyses were conducted. Results: Functional pathway enrichment analyses of differentially expressed genes revealed strong suppression of mitochondrial function. This suppression included the “aerobic electron transport chain” and “oxidative phosphorylation” pathways, indicating impaired energy production. Conversely, there was an upregulation of genes associated with adhesion and extracellular matrix-related pathways, indicating active restoration of muscle function in ER cases. Conclusions: The study demonstrated that muscle tissue exhibited signs of suppressed mitochondrial function and increased extracellular matrix development. Both of these facilitate muscle recovery within several months after an ER episode. Full article
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29 pages, 3012 KiB  
Article
Investigating Multi-Omic Signatures of Ethnicity and Dysglycaemia in Asian Chinese and European Caucasian Adults: Cross-Sectional Analysis of the TOFI_Asia Study at 4-Year Follow-Up
by Saif Faraj, Aidan Joblin-Mills, Ivana R. Sequeira-Bisson, Kok Hong Leiu, Tommy Tung, Jessica A. Wallbank, Karl Fraser, Jennifer L. Miles-Chan, Sally D. Poppitt and Michael W. Taylor
Metabolites 2025, 15(8), 522; https://doi.org/10.3390/metabo15080522 - 1 Aug 2025
Viewed by 253
Abstract
Background: Type 2 diabetes (T2D) is a global health epidemic with rising prevalence within Asian populations, particularly amongst individuals with high visceral adiposity and ectopic organ fat, the so-called Thin-Outside, Fat-Inside phenotype. Metabolomic and microbiome shifts may herald T2D onset, presenting potential biomarkers [...] Read more.
Background: Type 2 diabetes (T2D) is a global health epidemic with rising prevalence within Asian populations, particularly amongst individuals with high visceral adiposity and ectopic organ fat, the so-called Thin-Outside, Fat-Inside phenotype. Metabolomic and microbiome shifts may herald T2D onset, presenting potential biomarkers and mechanistic insight into metabolic dysregulation. However, multi-omics datasets across ethnicities remain limited. Methods: We performed cross-sectional multi-omics analyses on 171 adults (99 Asian Chinese, 72 European Caucasian) from the New Zealand-based TOFI_Asia cohort at 4-years follow-up. Paired plasma and faecal samples were analysed using untargeted metabolomic profiling (polar/lipid fractions) and shotgun metagenomic sequencing, respectively. Sparse multi-block partial least squares regression and discriminant analysis (DIABLO) unveiled signatures associated with ethnicity, glycaemic status, and sex. Results: Ethnicity-based DIABLO modelling achieved a balanced error rate of 0.22, correctly classifying 76.54% of test samples. Polar metabolites had the highest discriminatory power (AUC = 0.96), with trigonelline enriched in European Caucasians and carnitine in Asian Chinese. Lipid profiles highlighted ethnicity-specific signatures: Asian Chinese showed enrichment of polyunsaturated triglycerides (TG.16:0_18:2_22:6, TG.18:1_18:2_22:6) and ether-linked phospholipids, while European Caucasians exhibited higher levels of saturated species (TG.16:0_16:0_14:1, TG.15:0_15:0_17:1). The bacteria Bifidobacterium pseudocatenulatum, Erysipelatoclostridium ramosum, and Enterocloster bolteae characterised Asian Chinese participants, while Oscillibacter sp. and Clostridium innocuum characterised European Caucasians. Cross-omic correlations highlighted negative correlations of Phocaeicola vulgatus with amino acids (r = −0.84 to −0.76), while E. ramosum and C. innocuum positively correlated with long-chain triglycerides (r = 0.55–0.62). Conclusions: Ethnicity drove robust multi-omic differentiation, revealing distinctive metabolic and microbial profiles potentially underlying the differential T2D risk between Asian Chinese and European Caucasians. Full article
(This article belongs to the Section Endocrinology and Clinical Metabolic Research)
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24 pages, 2735 KiB  
Article
Dietary Intake of a Milk Sphingolipid-Rich MFGM/EV Concentrate Ameliorates Age-Related Metabolic Dysfunction
by Richard R. Sprenger, Kat F. Kiilerich, Mikael Palner, Arsênio Rodrigues Oliveira, Mikaël Croyal, Marie S. Ostenfeld, Ann Bjørnshave, Gitte M. Knudsen and Christer S. Ejsing
Nutrients 2025, 17(15), 2529; https://doi.org/10.3390/nu17152529 - 31 Jul 2025
Viewed by 242
Abstract
Background/Objectives: Nutraceuticals containing milk fat globule membranes (MFGMs) and extracellular vesicles (EVs) are purported to abate age-related metabolic dysfunction due to their richness in milk sphingolipids. As such, nutraceuticals offer a compelling strategy to improve metabolic health through dietary means, especially for elderly [...] Read more.
Background/Objectives: Nutraceuticals containing milk fat globule membranes (MFGMs) and extracellular vesicles (EVs) are purported to abate age-related metabolic dysfunction due to their richness in milk sphingolipids. As such, nutraceuticals offer a compelling strategy to improve metabolic health through dietary means, especially for elderly persons who are unable to adhere to common therapeutic interventions. To address this, we examined the effects of supplementing aged sedentary rats with an MFGM/EV-rich concentrate. Methods/Results: In a 25-week study, 89-week-old male rats received either a milk sphingolipid-rich MFGM/EV concentrate or a control supplement. Analysis of metabolic health using a battery of tests, including MSALL lipidomics of plasma, liver, and other peripheral tissues, revealed that MFGM/EV supplementation promotes accretion of unique sphingolipid signatures, ameliorates ceramide biomarkers predictive of cardiovascular death, and has a general lipid-lowering effect. At the functional level, we find that these health-promoting effects are linked to increased lipoprotein particle turnover, showcased by reduced levels of triglyceride-rich particles, as well as a metabolically healthier liver, assessed using whole-body lipidomic flux analysis. Conclusions: Altogether, our work unveils that MFGM/EV-containing food holds a potential for ameliorating age-related metabolic dysfunction in elderly individuals. Full article
(This article belongs to the Special Issue Diet and Nutrition: Metabolic Diseases---2nd Edition)
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31 pages, 638 KiB  
Systematic Review
Exploring the Autistic Brain: A Systematic Review of Diffusion Tensor Imaging Studies on Neural Connectivity in Autism Spectrum Disorder
by Giuseppe Marano, Georgios D. Kotzalidis, Maria Benedetta Anesini, Sara Barbonetti, Sara Rossi, Miriam Milintenda, Antonio Restaino, Mariateresa Acanfora, Gianandrea Traversi, Giorgio Veneziani, Maria Picilli, Tommaso Callovini, Carlo Lai, Eugenio Maria Mercuri, Gabriele Sani and Marianna Mazza
Brain Sci. 2025, 15(8), 824; https://doi.org/10.3390/brainsci15080824 (registering DOI) - 31 Jul 2025
Viewed by 219
Abstract
Background/Objectives: Autism spectrum disorder (ASD) has been extensively studied through neuroimaging, primarily focusing on grey matter and more in children than in adults. Studies in children and adolescents fail to capture changes that may dampen with age, thus leaving only changes specific [...] Read more.
Background/Objectives: Autism spectrum disorder (ASD) has been extensively studied through neuroimaging, primarily focusing on grey matter and more in children than in adults. Studies in children and adolescents fail to capture changes that may dampen with age, thus leaving only changes specific to ASD. While grey matter has been the primary focus, white matter (WM) may be more specific in identifying the particular biological signature of the neurodiversity of ASD. Diffusion tensor imaging (DTI) is the more appropriate tool to investigate WM in ASD. Despite being introduced in 1994, its application to ASD research began in 2001. Studies employing DTI identify altered fractional anisotropy (FA), mean diffusivity, and radial diffusivity (RD) in individuals with ASD compared to typically developing (TD) individuals. Methods: We systematically reviewed literature on 21 May 2025 on PubMed using the following strategy: (“autism spectrum”[ti] OR autistic[ti] OR ASD[ti] OR “high-functioning autism” OR Asperger*[ti] OR Rett*[ti]) AND (DTI[ti] OR “diffusion tensor”[ti] OR multimodal[ti] OR “white matter”[ti] OR tractograph*[ti]). Our search yielded 239 results, of which 26 were adult human studies and eligible. Results: Analysing the evidence, we obtained regionally diverse WM alterations in adult ASD, specifically in FA, MD, RD, axial diffusivity and kurtosis, neurite density, and orientation dispersion index, compared to TD individuals, mostly in frontal and interhemispheric tracts, association fibres, and subcortical projection pathways. These alterations were less prominent than those of children and adolescents, indicating that individuals with ASD may improve during brain maturation. Conclusions: Our findings suggest that white matter alterations in adults with ASD are regionally diverse but generally less pronounced than in younger populations. This may indicate a potential improvement or adaptation of brain structure during maturation. Further research is needed to clarify the neurobiological mechanisms underlying these changes and their implications for clinical outcomes. Full article
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25 pages, 2023 KiB  
Article
Geographical Origin Authentication of Leaves and Drupes from Olea europaea via 1H NMR and Excitation–Emission Fluorescence Spectroscopy: A Data Fusion Approach
by Duccio Tatini, Flavia Bisozzi, Sara Costantini, Giacomo Fattori, Amedeo Boldrini, Michele Baglioni, Claudia Bonechi, Alessandro Donati, Cristiana Tozzi, Angelo Riccaboni, Gabriella Tamasi and Claudio Rossi
Molecules 2025, 30(15), 3208; https://doi.org/10.3390/molecules30153208 - 30 Jul 2025
Viewed by 198
Abstract
Geographical origin authentication of agrifood products is essential for ensuring their quality, preventing fraud, and maintaining consumers’ trust. In this study, we used proton nuclear magnetic resonance (1H NMR) and excitation–emission matrix (EEM) fluorescence spectroscopy combined with chemometric methods for the [...] Read more.
Geographical origin authentication of agrifood products is essential for ensuring their quality, preventing fraud, and maintaining consumers’ trust. In this study, we used proton nuclear magnetic resonance (1H NMR) and excitation–emission matrix (EEM) fluorescence spectroscopy combined with chemometric methods for the geographical origin characterization of olive drupes and leaves from different Tuscany subregions, where olive oil production is relevant. Single-block approaches were implemented for individual datasets, using principal component analysis (PCA) for data visualization and Soft Independent Modeling of Class Analogy (SIMCA) for sample classification. 1H NMR spectroscopy provided detailed metabolomic profiles, identifying key compounds such as polyphenols and organic acids that contribute to geographical differentiation. EEM fluorescence spectroscopy, in combination with Parallel Factor Analysis (PARAFAC), revealed distinctive fluorescence signatures associated with polyphenolic content. A mid-level data fusion strategy, integrating the common dimensions (ComDim) method, was explored to improve the models’ performance. The results demonstrated that both spectroscopic techniques independently provided valuable insights in terms of geographical characterization, while data fusion further improved the model performances, particularly for olive drupes. Notably, this study represents the first attempt to apply EEM fluorescence for the geographical classification of olive drupes and leaves, highlighting its potential as a complementary tool in geographic origin authentication. The integration of advanced spectroscopic and chemometric methods offers a reliable approach for the differentiation of samples from closely related areas at a subregional level. Full article
(This article belongs to the Section Food Chemistry)
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36 pages, 9354 KiB  
Article
Effects of Clouds and Shadows on the Use of Independent Component Analysis for Feature Extraction
by Marcos A. Bosques-Perez, Naphtali Rishe, Thony Yan, Liangdong Deng and Malek Adjouadi
Remote Sens. 2025, 17(15), 2632; https://doi.org/10.3390/rs17152632 - 29 Jul 2025
Viewed by 152
Abstract
One of the persistent challenges in multispectral image analysis is the interference caused by dense cloud cover and its resulting shadows, which can significantly obscure surface features. This becomes especially problematic when attempting to monitor surface changes over time using satellite imagery, such [...] Read more.
One of the persistent challenges in multispectral image analysis is the interference caused by dense cloud cover and its resulting shadows, which can significantly obscure surface features. This becomes especially problematic when attempting to monitor surface changes over time using satellite imagery, such as from Landsat-8. In this study, rather than simply masking visual obstructions, we aimed to investigate the role and influence of clouds within the spectral data itself. To achieve this, we employed Independent Component Analysis (ICA), a statistical method capable of decomposing mixed signals into independent source components. By applying ICA to selected Landsat-8 bands and analyzing each component individually, we assessed the extent to which cloud signatures are entangled with surface data. This process revealed that clouds contribute to multiple ICA components simultaneously, indicating their broad spectral influence. With this influence on multiple wavebands, we managed to configure a set of components that could perfectly delineate the extent and location of clouds. Moreover, because Landsat-8 lacks cloud-penetrating wavebands, such as those in the microwave range (e.g., SAR), the surface information beneath dense cloud cover is not captured at all, making it physically impossible for ICA to recover what is not sensed in the first place. Despite these limitations, ICA proved effective in isolating and delineating cloud structures, allowing us to selectively suppress them in reconstructed images. Additionally, the technique successfully highlighted features such as water bodies, vegetation, and color-based land cover differences. These findings suggest that while ICA is a powerful tool for signal separation and cloud-related artifact suppression, its performance is ultimately constrained by the spectral and spatial properties of the input data. Future improvements could be realized by integrating data from complementary sensors—especially those operating in cloud-penetrating wavelengths—or by using higher spectral resolution imagery with narrower bands. Full article
(This article belongs to the Section Environmental Remote Sensing)
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45 pages, 770 KiB  
Review
Neural Correlates of Burnout Syndrome Based on Electroencephalography (EEG)—A Mechanistic Review and Discussion of Burnout Syndrome Cognitive Bias Theory
by James Chmiel and Agnieszka Malinowska
J. Clin. Med. 2025, 14(15), 5357; https://doi.org/10.3390/jcm14155357 - 29 Jul 2025
Viewed by 320
Abstract
Introduction: Burnout syndrome, long described as an “occupational phenomenon”, now affects 15–20% of the general workforce and more than 50% of clinicians, teachers, social-care staff and first responders. Its precise nosological standing remains disputed. We conducted a mechanistic review of electroencephalography (EEG) studies [...] Read more.
Introduction: Burnout syndrome, long described as an “occupational phenomenon”, now affects 15–20% of the general workforce and more than 50% of clinicians, teachers, social-care staff and first responders. Its precise nosological standing remains disputed. We conducted a mechanistic review of electroencephalography (EEG) studies to determine whether burnout is accompanied by reproducible brain-function alterations that justify disease-level classification. Methods: Following PRISMA-adapted guidelines, two independent reviewers searched PubMed/MEDLINE, Scopus, Google Scholar, Cochrane Library and reference lists (January 1980–May 2025) using combinations of “burnout,” “EEG”, “electroencephalography” and “event-related potential.” Only English-language clinical investigations were eligible. Eighteen studies (n = 2194 participants) met the inclusion criteria. Data were synthesised across three domains: resting-state spectra/connectivity, event-related potentials (ERPs) and longitudinal change. Results: Resting EEG consistently showed (i) a 0.4–0.6 Hz slowing of individual-alpha frequency, (ii) 20–35% global alpha-power reduction and (iii) fragmentation of high-alpha (11–13 Hz) fronto-parietal coherence, with stage- and sex-dependent modulation. ERP paradigms revealed a distinctive “alarm-heavy/evaluation-poor” profile; enlarged N2 and ERN components signalled hyper-reactive conflict and error detection, whereas P3b, Pe, reward-P3 and late CNV amplitudes were attenuated by 25–50%, indicating depleted evaluative and preparatory resources. Feedback processing showed intact or heightened FRN but blunted FRP, and affective tasks demonstrated threat-biassed P3a latency shifts alongside dampened VPP/EPN to positive cues. These alterations persisted in longitudinal cohorts yet normalised after recovery, supporting trait-plus-state dynamics. The electrophysiological fingerprint differed from major depression (no frontal-alpha asymmetry, opposite connectivity pattern). Conclusions: Across paradigms, burnout exhibits a coherent neurophysiological signature comparable in magnitude to established psychiatric disorders, refuting its current classification as a non-disease. Objective EEG markers can complement symptom scales for earlier diagnosis, treatment monitoring and public-health surveillance. Recognising burnout as a clinical disorder—and funding prevention and care accordingly—is medically justified and economically imperative. Full article
(This article belongs to the Special Issue Innovations in Neurorehabilitation)
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23 pages, 4210 KiB  
Article
CT-Based Habitat Radiomics Combining Multi-Instance Learning for Early Prediction of Post-Neoadjuvant Lymph Node Metastasis in Esophageal Squamous Cell Carcinoma
by Qinghe Peng, Shumin Zhou, Runzhe Chen, Jinghui Pan, Xin Yang, Jinlong Du, Hongdong Liu, Hao Jiang, Xiaoyan Huang, Haojiang Li and Li Chen
Bioengineering 2025, 12(8), 813; https://doi.org/10.3390/bioengineering12080813 - 28 Jul 2025
Viewed by 350
Abstract
Early prediction of lymph node metastasis (LNM) following neoadjuvant therapy (NAT) is crucial for timely treatment optimization in esophageal squamous cell carcinoma (ESCC). This study developed and validated a computed tomography-based radiomic model for predicting pathologically confirmed LNM status at the time of [...] Read more.
Early prediction of lymph node metastasis (LNM) following neoadjuvant therapy (NAT) is crucial for timely treatment optimization in esophageal squamous cell carcinoma (ESCC). This study developed and validated a computed tomography-based radiomic model for predicting pathologically confirmed LNM status at the time of surgery in ESCC patients after NAT. A total of 469 ESCC patients from Sun Yat-sen University Cancer Center were retrospectively enrolled and randomized into a training cohort (n = 328) and a test cohort (n = 141). Three signatures were constructed: the tumor-habitat-based signature (Habitat_Rad), derived from radiomic features of three tumor subregions identified via K-means clustering; the multiple instance learning-based signature (MIL_Rad), combining features from 2.5D deep learning models; and the clinicoradiological signature (Clinic), developed through multivariate logistic regression. A combined radiomic nomogram integrating these signatures outperformed the individual models, achieving areas under the curve (AUCs) of 0.929 (95% CI, 0.901–0.957) and 0.852 (95% CI, 0.778–0.925) in the training and test cohorts, respectively. The decision curve analysis confirmed a high net clinical benefit, highlighting the nomogram’s potential for accurate LNM prediction after NAT and guiding individualized therapy. Full article
(This article belongs to the Special Issue Machine Learning Methods for Biomedical Imaging)
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20 pages, 2792 KiB  
Article
Capturing High-Frequency Harmonic Signatures for NILM: Building a Dataset for Load Disaggregation
by Farid Dinar, Sébastien Paris and Éric Busvelle
Sensors 2025, 25(15), 4601; https://doi.org/10.3390/s25154601 - 25 Jul 2025
Viewed by 255
Abstract
Advanced Non-Intrusive Load Monitoring (NILM) research is important to help reduce energy consumption. Very-low-frequency approaches have traditionally faced challenges in separating appliance uses due to low discriminative information. The richer signatures available in high-frequency electrical data include many harmonic orders that have the [...] Read more.
Advanced Non-Intrusive Load Monitoring (NILM) research is important to help reduce energy consumption. Very-low-frequency approaches have traditionally faced challenges in separating appliance uses due to low discriminative information. The richer signatures available in high-frequency electrical data include many harmonic orders that have the potential to advance disaggregation. This has been explored to some extent, but not comprehensively due to a lack of an appropriate public dataset. This paper presents the development of a cost-effective energy monitoring system scalable for multiple entries while producing detailed measurements. We will detail our approach to creating a NILM dataset comprising both aggregate loads and individual appliance measurements, all while ensuring that the dataset is reproducible and accessible. Ultimately, the dataset can be used to validate NILM, and we show through the use of machine learning techniques that high-frequency features improve disaggregation accuracy when compared with traditional methods. This work addresses a critical gap in NILM research by detailing the design and implementation of a data acquisition system capable of generating rich and structured datasets that support precise energy consumption analysis and prepare the essential materials for advanced, real-time energy disaggregation and smart energy management applications. Full article
(This article belongs to the Section Intelligent Sensors)
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14 pages, 1895 KiB  
Article
MicroRNA Signatures in Dental Pulp Stem Cells Following Nicotine Exposure
by David Vang, Leyla Tahrani Hardin, Nabil Abid, Der Thor and Nan Xiao
Dent. J. 2025, 13(8), 338; https://doi.org/10.3390/dj13080338 - 23 Jul 2025
Viewed by 259
Abstract
Background and Objectives: Nicotine is the most well-studied toxic substance in cigarette smoke and e-cigarette vape. However, smoke and vape are composed of other components that have a negative impact on health. The objective of this study is to investigate whether nicotine has [...] Read more.
Background and Objectives: Nicotine is the most well-studied toxic substance in cigarette smoke and e-cigarette vape. However, smoke and vape are composed of other components that have a negative impact on health. The objective of this study is to investigate whether nicotine has a distinctive impact on molecular mechanisms in stem cells. Methods: The cellular impact of nicotine on the regenerative capacity of human dental pulp stem cells (DPSCs) and the microRNA (miRNA) profile was examined. Bioinformatic analysis was performed to identify miRNA-regulated cellular pathways associated with nicotine exposure. These pathways were then compared to those induced by cigarette smoke condensate (CSC). Results: Prolonged exposure to nicotine significantly impaired the regeneration of DPSCs and changed the expression of miRNAs. Nicotine upregulated the expression of hsa-miR-7977, hsa-miR-3178, and hsa-miR-10400-5p compared to vehicle control. Interestingly, nicotine did not change the expression of hsa-miR-29b-3p, hsa-miR-199b-5p, hsa-miR-26b-5p, or hsa-miR-26a-5p compared to the control. However, the expressions of these miRNAs were significantly altered when compared to CSC treatment. Further analysis revealed that nicotine was distinctively associated with certain miRNA-targeted pathways including apoptosis, ErbB, MAPK signaling, PI3K-Akt, TGF-b signaling, and Wnt signaling. Conclusions: Our work provides evidence on the distinctive miRNA signature induced by nicotine. The information will be important for identifying the unique molecular pathways downstream of nicotine from smoking and vaping in different individuals, providing a new direction for personalized disease prevention, prognosis, and treatment. Full article
(This article belongs to the Special Issue Recreational Drugs, Smoking, and Their Impact on Oral Health)
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14 pages, 896 KiB  
Article
Systemic Uremic Toxin Burden in Autism Spectrum Disorder: A Stratified Urinary Metabolite Analysis
by Joško Osredkar, Teja Fabjan, Uroš Godnov, Maja Jekovec-Vrhovšek, Joanna Giebułtowicz, Barbara Bobrowska-Korczak, Gorazd Avguštin and Kristina Kumer
Int. J. Mol. Sci. 2025, 26(15), 7070; https://doi.org/10.3390/ijms26157070 - 23 Jul 2025
Viewed by 231
Abstract
Autism spectrum disorder (ASD) is increasingly associated with microbial and metabolic disturbances, including the altered production of gut-derived uremic toxins. We investigated urinary concentrations of five representative uremic toxins—indoxyl sulfate (IS), p-cresyl sulfate (PCS), trimethylamine N-oxide (TMAO), asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine [...] Read more.
Autism spectrum disorder (ASD) is increasingly associated with microbial and metabolic disturbances, including the altered production of gut-derived uremic toxins. We investigated urinary concentrations of five representative uremic toxins—indoxyl sulfate (IS), p-cresyl sulfate (PCS), trimethylamine N-oxide (TMAO), asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA)—in 161 children with ASD and 71 healthy controls. Toxins were measured using LC-MS/MS and were normalized to creatinine. Subgroup analyses were performed by sex, age group (2–5.9 vs. 6–17 years), and autism severity based on the Childhood Autism Rating Scale (CARS). In addition to individual concentrations, we calculated the total toxin burden, proportional contributions, and functional ratios (IS/PCS, PCS/TMAO, and IS/ADMA). While individual toxin levels did not differ significantly between groups, stratified analyses revealed that PCS was higher in girls and in severe cases of ASD, whereas IS and TMAO were reduced in younger and more severely affected children. The functional ratios shifted consistently with severity—IS/PCS declined from 1.69 in controls to 0.99 in severe cases of ASD, while PCS/TMAO increased from 12.2 to 20.5. These patterns suggest a phenolic-dominant microbial signature and an altered host–microbial metabolic balance in ASD. Functional toxin profiling may offer a more sensitive approach to characterizing metabolic disturbances in ASD than concentration analysis alone. Full article
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23 pages, 43055 KiB  
Article
Tumor-Associated Macrophages and Collagen Remodeling in Mammary Carcinomas: A Comparative Analysis in Dogs and Humans
by Ana Paula Vargas Garcia, Marisa Salvi, Luana Aparecida Reis, Bárbara Regina Melo Ribeiro, Cristiana Buzelin Nunes, Ana Maria de Paula and Geovanni Dantas Cassali
Int. J. Mol. Sci. 2025, 26(14), 6928; https://doi.org/10.3390/ijms26146928 - 18 Jul 2025
Viewed by 470
Abstract
The tumor microenvironment (TME) plays a central role in cancer progression, with tumor-associated macrophages (TAMs) and extracellular matrix (ECM) components such as collagen being key modulators of invasiveness and immune regulation. Although macrophage infiltration and ECM remodeling are well-documented individually, their coordinated contribution [...] Read more.
The tumor microenvironment (TME) plays a central role in cancer progression, with tumor-associated macrophages (TAMs) and extracellular matrix (ECM) components such as collagen being key modulators of invasiveness and immune regulation. Although macrophage infiltration and ECM remodeling are well-documented individually, their coordinated contribution to mammary carcinoma aggressiveness remains underexplored, particularly in comparative oncology models. This study analyzed 117 mammary carcinoma samples—59 from dogs and 58 from women—using immunohistochemistry, immunofluorescence, and second-harmonic-generation (SHG) microscopy. We quantified TAM density and phenotype (CD206, iNOS, and S100A8/A9), assessed collagen fiber organization, and examined correlations with clinical–pathological variables and overall survival. Increased TAM infiltration was associated with a higher histological grade, aggressive molecular subtypes, enhanced cell proliferation, and shortened survival in dogs. High TAM density also correlated with decreased collagen fiber length and increased alignment, suggesting active immune–matrix remodeling in aggressive tumors. Macrophage phenotyping revealed heterogeneous populations, with CD206+ cells predominating in high-grade tumors, while S100A8/A9+/iNOS+ phenotypes were enriched in less aggressive subtypes. The findings were consistent across species, reinforcing the relevance of canine models. Our results identify macrophage–collagen interactions as critical determinants of tumor aggressiveness in mammary carcinomas. This study bridges comparative oncology and translational research by proposing immune–ECM signatures as potential prognostic biomarkers and therapeutic targets. These insights contribute to the advancement of molecular oncology in Brazil by supporting innovative strategies that integrate immune modulation and matrix-targeted interventions in breast cancer. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Oncology in Brazil, 3rd Edition)
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17 pages, 3908 KiB  
Article
Metagenomic Characterization of Gut Microbiota in Individuals with Low Cardiovascular Risk
by Argul Issilbayeva, Samat Kozhakhmetov, Zharkyn Jarmukhanov, Elizaveta Vinogradova, Nurislam Mukhanbetzhanov, Assel Meiramova, Yelena Rib, Tatyana Ivanova-Razumova, Gulzhan Myrzakhmetova, Saltanat Andossova, Ayazhan Zeinoldina, Malika Kuantkhan, Bayan Ainabekova, Makhabbat Bekbossynova and Almagul Kushugulova
J. Clin. Med. 2025, 14(14), 5097; https://doi.org/10.3390/jcm14145097 - 17 Jul 2025
Viewed by 392
Abstract
Background/Objectives: Cardiovascular diseases remain the leading cause of global mortality, with the gut microbiome emerging as a critical factor. This study aimed to characterize gut microbiome composition and metabolic pathways in individuals with low cardiovascular risk (LCR) compared to healthy controls to reveal [...] Read more.
Background/Objectives: Cardiovascular diseases remain the leading cause of global mortality, with the gut microbiome emerging as a critical factor. This study aimed to characterize gut microbiome composition and metabolic pathways in individuals with low cardiovascular risk (LCR) compared to healthy controls to reveal insights into early disease shifts. Methods: We performed shotgun metagenomic sequencing on fecal samples from 25 LCR individuals and 25 matched healthy controls. Participants underwent a comprehensive cardiovascular evaluation. Taxonomic classification used MetaPhlAn 4, and functional profiling employed HUMAnN 3. Results: Despite similar alpha diversity, significant differences in bacterial community structure were observed between groups (PERMANOVA, p < 0.05). The LCR group showed enrichment of Faecalibacterium prausnitzii (p = 0.035), negatively correlating with atherogenic markers, including ApoB (r = −0.3, p = 0.025). Conversely, Fusicatenibacter saccharivorans positively correlated with ApoB (r = 0.4, p = 0.006). Metabolic pathway analysis revealed upregulation of nucleotide biosynthesis, glycolysis, and sugar degradation pathways in the LCR group, suggesting altered metabolic activity. Conclusions: We identified distinct gut microbiome signatures in LCR individuals that may represent early alterations associated with cardiovascular disease development. The opposing correlations between F. prausnitzii and F. saccharivorans with lipid parameters highlight their potential roles in cardiometabolic health. These findings suggest gut microbiome signatures may serve as indicators of early metabolic dysregulation preceding clinically significant cardiovascular disease. Full article
(This article belongs to the Section Cardiovascular Medicine)
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24 pages, 2173 KiB  
Article
A Novel Ensemble of Deep Learning Approach for Cybersecurity Intrusion Detection with Explainable Artificial Intelligence
by Abdullah Alabdulatif
Appl. Sci. 2025, 15(14), 7984; https://doi.org/10.3390/app15147984 - 17 Jul 2025
Viewed by 571
Abstract
In today’s increasingly interconnected digital world, cyber threats have grown in frequency and sophistication, making intrusion detection systems a critical component of modern cybersecurity frameworks. Traditional IDS methods, often based on static signatures and rule-based systems, are no longer sufficient to detect and [...] Read more.
In today’s increasingly interconnected digital world, cyber threats have grown in frequency and sophistication, making intrusion detection systems a critical component of modern cybersecurity frameworks. Traditional IDS methods, often based on static signatures and rule-based systems, are no longer sufficient to detect and respond to complex and evolving attacks. To address these challenges, Artificial Intelligence and machine learning have emerged as powerful tools for enhancing the accuracy, adaptability, and automation of IDS solutions. This study presents a novel, hybrid ensemble learning-based intrusion detection framework that integrates deep learning and traditional ML algorithms with explainable artificial intelligence for real-time cybersecurity applications. The proposed model combines an Artificial Neural Network and Support Vector Machine as base classifiers and employs a Random Forest as a meta-classifier to fuse predictions, improving detection performance. Recursive Feature Elimination is utilized for optimal feature selection, while SHapley Additive exPlanations (SHAP) provide both global and local interpretability of the model’s decisions. The framework is deployed using a Flask-based web interface in the Amazon Elastic Compute Cloud environment, capturing live network traffic and offering sub-second inference with visual alerts. Experimental evaluations using the NSL-KDD dataset demonstrate that the ensemble model outperforms individual classifiers, achieving a high accuracy of 99.40%, along with excellent precision, recall, and F1-score metrics. This research not only enhances detection capabilities but also bridges the trust gap in AI-powered security systems through transparency. The solution shows strong potential for application in critical domains such as finance, healthcare, industrial IoT, and government networks, where real-time and interpretable threat detection is vital. Full article
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15 pages, 5441 KiB  
Article
Task-Related EEG as a Biomarker for Preclinical Alzheimer’s Disease: An Explainable Deep Learning Approach
by Ziyang Li, Hong Wang and Lei Li
Biomimetics 2025, 10(7), 468; https://doi.org/10.3390/biomimetics10070468 - 16 Jul 2025
Viewed by 457
Abstract
The early detection of Alzheimer’s disease (AD) in cognitively healthy individuals remains a major preclinical challenge. EEG is a promising tool that has shown effectiveness in detecting AD risk. Task-related EEG has been rarely used in Alzheimer’s disease research, as most studies have [...] Read more.
The early detection of Alzheimer’s disease (AD) in cognitively healthy individuals remains a major preclinical challenge. EEG is a promising tool that has shown effectiveness in detecting AD risk. Task-related EEG has been rarely used in Alzheimer’s disease research, as most studies have focused on resting-state EEG. An interpretable deep learning framework—Interpretable Convolutional Neural Network (InterpretableCNN)—was utilized to identify AD-related EEG features. EEG data were recorded during three cognitive task conditions, and samples were labeled based on APOE genotype and polygenic risk scores. A 100-fold leave-p%-subjects-out cross-validation (LPSO-CV) was used to evaluate model performance and generalizability. The model achieved an ROC AUC of 60.84% across the tasks and subjects, with a Kappa value of 0.22, indicating fair agreement. Interpretation revealed a consistent focus on theta and alpha activity in the parietal and temporal regions—areas commonly associated with AD pathology. Task-related EEG combined with interpretable deep learning can reveal early AD risk signatures in healthy individuals. InterpretableCNN enhances transparency in feature identification, offering a valuable tool for preclinical screening. Full article
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