Tag: statistics

PLoS One. 2025 Jun 3;20(6):e0321636. doi: 10.1371/journal.pone.0321636. eCollection 2025.

ABSTRACT

BACKGROUND: Cuproptosis may be a new clue to illustrate the pathogenesis of the disease. There was no study focused on the relationship between the cuproptosis genes and diabetic nephropathy (DN). This study aimed to reveal the relationship between cuproptosis genes and the immune microenvironment in DN and distinguish different phenotypes to describe disease heterogeneity through consensus clustering based on cuproptosis genes.

METHODS: We downloaded RNA sequencing data sets of DN glomerular and normal renal tissue samples (GSE142025, GSE30528, and GSE96804) from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between DN and control samples were screened. Immune cell subtype infiltration and immune score were figured out via different algorithms. Consensus clustering was performed by Ward’s method to determine different phenotypes of DN. Key genes between phenotypes were identified via a machine-learning algorithm. Logistic regression analysis was applied to establish a nomogram for assessing the disease risk of DN. The role of related genes was verified by cell experiments.

RESULTS: In DN samples, NOD-like receptor thermal protein domain associated protein 3(NLRP3) and cyclin-dependent kinase inhibitor 2A Gene(CDKN2A) were positively correlated to immune score. Nuclear factor erythroid 2-related factor 2(NFE2L2), Lipoic Acid Synthetase(LIAS), Lipoyltransferase 1(LIPT1), Dihydrolipoamide dehydrogenase(DLD), Dihydrolipoamide Branched Chain Transacylase E2(DBT) and Dihydrolipoamide S-Succinyltransferase(DLST) were negatively correlated to immune score. Via Consensus clustering based on cuproptosis genes, the DN samples were divided into cluster C1 and cluster C2. Cluster C1 was characterized by low cuproptosis gene expression, high immune cell subtype infiltration, and high enrichment of immune-related pathways. Cluster C2 was on the contrary. Dicarbonyl/l-xylulose reductase (DCXR) and heat-responsive protein 12 (HRSP12) were key genes related to clinical traits and immune microenvironment, negatively correlated with most immune cell subtypes. The nomogram constructed based on DCXR and HRSP12 showed good efficiency for DN diagnosis.

CONCLUSION: Immune microenvironment imbalance and metabolic disorders may lead to the occurrence of DN. Cuproptosis genes, with the ability to regulate the immune microenvironment and metabolism, can be used for disease clustering to describe the heterogeneity and characterize the immune microenvironment. HRSP12 and DCXR, as key genes related to disease phenotypes and immune microenvironment characteristics, were jointly constructed as nomograms for DN diagnosis with high accuracy and reliability. HRSP12 and DCXR may be potential biological markers and renal protective factors.

PMID:40460381 | DOI:10.1371/journal.pone.0321636

PLoS One. 2025 Jun 3;20(6):e0324147. doi: 10.1371/journal.pone.0324147. eCollection 2025.

ABSTRACT

This study examines the relationship between integrated reporting quality (IRQ) disclosures, corporate governance quality (CGQ), and the implied cost of equity capital (ICC) in developed markets, focusing on Australia and New Zealand. The increasing adoption of integrated reporting and its potential implications for firms’ ICC motivates this research. Moreover, the study highlights the role of IRQ in mitigating information asymmetry between firms and investors, emphasizing the need for high-quality disclosures. Using a quantitative approach with panel data analysis, the research analyzes a sample of the top 174 companies by Standard and Poor’s market capitalization in Australia and New Zealand from 2018 to 2022, encompassing 870 observations post-IRQ implementation. Statistical methods, including fixed-effects, IV2SLS, two-step system-GMM, pooled OLS, and medium quantile regression, were applied to ensure robust findings. The results reveal a significant negative relationship between IRQ disclosure and ICC, with CGQ playing a moderating role in strengthening this association. Consistent with agency theory, the findings suggest that to reduce information asymmetry, firms issue more information which allows to reduce the cost of capital. Therefore, a more comprehensive firms’ reporting, including information about their strategy and risks, increases investors’ confidence, hence it may reduce the cost of capital. This study provides valuable insights for regulators and policymakers by emphasizing the importance of integrated reporting frameworks and robust corporate governance practices to promote transparency, reduce information asymmetry, and optimize capital allocation efficiency in developed markets.

PMID:40460376 | DOI:10.1371/journal.pone.0324147

PLoS One. 2025 Jun 3;20(6):e0323347. doi: 10.1371/journal.pone.0323347. eCollection 2025.

ABSTRACT

Stable nanofluid dispersion with SiO2 particles of 15, 50, and 100 nm is generated in a base liquid composed of water and glycerol in a 7:3 ratio and tested for physical characteristics in the temperature range of 20-100oC. The nanofluid showed excellent stability for over a month. Experiments are undertaken for the flow of nanofluid in a copper pipe and measured for their heat transfer coefficient and flow behavior. The convection heat transfer coefficient increases with the flow Reynolds number in the transition-turbulent flow regime. The experimental results further reveal that the friction factor enhancement with 0.5% concentration has increased by 6% as compared to the base liquid. It was employed for prognostic model development using XGBoost and multi-gene genetic programming (MGGP) to model and predict the complex and nonlinear data acquired during experiments. Both techniques provided robust predictions, as witnessed by the statistical evaluation. The R2 statistics of the XGBoost-based model was 0.9899 throughout the model test, while it was lowered to 0.9455 for the MGGP-based model. However, the change was insignificant. The mean squared value was 8.37 for XGBoost, while it increased in the MGGP model to 45.12. Similarly, the mean absolute error (MAE) value was higher (6.623) in the case of MGGP than in XGBoost at 2.733. The statistical evaluation, Taylor diagrams, and violin plots helped determine that XGBoost was superior to MGGP in the present work.

PMID:40460369 | DOI:10.1371/journal.pone.0323347

PLoS One. 2025 Jun 3;20(6):e0325200. doi: 10.1371/journal.pone.0325200. eCollection 2025.

ABSTRACT

In this study, we report for the first time an exploration of the physicochemical characteristics and the prokaryotic diversity of three different types of microbial mats from karstic habitats located in Sisal, Progreso and Ría Lagartos, in the Yucatan Peninsula, Mexico. Our results showed that lift-off mats were found in the lower salinity (2.2%) area (Sisal), while flat and pustular mats were detected in hypersaline (6-9%) sites (Progreso and Ría Lagartos). Notably, some of these microbial mat structures were in close proximity to mangrove forest ecosystems with both degraded and restored regimes. XRD analysis revealed different mineral compositions of the mats; however, aragonite, calcite, and halite were commonly found in all samples studied. High-throughput sequencing of the 16S rRNA gene identified differences in microbial communities across the different mat types, and statistical analyses revealed that salinity, redox potential, and temperature were significant factors in explaining the variance of the prokaryotic assemblages. Microbial groups identified in this study include those known to be important in the biogeochemical cycling of key elements, such as carbon, nitrogen, and sulfur. Interestingly, the community composition of flat and pustular mats from Progreso was similar, with Bacteroidia, Anaerolineae, and Phycisphaerae being the most abundant microbial groups in flat mats; and Bacteroidia, Anaerolineae, and Alphaproteobacteria dominating pustular mats. By contrast, flat mats from Ría Lagartos were dominated by Halobacteria, Cyanobacteria and Bacteroidota, while Bacteroidia, Gammaproteobacteria and Cyanobacteria dominated lift-off mats from Sisal. This work contributes to understanding the distribution, physicochemical characteristics and microbial diversity of coastal microbial mats, providing valuable new insights into microbial mats that develop in karstic ecosystems. This information is relevant to ongoing and future efforts to manage and preserve coastal ecosystems in the Yucatan Peninsula.

PMID:40460360 | DOI:10.1371/journal.pone.0325200

Neurology. 2025 Jun 24;104(12):e213673. doi: 10.1212/WNL.0000000000213673. Epub 2025 Jun 3.

ABSTRACT

BACKGROUND AND OBJECTIVES: Older chronological age is associated with decreased multiple sclerosis (MS) relapse rates and increased risk of progressive disease. Measurement of biological age may be more precise than birthdate in understanding these aging effects. In addition to normal aging, MS-related accelerated aging may contribute. Measurement of biological age in adults may be confounded by the effects of natural aging and age-related comorbidities. Examining age extremes can be informative, and demonstrating accelerated biological aging in children would support a hypothesis of MS driving premature aging. We sought to compare epigenetic age in participants with pediatric-onset MS (POMS) and age-similar controls.

METHODS: We performed a multicenter case-control analysis of epigenetic age in a prospectively collected set of whole blood DNA samples and clinical data. Quantitative methylation scores were derived for approximately 850,000 cytosine-phosphate-guanine (CpG) sites. Epigenetic age was calculated based on 4 established epigenetic clock algorithms. Epigenetic age and age acceleration residual (AAR) were compared between participants with POMS and age-similar controls using multivariate regression analysis, adjusted for demographic variables.

RESULTS: Epigenetic age and AAR were greater in cases (n = 125, mean age 15.7 years [SD = 2.6], 63.2% female) compared with controls (n = 145, mean age 15.3 years [SD = 3.4], 63.5% female) after adjusting for age, sex, body mass index, tobacco exposure, and socioeconomic status. This difference was statistically significant for 2 of the 4 epigenetic clocks used (Horvath β = 0.31 years [CI = -0.32-0.94], p = 0.33; Hannum β = 1.50 years [CI = 0.58-2.42], p = 0.002; GrimAge β = 0.33 years [CI = -0.30-0.96], p = 0.29; PhenoAge β = 1.72 years [CI = 0.09-3.35], p = 0.004).

DISCUSSION: We observed greater point estimates of epigenetic age in participants with POMS compared with healthy controls in all epigenetic clocks tested. This difference was statistically significant for the Hannum and PhenoAge clocks after multivariable modeling. These results are consistent with those of studies in adult MS and suggest that accelerated aging may be present even in the youngest people living with MS.

PMID:40460354 | DOI:10.1212/WNL.0000000000213673

J Org Chem. 2025 Jun 3. doi: 10.1021/acs.joc.5c00616. Online ahead of print.

ABSTRACT

We report an intermolecular, cross-selective [2 + 2] cycloaddition between cyclic styrenes and olefin acceptors proceeding via visible-light irradiation, enabled by the extended triplet lifetime of cyclic styrenes. A broad range of olefins, including electron-deficient and simple alkenes, (hetero)styrenes, arylimines, vinyl boronate esters, among others, underwent efficient cycloaddition with cyclic styrenes constrained by four-, five-, and rigidified six-membered rings, providing rapid access to sp³-rich fused cyclobutane scaffolds. Notably, the [2 + 2] cycloaddition between two electronically similar styrenes, which typically gives statistical mixtures of homo- and heterodimers, proceeded with excellent chemoselectivity and yield between cyclic and acyclic styrenes without requiring a large excess of one reactant, facilitated by the significant difference in triplet lifetime between the reacting partners. Mechanistic studies and DFT calculations support a Dexter energy transfer mechanism of substrate activation and underscore the critical role of triplet lifetime extension in enabling the observed reactivity. The utility of this method is demonstrated in the total synthesis of lindleyanin, requiring only two steps.

PMID:40460348 | DOI:10.1021/acs.joc.5c00616

PLoS One. 2025 Jun 3;20(6):e0325318. doi: 10.1371/journal.pone.0325318. eCollection 2025.

ABSTRACT

Rock deterioration under uniaxial compression is significantly influenced by changes in meso-structure, which plays a key role in determining the mechanical behavior and stability of rock materials. Understanding how different loading stresses affect the evolution of meso-structure is crucial for assessing rock stability in engineering applications, such as tunneling and landslide prevention. This study investigates the damage mechanisms and meso-structural evolution of sandstone subjected to uniaxial compression at different loading stresses (0, 5, 15, 30, and 40 MPa). Utilizing Nuclear Magnetic Resonance (NMR), Scanning Electron Microscopy (SEM) and quantitative statistical analysis (e.g., Single-factor analysis of variance (ANOVA), Pearson correlation coefficients), the study analyzes how different stress levels influence the internal structural changes within the sandstone. The results revel that low loading stresses (5 and 15 MPa) primarily induce microdefect compaction and limited intergranular crack propagation, causing notable changes in failure strain without significant structural damage. In contrast, higher loading stresses (30 and 40 MPa) induce the formation of transgranular cracks, drastically reducing both failure strength and overall structural integrity. Meso-mechanical analysis identifies mineral rotation and crack propagation as critical factors driving these structural transformations. These findings demonstrate that rock deterioration is stress-dependent, with distinct characteristics at low versus high loading conditions. This research enhances the understanding of the underlying mechanisms of rock deterioration, providing valuable insights into rock stability evaluation. The findings are essential for predicting and mitigating geological hazards, offering critical implications for engineering practices aimed at enhancing rock stability and preventing disasters.

PMID:40460344 | DOI:10.1371/journal.pone.0325318

PLoS One. 2025 Jun 3;20(6):e0325150. doi: 10.1371/journal.pone.0325150. eCollection 2025.

ABSTRACT

OBJECTIVE: This meta-analysis investigates the differential risks of suicidal behaviors (ideation, attempts, mortality) associated with current asthma and asthma history.

METHOD: Retrieve cohort studies on the association between asthma and suicide from PubMed, Embase, and Cochrane library database. Use the Newcastle Ottawa Quality Assessment Scale (NOS) to assess the risk of bias. The risk ratio (RR) of 95% confidence interval (CI) was summarized using a random effects model, and publication bias was evaluated using funnel plots and Egger’s trials.

RESULT: A total of 12 cohort studies were included and published between 2005 and 2024. The NOS scores for the 12 cohort studies included in this meta-analysis ranged from 7 to 9. Most studies received scores of 7 or 8, indicating a generally high quality. Current asthma conferred a 62% increased risk of suicidal behaviors (RR = 1.62, 95% CI: 1.38-1.88), with suicide attempts showing the strongest association (RR = 2.27, 95% CI: 1.33-3.89). Asthma history was linked only to elevated suicide mortality (RR = 1.87, 95% CI: 1.64-2.14), not non-fatal suicidal behaviors.

CONCLUSION: Current asthma status is associated with an increased risk of suicidal behaviors, but a history of asthma correlates only with elevated suicide mortality. This finding highlights the need for proactive mental health screening in asthma management protocols, especially during periods of active disease.

PMID:40460338 | DOI:10.1371/journal.pone.0325150

PLoS One. 2025 Jun 3;20(6):e0306587. doi: 10.1371/journal.pone.0306587. eCollection 2025.

ABSTRACT

Muscle-tendon unit (MTU) assessments can be categorised into local (e.g., tendon strain) or global (e.g., jump height) assessments. Although menstrual cycle phase may be a key consideration when implementing these assessments in female athletes, the reliability of many MTU assessments is not well defined within female populations. Therefore, the purpose of this study was to report the test-retest reliability of local and global MTU assessments during the early follicular phase of the menstrual cycle. Seventeen naturally menstruating females (age 28.5 ± 7.3 years) completed local and global MTU assessments during two testing sessions separated over 24-72 hours. Local tests included Achilles’ tendon mechanical testing and isometric strength of ankle plantar flexors and knee extensors, whereas global tests included countermovement, squat, and drop jumps, and the isometric midthigh pull. Based on intraclass correlation coefficient (ICC) statistics, poor to excellent reliability was found for local measures (ICC: 0.096-0.936). Good to excellent reliability was found for all global measures (ICC: 0.788-0.985), excluding the eccentric utilisation ratio (ICC 0.738) and most rate of force development metrics (ICC: 0.635-0.912). Isometric midthigh pull peak force displayed excellent reliability (ICC: 0.966), whereas force-time metrics ranged from moderate to excellent (ICC: 0.635-0.970). Excluding rate of force development (coefficient of variation [CV]: 10.6-35.9%), global measures (CV: 1.6-12.9%) were more reproducible than local measures (CV: 3.6-64.5%). However, local metrics directly measure specific properties of the MTU, and therefore provide valuable information despite lower reproducibility. The novel data reported here provides insight into the natural variability of MTU assessments within female athletes which can be used to enhance the interpretation of other female athlete data, especially that which aims to investigate other aspects of variability, such as the menstrual cycle.

PMID:40460334 | DOI:10.1371/journal.pone.0306587

JCO Clin Cancer Inform. 2025 Jun;9:e2400331. doi: 10.1200/CCI-24-00331. Epub 2025 Jun 3.

ABSTRACT

PURPOSE: Rapid advancements in natural language processing have led to the development of sophisticated language models. Inspired by their success, these models are now used in health care for tasks such as clinical documentation and medical record classification. However, language models are prone to errors, which can have serious consequences in critical domains such as health care, ensuring that their reliability is essential to maintain patient safety and data integrity.

METHODS: To address this, we propose an innovative auditing process based on principles from clinical trial design. Our approach involves subject matter experts (SMEs) manually reviewing pathology reports without previous knowledge of the model’s classification. This single-blind setup minimizes bias and allows us to apply statistical rigor to assess model performance.

RESULTS: Deployed at the British Columbia Cancer Registry, our audit process effectively identified the core issues in the operational models. Early interventions addressed these issues, maintaining data integrity and patient care standards.

CONCLUSION: The audit provides real-world performance metrics and underscores the importance of human-in-the-loop machine learning. Even advanced models require SME oversight to ensure accuracy and reliability. To our knowledge, we have developed the first continuous audit process for language models in health care, modeled after clinical trial principles. This methodology ensures that audits are statistically sound and operationally feasible, setting a new standard for evaluating language models in critical applications.

PMID:40460332 | DOI:10.1200/CCI-24-00331