title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=108 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A cost-effective predictive tool for AFP-negative focal hepatic lesions of retrospective study: enhancing clinical triage and decision-making link: https://peerj.com/articles/19150 last-modified: 2025-03-26 description: BackgroundIdentifying alpha-fetal protein (AFP)-negative focal hepatic lesions presents a significant challenge, particularly in China. We sought to develop an economically portable tool for the diagnosis of benign and malignant liver lesions with AFP-negative status, and explore its clinical diagnostic efficiency.MethodsA retrospective study was conducted at Peking University Shenzhen Hospital from January 2017 to February 2023, including a total of 348 inpatients with AFP-negative liver space-occupying lesions. The study used a training set of 252 inpatients from January 2017 to September 2021 to establish a diagnostic model for differentiating benign and malignant AFP-negative liver space-occupying lesions. Additionally, a validation cohort of 96 inpatients from October 2021 to February 2023 was used to confirm the diagnostic performance of the model. From January 2017 to February 2023, patients at JingNing People’s Hospital, Gansu Province were assigned to the external cohort (n = 78).ResultsA predictive tool was established by screening age, gender, hepatitis B virus (HBV)/hepatitis C virus (HCV) infected, single lesion, alanine amino transferase (ALT), and lymphocyte-to-monocyte ratio (LMR) using multivariate logistic regression analysis and clinical practice. The area under the curve (AUC) of the model was 0.911 (95% CI [0.873–0.949]) in the training set and 0.882 (95% CI [0.815–0.949]) in the validation cohort. In addition, the model achieved an area under the curve of 0.811 (95% CI [0.687–0.935]) in the external validation cohort.ConclusionOur results demonstrated that the predictive tool has the characteristics of good diagnostic efficiency, economy and convenience, which is helpful for the clinical triage and decision-making of AFP-negative liver space-occupying lesions. creator: Yu Lin creator: Qianyi Wang creator: Minxuan Feng creator: Jize Lao creator: Changmeng Wu creator: Houlong Luo creator: Ling Ji creator: Yong Xia uri: https://doi.org/10.7717/peerj.19150 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lin et al. title: Electroencephalographic power spectrum patterns related to the intelligence of children with learning disorders link: https://peerj.com/articles/19138 last-modified: 2025-03-26 description: Children with learning disorders (LD) perform below average in tests of academic abilities and intelligence. These children also have a significantly abnormal resting-state electroencephalogram (EEG) compared to children with typical development (TD), i.e., an excess of slow brain oscillations such as delta and theta that may be markers of inefficient cognitive processing. We aimed to explore the relationship between the performance in an intelligence test and the resting-state EEG power spectrum of children with LD. Ninety-one children with LD and 45 control children with TD were evaluated with the Wechsler Intelligence Scale for Children 4th Edition (WISC-IV) test of intelligence and a 19-channel EEG during an eyes-closed resting-state condition. The EEG dimensionality was reduced with a principal component analysis that yielded several components representing EEG bands with functional meaning. The first seven EEG components and the intelligence values were analyzed with multiple linear regression and a between-group discriminant analysis. The EEG power spectrum was significantly related to children’s intelligence, predicting 13.1% of the IQ variance. Generalized delta and theta power were inversely related to IQ, whereas frontoparietal gamma activity was directly related. The intelligence test and the resting state EEG had a combined 82.4% success rate to discriminate between children with TD and those with LDs. creator: Benito Javier Martínez-Briones creator: Thalía Fernández creator: Juan Silva-Pereyra uri: https://doi.org/10.7717/peerj.19138 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Martínez-Briones et al. title: EGCG’s anticancer potential unveiled: triggering apoptosis in lung cancer cell lines through in vitro investigation link: https://peerj.com/articles/19135 last-modified: 2025-03-26 description: BackgroundNovel treatment techniques are needed since lung cancer is still a major worldwide health concern. Green tea contains a component called epigallocatechin-3-gallate (EGCG), which has demonstrated potential anticancer properties. This work sought to understand how EGCG affects the phosphatidylinositol-3-kinase protein kinase B (PI3K/Akt) signaling pathway, which in turn causes apoptosis in H1299 lung cancer cells.MethodsIn this experiment, multiple dosages of EGCG were applied to five H1299 cells and five A549 cell lines for a duration of 72 h. Apoptotic pathways, cellular responses, and protein expression levels were investigated in relation to EGCG by morphological, biochemical, and proliferation/migration investigations.ResultsIn H1299 and A549 cells, EGCG raised apoptosis rates and, in a dose-dependent way, hindered cell growth. The levels of phosphorylated Akt (p-Akt) and PI3K (p-PI3K) dramatically reduced following EGCG administration, despite no significant alterations in Akt and PI3K expressions. These results imply that EGCG inhibits the activation of the PI3K/Akt signaling pathway, which in turn causes apoptosis in H1299 and A549 cells.ConclusionThe research provides insights into the effects of EGCG on proliferation and migratory inhibition, as well as highlighting its potential to induce apoptosis in lung cancer cells. These results support EGCG’s promise as a therapeutic agent in the treatment of lung cancer and further our understanding of the processes underlying its anticancer activities. creator: Al Moutassem Billah Khair creator: Alexander Maniangat Luke creator: Rajashree Patnaik creator: Luca Testarelli uri: https://doi.org/10.7717/peerj.19135 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Khair et al. title: Enhancing the classification of isolated theropod teeth using machine learning: a comparative study link: https://peerj.com/articles/19116 last-modified: 2025-03-26 description: Classifying objects, such as taxonomic identification of fossils based on morphometric variables, is a time-consuming process. This task is further complicated by intra-class variability, which makes it ideal for automation via machine learning (ML) techniques. In this study, we compared six different ML techniques based on datasets with morphometric features used to classify isolated theropod teeth at both genus and higher taxonomic levels. Our model also intends to differentiate teeth from different positions on the tooth row (e.g., lateral, mesial). These datasets present different challenges like over-representation of certain classes and missing measurements. Given the class imbalance, we evaluate the effect of different standardization and oversampling techniques on the classification process for different classification models. The obtained results show that some classification models are more sensitive to class imbalance than others. This study presents a novel comparative analysis of multi-class classification methods for theropod teeth, evaluating their performance across varying taxonomic levels and dataset balancing techniques. The aim of this study is to evaluate which ML methods are more suitable for the classification of isolated theropod teeth, providing recommendations on how to deal with imbalanced datasets using different standardization, oversampling, and classification tools. The trained models and applied standardizations are made publicly available, providing a resource for future studies to classify isolated theropod teeth. This open-access methodology will enable more reliable cross-study comparisons of fossil records. creator: Carolina S. Marques creator: Emmanuel Dufourq creator: Soraia Pereira creator: Vanda F. Santos creator: Elisabete Malafaia uri: https://doi.org/10.7717/peerj.19116 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Marques et al. title: Back pain in the midwifery profession in northern Poland link: https://peerj.com/articles/19079 last-modified: 2025-03-26 description: BackgroundNeck pain (NP) and low back pain (LBP) are increasingly significant medical, social, and economic concerns. The midwifery profession, similar to other healthcare occupations, is particularly predisposed to these issues.MethodsThis study aimed to analyze the prevalence of back pain among midwives and evaluate the associated disability levels using the Neck Disability Index (NDI) and the Oswestry Disability Index (ODI). The study group included 208 actively practicing midwives aged 23 to 67 years (mean ± SD: 48.1 ± 10.7 years). Participants completed an anonymous survey comprising a custom-designed questionnaire, the Polish language versions of the NDI and ODI, and the Visual Analog Scale (VAS) for pain intensity.ResultsThe analysis revealed a statistically significant correlation between VAS pain intensity and both age (r = 0.2476) and work experience (r = 0.2758), indicating higher pain scores with increasing age and seniority. No significant association was found between BMI and VAS scores (r = 0.0011). Additionally, NDI and ODI scores correlated significantly with age (r = 0.1731; r = 0.3338), BMI (r = 0.1685; r = 0.2718), and work experience (r = 0.1987; r = 0.4074). Higher values for age, BMI, and seniority were associated with increased disability levels.ConclusionsNeck and low back pain represent prevalent and impactful issues for midwives in Poland, contributing to mild to moderate disability, absenteeism, reliance on pain medication, and limited physical activity. Key contributing factors include age, professional experience, BMI, and low levels of physical activity. creator: Aleksandra Bryndal creator: Sebastian Glowinski creator: Kazimiera Hebel creator: Agnieszka Grochulska uri: https://doi.org/10.7717/peerj.19079 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bryndal et al. title: Association of gender and metabolic factors with thyroid nodules in T2DM: a retrospective study link: https://peerj.com/articles/19068 last-modified: 2025-03-26 description: AimsSex differences in the incidence of thyroid nodules (TNs) are broadly recognized, but further analysis is lacking. Thus, the aim of this study was to evaluate the association between TNs and anthropometric parameters in type 2 diabetic males and females.Materials and MethodsThis cross-sectional study included 747 patients with type 2 diabetes mellitus (T2DM). All patients underwent clinical examination, thyroid ultrasound, laboratory tests, anthropometrics and body composition. Multivariable logistic regression assessed factors associated with TNs, and a simple nomogram was finally developed.ResultsIn total, the incidence of TNs was 36.95% (276/747) and was significantly higher in females (52.75%) than in males (27.85%). Age was positively correlated with TNs risk in patients with T2DM (males: OR = 4.141, 95% CI [1.999–8.577], females: OR = 4.630, 95% CI [1.845–11.618]). Obesity (OR = 2.655, 95% CI [1.257–5.607]) and hyperuricemia (OR = 1.997, 95% CI [1.030–3.873]) were only associated with the risk of TNs independent of other risk factors in type 2 diabetic females, as well as other obesity factors such as weight, BMI, waist-hip ratio, percent body fat, visceral curve area, and upper arm circumference, but not in type 2 diabetic males. However, the diameter of the largest thyroid nodule was only related to age (R = 0.226, p < 0.01). Finally, the nomogram for evaluating TNs in female T2DM patients was established, and the C-index of the nomogram was 0.704 (95% CI [0.89–0.94]).ConclusionTNs occur with a significantly higher frequency in type 2 diabetic females than in males, especially those with hyperuricemia and obesity. Modifiable metabolic factors, such as obesity and hyperuricemia, are a major focus for improving TNs risk in women. creator: Xi Yuan creator: Xin Wang creator: Xinwen Yu creator: Yuxin Jin creator: Aili Yang creator: Xiaorui Jing creator: Shengru Liang creator: Chunni Heng creator: Na Zhang creator: Lijuan Chao creator: Langlang Liu creator: Meiying Wang creator: Yufei Liu creator: Guohong Zhao creator: Bin Gao uri: https://doi.org/10.7717/peerj.19068 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yuan et al. title: Effects of different proportions of organic substitution for mineral fertilizers on soil methanogenic and methanotrophic communities in paddy fields link: https://peerj.com/articles/19000 last-modified: 2025-03-26 description: Mineral fertilizers are widely used to improve rice yields, but their overuse has caused severe environmental problems. Replacing mineral fertilizers with organic alternatives might be an effective practice for enhancing agro-ecosystems. This study investigated treatments with varying proportions of organic substitution to determine the optimal approach for increasing soil fertility and rice yield. In addition, the relationship between soil methane emission characteristics and associated microbial communities was studied by microcosm experiments and high-throughput sequencing to assess greenhouse gas emissions. Compared with mineral fertilizers alone, treatment with organic substitution, especially at high proportions, increased soil pH, fertility, and crop yield. Treatment with a medium proportion of organic substitution increased cumulative methane (CH4) emissions by 44.8% relative to mineral fertilization alone, but that with low and high proportions showed similar emissions compared with mineral fertilization alone. Organic substitution treatment significantly increased the gene copy numbers of soil methanogens and methanotrophs, with the highest increases observed under high proportions of organic substitution. The gene copy number of methanogens increased by 4.87 times, and that of methanophiles increased by 13.11 times. Additionally, organic substitution treatment significantly changed their community compositions. High organic substitution was associated with an exceptionally high abundance of methanotrophs. Treatment with a high proportion of organic substitution enhanced the relative abundance of Type I taxa of methanotrophs and increased soil pH to trigger higher pmoA abundance, thus strengthening methane oxidation capacity without additional cumulative CH4 emissions compared with mineral fertilizers alone. Besides, treatment with a high proportion of organic substitution increased crop yield and reduced the amount of mineral fertilizers needed, resulting in less environmental pollution. This study comprehensively evaluated the effects of organic substitution for mineral fertilizers, providing an essential theoretical basis for the sustainable development of agriculture. creator: Dandan Yuan creator: Keke Dang creator: Jing Yin creator: Han Liu creator: Tingting Ma creator: Jia Liu creator: Xingjia Xiang uri: https://doi.org/10.7717/peerj.19000 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yuan et al. title: Molecular profiling and phenotypic evaluation of thermo-sensitive genic male sterility genes for high-yielding rice hybrids (Oryza sativa L.) link: https://peerj.com/articles/18803 last-modified: 2025-03-26 description: Temperature-sensitive genic male sterility (TGMS) is crucial for boosting rice productivity and ensuring food security. In this study, we evaluated the morphological traits and genetic diversity of 57 rice TGMS lines under fertility-inducing (Gudalur) and sterility-inducing (Coimbatore) environments. Significant variations were observed in yield and floral characteristics, with flowering times ranging from 62.3 to 152.0 days. Lines such as TNAU 16S and TNAU 93S exhibited shorter plant heights and durations, along with higher numbers of productive tillers, making them promising candidates for hybrid breeding. Molecular profiling revealed that the tms8 gene was the most prevalent across the lines, with some carrying combinations of two or more TGMS genes. TNAU 38S and TNAU 60S possessed all four TGMS genes, ensuring stable sterility. These lines showed low fertility temperatures at Gudalur and low sterility temperatures at Coimbatore, indicating optimal conditions for hybrid seed production. Floral characteristics in lines like TNAU 19S, TNAU 126S-1 and TNAU 126S-2 were favorable, with total sterility under sterility-inducing conditions and increased fertility under fertility-inducing conditions, making them ideal for hybridization. For short-duration, semi-dwarf hybrids, TNAU 93S and TNAU 16S were identified as suitable female parents. Overall, this study highlights the significance of TGMS gene combinations for stable male sterility expression and identifies lines such as TNAU 37S, TNAU 60S and TNAU 85S as optimal for high-yielding two-line rice hybrids. The findings emphasize the potential for developing diverse, stable hybrids that can contribute to improved rice productivity and global food security. creator: B. Nagendra Naidu creator: Manonmani Swaminathan creator: Nivedha Rakkimuthu creator: Pushpam Ramamoorthy creator: Kumaresan Dharmalingam creator: Raveendran Muthurajan creator: Selvi Duraisamy creator: Tushar Arun Mohanty creator: Bonipas Antony John uri: https://doi.org/10.7717/peerj.18803 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Naidu et al. title: Psychometric evaluation of the Chinese version of Risky Loot Box Index (RLI) and cross-sectional investigation among gamers of China link: https://peerj.com/articles/19164 last-modified: 2025-03-25 description: Nowadays, many of the top-selling video games include options to purchase loot boxes as paid virtual items. As research progressed, loot boxes have been found to have similar characteristics to gambling, and there has been an ongoing debate as to whether loot boxes can be defined as gambling. In order to better study loot boxes, psychometrically meaningful scales are necessary. The Risky Loot Box Index (RLI) was developed by Brooks and Clark, which is the most commonly used tool to assess the use of loot boxes. This study aimed to translate the original RLI into Chinese and evaluate its psychometric properties. Two samples were recruited through online gaming forums (n = 143) and offline internet cafes (n = 236). An exploratory factor analysis of the online sample yielded a one-dimensional nine-item model, with the factor focused on risky behaviors associated with loot boxes. The confirmatory factor analysis carried out on the offline sample corroborated the results obtained from the exploratory factor analysis, and the Chinese version of the RLI displays satisfactory psychometric properties. Furthermore, the Problem Gambling Severity Index (r = 0.57, P < 0.001) and the Internet Gaming Disorder Scale-Short Form (r = 0.67, P < 0.001) were found to be significantly associated with the RLI. We also found that players with high RLI scores may have higher levels of anxiety and depression, and they were more willing to spend money on loot boxes, with some spending nearly all their earnings. Interestingly, no significant correlations between age, gender, education, or income level, and the RLI were found. creator: Peidong Guo creator: Yueheng Liu creator: Luyin Tan creator: Yifan Xu creator: Haolin Huang creator: Qijian Deng uri: https://doi.org/10.7717/peerj.19164 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Guo et al. title: Physiological traits underlying sodicity tolerance in Jamun (Syzygium cumini L. Skeels) cultivars link: https://peerj.com/articles/19132 last-modified: 2025-03-25 description: BackgroundThere is a lack of research on how sodicity stress affects tree growth and physiological relations in jamun (Syzygium cumini L. Skeels). An understanding of cultivar-specific morpho-physiological changes under sodic conditions might aid in the development of more sodicity-tolerant cultivars through genetic improvement, and help identify cultivars suitable for degraded sodic soils.MethodsWe assessed the effects of sodicity stress on tree growth, physiological relations, and ion uptake in four cultivars of jamun including CISH J-37 (J-37), CISH J-42 (J-42), Konkan Bahadoli (KB), and Goma Priyanka (GP).ResultsJamun cultivars exhibited varying degrees of reduction in tree growth, leaf area, and gas exchange properties under sodic conditions. Elevated soil pH caused relatively larger declines in trunk cross sectional area (TCSA; >30%) and canopy volume (CV; >25%) in J-42 and KB. Reductions brought on by sodicity stress in leaf area were rather modest (<10%) across cultivars, suggesting that maintaining leaf area may be a key adaptive trait in jamun to cope with sodic conditions. In addition to displaying a notable increase in water use efficiency (WUE), cultivar J-37 also exhibited largely intact levels of relative chlorophyll and photosynthetic rate (Pn) under sodic conditions. Despite a high intrinsic Pn under control treatment, cultivar GP displayed a large drop in Pn (37.16%) when exposed to sodicity stress. Comparatively greater increases in leaf phenolics in KB and GP seemed to be at the expense of growth and photosynthesis under sodic conditions. While superoxide dismutase (SOD) and catalase (CAT) activities showed notable spikes in both J-37 and GP, proline accumulation increased substantially only in cultivar J-37 in response to sodicity stress. Despite significant increases in leaf Na+ and Cl− concentrations, J-37 was found to be comparatively efficient in Na+ and Cl− exclusion from leaves when compared to other cultivars. Surprisingly, sodicity stress did not alter leaf K+, Ca2+ and Mg2+ levels noticeably across cultivars. Correlation analysis suggested that elevated leaf Cl− likely inhibited tree growth more than leaf Na+. Principal component analysis was reasonably efficient in discerning the shared and divergent responses to sodicity stress of the studied cultivars.ConclusionsMembership function analysis revealed a reasonable resilience to sodicity stress only in cultivar J-37. Maintenance of photosynthesis, reduced uptake of Na+ and Cl− ions, increased and synergistic activities of SOD and CAT, and a higher leaf K+/Na+ ratio likely accounted for better performance of J-37 trees in sodic soils. Further investigations are needed to elucidate the molecular underpinnings of sodicity tolerance. creator: Anshuman Singh creator: Ashwani Kumar creator: Jai Prakash creator: Daya Shankar Mishra uri: https://doi.org/10.7717/peerj.19132 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Singh et al.