title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=100 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: An update on Aenocyon dirus in the interior of North America: new records, radiocarbon dates, ZooMS spectra, and isotopic data for an iconic late Pleistocene carnivore link: https://peerj.com/articles/19219 last-modified: 2025-04-11 description: Aenocyon dirus played a crucial role as a predator in late Quaternary megafaunal communities throughout southern North America. This article presents two new occurrences of the species from southwest Iowa on the eastern Great Plains, updates the Peccary Cave record in the southern Ozark Highlands, and amends the fossil record of the species. In southern North America, there are 166 occurrences of A. dirus, spanning Marine Isotope Stage (MIS) 2-19, with at least two-thirds (n = 112) of the occurrences dating to MIS 2-3 (11,600–57,000 cal B.P.). A. dirus fossils are found across this region, with notable concentrations in California, Florida, the Ozark Highlands, and broadly across the southern Great Plains. Consideration of Canis specimens from the lead region (covering contiguous parts of Illinois, Wisconsin, and Iowa) previously identified as Canis mississippiensis (and sometimes synonymized with A. dirus or C. lupus) reveals they are actually C. lupus. The terminal extinction of A. dirus occurred sometime after 12,800 cal B.P.The Iowa finds, consisting of a radius and a partial cranium, are the first records for the state. Zooarchaeology by mass spectrometry confirms these records, as well as the Peccary Cave record, are A. dirus, as opposed to C. lupus. The Iowa specimens are directly dated to 29,040–28,410 cal B.P. and 14,325–14,075 cal B.P., while Peccary Cave is dated to 25,350–21,405 cal B.P. These results place A. dirus in the interior of southern North America before, during, and after the Last Glacial Maximum (26,500–19,000 cal B.P.). Stable nitrogen isotope (δ15N) values of bone collagen from the younger of the two Iowa records suggest this individual did not regularly compete for prey with Smilodon fatalis during the Bølling-Allerød Chronozone (14,640–12,850 cal B.P.). To the south, at Peccary Cave, considerations of prey size, prey abundance, and isotopic data strongly suggest Platygonus compressus was the focal prey species. creator: Matthew G. Hill creator: Christopher C. Widga creator: Todd A. Surovell creator: Kurt M. Wilson creator: Sarah A. Allaun creator: McKenna L. Litynski creator: Jason Titcomb uri: https://doi.org/10.7717/peerj.19219 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hill et al. title: RAD51 expression and prognostic impact in patients with stomach adenocarcinoma link: https://peerj.com/articles/19179 last-modified: 2025-04-11 description: BackgroundStomach adenocarcinoma (STAD) is the most common gastrointestinal cancer. A clear diagnosis and molecular targeted therapy have important implications for prolonging survival of patients. RAD51 is the central catalyst of homologous recombination that plays important role in maintaining genomic integrity. However, the clinical significance of RAD51 expression in STAD patients remains unclear. This study aimed to assess the association of RAD51 expression with clinicopathological characteristics and patient outcomes.MethodsIn this study, RAD51 mRNA expression in STAD patients was assessed using the UALCAN and GEPIA databases. The diagnostic value of RAD51 was evaluated by analyzing the ROC curve (data from the The Cancer Genome Atlas (TCGA) database). The protein expression level of RAD51 in STAD patients and its relationship with clinicopathological characteristics and prognosis were evaluated by immunohistochemistry. Co-expression analysis of RAD51 in STAD was performed by Coexpedia and Gene Expression Profiling Interactive Analysis (GEPIA) databases. The associations of RAD51 and its co-expression genes with immune infiltrates were analyzed in TIMER database.ResultsOur bioinformatic analysis revealed that RAD51 demonstrates elevated expression in STAD. The ROC curve analysis yielded an AUC value of 0.9366 (95% CI [0.9075–0.9658]), confirming its potential as a biomarker for STAD. Immunohistochemical assessments validated the up-regulation of RAD51 in STAD, highlighting its significant correlation with TNM stage and T stage, but not with age, sex, grade, N stage, M stage, or P53 expression. Patients exhibiting high RAD51 expression exhibited significantly reduced overall survival. Multivariate analysis identified RAD51 expression may serve as an independent prognostic biomarker of poor prognosis in patients with STAD. Additionally, our bioinformatic analysis identified eight RAD51 co-expression genes (AURKA, CKS1B, NUSAP1, PFDN4, CCNE1, CDCA4, KIF4A, and MCM10) in STAD. Moreover, we discovered that RAD51 and its main co-expressed genes were significantly negatively associated with most or all immune cell infiltration.ConclusionsRAD51 overexpression was related to disease progression and poor prognosis, as well as infiltration of immune cells in gastric cancer. creator: Baiyu Jian creator: Hao Zhang creator: Li Fan creator: Yang Li creator: Nan Wu creator: Ningning Wang creator: Lingmin Li creator: Xueyan Li creator: Pengling Ge creator: Yingcai Niu creator: Jicheng Liu uri: https://doi.org/10.7717/peerj.19179 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Jian et al. title: Phytochemical production and antioxidant activity improvement of Rhinacanthus nasutus (L.) Kurz calli by in vitro polyploidization link: https://peerj.com/articles/19160 last-modified: 2025-04-11 description: BackgroundRhinacanthus nasutus (L.) Kurz is a multipurpose ethnomedicinal shrub containing various bioactive compounds and phytochemicals. Inducing polyploidy is an alternative way to enhance the production of secondary metabolites in medicinal plants. The main objectives of this research were to study the effect of polyploidization on the phytochemical content and antioxidant activity of R. nasutus calli.MethodsIn vitro polyploidy was induced by soaking calli in colchicine at different concentrations and for different exposure times. To determine callus polyploidy, the relative DNA contents of each sample were examined using flow cytometry. Diploid, tetraploid, and mixoploid calli were extracted to determine the total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activity.Results and conclusionResults showed that the callus survival rate decreased with increasing colchicine concentration and exposure time. The highest percentage of induced tetraploid (66.67%) and mixoploid (66.67%) calli were obtained at 0.05% and 0.2% colchicine with exposure times of 48 and 24 h, respectively. Tetraploid calli showed the highest TPC (81.28 mg GAE/g extract), TFC (35.33 mg QE/g extract), and antioxidant activity compared to diploid and mixoploid calli. Additionally, tetraploid calli demonstrated an approximately twofold greater increase in TPC and TFC compared to diploid calli. The analysis of polyploid callus samples revealed that tetraploid calli exhibited the highest antioxidant activity, whereas diploid calli demonstrated the lowest antioxidant activity across all applied assays. Therefore, inducing a tetraploid of R. nasutus calli plays a critical role in modifying phytochemical content and antioxidant activity. creator: Wipa Yaowachai creator: Prathan Luecha creator: Worasitikulya Taratima uri: https://doi.org/10.7717/peerj.19160 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Yaowachai et al. title: Maize leaves salt-responsive genes revealed by comparative transcriptome of salt-tolerant and salt-sensitive cultivars during the seedling stage link: https://peerj.com/articles/19268 last-modified: 2025-04-10 description: Maize (Zea mays) is a crop of significant global importance, yet its productivity is considerably hindered by salt stress. In this study, we investigated two maize cultivars, one exhibiting high salt tolerance (ST) and the other showing salt sensitivity (SS) at the seedling stage. The ST cultivar demonstrated superior seedling survival rates, higher relative water content, and lower electrolyte leakage and malondialdehyde levels in its leaves after both 3-day and 7-day salt treatments, when compared to the SS cultivar. To explore the molecular basis of these differences, we performed comparative transcriptome sequencing under varying salt treatment durations. A total of 980 differentially expressed genes (DEGs) were identified. Gene ontology (GO) functional enrichment analysis of DEGs indicated that the oxidation-reduction process, phosphorylation, plasma membrane, transferase activity, metal ion binding, kinase activity, protein kinase activity and oxidoreductase activity process is deeply involved in the response of ST and SS maize varieties to salt stress. Further analysis highlighted differences in the regulatory patterns of transcription factors encoded by the DEGs between the ST and SS cultivars. Notably, transcription factor families such as AP2/ERF, bZIP, MYB, and WRKY were found to play crucial roles in the salt stress regulatory network of maize. These findings provide valuable insights into the molecular mechanisms underlying salt stress tolerance in maize seedlings. creator: Mingfang Ji creator: Sirui Xu creator: Zhongxian Ma creator: Chengnan Xiao creator: Jiangting Xu creator: Yanfang Zhu creator: Ronghao Cai creator: Chen Bo uri: https://doi.org/10.7717/peerj.19268 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ji et al. title: Genome-wide identification and characterization of the KNOX gene family in Vitis amurensis link: https://peerj.com/articles/19250 last-modified: 2025-04-09 description: BackgroundThe KNOX (KNOTTED1-like homeobox gene) gene family plays a pivotal role in controlling plant growth, maturation, and morphogenesis. However, the function of KNOX in Vitis amurensis has not yet been reported. This study identified and characterized the entire KNOX gene family in Vitis amurensis.MethodsBy employing bioinformatic approaches, the phylogenetic relationships, chromosomal positions, gene architectures, conserved motifs, cis-regulatory elements present in promoter regions, and gene expression profiles of KNOX gene family members in Vitis amurensis were identified and analyzed.ResultsTen KNOX genes spanning nine chromosomes were discovered, and these genes were subsequently categorized into two distinct subclasses. The promoter regions of members of the KNOX gene family include cis-acting elements that are involved in plant growth, hormonal regulation, and stress and light responses. An examination of the expression profiles of KNOX genes in different tissues of Vitis amurensis revealed that genes in Class I presented tissue-specific expression patterns, whereas genes belonging to Class II presented more ubiquitous expression across various tissues. The expression levels of Vitis amurensis KNOTTED1-like homeobox (VaKNOX)2, VaKNOX3, and VaKNOX5 were highest in fruits. VaKNOX2, VaKNOX3, and VaKNOX5 can serve as candidate genes for enhancing fruit quality. The expression levels of VaKNOX6 and VaKNOX7 were much higher in cold environments than in normal conditions. Through in-depth research into the functions of VaKNOX6 and VaKNOX7, we aimed to improve the cold resistance of grapevine varieties. creator: Linling Liu creator: Wenpeng Lu creator: Shutian Fan creator: Yiming Yang uri: https://doi.org/10.7717/peerj.19250 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Machine learning-based prediction of LDL cholesterol: performance evaluation and validation link: https://peerj.com/articles/19248 last-modified: 2025-04-09 description: ObjectiveThis study aimed to validate and optimize a machine learning algorithm for accurately predicting low-density lipoprotein cholesterol (LDL-C) levels, addressing limitations of traditional formulas, particularly in hypertriglyceridemia.MethodsVarious machine learning models—linear regression, K-nearest neighbors (KNN), decision tree, random forest, eXtreme Gradient Boosting (XGB), and multilayer perceptron (MLP) regressor—were compared to conventional formulas (Friedewald, Martin, and Sampson) using lipid profiles from 120,174 subjects (2020–2023). Predictive performance was evaluated using R-squared (R2), mean squared error (MSE), and Pearson correlation coefficient (PCC) against measured LDL-C values.ResultsMachine learning models outperformed traditional methods, with Random Forest and XGB achieving the highest accuracy (R2 = 0.94, MSE = 89.25) on the internal dataset. Among the traditional formulas, the Sampson method performed best but showed reduced accuracy in high triglyceride (TG) groups (TG > 300 mg/dL). Machine learning models maintained high predictive power across all TG levels.ConclusionMachine learning models offer more accurate LDL-C estimates, especially in high TG contexts where traditional formulas are less reliable. These models could enhance cardiovascular risk assessment by providing more precise LDL-C estimates, potentially leading to more informed treatment decisions and improved patient outcomes. creator: Jing-Bi Meng creator: Zai-Jian An creator: Chun-Shan Jiang uri: https://doi.org/10.7717/peerj.19248 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Meng et al. title: Caregiver factors influencing family-based treatment for child and adolescent eating disorders: a systematic review and conceptual model link: https://peerj.com/articles/19247 last-modified: 2025-04-09 description: IntroductionThe need to assess and manage familial factors influencing family-based treatment (FBT) has been identified in the literature in the context of improving outcomes. While some studies have attempted to address this need, results have not been unified into a framework and to date, no conceptual model exists to bring these factors together for use in clinical practice. A systematic review was conducted to fill this gap and addressed the following question: which caregiver factors influence FBT outcome for child and adolescent eating disorders?MethodologyThe protocol was registered in PROSPERO (CRD42022338843) and utilized the PRISMA framework. A total of 1,994 results were returned from EBSCO Host, Embase, ProQuest, PubMed Central, SCOPUS and Web of Science. Screening returned 164 studies for full-text-review with third-party replication to reduce risk of bias. Thirty-nine articles were included and organized in an evidence hierarchy including both quantitative and qualitative methodologies. Heterogeneity of the data precluded meta-analysis; results were synthesized and grouped using a systematic-narrative approach.ResultsInfluential caregiver factors were identified and grouped into eight domains: caregiver capacity, confidence, readiness, internalizing factors, externalizing factors, food-related factors, support network and family function. Factors within each domain and their influence on treatment outcome were reported. A conceptual model, caregiver factors influencing treatment (Care-FIT) was produced as a graphical representation of the identified domains and factors by frequency of appearance.ConclusionCaregiver factors can significantly impact FBT outcome, and given the importance of their role in treatment, effective identification and management of caregiver factors is warranted. The conceptual model can be used in clinical case formulation and to support further exploration of the degree to which factors are influential. Identifying caregiver factors likely to influence treatment can facilitate support to enhance treatment and recovery. creator: Alex McCord creator: Kylie Rice creator: Adam Rock uri: https://doi.org/10.7717/peerj.19247 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 McCord et al. title: Unveiling the potentials of Lawsonia inermis L.: its antioxidant, antimicrobial, and anticancer potentials link: https://peerj.com/articles/19170 last-modified: 2025-04-09 description: BackgroundLawsonia inermis L., commonly known as henna, is a traditional medicinal Indian plant used for anti-dandruff and antifungal purposes. The plant is rich in phytochemicals and is believed to have significant bioactivity potential. However, limited information is available on the phytochemical compositions of L. inermis cultivars in Thailand. Therefore, this study aims to assess the phytochemical constituents and investigate the bioactivity of L. inermis extract.MethodsL. inermis leaf extracts were prepared by macerating in ethanol (HenE), methanol (HenM), chloroform (HenC), hexane (HenH), and water boiling (HenW). The phenolic and flavonoid contents were determined by Folin-Ciocalteu and aluminum chloride colorimetric methods. High-performance liquid chromatography (HPLC) was performed to qualify polyphenolic contents. Antioxidant activities were evaluated by using 2,2-Diphenyl-1-picrylhydrazyl (DPPH), 2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and ferric reducing antioxidant power (FRAP) methods. Moreover, antibacterial activity was tested against two gram-positive and four gram-negative bacteria by the agar well diffusion and the broth dilution methods, and antifungal activity was carried out using the poisoned food technique. Additionally, the cytotoxicity of the extracts against MDA-MB-231, SW480, A549 and A549RT-eto cancer cell lines was determined by using (3-(4, 5-dimethylthiazolyl-2)-2, 5-diphenyltetrazolium bromide) (MTT) assay. The scratch wound healing assay was performed to determine the effect of anti-migration on A549 cells.ResultsQuantitative analysis revealed that HenE and HenM extracts had high phenolic and flavonoid contents. Gallic acid, catechin, ellagic acid, apigetrin, lawsone and quercetin were identified by HPLC. The HenE and HenM extracts exhibited strong antioxidant properties, and the extracts showed different inhibition growth against bacteria tested, especially B. cereus and S. aureus. In addition, all extracts had potential inhibitory activity to all fungal strains, especially HenE and Hen M, which exhibited strong antifungus activity against Penicillium sp. All extracts showed cytotoxic effects in the cell lines MDA-MB-231, SW480, A549 and A549RT-eto, except HenH. The HenE and HenM exhibited the best IC50 values of 57.33 ± 5.56 µg/ml and 65.00 ± 7.07 µg/ml against SW480 cells, respectively. The HenC, HenW, and HenH were found to suppress A549 cells migration.Discussion and ConclusionThis study revealed that the L. inermis extracts, particularly those obtained from polar solvents (HenE and HenM), had a strong potency for antioxidant, antibacterial, and anticancer properties. Our findings highlight the valuable biological properties of extracts that can be promoted through additional investigation into their applications in Thailand for medicinal and industrial purposes. creator: Nantikan Joyroy creator: Lukana Ngiwsara creator: Siriporn Wannachat creator: Ratchanee Mingma creator: Jisnuson Svasti creator: Jintanart Wongchawalit uri: https://doi.org/10.7717/peerj.19170 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Joyroy et al. title: Psychometric properties of the Chinese version physical literacy assessment questionnaire among high school students in Gansu, China link: https://peerj.com/articles/19093 last-modified: 2025-04-09 description: IntroductionThe concept of physical literacy (PL) originated from the philosophy of lifelong sports, and its development is crucial for achieving lifelong sports goals. The Portuguese Physical Literacy Assessment Questionnaire (PPLA-Q) is a tool designed to assess the physical literacy of high school students, demonstrating good reliability and validity. The aim of this study is to translate and adapt the PPLA-Q into Chinese (PPLA-Q-C) and validate its applicability among adolescents in Gansu, China through confirmatory factor analysis (CFA).MethodsA total of 780 middle school students from Gansu Province, China, aged 15–18, participated. After screening, the final sample size was 729. The English PPLA-Q was translated into Chinese and validated through expert review and pre-testing. Data were collected in September 2022 via a self-reported survey, with an effective response rate of 93.5%. Data analysis was conducted using Mplus 8.3 with the robust maximum likelihood (MLR) estimator. Confirmatory factor analysis (CFA) assessed model fit using standardized root mean square residual (SRMR), root mean square error of approximation (RMSEA), Tucker-Lewis index (TLI), and comparative fit index (CFI) indices. Construct validity was evaluated through composite reliability (CR), average variance extracted (AVE), and factor correlations. The study followed ethical guidelines and received approval from Universiti Sains Malaysia’s ethics committee.ResultsAll observed items exhibited high factor loadings, confirming that the assumed model, consisting of 40 items grouped into four latent variables, was consistent with the original model. The CFA model demonstrated a good fit with the data, as indicated by fit indices: RMSEA = .024 (90% CI [.020–.027]), CFI = .978, TLI = .977, SRMR = .032.ConclusionThe final measurement model comprised 40 items, all retained and considered acceptable for the sample. The study results suggest that the Chinese version of PPLA-Q (PPLA-Q-C) is effective and reliable for assessing the PL of high school students in Gansu Province, China. Education practitioners and policymakers can utilize the PPLA-Q-C framework in their future work to assess the PL of Chinese-speaking students. creator: Zilu Qu creator: Jiarun Wu creator: Yee Cheng Kueh creator: Dongqing Ye creator: Garry Kuan uri: https://doi.org/10.7717/peerj.19093 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Qu et al. title: Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing link: https://peerj.com/articles/19260 last-modified: 2025-04-08 description: The gut microbiota is integral to an animal’s physiology, influencing nutritional metabolism, immune function, and environmental adaptation. Despite the significance of gut microbiota in wild rodents, the Korean field mouse (Apodemus peninsulae) and the gray red-backed vole (Myodes rufocanus) remain understudied. To address this, a metagenomic sequencing analysis of the gut microbiome of these sympatric rodents in northeast China’s temperate forests was conducted. Intestinal contents were collected from A. peninsulae and M. rufocanus within the Mudanfeng National Nature Reserve. High-throughput sequencing elucidated the gut microbiome’s composition, diversity, and functional pathways. Firmicutes, Bacteroidetes, and Proteobacteria were identified as the dominant phyla, with M. rufocanus showing greater microbiome diversity. Key findings indicated distinct gut bacterial communities between the species, with M. rufocanus having a higher abundance of Proteobacteria. The gut microbiota of A. peninsulae and M. rufocanus differed marginally in functional profiles, specifically in the breakdown of complex carbohydrates, which might reflect their distinct food preferences albeit both being herbivores with a substantial dietary overlap. The investigation further elucidated gut microbiota’s contributions to energy metabolism and environmental adaptation mechanisms. This study aligns with information on rodent gut microbiota in literature and highlights the two understudied rodent species, providing comparative data for future studies investigating the role of gut microbiota in wildlife health and ecosystem functioning. creator: Jing Cao creator: Shengze Wang creator: Ruobing Ding creator: Yijia Liu creator: Baodong Yuan uri: https://doi.org/10.7717/peerj.19260 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Cao et al.