title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=2 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A non-invasive secreted protein-based gene signature for prognostic stratification and tumor microenvironment assessment in gastric cancer link: https://peerj.com/articles/20517 last-modified: 2026-01-13 description: BackgroundGastric cancer (GC) is a highly heterogeneous malignancy with poor prognosis. Current prognostic models for GC rely on invasive tissue-based high-throughput sequencing. Secreted proteins, detectable non-invasively and involved in tumor microenvironment (TME) remodeling, offer promising biomarkers. We aimed to develop a non-invasive prognostic signature based on secreted protein-coding genes (SPCGs) to stratify GC patients and predict TME characteristics.MethodsWe obtained RNA sequencing data and clinical information from 375 GC and 32 paracancerous tissue samples from The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD). Differentially expressed SPCGs were identified by intersecting differentially expressed genes with 731 Human Protein Atlas (HPA) secreted protein genes. An 8-SPCG signature was constructed using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses. The model’s predictive performance was validated through Kaplan–Meier survival curves, time-dependent receiver operating characteristic (ROC) analysis, and multivariable Cox regression. A nomogram integrating risk scores and clinical parameters was developed and validated using calibration curves. Functional annotation was conducted through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA). Tumor mutational burden (TMB) profiles and immune cell infiltration were compared between risk subgroups. The biological properties and clinical significance of SERPINE1 were validated through in vitro experiments and clinical data from our center.ResultsAn 8-SPCG signature (SERPINE1, C6, GRP, GCG, IL1F10, IGFBP1, ITIH2, and APOD) was identified and validated to predict overall survival in GC patients. The risk score derived from this signature was significantly associated with TME characteristics, including TME scores, immune cell infiltration, and immune checkpoint expression. High-risk patients exhibited an immunosuppressive microenvironment and lower TMB. Functional enrichment analysis indicated that the high-risk group was enriched in extracellular matrix-related pathways, while the low-risk group was associated with cellular metabolism and gene expression pathways. SERPINE1 was overexpressed in GC tissues, peripheral blood, and malignant effusions, and its high expression correlated with poor prognosis. In vitro experiments demonstrated that SERPINE1 promoted GC cell proliferation and invasion, and its expression was enhanced by cancer-associated fibroblasts (CAFs) through the EGF-ERBB signaling pathway.ConclusionsWe established a non-invasive 8-SPCG signature that may serve as a potential predictor for GC prognosis and TME features. SERPINE1 was identified as a promising mediator linking GC progression to CAFs interactions, supporting its further investigation as a therapeutic target. creator: Qiuxia Liu creator: Haofeng Yin creator: Ziming Wang creator: Qianlong Shen creator: Jianguo Zhao creator: Xianhe Xie uri: https://doi.org/10.7717/peerj.20517 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2026 Liu et al. title: Snow cover mapping with Meteosat third generation FCI: initial evaluation of the European Organisation for the Exploitation of Meteorological Satellites H SAF H43 snow mask product link: https://peerj.com/articles/20495 last-modified: 2026-01-13 description: This study presents the results of the initial validation of the EUMETSAT H SAF H43 snow cover product, the first operational snow product derived from the Flexible Combined Imager (FCI) onboard Meteosat Third Generation (MTG). The evaluation, covering the period from December 2024 to February 2025, includes a direct comparison with the earlier H34 product, generated from SEVIRI observations onboard Meteosat Second Generation (MSG). Analyses were conducted over three mountainous regions—the Alps, Turkey, and Georgia—using MODIS-based reference snow cover maps and in-situ snow-depth measurements from WMO synoptic stations. As snow cover in mountainous terrain plays a critical role in hydrology and water resources management, special attention was given to high-elevation zones (above 1,000 m), where snow is seasonally persistent and detection accuracy most relevant. The evaluation employed standard accuracy metrics—Probability of Detection (POD), False Alarm Ratio (FAR), and Overall Accuracy (ACC)—to assess performance across elevation, aspect, and land-cover classes. Results indicate that H43 provides consistent yet moderate improvements over H34, with miss-rate reductions of up to 40% above 2,000 m elevation and FAR values remaining below 30% across land-cover types. These improvements are supported by the enhanced radiometric performance and 10-min temporal resolution of the FCI sensor, which enable more effective cloud detection and frequent scene refresh. Combined with its near-real-time availability, these features make H43 a promising tool for operational snow monitoring, hydrological forecasting, and early-warning applications across topographically complex regions. creator: Semih Kuter creator: Cagri Hasan Karaman creator: Mustafa Berkay Akpinar creator: Zuhal Akyurek uri: https://doi.org/10.7717/peerj.20495 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2026 Kuter et al. title: Risk factors for systemic lupus erythematosus complicated with tuberculosis infection: meta-analyses and systematic reviews link: https://peerj.com/articles/20448 last-modified: 2026-01-13 description: BackgroundTo unravel the risk factors of systemic lupus erythematosus (SLE) complicated with tuberculosis (TB) infection through a systematic review and meta-analysis.MethodsPubMed, Embase, Cochrane Library, and Web of Science databases were searched for relevant research articles on systemic lupus erythematosus with TB infection from inception to June 12, 2024. Analyses of the data were performed with Stata 15.0.ResultsThe analysis incorporated 19 articles, comprising nine case-control and 10 cohort studies. In these studies, 1,292 patients with SLE complicated with TB infection and 5,703 SLE patients without TB infection were evaluated. The meta-analysis findings elucidated several pivotal risk factors with statistical significance: male (odds ratio (OR) = 1.32, 95% confidence interval (CI) [1.06–1.64], probability value (P) = 0.011), lymphocytopenia (OR = 2.65, 95% CI [1.98–3.55], P = 0.000), anemia (OR = 2.53, 95% CI [1.11–5.77], P = 0.001), hypoalbuminemia (OR = 3.46, 95% CI [1.26–9.50], P = 0.016), diabetes (OR = 3.05, 95% CI [1.63–5.71], P = 0.000). Results of multivariate analysis identified lymphocytopenia (OR = 2.90, 95% CI [1.89–4.45], P = 0.000), cumulative glucocorticoids dosage (OR = 4.88, 95% CI [1.85–12.91], P = 0.001), and a history of TB exposure (OR = 3.38, 95% CI [1.16–9.86], P = 0.026) as risk factors for SLE complicated with TB infection.ConclusionBased on available evidence, males, lymphocytopenia, anemia, hypoalbuminemia, diabetes, cumulative glucocorticoids dosage, and the TB exposure history are risk factors for SLE complicated with TB infection.PROSPERO registry numberCRD42024583278. creator: Xiaoyi Zhang creator: Hai Zheng creator: Peng Zhou creator: Wenfeng Hu creator: Yuxin Si creator: Xianhui Wu creator: Chen Shen uri: https://doi.org/10.7717/peerj.20448 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2026 Zhang et al. title: Determination of the biological parameters of Nabis pseudoferus orientarius Remane, 1962 (Hemiptera: Nabidae) under laboratory conditions link: https://peerj.com/articles/20267 last-modified: 2026-01-13 description: Cotton is an important industrial crop that is used in the textile and oil industries, in animal husbandry, and has economic value. Many insect species cause damage in cotton production areas. Nabis species are important predatory insects that feed on many soft-bodied insects, larvae, and eggs found in cotton fields. In this study, some biological parameters of Nabis pseudoferus orientarius were examined under laboratory conditions with 25 ± 1 °C temperature, 65 ± 5% humidity, and 16:8 L: D conditions. In the results of working, the average egg hatching time of N. pseudoferus orientarius was found with 9.83 days, the average preadult development time was 26.85 days, and the average adult life was 62.6 days. The average preoviposition, oviposition, and postoviposition periods of N. pseudoferus orientarius were determined as 9, 58.3, and 4.8 days, respectively. A female lays an average of 446.1 (267–576) eggs throughout her life. In the study, hereditary reproductive ability (r) was determined as 9.15, the increase rate limit (λ) was 1.10, the net reproductive rate (R0) was 193.13, and the average reproductive duration (T) was 57.50. The age-specific survival rate (lx) was calculated as 4.35, the age- and period-specific survival rate (Sxj) was calculated as 80.30, and the age-specific reproduction rate (mx) was calculated as 14. creator: Muhlis Sezgin creator: Selime Olmez Bayhan creator: Erol Bayhan uri: https://doi.org/10.7717/peerj.20267 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2026 Sezgin et al. title: Past and present genetic structure of the tropical rainforest palm Astrocaryum mexicanum: effects of anthropogenic fragmentation link: https://peerj.com/articles/19784 last-modified: 2026-01-13 description: To assess whether fragmentation of the lowland rainforest of Los Tuxtlas natural reserve has altered the genetic structure of understory palm Astrocaryum mexicanum, we analyzed populations from undisturbed forest and forest fragments. The questions that this study addressed were: Has habitat fragmentation reduced gene flow and within-population genetic variation (allele loss)? Has this process, in turn, increased population genetic differentiation of populations in fragments? We expected that reduced population sizes and gene flow, in fragments, has increased the effects of genetic drift, thus affecting genetic structure. The design of the study allows control for pre-fragmentation genetic structure, a common criticism against fragmentation studies, and addresses this question for a community-level important palm tree species of the tropical rain forests of southern Mexico. We sampled two cohorts (i.e., pre- and post-fragmentation palms) in each of eight populations (thirty individuals per cohort or generation, and a separation of four to nine km between populations), one composed by adult palms (80–140 years old), and the other of seedlings <3 years old. We estimated RST, inbreeding coefficient, number of alleles, heterozygosity, linkage disequilibrium, and number of migrants per generation, using variation at eight novel microsatellite loci, developed ex profeso for this study. Results indicate lack of differentiation between population pairs, and most genetic variation exists within subpopulations, implying high historical connectivity. Fragments were not genetically distinct from continuous forest populations. Simulations suggest a severe effective population size reduction at the outset of the Last Glacial Maximum 26,000 YBP, after which the area was recolonized by individuals from Central America. It is possible that the number of reproductive events that have passed since the onset of fragmentation has been insufficient to detect an effect on genetic variation, or that the extant number of palm trees in fragments is high enough to maintain the genetic diversity; bottleneck simulations agree with the first explanation. Notwithstanding, evidence suggests that populations in fragments face harsher environmental conditions, selecting against homozygotes, a situation that can jeopardize their persistence in fragments if population size is too small. creator: Jorge O. Juárez-Ramírez creator: Juan Núñez-Farfán uri: https://doi.org/10.7717/peerj.19784 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2026 Juárez-Ramírez and Núñez-Farfán title: Determinants of subclinical leprosy among household contacts in Indonesia: serological and socio-demographic factors link: https://peerj.com/articles/20631 last-modified: 2026-01-12 description: BackgroundLeprosy remains a public health challenge in Indonesia, which ranks third globally after India and Brazil. Subclinical infection among household contacts contributes to ongoing transmission, as individuals infected with Mycobacterium leprae (M. leprae) without symptoms may serve as undetected reservoirs. This study investigated serological and sociodemographic determinants associated with subclinical M. leprae infection among household contacts of leprosy patients in Tangerang, Indonesia.MethodsA cross-sectional study was conducted in 2020 among 320 household contacts of confirmed leprosy index cases recruited through purposive sampling. Anti-Phenolic Glycolipid-1 (PGL-1) IgM antibodies were detected using an in-house enzyme-linked immunosorbent assay (ELISA). Bivariate analysis using Chi-square and t-tests assessed preliminary associations, and multivariate logistic regression was applied to identify independent predictors of seropositivity, adjusting for potential confounders.ResultsOverall, 43.8% of household contacts were seropositive for anti-PGL-1 IgM antibodies. Multivariate analysis revealed that a history of Bacille Calmette-Guerin (BCG) vaccination was associated with significantly lower odds of seropositivity (adjusted OR = 0.514; 95% CI [0.291–0.907]; p = 0.018), while the presence of a visible BCG scar was associated with nearly twofold higher odds (adjusted OR = 1.953; 95% CI [1.117–3.415]; p = 0.024). No significant associations were found between sociodemographic factors such as age, sex, or contact duration, and seropositivity.ConclusionBCG vaccination status and visible BCG scars were key determinants of anti-PGL-1 seropositivity, suggesting complex interactions between vaccination, immune response, and exposure to M. leprae. The study highlights the protective role of BCG-induced immunity while emphasizing the need for standardized scar assessment and continuous surveillance of household contacts. Although limited by its cross-sectional and purposive design, the integration of immunological and epidemiological data represents a strength, providing evidence to support Indonesia’s Zero Leprosy 2030 control strategy. creator: Khariri Khariri creator: Sunarno Sunarno creator: Novaria Sari Dewi Panjaitan creator: Putu Yuliandari creator: Sarwo Handayani creator: Rita Marleta Dewi creator: Nastiti Intan Permata Sari creator: Fitriana Fitriana creator: Agriani Dini Pasiana creator: Ina Kusrini creator: Edwin Nugroho Njoto uri: https://doi.org/10.7717/peerj.20631 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2026 Khariri et al. title: Serum osmolarity as a predictor of mortality in ICU COVID-19 patients: a retrospective analysis link: https://peerj.com/articles/20590 last-modified: 2026-01-12 description: BackgroundSerum osmolarity, reflecting fluid and electrolyte balance, may serve as a prognostic marker in critically ill patients, but its role in COVID-19 is not well established. This study evaluated the association between admission serum osmolarity and in-hospital mortality in critically ill COVID-19 patients.MethodsWe conducted a retrospective study including 267 critically ill COVID-19 patients admitted from the ED to the ICU of a tertiary-care hospital between March 2020 and April 2022. Data on demographics, thoracic computed tomography (CT) findings, vasopressor use, ventilation support, laboratory values, and in-hospital mortality were obtained. Serum osmolarity was calculated using the formula. The primary outcome was in-hospital mortality; secondary outcomes included vasopressor use, endotracheal intubation (ETI), and laboratory parameters. Statistical analyses included Mann–Whitney U and chi-square tests, logistic regression, and receiver operating characteristic (ROC) curve analysis.ResultsOf 267 patients, 203 were non-survivors and 64 survivors (mortality 76%); mean age was 53.8 ± 12.3 years, 59.6% male. Survivors had higher median serum osmolarity (288.37 vs. 285.75 mOsm/L, p = 0.034) and sodium (Na) (135 vs. 133 mEq/L, p = 0.004). Sodium demonstrated slightly superior discrimination (AUC = 0.620) compared to osmolarity (area under the curve (AUC) = 0.588). In multivariate logistic regression, serum sodium (OR = 0.89, 95% CI 0.82–0.97), inotropic agent use (OR = 3.73, 95% CI [1.65–8.42]), and endotracheal intubation (OR = 5.20, 95% CI [2.11–12.84]) were independent predictors of mortality. The model’s c-statistic was 0.713 (95% CI [0.654–0.771]) with 70.4% sensitivity and 65.8% specificity.ConclusionsLower admission serum osmolarity and hyponatremia were independently associated with increased in-hospital mortality in critically ill COVID-19 patients. Although Na slightly outperformed calculated osmolarity, the latter remains a practical, integrative prognostic tool for early risk stratification. Prospective studies should evaluate whether timely correction of hypo-osmolar or hyponatremic states improves outcomes. creator: Mehmet Toptas creator: Özlem Dikme creator: Ozgur Dikme creator: Abdurrahman Tünay creator: Mensure Yilmaz Cakirgoz creator: İbrahim Akkoç uri: https://doi.org/10.7717/peerj.20590 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2026 Toptas et al. title: A new defoliating threat to eucalyptus plantations: biology and foliar consumption of Physocleora dukinfeldia (Lepidoptera: Geometridae) link: https://peerj.com/articles/20589 last-modified: 2026-01-12 description: The defoliator Physocleora dukinfeldia Schaus 1897 (Lepidoptera: Geometridae) was recently reported attacking Eucalyptus urograndis (Myrtaceae) plantations in Brazil, raising concerns about its potential impact on commercial forestry. In this context, early characterization of pest biology plays a critical role in understanding host-use patterns and forecasting potential impacts on forest ecosystems. This study aimed to characterize the biology and foliar consumption of P. dukinfeldia on E. urograndis and its native host, Schinus terebinthifolia (Anacardiaceae), by recording molting, mortality, pupation, and emergence of imago, measuring larval head capsule width, pupal weight, and size, and calculating stage duration and viability under controlled conditions. The insect completed its life cycle on both host plants, with significantly longer development time and reduced pupal viability observed on E. urograndis. Although larval survival was low on both host species, nearly one-third of the individuals successfully reached adulthood. No significant differences in leaf consumption were detected between the two eucalyptus species evaluated in this study. These findings indicate that P. dukinfeldia has the biological capacity to adapt to eucalyptus and should be closely monitored in forest production areas. This is the first report to detail the life cycle and feeding behavior of this species on eucalyptus, providing critical baseline information for future pest management strategies. creator: Paula Gregorini Silva creator: Aline Marques Pinheiro creator: Thais Lohaine Braga Santos creator: Laura Vilas Bôas Gianezi creator: Daniel Somma Araújo creator: Bruna Ferreira Anjos creator: Carlos Gilberto Raetano creator: Carlos Frederico Wilcken uri: https://doi.org/10.7717/peerj.20589 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2026 Silva et al. title: Human landscape disturbance and wildlife gut microbiota: global knowledge gaps link: https://peerj.com/articles/20545 last-modified: 2026-01-12 description: Wildlife gut microbiota (GM) comprises a dynamic microbial community that plays a key role in host adaptation, ecological interactions and health. Human landscape disturbances (e.g., habitat loss and fragmentation) may alter the diversity and composition of wildlife GM. Therefore, it is important to understand whether these changes are driven by habitat loss, fragmentation per se, or a combination of fragmentation and additional disturbances (e.g., human activities, interaction with domestic animals). We reviewed recent literature (2013–2023) concerning the effects of human landscape disturbance on wildlife GM alpha diversity, focusing on studies employing quantitative or qualitative landscape metrics. Of 119 reviewed studies, 62.2% (n = 74) used some type of landscape metrics, 58% (n = 69) incorporated landscape disturbance as a variable in their analyses, and 49.5% (n = 59) reported significant differences in at least one alpha diversity index. Among studies on free-ranging wildlife that found significant differences in any alpha diversity index (n = 52), 69.2% (n = 36) employed landscape metrics, and 55.8% (n = 29) explicitly described the type of disturbance associated with changes in GM alpha diversity index, with higher values in less disturbed landscapes compared to more disturbed landscapes (binomial sign test; p = 0.04). With respect to host species exhibiting significant variations in their GM alpha diversity index due to human landscape disturbance, there is an overrepresentation of species classified as “Least Concern” and an underrepresentation of species from certain regions, particularly South America. Despite growing research interest in this field, the available studies remain insufficiently extensive to establish clear overall patterns and trends, both globally and across different taxonomic groups. This review identifies methodological and geographical biases and emphasizes the need for more comprehensive studies in this field, considering host species ecology and quantitative landscape metrics as a substantial contribution for predicting ecosystem-level responses and informing effective conservation efforts. creator: Rocío Paleo-López creator: Carolina S. Ugarte creator: Camila J. Stuardo creator: Andrea X. Silva creator: Constanza Napolitano uri: https://doi.org/10.7717/peerj.20545 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2026 Paleo-López et al. title: Dental caries risk assessment using caries management by risk assessment (CAMBRA) tool in Yanbu city, Saudi Arabia—a cross sectional study link: https://peerj.com/articles/20540 last-modified: 2026-01-12 description: IntroductionDental caries affects billions of people globally with complications leading to a reduced quality of life. Investigating dental caries risk factors is of the utmost importance to prevent future carious lesions. To date, most oral health research focused on measuring the prevalence of the disease at the expense of investigating the caries risk. This study aims to establish a baseline record on the level of dental caries risk in Yanbu city and to explore the factors associated with an increased risk in permanent dentition.MethodsContact information was obtained from all Ministry of Health facilities across Yanbu city. Participants aged ≥18 years with permanent dentition were included via simple random sampling. Clinical examinations were conducted to collect potential risk and protective factors using CAMBRA tool. In addition, other factors including demographic characteristics, dental attendance, smoking history, dental anxiety, and the presence of comorbidities, were collected. Descriptive, chi2 test, and multivariate linear regression analyses were performed to determine major potential risk factors and the level of caries risk.ResultsA total of 141 participants were included in the study. The most prevalent risk factor was the presence of heavy plaque (51.1%), 97.2% of the participants presented with cavitated teeth. Factors such as the use of fluoridated toothpaste once/twice daily and a chlorhexidine gluconate mouth rinse were associated with a decreased risk of caries (p-value < 0.05). Conversely, frequent snacking, medications-induced hyposalivation, the presence of heavy plaque, deep pits and fissures, exposed tooth roots, white spot lesions, new non-cavitated lesions in enamel and existing restorations were associated with an increased risk for dental caries (p-value < 0.05).ConclusionThis study represents a foundational assessment of caries risk via the CAMBRA protocol among an underreported population in Saudi Arabia. This work addresses a critical gap and highlights important key factors that can be utilized in managing dental caries clinically and in the implementation of larger-scale caries preventive programs in the region. creator: Wallaa Albishi creator: Sumyia Mehrin creator: Mai Kadi creator: Ghadah Althubyani creator: Abdulelah Alblawi creator: Ghadeer Baqais creator: Nouf Alnazawi uri: https://doi.org/10.7717/peerj.20540 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2026 Albishi et al.