Search Results (218)

Factor analysis is a well-known statistical method to describe the variability of observed variables in terms of a smaller number of unobserved latent variables called factors. Even though latent factors are conceptually independent of each other, their influence on the observed variables is often joint and synergistic. We propose to quantify the synergy of the joint influence of factors on the observed variables using O-information, a recently introduced metric to assess high-order dependencies in complex systems; in the proposed framework, latent factors and observed variables are jointly analyzed in terms of their joint informational character. Two case studies are reported: analyzing resting fMRI data, we find that DMN and FP networks show the highest synergy, consistent with their crucial role in higher cognitive functions; concerning HeLa cells, we find that the most synergistic gene is STK-12 (AURKB), suggesting that this gene is involved in controlling the HeLa cell cycle. We believe that our approach, representing a bridge between factor analysis and the field of high-order interactions, will find wide application across several domains. Full article

RKIP and LKB1, encoded by PEBP1 and STK11, respectively, have emerged as key regulators of cancer pathophysiology. However, their role in shaping tumor progression through modulation of the tumor microenvironment (TME) is not yet fully understood. To address this, we performed a comprehensive pan-cancer analysis using TCGA transcriptomic data across 33 cancer types, grouped by their tissue of origin. We investigated PEBP1/STK11 co-expression and its association with transcriptomic reprogramming in major TME components, including immune, mechanical, metabolic, and hypoxic subtypes. Our results revealed both positive and inverse correlations between PEBP1/STK11 co-expression and TME-related molecular signatures, which did not align with classical cancer categorizations. In a subset of tumors, PEBP1/STK11 co-expression was significantly associated with improved overall survival and reduced mortality (HR < 1). Notably, we predominantly observed inverse correlations with pro-inflammatory and immunosuppressive chemokines, immune checkpoints, extracellular matrix components, and key regulators of epithelial-to-mesenchymal transition. In contrast, we found positive associations with anti-inflammatory chemokines and their receptors. Importantly, PEBP1/STK11 co-expression was consistently linked to reduced expression of drug resistance genes and greater chemosensitivity across multiple tumor types. Our findings underscore the co-expression of PEBP1 and STK11 as a promising target for future studies aimed at elucidating its potential as a biomarker for prognosis and therapeutic response in precision oncology. Full article

Background/Objectives: The clinical value of KRAS mutations in lung adenocarcinoma, alone or in combination with other mutations, has been assessed especially in advanced stages. This study evaluates how KRAS and the presence of co-mutations could affect survival in early-stage lung. Methods: We analyzed a real-world cohort including all staged NSCLC patients diagnosed and treated from 2018 to 2022 at our Institute with availability of NGS molecular data. Statistical analyses were made using log-rank test, the two-tailed Fisher’s exact test and Kaplan-Meier survival curves. Results: KRAS mutations were observed in 179/464 cases (38.6%). The majority of KRAS co-mutations were in TP53 (74%) and STK11 (14.3%) genes. KRAS+TP53 co-mutations were more frequent compared to KRAS-only tumors in stage IV NSCLC (p = 0.01). In early stage and locally advanced cases (stage I-III), better prognosis was associated to KRAS-only mutated NSCLC and to KRAS+STK11 mutated cases compared to KRAS+TP53 (p = 0.008). In particular, patients carrying KRAS+TP53 in stage I and II displayed a shorter survival, similar to patients diagnosed at stage III. Conclusions: Routine NGS provides important information for potential actionable mutations but also for the prognostic and predictive role of the presence of co-occurring mutations. In particular, the presence of KRAS+TP53 in stage I and II NSCLC may be considered an unfavorable prognostic marker possibly leading to adapt the perioperative chemo-immunotherapy. Full article

Worldwide, lung cancer is one of the most common cancers, with non-small cell lung cancer (NSCLC) including up to 80–85% of all lung cancer diagnoses. The landscape of NSCLC is characterized by a heterogeneous spectrum of gene alterations, with tyrosine kinase inhibitors (TKIs) and targeted treatments that significantly improve survival outcomes for patients with oncogene-addicted NSCLC, offering superior efficacy, and often favorable safety and tolerability profiles compared to chemotherapy-based treatments. However, the complexity of NSCLC extends to co-occurring genomic alterations or amplifications in tumor suppressors and other oncogenes, such as TP53, STK11, KEAP1, PIK3CA, RB1, and others, that significantly influence disease progression, therapeutic resistance, and clinical outcomes. These co-mutations often contribute to the development of primary and acquired resistance to targeted therapies, complicating decision-making strategies. This review provides a timely and comprehensive synthesis of current insights into co-mutations in NSCLC, with a particular focus on their clinical implications, and offers a novel perspective by integrating recent molecular insights with therapeutic challenges, addressing existing knowledge gaps through a more integrative and clinically oriented analysis of co-mutations. Advances in next-generation sequencing (NGS) and molecular profiling have enabled the identification of these co-alterations, paving the way for more personalized therapeutic approaches. However, challenges remain in interpreting the functional interplay of co-mutations and translating these insights into effective clinical interventions. This review also highlights the significance of co-mutations in shaping NSCLC biology, and discusses their impact on current therapeutic paradigms, emphasizing the need for integrative biomarker-driven approaches to improve outcomes in NSCLC. Full article

Background: Alcohol-associated liver disease (ALD) is characterized by gut–liver axis dysfunction and metabolic dysregulation, yet the therapeutic potential of probiotics remains underexplored. This study aimed to investigate the protective effects and mechanisms of Lacticaseibacillus paracasei 36 (LP36) against ethanol-induced ALD in mice. Methods: Mice were pretreated with LP36 prior to ethanol exposure. Liver injury was assessed through serum ALT/AST levels, hepatic steatosis (TC/TG content), and ethanol detoxification capacity (ADH/ALDH activity). Intestinal barrier integrity was evaluated via Mucin2 and ZO-1 expression, and gut microbiota alterations were analyzed by 16S rRNA sequencing. Hepatic transcriptomics (RNA-seq) was performed to identify key regulatory pathways. Results: LP36 significantly attenuated ethanol-induced liver injury, evidenced by reduced ALT/AST, improved hepatic steatosis (lower TC/TG), and enhanced ADH/ALDH activity. Mechanistically, LP36 restored intestinal barrier function (upregulated Mucin2 and ZO-1), modulated gut microbiota (suppressed Parasutterella, Romboutsia, and Christensenellaceae_R-7_group; enriched Faecalibaculum and Tuzzerella), and reduced systemic inflammation. Transcriptomics revealed LP36-mediated rescue of AMPK signaling, involving regulation of Stk11, Prkag3, lipid synthesis genes (Fasn, Acaca), and metabolic modulators (Creb3l3, G6pc3, mTOR, Rps6kb2).Conclusions: LP36 ameliorates ethanol-induced ALD by enhancing intestinal barrier integrity, reshaping gut microbiota, and restoring AMPK-dependent metabolic homeostasis. These findings highlight LP36 as a promising probiotic candidate for ALD prevention. Full article

The increasing congestion of low Earth orbit (LEO) has raised the need for efficient collision avoidance strategies, especially for CubeSats without propulsion systems. This study proposes a methodology for evaluating passive collision avoidance maneuvers using aerodynamic control via a satellite’s Attitude Determination and Control System (ADCS). By adjusting orientation, the satellite modifies its exposed surface area, altering atmospheric drag and lift forces to shift its orbit. This new approach integrates atmospheric modeling (NRLMSISE-00), aerodynamic coefficient estimation using the ADBSat panel method, and orbital simulations in Systems Tool Kit (STK). The LUME-1 CubeSat mission is used as a reference case, with simulations at three altitudes (500, 460, and 420 km). Results show that attitude-induced drag modulation can generate significant orbital displacements—measured by Horizontal and Vertical Distance Differences (HDD and VDD)—sufficient to reduce collision risk. Compared to constant-drag models, the panel method offers more accurate, orientation-dependent predictions. While lift forces are minor, their inclusion enhances modeling fidelity. This methodology supports the development of low-resource, autonomous collision avoidance systems for future CubeSat missions, particularly in remote sensing applications where orbital precision is essential. Full article

Although immunotherapy has led to a breakthrough in the treatment of NSCLC, fast disease progression in some patients remains problematic. Great efforts are being made to identify the mechanisms of immune resistance and to establish new predictive and prognostic biomarkers. The aim of this study was to evaluate the association between PD-L1 expression, genetic alterations, and prognosis in patients diagnosed with metastatic NSCLC. PD-L1 expression and genetic profiling using NGS were assessed in 50 patients with advanced NSCLC who were negative for EGFR mutations. According to this study results, positive PD-L1 expression was detected in 62% of cases, whereas high TMB was detected in 34% of cases. Targetable mutations were detected in 33.4% of cases. The TP53 mutation was more likely to be found in tumours with higher PD-L1 and TMB levels (median 45 vs. 0, p = 0.005; median 10 vs. 4.5, p = 0.008, respectively). Meanwhile, STK11 mutation was associated with lower PD-L1 and higher TMB levels (median 0 vs. 17.5, p = 0.019; median 11.5 vs. 6, p = 0.047). Fast disease progression was observed in 22.2% of cases when immunotherapy alone or combined with chemotherapy was administered, with the most frequently detected TP53 (87.5%), STK11 (37.5%), and KEAP1 (37.5%) mutations in this part of the population. Progressive disease was more likely to be found in patients with KEAP1 mutation than in those with wild-type KEAP1 (75% vs. 18.8%, p = 0.02). To conclude, significant associations were found between PD-L1, TMB statuses and mutations in STK11 and TP53. Fast disease progression was established in 1/5 of the entire population treated with immunotherapy or chemo-immunotherapy. TP53, STK11, and KEAP1 mutations were most frequently detected in patients with fast disease progression. The KEAP1 mutation was associated with progressive disease in patients with advanced NSCLC. Our results suggest that a specific genetic profile could serve as a predictor of fast progression in a selected group of patients. Full article

Mango peel (MP), an abundant agro-industrial residue, was evaluated as a solid biofuel using combined physicochemical characterisation and non-isothermal thermogravimetric kinetics (TGA). Fourier transform infrared (FTIR), X-ray diffraction (XRD), and scanning electron microscopy (SEM) revealed hydroxyl-rich surfaces and porous microstructures. Thermogravimetric combustion, conducted at heating rates of 20–80 K min⁻¹, displayed three distinct stages. These stages correspond to dehydration (330–460 K), hemicellulose/cellulose oxidation (420–590 K), and cellulose/lignin oxidation (540–710 K). Kinetic analysis using six model-free methods (Friedman (FR), Flynn–Wall–Ozawa (FWO), Kissinger–Akahira–Sunose (KAS), Starink (STK), Kissinger (K), and Vyazovkin (VY)) yielded activation energies (E_a) of 52–197 kJ mol⁻¹, increasing with conversion (mean E_a ≈ 111 kJ mol⁻¹). Coats–Redfern (CR) fitting confirmed a three-dimensional diffusion mechanism (D3, R² > 0.99). Thermodynamic analysis revealed that the formation of the activated complex is endothermic, with activation enthalpy (ΔH) values of 45–285 kJ mol⁻¹. The process was found to be non-spontaneous under the studied conditions, with Gibbs free energy (ΔG) values ranging from 83 to 182 kJ mol⁻¹. With a high heating value (HHV) of 21.9 MJ kg⁻¹ and favourable combustion kinetics, MP is a promising supplementary fuel for industrial biomass boilers. However, its high potassium oxide (K₂O) content requires dedicated ash management strategies to mitigate slagging risks, a key consideration for its practical, large-scale application. Full article

Protein kinases and phosphatases are essential for post-translational regulation, enabling bacteria to adapt to environmental stresses and modulate virulence. While prior reviews have broadly covered their roles in stress response, antibiotic resistance, and virulence, this article updates specifically on the roles of histidine kinases (HKs) and serine/threonine kinases (STKs) in mediating phage-bacteria interactions. A key aspect is phage-encoded kinases, which hijack bacterial signalling by phosphorylating and disrupting host processes to promote infection. Despite their importance, significant gaps remain in understanding these regulatory networks. This microreview highlights both the unresolved mechanisms and the therapeutic potential of targeting kinase pathways—for instance, by disrupting phage evasion strategies or enhancing phage-based antimicrobial therapies. Full article

Alcoholic liver disease (ALD) is a type of liver disease with complex pathogenic factors. In 2019, alcohol caused 11 million life-years to be lost globally, and the mortality rate has continued to rise. This study aims to explore the exclusive gene profile of AH and construct an mRNA-lncRNA regulatory network through an integrative analysis and database validation to reveal potential key biomarkers. We obtained expression data for alcoholic hepatitis from the GEO database; screened differentially expressed genes (DEGs) through a weighted gene co-expression network analysis (WGCNA); conducted a GO&KEGG analysis; and focused on the enrichment pathways for the top 20 genes. Hub genes were selected using cytoHubba and MCODE to construct the mRNA-lncRNA regulatory network, and key genes were confirmed using GSE167308 and GSE28619. We obtained 2552 differentially expressed mRNAs and 555 differentially expressed lncRNAs from three databases. Differentially expressed genes are mainly involved in pathways such as lipid metabolism disorders, complement activation, the activation of cancer-related pathways, the excessive activation of inflammatory immunity, and the initiation of cell adhesion and fibrosis. Based on the hub gene analysis, we screened out 43 key genes. By constructing the key mRNA-lncRNA–pathway network, we identified 12 mRNAs (AQP1, ELOVL7, ITPR3, KRT19, KRT23, LAMC2, MMP7, PROM1, SPINT1, STK39, TNFRSF21, and VTCN1) and 14 lncRNAs that play an important role in the occurrence and development of alcoholic hepatitis. To sum up, this article mainly expounds upon the key genes in the occurrence and development of alcoholic hepatitis. The key genes are mainly concentrated within signaling pathways such as metabolic pathways, fatty acid metabolism, and cancer pathways. Twelve differentially expressed mRNAs in the co-expression network can be used as biomarkers and intervention targets for the diagnosis and treatment of alcoholic hepatitis. Full article

Osteosarcoma (OSA) is the most prevalent bone malignancy in people and dogs. Current survival rates show the need for advances in novel therapies to help overcome the growth, survival and metastatic progression of the cancer. Canine models are often used to advance prognostic and treatment opportunities for OSA due to the similarities in the disease between species. This study focusses on the genetic and molecular similarities of OSA between human and canine specimens. Differentially expressed genes (DEGs) were compared and identified in canine and human OSA tumours, revealing 86 common genes, 36 having high and 50 having low expression. Further immunohistochemical analysis of the corresponding proteins of three identified DEGs (ASPN, STK3, BAMBI) allowed for the visualisation of protein expression in canine OSA tissues (n = 19). Overall nuclear and cytoplasmic H-scores were generated, and nuclear and cytoplasmic scores in males and females and in different anatomical locations (axial versus appendicular) were also investigated, presenting unique opportunities to understand the expression in this cancer type. This study contributes to a deeper knowledge of genetic pathways changes and identifies avenues for the diagnosis, prognosis and treatment of OSA in people and dogs, whilst encompassing the One Health concept in medicine. Full article

Decentralized solar water disinfection systems (DSODIS) in continuous flow systems are alternatives for large-scale improved water access in rural contexts. However, DSODIS in rural Ghana are limited. An exploratory sequential mixed-methods design was used to explore the enablers of and barriers to, as well as reported barrier perceptions to, the effective implementation of DSODIS in the Sawla-Tuna-Kalba (STK) District of Ghana. The qualitative data (26 respondents) were analyzed thematically, and the quantitative data (1155 household heads) were subjected to Poisson regression analyses. Enablers were categorized into themes such as willingness to pay for DSODIS, household and community participation, and willingness to use water from DSODIS. Similarly, the barriers include environmental barriers, technological barriers, economic barriers, and political and legal barriers. Household characteristics such as main water source and income, age group, education, marital status, household size, being born in the community, and years living in the community are statistically associated with reported barrier perceptions. Households with unimproved water sources and high income (IRR = 1.432, p = 0.000) and improved water sources and high income (IRR = 1.295, p = 0.000) are 43% and 30% more likely, respectively, to report more barrier perceptions compared with households with unimproved water sources and low income. Females (IRR = 1.070, p = 0.032) are marginally more likely to report more barrier perceptions compared with males. The model output also indicates that household heads with higher educational attainment (IRR = 1.152, p = 0.001) are 15% more likely to report more barrier perceptions compared with those with no formal education. These findings provide valuable information for policymakers and stakeholders aiming to provide quality water in rural Ghana where centralized systems cannot be installed. Full article

Dysregulation of protein kinases is associated with developmental defects and various human diseases. The human kinome comprises 518 kinases, including several orphan kinases whose functions remain to be fully characterized. The NKF4 family, which includes STK35L1 and PDIK1L, is one such uncharacterized kinase family. STK35L1, also known as Clik1, was initially identified as a nuclear kinase associated with actin fibers. Subsequent studies have demonstrated that STK35L1 plays critical roles in cellular processes such as cell cycle regulation, migration, angiogenesis, the DNA damage response, and related processes such as spermatogenesis. STK35L1 has also been implicated in various developmental processes and its knockout mice exhibited defects in the testis, ovary, and eye. STK35L1 acts as a central regulator of the fundamental cellular functions, and its dysregulation leads to various diseases. Research has established that STK35L1 regulates tumor growth and proliferation in cancers such as osteosarcoma, colorectal cancer, and acute myeloid leukemia. Notably, it also affects chemosensitivity in colorectal cancer and metabolism in acute myeloid leukemia. Additionally, STK35L1 is crucial for the infection of hepatocytes by Plasmodium sporozoites during the liver stage of Malaria. This review discusses the current understanding of STK35L1, highlighting its role in various diseases. Full article

Background/Objectives: We aimed to discover genes with bimodal expression linked to patient outcomes, to reveal underlying oncogenotypes and identify new therapeutic insights in lung adenocarcinoma (LUAD). Methods: We performed meta-analysis to screen LUAD datasets for prognostic genes with bimodal expression patterns. Kynureninase (KYNU), a key enzyme in tryptophan catabolism, emerged as a top candidate. We then examined its relationship with LUAD mutations, metabolic alterations, immune microenvironment states, and expression patterns in human and mouse models using bulk and single-cell transcriptomics, metabolomics, and preclinical model datasets. Pan-cancer prognostic associations were also assessed. Results: Model-based clustering of KYNU expression outperformed median-based dichotomization in prognostic accuracy. KYNU was elevated in tumors with KEAP1 and STK11 co-mutations but remained a strong independent prognostic marker. Metabolomic analysis showed that KYNU-high tumors had increased anthranilic acid, a catalytic product, while maintaining stable kynurenine levels, suggesting a compensatory mechanism sustaining immunosuppressive signaling. Single-cell and bulk data showed KYNU expression was cancer cell-intrinsic in immune-cold tumors and myeloid-derived in immune-infiltrated tumors. In murine LUAD models, Kynu expression was predominantly immune-derived and uncoupled from Nrf2/Lkb1 signaling, indicating poor model fidelity. KYNU’s prognostic associations extended across cancer types, with poor outcomes in pancreatic and kidney cancers but favorable outcomes in melanoma, underscoring the need for lineage-specific considerations in therapy development. Conclusions:KYNU is a robust prognostic biomarker and potential immunometabolic target in LUAD, especially in STK11 and KEAP1 co-mutated tumors. Its cancer cell-intrinsic expression and immunosuppressive metabolic phenotype offer translational potential, though species-specific expression patterns pose challenges for preclinical modeling. Full article

This study presents a comprehensive kinetic and thermodynamic investigation of dried orange peel (OP) combustion, employing thermogravimetric analysis (TGA) and differential thermogravimetry (DTG) at high heating rates (20–80 K min⁻¹). This gap in high heating rate analysis motivates the novelty of present study, by investigating OP combustion at 20, 40, 60, and 80 K min⁻¹ using TGA, to closely simulate rapid thermal conditions typical of industrial combustion processes. Thermal decomposition occurred in three distinct stages corresponding sequentially to the dehydration, degradation of hemicellulose, cellulose, and lignin. Activation energy (E_a) was calculated using six model-free methods—Friedman (FR), Flynn–Wall–Ozawa (FWO), Kissinger–Akahira–Sunose (KAS), Starink (STK), Kissinger (K), and Vyazovkin (VY)—yielding values between 64 and 309 kJ mol⁻¹. The E_a increased progressively from the initial to final degradation stages, reflecting the thermal stability differences among biomass constituents. Further kinetic analysis using the Coats–Redfern (CR) model-fitting method identified that first-order (F1), second-order (F2), and diffusion-based mechanisms (D1, D2, D3) effectively describe OP combustion. Calculated thermodynamic parameters—including enthalpy (ΔH), Gibbs free energy (ΔG), and entropy (ΔS)—indicated the endothermic and increasingly non-spontaneous nature of the reactions at higher conversions. These findings demonstrate the potential of OP, an abundant agricultural waste product, as a viable bioenergy resource, contributing valuable insights into sustainable combustion processes. Full article