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Search Results (1,874)

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14 pages, 2544 KiB  
Article
Colorectal Cancer Risk in Korean Patients with Inflammatory Bowel Disease: A Nationwide Big Data Study of Subtype and Socioeconomic Disparities
by Kyeong Min Han, Ho Suk Kang, Joo-Hee Kim, Hyo Geun Choi, Dae Myoung Yoo, Nan Young Kim, Ha Young Park and Mi Jung Kwon
J. Clin. Med. 2025, 14(15), 5503; https://doi.org/10.3390/jcm14155503 - 5 Aug 2025
Abstract
Background/Objectives: The two major subtypes of inflammatory bowel disease (IBD)—Crohn’s disease (CD) and ulcerative colitis (UC)—are known to increase the likelihood of developing colorectal cancer (CRC). While this relationship has been well studied in Western populations, evidence from East Asia remains limited [...] Read more.
Background/Objectives: The two major subtypes of inflammatory bowel disease (IBD)—Crohn’s disease (CD) and ulcerative colitis (UC)—are known to increase the likelihood of developing colorectal cancer (CRC). While this relationship has been well studied in Western populations, evidence from East Asia remains limited and inconsistent. Using nationwide cohort data, this study explored the potential connection between IBD and CRC in a large Korean population. Methods: We conducted a retrospective cohort study using data from the Korean National Health Insurance Service–National Sample Cohort from 2005 to 2019. A total of 9920 CRC patients were matched 1:4 with 39,680 controls using propensity scores based on age, sex, income, and region. Overlap weighting and multivariable logistic regression were used to evaluate the association between IBD and CRC. Subgroup analyses were conducted to assess effect modification by demographic and clinical factors. Results: IBD markedly increased the likelihood of developing CRC (adjusted odds ratio (aOR) = 1.38; 95% confidence interval (CI): 1.20–1.58; p < 0.001), with the association primarily driven by UC (aOR = 1.52; 95% CI: 1.27–1.83). CD appeared unrelated to heightened CRC risk overall, though a significant association was observed among low-income CD patients (aOR = 1.58; 95% CI: 1.15–2.16). The UC–CRC association persisted across all subgroups, including patients without comorbidities. Conclusions: Our findings support an independent association between IBD—particularly UC—and increased CRC risk in Korea. These results underscore the need for personalized CRC surveillance strategies that account for disease subtype, comorbidity burden, and socioeconomic status, especially in vulnerable subpopulations. Full article
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25 pages, 1751 KiB  
Review
Large Language Models for Adverse Drug Events: A Clinical Perspective
by Md Muntasir Zitu, Dwight Owen, Ashish Manne, Ping Wei and Lang Li
J. Clin. Med. 2025, 14(15), 5490; https://doi.org/10.3390/jcm14155490 - 4 Aug 2025
Abstract
Adverse drug events (ADEs) significantly impact patient safety and health outcomes. Manual ADE detection from clinical narratives is time-consuming, labor-intensive, and costly. Recent advancements in large language models (LLMs), including transformer-based architectures such as Bidirectional Encoder Representations from Transformers (BERT) and Generative Pretrained [...] Read more.
Adverse drug events (ADEs) significantly impact patient safety and health outcomes. Manual ADE detection from clinical narratives is time-consuming, labor-intensive, and costly. Recent advancements in large language models (LLMs), including transformer-based architectures such as Bidirectional Encoder Representations from Transformers (BERT) and Generative Pretrained Transformer (GPT) series, offer promising methods for automating ADE extraction from clinical data. These models have been applied to various aspects of pharmacovigilance and clinical decision support, demonstrating potential in extracting ADE-related information from real-world clinical data. Additionally, chatbot-assisted systems have been explored as tools in clinical management, aiding in medication adherence, patient engagement, and symptom monitoring. This narrative review synthesizes the current state of LLMs in ADE detection from a clinical perspective, organizing studies into categories such as human-facing decision support tools, immune-related ADE detection, cancer-related and non-cancer-related ADE surveillance, and personalized decision support systems. In total, 39 articles were included in this review. Across domains, LLM-driven methods have demonstrated promising performances, often outperforming traditional approaches. However, critical limitations persist, such as domain-specific variability in model performance, interpretability challenges, data quality and privacy concerns, and infrastructure requirements. By addressing these challenges, LLM-based ADE detection could enhance pharmacovigilance practices, improve patient safety outcomes, and optimize clinical workflows. Full article
(This article belongs to the Section Pharmacology)
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28 pages, 1877 KiB  
Review
Unconventional Immunotherapies in Cancer: Opportunities and Challenges
by Meshael Alturki, Abdullah A. Alshehri, Ahmad M. Aldossary, Mohannad M. Fallatah, Fahad A. Almughem, Nojoud Al Fayez, Majed A. Majrashi, Ibrahim A. Alradwan, Mohammad Alkhrayef, Mohammad N. Alomary and Essam A. Tawfik
Pharmaceuticals 2025, 18(8), 1154; https://doi.org/10.3390/ph18081154 - 4 Aug 2025
Abstract
Conventional immunotherapy, including immune checkpoint blockade and chimeric antigen receptor (CAR)-T cells, has revolutionized cancer therapy over the past decade. Yet, the efficacy of these therapies is limited by tumor resistance, antigen escape mechanisms, poor persistence, and T-cell exhaustion, particularly in the treatment [...] Read more.
Conventional immunotherapy, including immune checkpoint blockade and chimeric antigen receptor (CAR)-T cells, has revolutionized cancer therapy over the past decade. Yet, the efficacy of these therapies is limited by tumor resistance, antigen escape mechanisms, poor persistence, and T-cell exhaustion, particularly in the treatment of solid tumors. The emergence of unconventional immunotherapies offers novel opportunities by leveraging diverse immune cell subsets and synthetic biologics. This review explores various immunotherapy platforms, including gamma delta T cells, invariant natural killer T cells, mucosal-associated invariant T cells, engineered regulatory T cells, and universal CAR platforms. Additionally, it expands on biologics, including bispecific and multispecific antibodies, cytokine fusions, agonists, and oncolytic viruses, showcasing their potential for modular engineering and off-the-shelf applicability. Distinct features of unconventional platforms include independence from the major histocompatibility complex (MHC), tissue-homing capabilities, stress ligand sensing, and the ability to bridge adaptive and innate immunity. Their compatibility with engineering approaches highlights their potential as scalable, efficient, and cost-effective therapies. To overcome translational challenges such as functional heterogeneity, immune exhaustion, tumor microenvironment-mediated suppression, and limited persistence, novel strategies will be discussed, including metabolic and epigenetic reprogramming, immune cloaking, gene editing, and the utilization of artificial intelligence for patient stratification. Ultimately, unconventional immunotherapies extend the therapeutic horizon of cancer immunotherapy by breaking barriers in solid tumor treatment and increasing accessibility. Continued investments in research for mechanistic insights and scalable manufacturing are key to unlocking their full clinical potential. Full article
(This article belongs to the Section Biopharmaceuticals)
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21 pages, 632 KiB  
Review
DNA Methylation in Bladder Cancer: Diagnostic and Therapeutic Perspectives—A Narrative Review
by Dragoş Puia, Marius Ivănuță and Cătălin Pricop
Int. J. Mol. Sci. 2025, 26(15), 7507; https://doi.org/10.3390/ijms26157507 (registering DOI) - 3 Aug 2025
Viewed by 60
Abstract
Bladder cancer pathogenesis is closely linked to epigenetic alterations, particularly DNA methylation and demethylation processes. Environmental carcinogens and persistent inflammatory stimuli—such as recurrent urinary tract infections—can induce aberrant DNA methylation, altering gene expression profiles and contributing to malignant transformation. This review synthesizes current [...] Read more.
Bladder cancer pathogenesis is closely linked to epigenetic alterations, particularly DNA methylation and demethylation processes. Environmental carcinogens and persistent inflammatory stimuli—such as recurrent urinary tract infections—can induce aberrant DNA methylation, altering gene expression profiles and contributing to malignant transformation. This review synthesizes current evidence on the role of DNA methyltransferases (DNMT1, DNMT3a, DNMT3b) and the hypermethylation of key tumour suppressor genes, including A2BP1, NPTX2, SOX11, PENK, NKX6-2, DBC1, MYO3A, and CA10, in bladder cancer. It also evaluates the therapeutic application of DNA-demethylating agents such as 5-azacytidine and highlights the impact of chronic inflammation on epigenetic regulation. Promoter hypermethylation of tumour suppressor genes leads to transcriptional silencing and unchecked cell proliferation. Urine-based DNA methylation assays provide a sensitive and specific method for non-invasive early detection, with single-target approaches offering high diagnostic precision. Animal models are increasingly employed to validate these findings, allowing the study of methylation dynamics and gene–environment interactions in vivo. DNA methylation represents a key epigenetic mechanism in bladder cancer, with significant diagnostic, prognostic, and therapeutic implications. Integration of human and experimental data supports the use of methylation-based biomarkers for early detection and targeted treatment, paving the way for personalized approaches in bladder cancer management. Full article
(This article belongs to the Section Molecular Oncology)
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16 pages, 914 KiB  
Article
APTIMA mRNA vs. DNA-Based HPV Assays: Analytical Performance Insights from a Resource-Limited South African Setting
by Varsetile Varster Nkwinika, Kelvin Amoh Amissah, Johnny Nare Rakgole, Moshawa Calvin Khaba, Cliff Abdul Magwira and Ramokone Lisbeth Lebelo
Int. J. Mol. Sci. 2025, 26(15), 7450; https://doi.org/10.3390/ijms26157450 (registering DOI) - 1 Aug 2025
Viewed by 223
Abstract
Cervical cancer remains a major health burden among women in sub-Saharan Africa, where screening is often limited. Persistent high-risk human papillomavirus (HR-HPV) infection is the principal cause, highlighting the need for accurate molecular diagnostics. This cross-sectional study evaluated the analytical performance of one [...] Read more.
Cervical cancer remains a major health burden among women in sub-Saharan Africa, where screening is often limited. Persistent high-risk human papillomavirus (HR-HPV) infection is the principal cause, highlighting the need for accurate molecular diagnostics. This cross-sectional study evaluated the analytical performance of one mRNA assay, APTIMA® HPV assay (APTIMA mRNA), and two DNA-based assays, the Abbott RealTime High Risk HPV assay (Abbott DNA) and Seegene Allplex™ II HPV28 assay (Seegene DNA), in 527 cervical samples from a South African tertiary hospital, focusing on 14 shared HR-HPV genotypes. Seegene DNA yielded the highest detection rate (53.7%), followed by Abbott DNA (48.2%) and APTIMA mRNA (45.2%). APTIMA mRNA showed a strong agreement with Abbott DNA (87.9%, κ = 0.80), 89.9% sensitivity, 91.2% NPV, and the highest accuracy (AUC = 0.8804 vs. 0.8681). The agreement between APTIMA mRNA and Seegene DNA was moderate (83.4%, κ = 0.70), reflecting target differences. Many DNA-positive/mRNA-negative cases likely represent transient infections, though some may be latent with reactivation potential, warranting a follow-up. In resource-constrained settings, prioritizing transcriptionally active infections through mRNA testing may enhance screening efficiency and reduce burden. Scalable, cost-effective assays with strong clinical utility are essential for broadening access and improving cervical cancer prevention. Further studies should assess the integration of mRNA testing into longitudinal screening algorithms. Full article
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22 pages, 6758 KiB  
Article
Screening of an FDA-Approved Drug Library: Menadione Induces Multiple Forms of Programmed Cell Death in Colorectal Cancer Cells via MAPK8 Cascades
by Liyuan Cao, Weiwei Song, Jinli Sun, Yang Ge, Wei Mu and Lei Li
Pharmaceuticals 2025, 18(8), 1145; https://doi.org/10.3390/ph18081145 - 31 Jul 2025
Viewed by 232
Abstract
Background: Colorectal cancer (CRC) is a prevalent gastrointestinal malignancy, ranking third in incidence and second in cancer-related mortality. Despite therapeutic advances, challenges such as chemotherapy toxicity and drug resistance persist. Thus, there is an urgent need for novel CRC treatments. However, developing [...] Read more.
Background: Colorectal cancer (CRC) is a prevalent gastrointestinal malignancy, ranking third in incidence and second in cancer-related mortality. Despite therapeutic advances, challenges such as chemotherapy toxicity and drug resistance persist. Thus, there is an urgent need for novel CRC treatments. However, developing new drugs is time-consuming and resource-intensive. As a more efficient approach, drug repurposing offers a promising alternative for discovering new therapies. Methods: In this study, we screened 1068 small molecular compounds from an FDA-approved drug library in CRC cells. Menadione was selected for further study based on its activity profile. Mechanistic analysis included a cell death pathway PCR array, differential gene expression, enrichment, and network analysis. Gene expressions were validated by RT-qPCR. Results: We identified menadione as a potent anti-tumor drug. Menadione induced three programmed cell death (PCD) signaling pathways: necroptosis, apoptosis, and autophagy. Furthermore, we found that the anti-tumor effect induced by menadione in CRC cells was mediated through a key gene: MAPK8. Conclusions: By employing methods of cell biology, molecular biology, and bioinformatics, we conclude that menadione can induce multiple forms of PCD in CRC cells by activating MAPK8, providing a foundation for repurposing the “new use” of the “old drug” menadione in CRC treatment. Full article
(This article belongs to the Section Medicinal Chemistry)
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13 pages, 1149 KiB  
Article
Not All Weight Loss Is Equal: Divergent Patterns and Prognostic Roles in Head and Neck Cancer Versus High-Grade B-Cell Lymphoma
by Judith Büntzel, Gina Westhofen, Wilken Harms, Markus Maulhardt, Alexander Casimir Angleitner and Jens Büntzel
Nutrients 2025, 17(15), 2530; https://doi.org/10.3390/nu17152530 - 31 Jul 2025
Viewed by 155
Abstract
Background: Malnutrition and unintended weight loss are frequent in cancer patients and linked to poorer outcomes. However, data on long-term weight trajectories, particularly comparing different cancer entities, remain limited. Methods: In this retrospective, multicenter study, we analyzed 145 patients diagnosed with either head [...] Read more.
Background: Malnutrition and unintended weight loss are frequent in cancer patients and linked to poorer outcomes. However, data on long-term weight trajectories, particularly comparing different cancer entities, remain limited. Methods: In this retrospective, multicenter study, we analyzed 145 patients diagnosed with either head and neck cancer (HNC; n = 48) or high-grade B-cell lymphoma (HGBCL; n = 97). Body weight, C-reactive protein (CrP), albumin, and modified Glasgow Prognostic Score (mGPS) were assessed at diagnosis and at 3, 6, 9, and 12 months. Clinically relevant weight loss was defined as >5% from baseline. Survival analyses were performed for HGBCL patients. Results: Weight loss was common in both cohorts, affecting 32.2% at 3 months and persisting in 42.3% at 12 months. Nearly half of HNC patients had sustained >5% weight loss at one year, whereas HGBCL patients were more likely to regain weight, with significantly higher rates of weight gain at 6 and 12 months (p = 0.04 and p = 0.02). At baseline, HGBCL patients showed elevated CrP and lower albumin compared to HNC (both p < 0.001). Weight loss at 6 months was significantly associated with reduced overall survival in HGBCL (p < 0.01). Both Δweight at 6 months and mGPS emerged as useful prognostic indicators. Conclusions: This study reveals distinct patterns of weight change and systemic inflammation between HNC and HGBCL patients during the first year after diagnosis. These findings highlight the need for entity-specific nutritional monitoring and tailored supportive care strategies extending into survivorship. Prospective studies integrating body composition analyses are warranted to better guide long-term management. Full article
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31 pages, 419 KiB  
Review
Neoadjuvant Treatment for Locally Advanced Rectal Cancer: Current Status and Future Directions
by Masayoshi Iwamoto, Kazuki Ueda and Junichiro Kawamura
Cancers 2025, 17(15), 2540; https://doi.org/10.3390/cancers17152540 - 31 Jul 2025
Viewed by 475
Abstract
Locally advanced rectal cancer (LARC) remains a major clinical challenge due to its high risk of local recurrence and distant metastasis. Although total mesorectal excision (TME) has been established as the gold standard surgical approach, high recurrence rates associated with surgery alone have [...] Read more.
Locally advanced rectal cancer (LARC) remains a major clinical challenge due to its high risk of local recurrence and distant metastasis. Although total mesorectal excision (TME) has been established as the gold standard surgical approach, high recurrence rates associated with surgery alone have driven the development of multimodal preoperative strategies, such as radiotherapy and chemoradiotherapy. More recently, total neoadjuvant therapy (TNT)—which integrates systemic chemotherapy and radiotherapy prior to surgery—and non-operative management (NOM) for patients who achieve a clinical complete response (cCR) have further expanded treatment options. These advances aim not only to improve oncologic outcomes but also to enhance quality of life (QOL) by reducing long-term morbidity and preserving organ function. However, several unresolved issues persist, including the optimal sequencing of therapies, precise risk stratification, accurate evaluation of treatment response, and effective surveillance protocols for NOM. The advent of molecular biomarkers, next-generation sequencing, and artificial intelligence (AI) presents new opportunities for individualized treatment and more accurate prognostication. This narrative review provides a comprehensive overview of the current status of preoperative treatment for LARC, critically examines emerging strategies and their supporting evidence, and discusses future directions to optimize both oncological and patient-centered outcomes. By integrating clinical, molecular, and technological advances, the management of rectal cancer is moving toward truly personalized medicine. Full article
(This article belongs to the Special Issue Multidisciplinary Management of Rectal Cancer)
12 pages, 1472 KiB  
Article
Furosemide Reduces Radionuclide Activity in the Bladder in 18F-PSMA-1007-PET/CT: A Single-Center Retrospective Intra-Individual Comparative Study
by Martin A. Cahenzli, Andreas S. Kreusch, Philipp Huber, Marco Dressler, Janusch P. Blautzik and Gregor Sommer
Diagnostics 2025, 15(15), 1931; https://doi.org/10.3390/diagnostics15151931 - 31 Jul 2025
Viewed by 154
Abstract
Background/Objectives: 18F-PSMA-1007 is one of the more widely used radioligands in prostate cancer imaging with PET/CT. Its major advantage lies in the low urinary tracer activity due to primarily hepatobiliary clearance, but unexpectedly high tracer accumulation in the bladder can occur, [...] Read more.
Background/Objectives: 18F-PSMA-1007 is one of the more widely used radioligands in prostate cancer imaging with PET/CT. Its major advantage lies in the low urinary tracer activity due to primarily hepatobiliary clearance, but unexpectedly high tracer accumulation in the bladder can occur, potentially hindering assessment of lesions near the prostate bed. This study assesses the impact of furosemide on 18F-PSMA-1007 tracer accumulation in the bladder. Methods: In this single-center, retrospective, intra-individual comparative analysis, 18 patients undergoing two consecutive 18F-PSMA-1007 PET/CT scans for biochemical relapse (BCR) or persistence (BCP)—one with and one without prior furosemide administration—were included. Images were acquired 60 min post-injection of 250 MBq of tracer activity. Standardized Uptake Values (SUVmax, SUVpeak, SUVmean) were measured in the bladder and in tissues with physiological uptake by three readers. Differences were analyzed using Wilcoxon signed-rank tests. The inter-reader agreement was assessed using intraclass correlation coefficient. Results: Furosemide significantly decreased bladder SUVmax, SUVpeak, and SUVmean (all p < 0.001). Mean bladder SUVmax decreased from 13.20 ± 10.40 to 3.92 ± 3.47, SUVpeak from 10.94 ± 8.02 to 3.47 ± 3.13, and SUVmean from 8.74 ± 6.66 to 2.81 ± 2.56, representing a large effect size (r ≈ 0.55). Physiological tracer uptake in most organs was not significantly influenced by furosemide (all p > 0.05). Conclusions: Despite the predominantly hepatobiliary clearance of 18F-PSMA-1007, furosemide-induced forced diuresis leads to a significant reduction in tracer activity in the bladder, which in clinical practice could help in early detection of tumor recurrence. Full article
(This article belongs to the Special Issue Research Update on Nuclear Medicine)
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35 pages, 887 KiB  
Review
Prognostic Factors in Colorectal Liver Metastases: An Exhaustive Review of the Literature and Future Prospectives
by Maria Conticchio, Emilie Uldry, Martin Hübner, Antonia Digklia, Montserrat Fraga, Christine Sempoux, Jean Louis Raisaro and David Fuks
Cancers 2025, 17(15), 2539; https://doi.org/10.3390/cancers17152539 - 31 Jul 2025
Viewed by 137
Abstract
Background: Colorectal liver metastasis (CRLM) represents a major clinical challenge in oncology, affecting 25–50% of colorectal cancer patients and significantly impacting survival. While multimodal therapies—including surgical resection, systemic chemotherapy, and local ablative techniques—have improved outcomes, prognosis remains heterogeneous due to variations in [...] Read more.
Background: Colorectal liver metastasis (CRLM) represents a major clinical challenge in oncology, affecting 25–50% of colorectal cancer patients and significantly impacting survival. While multimodal therapies—including surgical resection, systemic chemotherapy, and local ablative techniques—have improved outcomes, prognosis remains heterogeneous due to variations in tumor biology, patient factors, and institutional practices. Methods: This review synthesizes current evidence on prognostic factors influencing CRLM management, encompassing clinical (e.g., tumor burden, anatomic distribution, timing of metastases), biological (e.g., CEA levels, inflammatory markers), and molecular (e.g., RAS/BRAF mutations, MSI status, HER2 alterations) determinants. Results: Key findings highlight the critical role of molecular profiling in guiding therapeutic decisions, with RAS/BRAF mutations predicting resistance to anti-EGFR therapies and MSI-H status indicating potential responsiveness to immunotherapy. Emerging tools like circulating tumor DNA (ctDNA) and radiomics offer promise for dynamic risk stratification and early recurrence detection, while the gut microbiome is increasingly recognized as a modulator of treatment response. Conclusions: Despite advancements, challenges persist in standardizing resectability criteria and integrating multidisciplinary approaches. Current guidelines (NCCN, ESMO, ASCO) emphasize personalized strategies but lack granularity in terms of incorporating novel biomarkers. This exhaustive review underscores the imperative for the development of a unified, biomarker-integrated framework to refine CRLM management and improve long-term outcomes. Full article
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12 pages, 328 KiB  
Article
Polygenic Embryo Risk Scores: A Survey of Public Perception
by Alexandra Peyser, Cailey Brogan, Lilli Zimmerman and Randi H. Goldman
Reprod. Med. 2025, 6(3), 19; https://doi.org/10.3390/reprodmed6030019 - 31 Jul 2025
Viewed by 201
Abstract
Background: Preimplantation genetic testing for polygenic diseases (PGT-P) is a reproductive technology that has made it possible to assign risk scores to embryos for various complex polygenic conditions such as diabetes, hypertension, breast cancer, and schizophrenia. Whether there is public interest in utilizing [...] Read more.
Background: Preimplantation genetic testing for polygenic diseases (PGT-P) is a reproductive technology that has made it possible to assign risk scores to embryos for various complex polygenic conditions such as diabetes, hypertension, breast cancer, and schizophrenia. Whether there is public interest in utilizing PGT-P and what public opinions are regarding this technology is unknown. Therefore, the objective of our study was to evaluate the opinion of the general United States (US) public regarding PGT-P. Methods: A web-based questionnaire consisting of 25 questions was administered to a nationally representative sample of adult US residents according to age and sex. The survey contained a description of PGT-P, followed by questions with Likert-scale responses ranging from strongly agree to strongly disagree. Results: Of the 715 respondents recruited, 673 (94%) completed the survey. Most respondents agreed that use of PGT-P is ethical (54%), and another 37% were neutral; however, approximately 9% of respondents disagreed and were opposed to the use of PGT-P. Those that opposed PGT-P cited that it was “unethical” (46%) or “not natural” (39%), believed children could be negatively affected (31%), or stated that it went against their religion (15%). The majority of respondents did not know whether PGT-P was safe for embryos (68%) or children (67%) and felt that anyone should be able to utilize it (53%). Conclusions: Participants who were younger, were Atheist, or were Democrats were more likely to agree that “PGT-P is ethical”. This study identified that more than half of respondents supported the use of PGT-P. However, concerns regarding its safety and ethical implications persist. Full article
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25 pages, 2761 KiB  
Article
Leveraging Deep Learning, Grid Search, and Bayesian Networks to Predict Distant Recurrence of Breast Cancer
by Xia Jiang, Yijun Zhou, Alan Wells and Adam Brufsky
Cancers 2025, 17(15), 2515; https://doi.org/10.3390/cancers17152515 - 30 Jul 2025
Viewed by 274
Abstract
Background: Unlike most cancers, breast cancer poses a persistent risk of distant recurrence—often years after initial treatment—making long-term risk stratification uniquely challenging. Current tools fall short in predicting late metastatic events, particularly for early-stage patients. Methods: We present an interpretable machine [...] Read more.
Background: Unlike most cancers, breast cancer poses a persistent risk of distant recurrence—often years after initial treatment—making long-term risk stratification uniquely challenging. Current tools fall short in predicting late metastatic events, particularly for early-stage patients. Methods: We present an interpretable machine learning (ML) pipeline to predict distant recurrence-free survival at 5, 10, and 15 years, integrating Bayesian network-based causal feature selection, deep feed-forward neural network models (DNMs), and SHAP-based interpretation. Using electronic health record (EHR)-based clinical data from over 6000 patients, we first applied the Markov blanket and interactive risk factor learner (MBIL) to identify minimally sufficient predictor subsets. These were then used to train optimized DNM classifiers, with hyperparameters tuned via grid search and benchmarked against models from 10 traditional ML methods and models trained using all predictors. Results: Our best models achieved area under the curve (AUC) scores of 0.79, 0.83, and 0.89 for 5-, 10-, and 15-year predictions, respectively—substantially outperforming baselines. MBIL reduced input dimensionality by over 80% without sacrificing accuracy. Importantly, MBIL-selected features (e.g., nodal status, hormone receptor expression, tumor size) overlapped strongly with top SHAP contributors, reinforcing interpretability. Calibration plots further demonstrated close agreement between predicted probabilities and observed recurrence rates. The percentage performance improvement due to grid search ranged from 25.3% to 60%. Conclusions: This study demonstrates that combining causal selection, deep learning, and grid search improves prediction accuracy, transparency, and calibration for long-horizon breast cancer recurrence risk. The proposed framework is well-positioned for clinical use, especially to guide long-term follow-up and therapy decisions in early-stage patients. Full article
(This article belongs to the Special Issue AI-Based Applications in Cancers)
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21 pages, 604 KiB  
Review
Autoantibodies in COVID-19: Pathogenic Mechanisms and Implications for Severe Illness and Post-Acute Sequelae
by Lais Alves do-Nascimento, Nicolle Rakanidis Machado, Isabella Siuffi Bergamasco, João Vitor da Silva Borges, Fabio da Ressureição Sgnotto and Jefferson Russo Victor
COVID 2025, 5(8), 121; https://doi.org/10.3390/covid5080121 - 30 Jul 2025
Viewed by 246
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has led to a wide range of acute and chronic disease manifestations. While most infections are mild, a significant number of patients develop severe illness marked by respiratory failure, thromboinflammation, and multi-organ dysfunction. In addition, post-acute sequelae—commonly [...] Read more.
The COVID-19 pandemic, caused by SARS-CoV-2, has led to a wide range of acute and chronic disease manifestations. While most infections are mild, a significant number of patients develop severe illness marked by respiratory failure, thromboinflammation, and multi-organ dysfunction. In addition, post-acute sequelae—commonly known as long-COVID—can persist for months. Recent studies have identified the emergence of diverse autoantibodies in COVID-19, including those targeting nuclear antigens, phospholipids, type I interferons, cytokines, endothelial components, and G-protein-coupled receptors. These autoantibodies are more frequently detected in patients with moderate to severe disease and have been implicated in immune dysregulation, vascular injury, and persistent symptoms. This review examines the underlying immunological mechanisms driving autoantibody production during SARS-CoV-2 infection—including molecular mimicry, epitope spreading, and bystander activation—and discusses their functional roles in acute and post-acute disease. We further explore the relevance of autoantibodies in maternal–fetal immunity and comorbid conditions such as autoimmunity and cancer, and we summarize current and emerging therapeutic strategies. A comprehensive understanding of SARS-CoV-2-induced autoantibodies may improve risk stratification, inform clinical management, and guide the development of targeted immunomodulatory therapies. Full article
(This article belongs to the Section Host Genetics and Susceptibility/Resistance)
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26 pages, 7326 KiB  
Article
Cocoa Polyphenols Alter the Fecal Microbiome Without Mitigating Colitis in Mice Fed Healthy or Western Basal Diets
by Eliza C. Stewart, Mohammed F. Almatani, Marcus Hayden, Giovanni Rompato, Jeremy Case, Samuel Rice, Korry J. Hintze and Abby D. Benninghoff
Nutrients 2025, 17(15), 2482; https://doi.org/10.3390/nu17152482 - 29 Jul 2025
Viewed by 276
Abstract
Background/Objectives: Chronic inflammation and Western-style diets elevate colorectal cancer (CRC) risk, particularly in individuals with colitis, a feature of inflammatory bowel disease (IBD). Diets rich in polyphenol-containing functional foods, such as cocoa, may reduce gut inflammation and modulate the gut microbiome. This [...] Read more.
Background/Objectives: Chronic inflammation and Western-style diets elevate colorectal cancer (CRC) risk, particularly in individuals with colitis, a feature of inflammatory bowel disease (IBD). Diets rich in polyphenol-containing functional foods, such as cocoa, may reduce gut inflammation and modulate the gut microbiome. This study investigated the impact of cocoa polyphenol (CP) supplementation on inflammation and microbiome composition in mice with colitis, fed either a healthy or Western diet, before, during, and after the onset of disease. We hypothesized that CPs would attenuate inflammation and promote distinct shifts in the microbiome, especially in the context of a Western diet. Methods: A 2 × 2 factorial design tested the effects of the basal diet (AIN93G vs. total Western diet [TWD]) and CP supplementation (2.6% w/w CocoaVia™ Cardio Health Powder). Inflammation was induced using the AOM/DSS model of colitis. Results: CP supplementation did not reduce the severity of colitis, as measured by disease activity index or histopathology. CPs did not alter gene expression in healthy tissue or suppress the colitis-associated pro-inflammatory transcriptional profile in either of the two diet groups. However, fecal microbiome composition shifted significantly with CPs before colitis induction, with persistent effects on several rare taxa during colitis and recovery. Conclusions: CP supplementation did not mitigate inflammation or mucosal injury at the tissue level, nor did it affect the expression of immune-related genes. While CPs altered microbiome composition, most notably in healthy mice before colitis, these shifts did not correspond to changes in inflammatory signaling. Basal diet remained the primary determinant of inflammation, mucosal damage, and colitis severity in this model. Full article
(This article belongs to the Section Phytochemicals and Human Health)
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20 pages, 1859 KiB  
Systematic Review
From Evidence to Practice: A Systematic Review and Meta-Analysis on the Effects of Supervised Exercise on Fatigue in Breast and Prostate Cancer Survivors
by Arturo Cano-Uceda, Pablo García-Fernández, Blanca Peuyadé-Rueda, Ana María Cañuelo-Marquez, Cristian Solís-Mencía, Carmen Lucio-Allende, Luis De Sousa-De Sousa and José Luis Maté-Muñoz
Appl. Sci. 2025, 15(15), 8399; https://doi.org/10.3390/app15158399 - 29 Jul 2025
Viewed by 197
Abstract
Background: Breast and prostate cancer represent a significant global public health burden. Among the adverse effects of oncological treatments, fatigue is one of the most prevalent, persistent, and disabling symptoms. Therapeutic exercise has been shown to be effective for its management, with [...] Read more.
Background: Breast and prostate cancer represent a significant global public health burden. Among the adverse effects of oncological treatments, fatigue is one of the most prevalent, persistent, and disabling symptoms. Therapeutic exercise has been shown to be effective for its management, with supervision identified as a key factor that may enhance adherence, safety, and intensity control. This systematic review and meta-analysis aimed to compare the effects of supervised exercise programs versus usual care on cancer-related fatigue in patients with breast or prostate cancer. Methods: A systematic search (September–December 2024) was conducted in six databases (PubMed, Web of Science, Scopus, Cochrane, PEDro, Scielo), selecting RCTs from the past 10 years in English or Spanish. Studies compared supervised exercise with unsupervised exercise or usual care in stage I–III breast or prostate cancer patients within five years post-treatment. Methodological quality was assessed with the PEDro scale and risk of bias with Cochrane’s RoB 2.0. A random-effects model was used to calculate pooled effect sizes (ES, 95% CI), with heterogeneity (I2), sensitivity, subgroup, and publication bias analyses. Results: A total of 25 interventions from 19 randomized controlled trials involving over 2200 participants were included. Supervised exercise significantly reduced cancer-related fatigue compared to usual care (effect size = 0.34; 95% CI: 0.22–0.47; p < 0.001; I2 = 56%). Sensitivity analyses supported the robustness of the findings. Subgroup analyses revealed greater effects in combined exercise programs, in men, and in patients with prostate cancer. No evidence of publication bias was observed. While 73.7% of studies were rated as having good methodological quality, the risk of bias was often unclear or high. Conclusions: Supervised therapeutic exercise programs are effective and safe for reducing fatigue in breast and prostate cancer survivors. These interventions should be incorporated into comprehensive care plans, with individualization based on patients’ clinical and demographic characteristics. Further research is needed to identify the most effective and sustainable strategies for different patient subgroups. Full article
(This article belongs to the Special Issue Recent Advances in Exercise-Based Rehabilitation)
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