title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=11 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: High-fluorescent cells as a rapid screening tool for malignant effusions link: https://peerj.com/articles/20528 last-modified: 2025-12-18 description: ObjectiveElevated levels of high-fluorescent cells (HFCs) in serous effusions often suggest the presence of tumor cells. The purpose of this study was to evaluate the diagnostic value of HFC detection in the differentiation between benign and malignant serous effusions using the Sysmex XN-10 automated hematology analyzer in body fluid mode (BF mode).MethodsSerous effusion specimens, including 702 pleural effusions, 255 ascitic fluid samples and 21 pericardial effusions, were collected from 978 patients at the First Affiliated Hospital with Nanjing Medical University between June 2023 and June 2024. The absolute number (HFC#) and percentage (HFC%) of HFCs were detected using the Sysmex XN-10 automated hematology analyzer. Meanwhile, levels of carcinoembryonic antigen (CEA), lactate dehydrogenase (LDH) and other biomarkers in serous effusions were measured. The diagnostic performance for malignant effusions was evaluated using receiver operating characteristic (ROC) curves.ResultsThe HFC#, HFC% and CEA levels in the malignant effusion group were significantly higher than those in the benign effusion group (all P < 0.001). Multivariate logistic regression analysis revealed that HFC#, HFC%, CEA, and LDH were independently associated with malignant effusion. Receiver operating characteristic (ROC) analysis showed that CEA had the best diagnostic performance (AUC = 0.817), followed by HFC% (AUC = 0.727) and HFC# (AUC = 0.703). The diagnostic performance of HFC in combination with CEA is significantly better than that of CEA alone. For malignant effusions associated with lung cancer, the diagnostic performance of CEA was better than HFC and cytokeratin 19 fragment (CYFRA21-1), but there was no significant difference between HFC and CYFRA21-1.ConclusionHFC demonstrates high diagnostic value in identifying malignant serous effusions, especially when used in combination with CEA. As a rapid laboratory parameter based on cellular nucleic acid characteristics, HFC can serve as a useful auxiliary tool for screening malignant effusions. creator: Hongmei Ding creator: Yuexinzi Jin creator: Chu Chu creator: Lin Wang uri: https://doi.org/10.7717/peerj.20528 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ding et al. title: The clinical significance of gut microbiota of chronic obstructive pulmonary disease with functional abdominal bloating and distension link: https://peerj.com/articles/20526 last-modified: 2025-12-18 description: BackgroundChronic obstructive pulmonary disease (COPD) is a disease with high morbidity and mortality. Functional abdominal bloating/distension (FABD), a functional gastrointestinal disorder characterized by recurrent sensations of abdominal fullness and/or visible abdominal distension without identifiable organic causes. FABD mainly impairs gastrointestinal functions—particularly intestinal transit and gas handling—rather than pulmonary function. This study characterized fecal microbiota in COPD patients with FABD to identify precision medicine biomarkers.MethodsFecal samples from 20 COPD & FABD, 20 COPD, and 10 healthy controls (HC) were analyzed via metagenomic analysis. Gut microbiota diversity/composition were compared, and immune parameters (serum IgG, CD4+/CD8+ T cells) were assessed.ResultsCOPD/COPD & FABD patients showed significantly higher fecal microbiota α-diversity (COPD vs. HC: Chao1, P = 0.12; ACE, P = 0.14; Shannon, P = 0.0016; Simpson, P = 0.0013; COPD & FABD vs. HC: Chao1, P = 0.031; ACE, P = 0.031; Shannon, P = 0.00032; Simpson, P = 0.0005) vs. HC. β-Diversity analyses (PCA/PCoA) revealed distinct clustering between patients and HC (PCA, P = 0.014; PCoA, P = 0.013), but no separation between COPD and COPD & FABD (P > 0.05). Linear discriminant analysis (LEfSe) identified 50 discriminative biomarkers: 41 enriched in HC (Bacteroides uniformis), five in COPD & FABD (Bacilli, Enterococcus faecium), and four in COPD (Streptococcus parasanguinis). Notably, Enterococcus faecium was highly abundant in patients (22.04–26.92%) but absent in HC, suggesting a potential association with the COPD-FABD condition. Random forest models showed moderate diagnostic accuracy for all microbes (AUC = 0.632) and strong performance for fungal biomarkers (Clostridium fessum, Clostridioides difficile; AUC = 0.856).ConclusionGut microbiota signatures, particularly Enterococcus faecium and fungal taxa, may serve as non-invasive biomarkers for COPD progression and FABD diagnosis, warranting clinical validation. creator: Xiaowei Lu creator: Haiyun Dai creator: Xiang Gu creator: Jing Xie creator: Xianhong Zhong creator: Xiaofen Dong creator: Bing Su creator: Jia Su creator: Linlin Wang creator: Tingting Sun creator: Lihui Geng uri: https://doi.org/10.7717/peerj.20526 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lu et al. title: Simpler predictive models provide higher accuracy for ovarian cancer detection link: https://peerj.com/articles/20525 last-modified: 2025-12-18 description: Ovarian cancer remains a danger to women’s health, and accurate screening tests would likely increase survival. Two established protein biomarkers, CA125 and HE4, have been shown to work well in isolation, but achieve even higher accuracy when combined using logistic regression (LR). This LR-based combination of protein concentrations achieves high accuracy when distinguishing healthy samples from cancer samples (area under the curve (AUC) = 0.99). The dataset we use was obtained from a previous publication that described DELFI-Pro, an LR model combining features derived from cell-free DNA (cfDNA) with the two proteins’ concentrations. We show that many of DELFI-Pro’s cfDNA features are affected by confounding technical variation within training data, which impacts the previously reported results. A minority of the training data’s cancer samples (42 of 94) have chromosomal copy number values that are markedly different from the other samples used to evaluate the DELFI-Pro screening model. After removing those 42 samples from the training data, we find that DELFI-Pro does not outperform CA125 or CA125+HE4 protein-only screening classifiers even in cross validation, including a two-protein model published alongside the DELFI-Pro model. We conclude that DELFI-Pro does not adequately justify the inclusion of its cfDNA features. Our results are in line with the principle that simpler machine learning models will tend to exhibit better generalizability on new data. creator: Derrick E. Wood creator: Joseph Roy creator: Bari J. Ballew uri: https://doi.org/10.7717/peerj.20525 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Wood et al. title: Perception of King Khalid University students regarding the benefits, barriers, self-efficacy, knowledge, and practices related to healthy eating: a cross-sectional study link: https://peerj.com/articles/20523 last-modified: 2025-12-18 description: BackgroundMaintaining healthy eating habits is crucial for promoting better nutritional status, especially among university students who face challenges. Therefore, this study aimed to assess the perceptions of King Khalid University students regarding the benefits and barriers to healthy eating, their self-efficacy, nutritional knowledge, and dietary practices.MethodsThis study employed a descriptive cross-sectional design. A total of 385 students participated by completing a pretested, self-administered questionnaire consisting of 87 items.ResultsFindings revealed a high perception of the benefits of healthy eating (Mean = 4.23, SD = 0.83). However, participants reported significant perceived barriers (Mean = 3.12, SD = 1.19), particularly the high cost of healthy foods (Mean = 3.89, SD = 1.15). Self-efficacy in adopting healthy eating was moderate (Mean = 3.25, SD = 1.21). Knowledge of the health benefits of fruits and vegetables was high, whereas awareness of whole grains and flaxseeds was limited. Regression analysis indicated that perceived barriers (B = –0.181, p < 0.001), self-efficacy (B = 0.078, p = 0.003), and knowledge of food healthiness (B = 0.125, p < 0.001) were significant predictors of healthy food practices.ConclusionAlthough students had positive perceptions, barriers and knowledge gaps persisted. Interventions should focus on reducing barriers, enhancing self-efficacy, and improving nutrition literacy to promote healthier behaviors among university students. creator: Amani Alhazmi creator: Manal Mohammed Hawash creator: Maha Ali creator: Haroon Ali creator: Farah Aziz creator: Khursheed Muzammil uri: https://doi.org/10.7717/peerj.20523 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Alhazmi et al. title: Preliminary insights into the gut microbiota of patients with rheumatoid arthritis in Vietnam link: https://peerj.com/articles/20521 last-modified: 2025-12-18 description: In Vietnam, rheumatoid arthritis accounts for more than 20% of all joint diseases, with a growing number of young patients. The disease progresses rapidly, but its exact cause remains not fully understood. Environmental and lifestyle factors, such as smoking, pollution, obesity, gut microbiota, and infections, play a role in rheumatoid arthritis development. The presence of Gram-positive bacteria in the gut might promote the release of toxic metabolites into the bloodstream, which in turn triggers joint inflammation. Therefore, this pilot study aimed to compare the gut microbiota in 22 patients with newly diagnosed rheumatoid arthritis and 20 healthy individuals recruited at the Bach Mai Hospital, Hanoi, Vietnam. To this end, we analyzed fecal samples from all participants by 16S rRNA metagenomic sequencing. The sequencing data analysis did not reveal any significant differences in alpha diversity between patients and healthy controls. Conversely, unweighted and weighted UniFrac distances (beta diversity metrics) allowed distinct clustering between groups. The abundance of the Lactococcus, Solobacterium, Faecalibaculum, and Corynebacterium genera was increased, and that of Bacteroides was decreased in patients with rheumatoid arthritis compared with healthy controls. Moreover, patients exhibited distinct gut microbiota profiles in function of their disease activity scores (DAS28-CRP, DAS-ESR), rheumatoid factor, and anti-citrullinated protein antibody concentrations. Overall, our study contributes to bridging this knowledge gap and provides a foundation for the study of gut microbial signatures of autoimmune disease in Vietnamese patients. It also highlights the potential role of gut microbes in rheumatoid arthritis diagnosis and management in Vietnam. creator: Bich Ngoc Nguyen creator: Lan Thi Ngoc Nguyen creator: Dinh Thi My Trinh creator: Hien Thao Nguyen creator: Tam Thi Thanh Tran uri: https://doi.org/10.7717/peerj.20521 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Nguyen et al. title: The connection between mindfulness levels and life satisfaction among breast cancer patients: the sequential mediating effects of body appreciation and stress perception link: https://peerj.com/articles/20485 last-modified: 2025-12-18 description: BackgroundResearch indicates a positive relationship between life satisfaction, mindfulness, and emotional perception. While this connection is observed in a variety of groups, it has been less studied in women with breast cancer. The research investigated correlation among mindfulness, body appreciation, emotional perception, and life satisfaction in Chinese breast cancer patients.MethodsIn Xiangyang City, a survey was conducted involving 312 individuals diagnosed with breast cancer. The instruments used for this assessment included the Revised Mindfulness Cognition and Affective Scale (CAMS-R), Body Appreciation Scale (BAS), Perceived Stress Scale (PSS), and Life Satisfaction Scale (SWLS).Results(1) Mindfulness may positively and substantially predict the life satisfaction of breast cancer patients (β = 0.439, P < 0.001); (2) body appreciation (β = 0.152, P < 0.01) and perceived stress (β =  − 0.183, P < 0.01), respectively, acted as a mediator to the influence of being mindful on fulfillment in life, and (3) mindfulness could also indirectly affect the life satisfaction of individuals diagnosed with breast cancer through the sequential influence of body appreciation and perceived stress.ConclusionThe mediating model has been fitted on cross-sectional data in this research. Breast cancer patients’ life satisfaction is significantly positively predicted by mindfulness, which includes indirect as well as direct outcomes of perceived stress and body appreciation. The connection between mindfulness and overall well-being is partially mediated through body appreciation and also perceived stress, and the chain mediation effect provides additional insight into the connection between mindfulness and overall well-being. Therefore, in clinical practice, mindfulness training can enhance the body appreciation levels of breast cancer patients, reduce their perception of stress, and subsequently improve their overall life satisfaction. creator: Junli Zhou creator: Xianhui Huang creator: Dan Yuan creator: Liyuan Wang creator: Minyu Liu creator: Xue Jiang creator: Lijuan Xing creator: Song Xu uri: https://doi.org/10.7717/peerj.20485 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhou et al. title: Mechanistic study on integrated water-fertilizer management to alleviate Na+ toxicity and enhance salt tolerance and yield of pakchoi under salt stress link: https://peerj.com/articles/20431 last-modified: 2025-12-18 description: The cultivation of salt-tolerant pakchoi is a promising strategy for utilizing coastal saline soils. However, supporting agronomic technologies are remain underdeveloped. This study investigates how coordinated water-fertilizer regulation mitigates sodium (Na+) toxicity under salt stress, thereby enhancing salt tolerance and yield in pakchoi and providing a scientific basis for optimizing agronomic management. A pot experiment was conducted with three irrigation methods (conventional, drip, and mulched drip) and three fertilizer types (conventional, controlled-release, and mixed), under soil salt stress adjusted by sodium chloride (NaCl) to 0.15% salinity by weight. The results showed that MP treatment (mulched drip irrigation + mixed fertilizer) can significantly improve yield performance, with fresh and dry weight increasing by 39% and 42% respectively, and enhancing ion balance by increasing potassium (K+) and calcium (Ca2+) and reducing Na+. In addition, MP enhanced antioxidant defense by increasing superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) activities and reducing oxidative damage. The treatment also maintains better water status and photosynthetic efficiency. MP treatment can improve growth, physiology, and stress tolerance. This integrated approach represents a novel water-fertilizer strategy with high application potential for sustainable vegetable production in saline regions. creator: Jin Li creator: Hongcheng Li creator: Zizheng Li creator: Huirong Su creator: Tingting Duan creator: Zhong Lin creator: Yinling Zhu creator: Xiaoli Chen creator: Xianmin Wang uri: https://doi.org/10.7717/peerj.20431 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Li et al. title: A systematic review of the role of methylase genes in antibiotic resistance: co-existence with extended spectrum β-lactamase and carbapenemase genes in Klebsiella pneumoniae link: https://peerj.com/articles/20428 last-modified: 2025-12-18 description: BackgroundAntibiotic resistance in multidrug-resistant Klebsiella pneumoniae (MDR-KP), particularly against carbapenems and colistin, is a critical concern, increasing morbidity and mortality among hospitalized patients. This systematic review aims to identify methylase genes in K. pneumoniae and examine their co-existence with β-lactamase and carbapenemase genes contributing to antibiotic resistance.MethodsA literature search was conducted across three electronic databases from inception until 6 December 2023. The quality assessment followed Critical Appraisal Skills Programme (CASP) criteria. Studies focusing on methylase genes and antibiotic resistance in K. pneumoniae were included. Two authors independently screened titles, abstracts, and full texts, with a third resolving disagreements.ResultsThirty-four studies met the inclusion criteria. Methylase genes in K. pneumoniae isolates were predominantly reported in Europe and Asia, particularly in Iran, China, Japan, and India (8.8%, N = 3). The most prevalent 16S rRNA methyltransferase genes identified were armA (76.5%, N = 26), rmtB (61.8%, N = 21), and rmtC (29.4%, N = 10). Common extended-spectrum β-lactamase (ESBL) genes included blaCTXM (64.7%, N = 22) and blaSHV (47%, N = 16), while blaKPC (26.5%, N = 9) and blaNDM (23.5%, N = 8) were the predominant carbapenemase genes. The coexistence of methylase genes with ESBL and carbapenemase genes conferred significant resistance to aminoglycosides (gentamicin, kanamycin, tobramycin, amikacin, arbekacin), cephalosporins (cefazolin, cefoxitin, cefotaxime), and carbapenems (imipenem, meropenem).ConclusionsThe widespread distribution of resistance mechanisms in K. pneumoniae highlights a global challenge, emphasizing the need for strategic antimicrobial use to reduce resistance rates. creator: Nur Husna Shahimi creator: Nabiha Bouafia creator: Mawaddah Mohd Azlan creator: Asma Nadia Ahmad Faris creator: Nur Ayunie Ahmad creator: Ali Rabaan creator: Amal Alfaraj creator: Bandar Albaradi creator: Tasneem Zaidan creator: Abdulsalam Alawfi creator: Amer Alshengeti creator: Zainab Almansour creator: Wadha Alfouzan creator: Amal Sabour creator: Maha Alshiekheid creator: Anizah Rahumatullah creator: Nik Yusnoraini Yusof uri: https://doi.org/10.7717/peerj.20428 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shahimi et al. title: Effects of glucose spraying and lactic acid bacteria inoculation applied to high-moisture alfalfa during pre- and post-harvest periods on silage fermentation and feed quality link: https://peerj.com/articles/20276 last-modified: 2025-12-18 description: BackgroundThe management of alfalfa silage in livestock production systems is crucial for achieving high-quality silage and optimal livestock production. Alfalfa (Medicago sativa L.) is known to be difficult to ensile due to its high buffering capacity (BC), low water-soluble carbohydrate (WSC) content, and low dry matter (DM) content. Therefore, using biological or chemical additives may be beneficial in improving the silage quality of alfalfa, particularly when it is harvested at relatively low DM content and high protein levels. Lactic acid bacteria (LAB) and glucose are commonly used as silage additives to enhance the ensiling process and improve fermentation quality.MethodsThis study aimed to estimate the effects of pre-harvest and post-harvest application of lactic acid bacteria inoculant (control, L. plantarum, and L. citerum) and glucose doses (0%, 3% and 6%) treatments on the chemical composition and fermentation profile of silage feed of alfalfa grown under field conditions in 2023. After 60 days of ensiling, silages were analyzed for fermentation and quality characteristics.ResultsSignificant two-way and three-way interactions were observed among harvest, inoculant, and glucose dose for several parameters, including pH (T0, T60), dry matter ratio (DMT0, T60) content, and lactic acid bacteria (LAB T0) counts and acid detergent lignin (ADL) content. These interactions indicate that the effect of treatment varied depending on their combinations. The lowest initial pH(T0) was recorded in the pre-harvest combination L. plantarum with 0% glucose (p < 0.001). The silage pH(T60) value the lowest (4.91) was observed in 6% glucose combined with L. plantarum, while the highest pH was found in the control group with %0 glucose (p < 0.02). The highest initial DM(T0) content (25.78%) was achieved with the pre-harvest combination L. citerum + 3% glucose (p < 0.02). The highest silage DM (T60) content was noted with L. citerum (24.00%) and L. plantarum (23.20%) applied pre-harvest (p < 0.001). ADL content was recorded at its lowest value in the pre-harvest L. citerum with 3% glucose added (p < 0.03). The timing of harvest also had a significant effect on the quality parameters of silage (p < 0.001). Yeasts (T60) count and ADF content was lower in the pre-harvest treatments and crude protein content was higher in the pre-harvest (p < 0.01). Increasing glucose dose from 0% to 6% increased DM content, crude protein content and LAB count (p < 0.001).ConclusionThe best results for low pH and improved fermentation stability were achieved with 6% glucose and L. plantarum applied 24 h before harvest, which is recommended for practical use under field conditions. To suppress the yeast population, 3% and 6% glucose contents of L. citerum pre-harvest can be used alternatively. creator: Fatma Akbay uri: https://doi.org/10.7717/peerj.20276 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Akbay title: Vast cryptic diversity in direct-developing frogs Pristimantis (Anura: Strabomantidae): a new subgenus and the description of a new species from the eastern Andes of Ecuador link: https://peerj.com/articles/20512 last-modified: 2025-12-17 description: Pristimantis, a genus of direct-developing frogs within the family Strabomantidae, comprises 617 recognized species, making it the most species-rich genus of vertebrates worldwide. This group include 264 described (43% of the world) species in Ecuador, being one of the countries in the region with the highest rate of species description, greatest diversity and endemism. In this study, we analyze the phylogenetic position and describe a new Pristimantis species from the Colonso Chalupas Biological Reserve and Llanganates National Park in northeastern Ecuador, using phylogenetic, genetic, morphological, and geographic evidence. Additionally, we propose a new subgenus within Pristimantis that includes the Pristimantis prolatus and Pristimantis bicantus species groups. Our results indicate that the new species and related species form a well-supported group with significant genetic divergence based on the 16S rRNA gene (average uncorrected p-distance = 2.8–7.5%), within the Pristimantis bicantus species group. Morphologically, the new species is characterized by a black to dark-gray dorsum and marbled venter (less intense or brown in males), being endemic to the Guacamayos mountain range and the Llanganates region in the northeastern Andean foothills of Ecuador. We emphasize the importance of including topotypic specimens to analyze and compare species groups to delimiting species, like Pristimantis. creator: Keyko D. Loza-Carvajal creator: Mario H. Yánez-Muñoz creator: Walter Quilumbaquin creator: H. Mauricio Ortega-Andrade uri: https://doi.org/10.7717/peerj.20512 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Loza-Carvajal et al.