Search Results (656)

The phage-resistant mutant (PRM) strains of Escherichia coli (E. coli) exhibited abundant genetic and phenotypic diversity. IS elements played a vital role in creating various genetic divergences and regulating gene functions under phage infection stress. Genetic variations of PRM strains derived from E. coli MG1655 and mutation frequencies of coevolved E. coli populations with phages were explored by high-throughput sequencing and resequencing. Infrequent-restriction-site PCR (IRS-PCR) and carbon utilization test revealed the genetic and phenotypic diversity of the PRM strains. Numerous and discrepant mutation sites (MSs) were observed in the PRM strains and the coevolved populations, and many MSs were related to the synthesis of flagella and LPS, which often serve as receptors in a phage invasion. The insertions of various IS elements in key gene locations were also frequently found in the PRM strains, which indicate for the first time that IS elements played a vital role in generating genetic divergence and regulating gene functions under phage infection stress. Resequencing revealed that the coevolved populations at three evolving stages had discrepant profiles of MSs, and nearly all detected MSs occurred in the coevolved populations, which led to coexisting phages that increased the mutation rates and expedited the occurrence of the defective MSs in E. coli populations. In summary, our results reveal that the widespread and abundant presence of phages may provide one important force driving bacterial genomic evolution and prompt bacterial genetic divergence via accelerated mutation and increased mutation rates in the E. coli genome. Full article

As a metallurgical solid waste rich in active calcium oxide, magnesium slag (MS) is endowed with significant carbon dioxide sequestration potential due to its inherent properties, providing a feasible path for the simultaneous solution of waste residue disposal and carbon dioxide emission reduction. However, current research has neither clarified the kinetic mechanism (core theoretical support for carbon dioxide sequestration industrialization) nor systematically evaluated the life cycle environmental impacts of MS’s two carbonation routes (direct or indirect leaching carbonation). To address this, this study explores kinetic laws via the single-factor control variable method, and combines life cycle assessment (LCA) to fill the gap, providing key theoretical support for process optimization and engineering promotion. Kinetic results show indirect carbon dioxide sequestration (ICDS) forms an inert silicon-rich layer (core-shrinkage model, mixed control, 28.4 kJ/mol activation energy), while direct carbon dioxide sequestration (DCDS) involves dual-layer formation and pore blockage (mixed control, 14.0 kJ/mol). The ICDS achieves a higher reaction rate of 89%, compared to 63% for the DCDS. In life cycle assessments, DCDS demonstrates outstanding overall environmental sustainability, particularly excelling in carbon dioxide sequestration and acidification control, while ICDS exhibits significant environmental drawbacks (such as high carbon dioxide emissions and ecological toxicity). However, ICDS possesses advantages such as high feedstock utilization and strong synthesis capabilities for high-value-added products. Through targeted optimization, its environmental indicators can be reduced in the future, making it suitable for specific scenarios like high-end calcium carbonate production and resource utilization of low-grade magnesium slag. Full article

Background/Objective: Pulmonary involvement in systemic sclerosis (SSc) is typically assessed using pulmonary function tests (PFTs), high-resolution CT (HRCT), and composite indices. Patient-reported outcomes (PRO), including ScleroID, provide insight into quality of life, but their relationship with clinical measures and role in overall disease assessment remain unclear. To assess the correlation between ScleroID scores and both lung involvement and disease activity/damage in a cohort of SSc-ILD patients from a large tertiary care center. Methods: Disease activity [European Scleroderma Study Group Activity Index (EScSG-AI), Scleroderma Clinical Trials Consortium Activity Index (SCTC-AI)], disease severity [Medsger severity scale (MSS)], and PRO measure ScleroID were assessed for associations with the extent and severity of SSc-ILD. Results: In 82 patients with SSc-ILD (mean age 56.0 ± 10.8 years; median disease duration 4.2 ± 4.7 years), higher fibrosis extent (>20%) was associated with worse lung function, greater exercise limitation, and higher ScleroID scores, particularly in fatigue, social life, and body mobility domains (all p ≤ 0.03). Patients with >20% fibrosis also had worse NYHA class and Borg scores during 6-MWD (p < 0.001). Cross-sectional correlations showed that ScleroID total and individual domains were negatively associated with FVC% and 6-MWD, and positively with ILD extent on HRCT. Fatigue, social impact, and mobility domains correlated most strongly with disease activity and severity scores, especially in patients with > 20% fibrosis (r = 0.384–0.635, all p ≤ 0.016), whereas breathlessness showed minimal associations (r < 0.2). Conclusions: In SSc-ILD, greater lung fibrosis and functional impairment are associated with worse patient-reported quality of life, particularly in fatigue, mobility, and social domains. ScleroID scores reflect both physiological severity and disease burden highlighting its value as a multidimensional outcome measure in patients with more advanced disease. Full article

Background: Metastatic colorectal cancer (mCRC) with TP53 gene mutations, which are commonly found in tumors that are microsatellite stable (MSS) and not prone to genetic errors seen in some cancers, is associated with aggressive cancer behavior and poor outcomes. While MSI-high (MSI-H, referring to high levels of gene instability) disease benefits markedly from PD-1-based immunotherapy (drugs that inhibit the PD-1 protein on immune cells), TP53-mutated MSS tumors rarely receive immune checkpoint inhibitors (ICIs, drugs that help immune cells attack cancer) outside of trials and often only in later lines of therapy. Objective: We aimed to synthesize translational and clinical evidence regarding the effects of early rationale-driven immunotherapy combinations on survival outcomes, in TP53-mutated metastatic colorectal cancer, with a focus on practical clinical implications. Methods: This narrative review was conducted in accordance with SANRA criteria. Literature searches were performed in PubMed/MEDLINE, Scopus, and Web of Science (2010–2025). Relevant ESMO and NCCN guidelines and key references were also reviewed. Results: In KEYNOTE-177 study (MSI-H/dMMR), pembrolizumab improved PFS (HR 0.60) and showed durable OS with >5-year follow-up. CheckMate-142 reported sustained activity with nivolumab ± ipilimumab. Preclinical/early clinical data in MSS/TP53 suggest that ICIs may become effective when combined with priming (chemo/DDR) and vascular normalization (anti-VEGF), particularly in subsets with elevated TMB. The randomized ROME trial supports the clinical utility of genomically matched, NGS-guided strategies. Conclusions: A precision approach integrating TP53 status, TMB, and TME modulation could extend the immunotherapy benefit beyond MSI-H to TP53-mutated MSS mCRC; prospective first-line trials are warranted. Full article

Marinesco–Sjögren syndrome (MSS) is a rare autosomal recessive disorder characterized by cerebellar ataxia, congenital cataracts, developmental delay, hypotonia, and progressive myopathy. Most reported cases are linked to pathogenic variants in SIL1, a gene encoding a co-chaperone essential for protein folding in the endoplasmic reticulum. Here, we present a comprehensive case study of a Turkish pediatric patient diagnosed with MSS, supported by genetic, bioinformatic, and structural modeling analyses. Whole-exome sequencing revealed a homozygous splice-site variant (SIL1 c.453+1G>T), confirmed by Sanger sequencing and segregation analysis. In silico annotation using Genomize, InterVar, Franklin, VarSome, ClinVar, OMIM, and PubMed classified the variant as pathogenic according to ACMG guidelines. Structural modeling by Phyre2 and I-TASSER demonstrated that the variant abolishes the intron 5 donor site, leading to truncation of the wild-type 461-amino-acid protein into a shortened ~189-amino-acid polypeptide. This truncation results in the loss of critical Armadillo (ARM) repeats required for HSPA5 interaction, explaining the observed instability and impaired chaperone function. Clinically, the patient presented with congenital cataracts, ataxia, developmental delay, and progressive muscle weakness, consistent with previously reported MSS cases. Comparison with the literature confirmed that splice-site variants frequently correlate with severe phenotypes, including early-onset ataxia and cataracts. This report highlights the importance of integrating genomic, structural, and clinical data to better understand genotype–phenotype correlations in MSS. Our findings expand the mutational spectrum of SIL1, reinforce the role of splicing defects in disease pathogenesis, and emphasize the necessity of comprehensive molecular diagnostics for rare neurogenetic syndromes. Full article

Immunotherapy has demonstrated significant efficacy in colorectal cancer (CRC), but its therapeutic effects remain limited in microsatellite stable (MSS) patients, indicating the critical role of the tumor immune microenvironment (TIME) in regulating immune responses. Lipid rafts, dynamic membrane microdomains enriched in cholesterol and sphingolipids, have emerged as potential targets for TIME remodeling through their integration of immune signal transduction, enrichment of cell death receptors, and regulation of immune cell functionality. This review outlines the pivotal mediating roles of lipid rafts in cellular survival, death, and tumor progression. Specifically, MSS-type CRC exhibits lipid raft structural remodeling driven by dysregulated lipid metabolism, which fosters multiple immune escape mechanisms through exosome-mediated immunosuppressive signaling, promotion of tumor-associated macrophage (TAM) M2 polarization, enhanced infiltration of regulatory T cells (Tregs), and functional exhaustion of effector cells, such as CD8⁺ T cells and NK cells. Finally, we discuss targeted therapeutic strategies based on lipid raft characteristics and CRC molecular profiles, proposing an innovative multidimensional treatment framework combining immune checkpoint inhibitors with lipid raft-targeted interventions and chemoradiotherapy. This approach provides theoretical and strategic support for overcoming CRC immunotherapy resistance and advancing clinical translation. Full article

In colorectal carcinoma (CRC), 5-fluorouracil (5-FU) remains the cornerstone of adjuvant systemic therapy, with folic acid (FA) serving as an essential adjunct. Expression of genes related to the metabolism and action of 5-FU and FA can be influenced by patient- and tumor-specific biological factors. In this study, we explore differential gene expression profiles of 180 genes representing 14 different gene sets associated with different 5-FU and FA metabolism processes, at both gene and pathway levels across clinical and molecular subgroups. In 71 patients with CRC, paired tumors and normal colonic tissues were analyzed. In CRC tissue, several gene sets (including Cell Cycle Checkpoint, Oxidative Stress Response, and Signaling Pathway, etc.) were upregulated, while three gene sets (Apoptotic, Tumor Suppressor, and Endoplasmic Reticulum Stress) were downregulated. Kirsten rat sarcoma virus (KRAS), tumor protein p53 (TP53), and microsatellite instability (MSI) status impacted gene expression across molecular subgroups. At the individual gene level, among cell cycle genes, the BUB3 mitotic checkpoint protein (BUB3) was upregulated in MSI tumors compared to MSS, whereas SMAD family member 4 (SMAD4) was downregulated in MSS tumors compared to MSI. DNA fragmentation factor alpha (DFFA) was downregulated in MSI and upregulated in MSS. Notably, thymidylate synthetase (TYMS) was more upregulated in MSI tumors (1.65-fold; 95% CI: 1.27–2.13) compared to MSS (1.19-fold; 95% CI: 1.02–1.39). Dysregulation of these genes across these factors will broaden our understanding of 5-FU-based treatment in CRC. Furthermore, targeting dysregulated pathways could form the basis for improved precision therapies tailored to CRC subtypes. Full article

Marinesco–Sjögren syndrome (MSS) is a rare autosomal recessive neuromuscular disorder marked by ataxia, muscle weakness, cataracts, and often intellectual and skeletal abnormalities. It is commonly caused by loss-of-function variants in the SIL1 gene, which impair binding immunoglobulin protein (BiP) function, leading to protein misfolding and activation of the unfolded protein response. In a 2-year-old patient with typical MSS symptoms, we identified a previously unreported c.1024G>A (p.E342K) variant in SIL1 via whole-exome sequencing. The pathogenicity of this Sil1 variant was supported by evidence of structural changes revealed through in silico predictions, circular dichroism, and native gel electrophoresis. Patient-derived fibroblasts exhibited reduced Sil1 protein levels, likely due to misfolding and degradation, which was partially rescued by proteasome inhibition. Proteomics revealed a profile similar to known MSS cases and a distinctive MSS transcriptional signature. Ultrastructural analysis confirmed typical MSS features, such as autophagic vacuoles and lipid droplets. Although the p.E342K phenotype appears milder than the reference pathogenic variant R111X, our findings support the reclassification of this novel variant as pathogenic, in accordance with the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) 2015 guidelines and the refinements proposed by the Clinical Genome Resource Sequence Variant Interpretation (ClinGen SVI) recommendations. Furthermore, the overall evidence also provides important insights into the genotype–phenotype correlation and the underlying pathogenic mechanism of the p.E342K variant. Full article

Background: Multiple Sclerosis (MS) is an inflammatory, autoimmune and neurodegenerative disease of the central nervous system that leads to the progressive loss of motor and sensory functions. Cognitive dysfunction is a common symptom that significantly affects quality of life and daily activities. The MS diagnosis involves progressive disability due to its neurodegenerative nature. Objective: to analyze the relationship between the Latin Norm Neuropsychological Assessment and Disability in Multiple Sclerosis (NLNAMS) battery and physical disability in patients with MS. Methods: A retrospective review of 100 medical records was conducted. Three sections of clinical information were analyzed: (1) sociodemographic data and medical history, (2) neurological examination including disability measures using the Expanded Disability Status Scale (EDSS) and the Multiple Sclerosis Severity Score (MSS), and (3) neuropsychological assessment results obtained through the NLNAMS battery to evaluate cognitive functioning across multiple domains. Results: High correlations were observed between EDSS scores and performance on the Symbol Digit Modalities Test (SDMT) and the Hopkins Verbal Learning Test–Revised (HVLT-R), which assess attention, processing speed and memory. Strong correlations were also found between EDSS and performance on verbal fluency tests, Trail Making Test (TMT), Rey–Osterrieth Complex Figure copy (ROCF), and the Modified Wisconsin Card Sorting Test (M-WCST). No significant correlation with MSS was found. Conclusions: The neuropsychological evaluation conducted with the NLNAMS battery showed a relationship between physical disability in multiple sclerosis and the domains of attention, processing speed, and memory. Therefore, this battery may provide valuable information for disease monitoring and prognosis. Full article

This paper introduces two generalized frameworks, the extended bipolar parametric b-metricspace (EBPbMS) and the extended bipolar fuzzy b-metric space (EBFbMS), which unify and extend several existing bipolar and fuzzy metric structures. Within these settings, new fixed-point results are established for covariant and contravariant Meir–Keeler-type contractions. A fundamental correspondence between EBFbMSs and EBPbMSs is developed, providing a unified basis for analyzing convergence and stability in generalized metric environments. An illustrative example and an application to a fractional blood flow model confirm the effectiveness of the proposed approach and ensure the existence and uniqueness of the solution. These results demonstrate the capability of extended bipolar structures to model nonlinear fractional systems with memory effects. Full article

Background: Colorectal cancer (CRC), particularly the microsatellite-stable (MSS) subtype, remains largely unresponsive to immune checkpoint inhibitors (ICIs) due to immune escape, tumor-associated macrophage (TAM) enrichment, and cytokine-driven suppression that sustain a TAM-dominant tumor microenvironment (TME). To overcome these barriers, a pH-responsive solid lipid nanoparticle (SLN) system was engineered to co-deliver CB-5083 (a VCP/p97 inhibitor), miR-142 (a PD-L1-targeting microRNA), and imiquimod (R, a TLR7 agonist) for spatially confined induction of endoplasmic reticulum stress (ERS) and immune reprogramming in MSS CRC. Methods: The SLNs were coated with PEG–PGA for pH-triggered de-shielding and functionalized with PD-L1- and EGFR-binding peptides plus an ER-homing peptide, enabling tumor-selective and subcellular targeting. Results: The nanoplatform displayed acid-triggered PEG–PGA detachment, selective CRC/TAM uptake, and ER localization. CB-mediated VCP inhibition activated IRE1α/XBP1s/LC3II, PERK/eIF2α/ATF4/CHOP, and JNK/Beclin signaling, driving apoptosis and autophagy, while miR-142 suppressed PD-L1 expression and epithelial–mesenchymal transition markers. R facilitated dendritic cell maturation and M1 polarization. Combined CB + miR + R/SLN-CSW suppressed IL-17, G-CSF, and CXCL1, increased infiltration of CD4⁺ and CD8⁺ T cells, reduced Tregs and M2-TAMs, and inhibited tumor growth in CT-26 bearing mice. The treatment induced immunogenic cell death, reprogramming the TME into a T cell-permissive state and conferring resistance to tumor rechallenge. Biodistribution analysis confirmed tumor-preferential accumulation with minimal off-target exposure, and biosafety profiling demonstrated low systemic toxicity. Conclusions: This TME-responsive nanoplatform therefore integrates ERS induction, checkpoint modulation, and cytokine suppression to overcome immune exclusion in MSS CRC, representing a clinically translatable strategy for chemo-immunotherapy in immune-refractory tumors. Full article

Sepsis is characterized by the over-production of pro-inflammatory cytokines. Cecal ligation and puncture (CLP) is a well-accepted model for recreating sepsis-induced renal injury in mice. The current study investigates how citronellol, a naturally occurring substance with a variety of biological characteristics, can prevent acute kidney inflammation brought on by CLP. In the CLP mouse model, citronellol was administered orally at doses of 50 and 100 mg/kg. Serum levels of creatinine and urea were used as markers of renal function, and the Murine Sepsis Score (MSS) was used to assess the severity of sepsis. According to our findings, CLP caused a decline in renal function, as shown by higher serum urea and creatinine levels in comparison to control mice. Nevertheless, administering citronellol as pretreatment at doses of 50 and 100 mg/kg alleviated the deterioration in renal functions. Citronellol decreased levels of serum urea and creatinine. Citronellol demonstrated an anti-inflammatory effect by reducing pro-inflammatory cytokines (TNF-α, NF-κB, AP-1) and KIM-1. Overall, our study suggests that citronellol holds a promise as a potential therapeutic agent for mitigating kidney inflammation. Full article

Targetable gene alterations have become increasingly important in the treatment of cancers. Thirty STK11-mutated lung cancers from 199 cases with molecular profiling performed during 2016–2024 were studied for clinical, morphologic, immunohistochemical (IHC) and molecular features. Of the 30 STK11-mutated lung cancers, 29 were lung adenocarcinomas (LADCs) and 1 was large cell neuroendocrine carcinoma (LCNEC). STK11 mutation was not found in other subtypes of lung cancers. Of the 29 STK11-mutated LADCs, 6 (21%) were mucinous and 23 (79%) were non-mucinous. Of the 19 non-mucinous LADCs with sufficient material for IHC, 9 (47%) displayed acinar/papillary/lepidic patterns, 8 (42%) were poorly differentiated (solid/trabecular/basaloid/complex glandular), and 2 (11%) had mixed solid and acinar patterns. The most common concurrent altered genes were KRAS (52%), followed by TP53 (38%), KEAP1 (34%), and DNA repair genes (BRCA2/ATM) (21%). A total of 6/15 (40%) LADCs with a KRAS mutation presented with mucinous morphology. Concurrent EGFR, ROS, or ALK alterations with STK11 mutation were rare or non-existent. Of the 3 LADCs with SMARCA4 deficiency, 2 were mucinous and 1 had basaloid/adenoid cystic-like features. All the cases were microsatellite stable (MSS). The majority (55%) had low TMB (<10). Most (86%) had PD-L1 TPS 0 or <5%. Among the 14 non-mucinous LADCs with IHC performed, 5 (36%) were TTF-1-negative and all displayed poorly differentiated morphology. Overall, 8/10 (80%) of poorly differentiated components in non-mucinous LADCs were negative for TTF-1. In contrast, all LADCs with better differentiated patterns (acini/papillary/lepidic) were positive for TTF-1. The majority (14/21, 67%) of patients with available follow-up presented with metastasis. Full article

Colorectal cancer (CRC) classification has progressed from consensus molecular subtypes (CMS) to epithelial–intrinsic consensus molecular subtypes (iCMS) and the layered intrinsic subtype-MSI-fibrosis (IMF) system that combines intrinsic state, MSI status, and fibrosis. This article reviews biological underpinnings of iCMS/IMF, their relationships to tumor-microenvironment crosstalk, and how single-cell and spatial transcriptomics refine therapeutic stratification by resolving tumor microenvironment heterogeneity and its impact on fibrosis. Prognostic and therapeutic implications are covered, including PD-1 blockade in MSI-high (MSI-H), MAPK-directed therapy in BRAF-mutant disease, and EGFR targeting in selected RAS wild-type (WT) left-sided tumors, and we suggest decision points specifically informed by the activity of the fibrosis axis. A step-by-step procedure is presented for the analysis of bulk and single-cell RNA and formalin-fixed, paraffin-embedded (FFPE) resources, along with open-source tools and reporting standards to make iCMS/IMF calling reproducible in clinics and trials. Future outlooks are outlined with near-term biomarker–drug hypotheses for microsatellite-stable (MSS)-iCMS3 and high fibrosis tumors and key gaps to close for clinical translation. This review outlines a roadmap for precision medicine in colorectal cancer by leveraging the iCMS/IMF framework to integrate pathology and digital pathology, molecular diagnostics, and therapy mapping with FAP-targeted imaging and therapy. Full article

This study proposes a method to quantitatively assess evacuation demographics during regional floods using Mobile Spatial Statistics (MSSs). It focuses on Koriyama City, affected by Typhoon Hagibis in 2019, as well as Yamagata City, which experienced torrential rains in July 2020, when COVID-19 infection risks in evacuation shelters could have affected evacuation behavior. Both events led to flooding. MSS provided by NTT Docomo were used to explore the dynamics of the population. Evacuees’ demographics, according to the changes in river levels, were presented by gender and age group. Our results show differences in evacuation dynamics between the two regions: In Koriyama, younger people were more likely to evacuate faster; in Yamagata, older people moved faster than other age groups. At the evacuation peak, the average relative evacuation ratios were 2.2 times higher for women in their 20s in Koriyama, and 2.5 times higher for women in their 30s in Yamagata. Gender differences indicate that women were more likely to evacuate than men. The effect of the COVID-19 pandemic on evacuation dynamics remains unclear; however, concerns about infection risk in shelters may have influenced people’s willingness to evacuate. MSSs provide a robust representation of evacuation dynamics in the local context and can help municipal governments develop more targeted evacuation policies, such as tailored warnings for specific age groups and enhanced support for older adults. Full article