title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=24 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The function and mechanisms of action of lysyl oxidase-like 3 (LOXL3) in cancers link: https://peerj.com/articles/20274 last-modified: 2025-11-13 description: Lysyl oxidase-like 3 (LOXL3) is a key member of the lysyl oxidase (LOX) family and belongs to the copper-dependent amine oxidase family. Its traditional core function is to catalyze the cross-linking of collagen and elastin in the extracellular matrix (ECM), thereby maintaining the structural integrity and normal physiological functions of the ECM. In recent years, studies on cancer molecular mechanisms have confirmed that LOXL3 exhibits abnormal expression in a variety of cancers: in common malignant tumors such as melanoma, liver cancer, gastric cancer, colorectal cancer, and breast cancer, its expression level is significantly higher than that in the corresponding normal tissues. Meanwhile, numerous prognostic analyses have demonstrated that high LOXL3 expression is an independent risk factor for poor prognosis in cancer patients. Such patients usually have shorter progression-free survival (PFS) and overall survival (OS), suggesting that LOXL3 may serve as a potential biomarker for evaluating cancer prognosis. At the functional and mechanistic level, the role of LOXL3 is not limited to ECM remodeling. It can directly affect key biological behaviors of cancer cells, including proliferation, invasion, metastatic potential, and sensitivity to chemotherapeutic drugs, by regulating a variety of intracellular signaling pathways. This article reviews the specific roles and potential molecular mechanisms of LOXL3 in cancer, covering its associations with key cancer pathological processes such as epithelial-mesenchymal transition, maintenance of genomic stability, and regulation of the tumor microenvironment. It focuses on clarifying the specific molecular pathways through which LOXL3 promotes pro-tumor activities in different tumors, as well as the regulatory effects of these pro-tumor activities on patients’ relevant prognosis. creator: Dan Zhao creator: Pu Su creator: Xuan Peng creator: Xue Cheng creator: Bin Li creator: Xi-min Tang creator: Shaoyang Huang creator: Zhengliang Li creator: Huaize Cao creator: Wei Xiong uri: https://doi.org/10.7717/peerj.20274 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhao et al. title: Differential responses of hard coral Montipora digitata and soft coral Xenia umbellata to nutrient stoichiometry under heat stress link: https://peerj.com/articles/20273 last-modified: 2025-11-13 description: The nitrogen-to-phosphorus (N:P) ratio of dissolved inorganic nutrients may influence coral susceptibility to heat stress, but comparative studies on how different N:P ratios affect soft and hard corals do not exist. This study thus investigated the effects of two different N:P ratios on two common Indo-Pacific reef corals: the pulsating soft coral Xenia umbellata and the hard coral Montipora digitata. Corals were exposed for five weeks to N:P 19:1 (37 µM nitrate, two µM phosphate) and N:P 5:1 (37 µM nitrate, eight µM phosphate), relative to a low nutrient control (N:P 3:1, 0.003 µM nitrate, 0.001 µM phosphate). After two weeks, temperatures were gradually increased from 26 to 32 °C. Nutrient enrichment alone did not affect any response parameter for M. digitata, whereas for X. umbellata, 9% mortality was observed, along with a reduction in pulsation rates (−100% under 5:1 ratio, −58% under 19:1 ratio). Heat stress alone significantly reduced Symbiodiniaceae density and chlorophyll a content of M. digitata, while X. umbellata was unaffected. Combined factors significantly increased mortality for M. digitata (100% and 92%) and X. umbellata (87% and 33%) under the 5:1 and 19:1 ratio, respectively. Symbiodiniaceae density and chlorophyll a content in M. digitata showed the same response as under heat stress alone, while these parameters were unaffected for X. umbellata. Pulsation of X. umbellata was reduced by 100% in both combined treatments. Nutrient enrichment alone likely compromised X. umbellata’s metabolism through the energy-intensive reduction of nitrate to ammonium, halting pulsation. Yet, under combined warming and nutrient addition, X. umbellata showed better fitness than M. digitata, suggesting it may better cope with the predicted environmental changes. Still, both corals were negatively affected, particularly by the 5:1 N:P ratio. The stronger impact of this low ratio likely resulted from exacerbated energy depletion by nitrogen assimilation, while the imbalanced 19:1 ratio may have limited nitrogen assimilation, thereby mitigating stress. These findings suggest that high phosphorus, in combination with high nitrogen, may accelerate coral stress. Hence, tailored nutrient management strategies to aid coral survival in a warming ocean should reduce nutrient concentrations and keep N:P ratios close to the Redfield ratio of 16:1. creator: Selma D. Mezger creator: Sophie Littke creator: Malte Ostendarp creator: Mareike de Breuyn creator: Christian Wild uri: https://doi.org/10.7717/peerj.20273 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mezger et al. title: Development of a prediction model for lower limb deep vein thrombosis in critically ill patients after intracranial hemorrhage at high altitude: a retrospective study link: https://peerj.com/articles/20245 last-modified: 2025-11-13 description: ObjectiveTo analyze the risk factors for lower limb deep vein thrombosis (LDVT) in critically ill patients admitted to the intensive care unit (ICU) following intracranial hemorrhage at high altitude, and to establish a predictive model.MethodsA retrospective analysis was conducted on 359 patients who underwent surgery for intracranial hemorrhage and were admitted to the ICU of Xizang Autonomous Region People’s Hospital between August 1, 2021, and December 31, 2023. Patients were categorized into an LDVT group (n = 86) and a non-LDVT group (n = 273) based on the occurrence of LDVT during their ICU stay. Demographic data, comorbidities, laboratory results, and treatment approaches were compared between the groups. Independent risk factors were identified through univariate and multivariate logistic regression analyses. A risk prediction model was developed using R software, and its performance was internally validated.ResultsCompared to the non-LDVT group, patients in the LDVT group had significantly longer ICU and overall hospital stays (p < 0.05). Multivariate logistic regression revealed hypoalbuminemia and elevated D-dimer levels as independent risk factors for LDVT, while aboriginal residency in high-altitude areas (≥ 4,500 m) was identified as a protective factor. A nomogram incorporating these variables was constructed. Internal validation demonstrated strong agreement between predicted and observed outcomes, with the area under the receiver operating characteristic (ROC) curve reaching 0.815 (95% CI [0.761–0.870]). The Hosmer-Lemeshow test indicated a good model fit (p = 0.088).ConclusionLDVT significantly prolongs ICU and hospital stays in critically ill patients. Hypoalbuminemia and elevated D-dimer levels are independent risk factors for LDVT, whereas aboriginal residency at high altitudes (≥ 4,500 m) serves as a protective factor. The developed risk prediction model shows strong predictive performance. creator: Zhuoma Ciren creator: Jianlei Fu creator: Guoying Lin creator: Qianwei Li creator: Bin Wang uri: https://doi.org/10.7717/peerj.20245 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 et al. title: Screening durum wheat cultivars for resistance traits against the stem-base pathogen Fusarium graminearum link: https://peerj.com/articles/20105 last-modified: 2025-11-13 description: Durum wheat is not a traditional crop in countries with a temperate climate, but the growing demand for semolina in the food processing industry has increased the popularity of this cereal species in the farming sector. The pathogens responsible for Fusarium crown rot (FCR), eyespot, and sharp eyespot contribute to lodging, disrupt the translocation of water and nutrients in plants, and decrease yields. The present study was conducted in several dozen locations in Poland to determine the severity of FCR, eyespot, and sharp eyespot in more than ten durum wheat cultivars, to identify stem-base pathogens, to analyze the virulence of Fusarium graminearum, and to evaluate the effectiveness of seed dressing in reducing the severity of infections in durum wheat seedlings. Durum wheat cultivars were screened in field and plot experiments in Poland. The virulence of F. graminearum and the effectiveness of biological and chemical seed dressing in reducing the incidence of FCR were determined in vivo. In the studied locations, symptoms of FCR and eyespot were observed on 16–76% and 1–36% of durum wheat stems, respectively, on average. Sharp eyespot was noted only in one year of the study in a single location (1–6%). The severity of the analyzed diseases was generally low. Fusarium avenaceum, F. culmorum, F. graminearum, F. oxysporum, F. poae, F. solani, and F. sporotrichioides were isolated from stems with symptoms of FCR. The number of F. graminearum and F. culmorum isolates was significantly positively correlated with the severity of FCR symptoms (r = 0.480 and r = 0.485, respectively). Fusarium graminearum was identified in 15 locations, and F. culmorum was detected in six locations. Seed treatment with triticonazole reduced the number of ungerminated kernels by 42.6% in comparison with the untreated control. Seed treatment involving Debaryomyces hansenii decreased the number of ungerminated kernels by 31.1% on average, but this effect was noted only in cv. Floradur. All durum wheat cultivars evaluated in Koch’s postulate test were severely infected, but F. graminearum isolates differed in virulence. Fusarium graminearum was the most prevalent pathogen in durum wheat stands, and it was highly virulent for seedlings. To decrease the incidence of FCR in durum wheat stands, new resistant varieties should be tested, suitable farming locations with desirable soil and environmental conditions should be identified, and new agricultural treatments should be developed. creator: Edyta Kwiatkowska creator: Urszula Wachowska creator: Weronika Giedrojć creator: Agata Wachowska creator: Dariusz Gontarz uri: https://doi.org/10.7717/peerj.20105 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kwiatkowska et al. title: Personality Assessment Inventory (PAI): obsolete norms identify psychopathology in nearly everyone link: https://peerj.com/articles/20340 last-modified: 2025-11-12 description: BackgroundThe Personality Assessment Inventory (PAI), a self-report personality test, is one of the frequently used measures to assess psychopathology in a wide variety of settings including in high stakes assessments, for example, in child custody disputes, employment settings and fitness for duty assessments. The PAI has never been normed on a Canadian population and the PAI users have simply assumed that the US norms also describe the Canadian population. Moreover, accumulated research demonstrates that the PAI’s 35 years outdated and obsolete norms no longer describe neither university students’ nor normal adult US populations.MethodWe administered the PAI to over 200 university students in a mid-size Canadian university.ResultsOur students scored on average in moderately elevated range (60T to 69T) on many of the PAI scales including anxiety (ANX), anxiety-related disorders (ARD), depression (DEP), schizophrenia (SCZ), and borderline features (BOR). Multivariate base rate analyses revealed that approximately 95% of our sample scored in elevated range on at least one out of the 22 PAI Scales. Furthermore, although some of the PAI reliabilities are adequate for research, the PAI reliabilities are too low for using the PAI in high stakes and forensic assessment, for example, in insurance benefits, child custody, employment, and fitness for duty assessments.DiscussionWe conclude that the PAI US norms are no longer appropriate for high-stakes assessments, ought to be withdrawn immediately, and new up-to-date norms ought to be established to prevent mislabelling and diagnostic misclassifications of and harm to examinees. Continued use of the PAI outdated norms in high stakes assessments carries ethical risks, is non-scientific, and likely amounts to malpractice. creator: Bob Uttl creator: Kiefer Sikma creator: Mikayla Tat uri: https://doi.org/10.7717/peerj.20340 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Uttl et al. title: The effect of the erythropoietin resistance index on brain hemorrhage and infarction risk in maintenance hemodialysis patients: a retrospective cohort study link: https://peerj.com/articles/20326 last-modified: 2025-11-12 description: BackgroundMaintenance hemodialysis (MHD) is the main renal replacement therapy for patients with end-stage renal disease, and erythropoietin (EPO) is the main therapy for renal anemia in patients receiving maintenance hemodialysis. However, the risks of brain hemorrhage and infarction in patients on hemodialysis with erythropoietin therapy remain unclear.MethodsPatients who underwent regular hemodialysis at the Blood Purification Center of the Northern Theater General Hospital from January 1, 2018, to January 1, 2022, were retrospectively selected. A total of 588 MHD patients were enrolled on the basis of the inclusion and exclusion criteria. The primary endpoint of follow-up was brain hemorrhage and infarction, or January 1, 2024. The secondary endpoint was all-cause death. The erythropoietin resistance index (ERI) was calculated as follows: erythropoiesis-stimulating agent (ESA) (IU/week)/body weight (kg)/hemoglobin level (g/dL). Patients were divided into four groups according to ERI quartile, and a Cox proportional risk model was applied to observe the associations between the ERI and the risks of brain hemorrhage and infarction and all-cause mortality.ResultsDuring a median follow-up of 6 years, brain hemorrhage events occurred in 41 (6.9%) MHD patients, and brain infarction events occurred in 61 (10.3%) MHD patients. According to the Kaplan–Meier curve, the incidence of brain hemorrhage and infarction was greater in the high-ERI subgroup than in the low-ERI subgroup (p < 0.001). Multivariate Cox regression analysis revealed that a high ERI was a significant predictor of brain hemorrhage (HR: 3.85, 95% CI [1.34–11.07], p = 0.012) and brain infarction (HR = 2.657, 95% CI [1.17–6.02], p = 0.020). A higher ERI was associated with an increased risk of all-cause death in MHD patients (HR: 1.72, 95% CI [1.05–2.82], p = 0.033).ConclusionsHigher ERI scores were associated with brain hemorrhage and infarction in MHD patients. creator: Mingyu Liu creator: Kaiming Ren creator: Qian Wang creator: Chen Zhao creator: Zhuo Ren creator: Jiuxu Bai creator: Ning Cao uri: https://doi.org/10.7717/peerj.20326 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al. title: Minos-mediated transgenesis in the pantry moth Plodia interpunctella link: https://peerj.com/articles/20249 last-modified: 2025-11-12 description: Transposon-mediated transgenesis has been widely used to study gene function in Lepidoptera, with piggyBac being the most commonly employed system. However, because the piggyBac transposase originates from a lepidopteran genome, it raises concerns about endogenous activation, remobilization, and silencing of transgenes, thus questioning its suitability as an optimal tool in Lepidoptera. As an alternative, we evaluated the dipteran-derived Minos transposase for stable germline transformation in the pantry moth, Plodia interpunctella. We injected syncytial embryos with transposase mRNA, along with donor plasmids encoding 3xP3::EGFP and 3xP3::mCherry markers of eye and glial tissues. Across multiple experiments, we found that G0 injectees could transmit Minos transgenes through the germline even in the absence of visible marker expression in the soma, and that large mating pools of G0 founders consistently produced transgenic offspring at efficiencies exceeding 10%. Using these methods, we generated transgenic lines with a dual expression plasmid, using 3xP3::mCherry for driving red fluorescence in eyes and glial tissues, as well as the Fibroin-L promoter expressing the recently developed mBaoJin fluorescent protein in the silk glands. This demonstrated the feasibility of screening two pairs of promoter activity in tissues of interest. Collectively, these results—along with previous findings in the silkworm Bombyx mori—demonstrate that Minos achieves robust germline integration of transgenes in Lepidoptera, offering a valuable pathway to the genetic modification of species where the remobilization or suppression of piggyBac elements might be rampant. creator: Donya N. Shodja creator: Luca Livraghi creator: Arnaud Martin uri: https://doi.org/10.7717/peerj.20249 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Shodja et al. title: The cuproptosis-related gene ITGB6 and LTBP1 may be associated with diabetic kidney disease progression and immune cell infiltration link: https://peerj.com/articles/20346 last-modified: 2025-11-11 description: ObjectiveCuproptosis, a newly discovered cell death mechanism, has been linked to the pathogenesis of multiple diseases. However, its role in diabetic kidney disease (DKD) remains unclear.MethodsBy analyzing datasets GPL17586 and GPL571 from the GEO database and applying machine learning, cuproptosis-related marker genes associated with DKD were identified. The expression levels of these genes were examined in Mouse Podocyte Cell Line (MPC5) podocytes cultured in vitro and treated with high glucose (30 mM) for 24, 48, and 72 h to explore their roles in the onset and progression of DKD.ResultsKey genes in the cuproptosis pathway, integrin β6 (ITGB6) and latent transforming growth factor beta-binding protein 1 (LTBP1), were significantly upregulated in DKD patients. Consistent with this, in high glucose-treated podocytes, the expression of ITGB6 and LTBP1 was significantly higher than in the control group at 24, 48, and 72 h. The area under the receiver operating characteristic (ROC) curve (AUC) for ITGB6 and LTBP1 in both the training set (GPL17586) and validation set (GPL571) exceeded 0.7, indicating good diagnostic efficacy for DKD. Furthermore, immune infiltration analysis further revealed that ITGB6 and LTBP1 were significantly positively correlated with activated B cells, central memory Cluster of Differentiation 4 (CD4) T cells, effector memory CD4 T cells, effector memory Cluster of Differentiation 8 (CD8) T cells, and immature B cells, while showing a significant negative correlation with neutrophils.ConclusionThis study suggests that cuproptosis-related genes ITGB6 and LTBP1 may be associated with the progression of DKD through their potential role in immune cell infiltration, and could serve as potential novel targets for the prevention and diagnosis of DKD. creator: Suying Hu creator: Mengdi Tian creator: Wenjia Hu creator: Liang Yao creator: Ying Tang creator: Wei Shen creator: Qing He creator: Jing Xu creator: Huan Yao creator: Lei Ji creator: Feifei Fan creator: Shiqiang Liu creator: Zhen Wang uri: https://doi.org/10.7717/peerj.20346 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hu et al. title: Decoding the bare necessities of decapod crustacean nomenclature through the ages link: https://peerj.com/articles/20337 last-modified: 2025-11-11 description: Though taxonomists have been classifying species since 1758, the methods and biases of their naming practices have recently come under scrutiny. Despite some compelling claims on e.g., historical imperialism in the published literature, the knowledge base for making such assertions is small, as nomenclatural trends have only been researched in a select few taxa. Here, we investigate naming practices in Decapoda, one of the most studied crustacean groups, thereby extending the knowledge base to the marine realm in contrast to a previously studied cohort of largely terrestrial taxa. To date almost 18,000 species of decapods are known, from which a total of 22,363 unique names are analysed, as neither nomenclatorial nor taxonomic status has any bearing on the naming process. Despite taxonomists being inspired by a multitude of cultural influences, historically the majority of names were derived from the morphology of the animals. This dominance declined in the Victorian era, with a concomitant rise in the use of both geographically inspired names and eponyms (species named after people). Post-1958, a near-even split is achieved between these three categories, while other etymological classifications stake a minority claim on the dataset. Although a historic and contemporary gender imbalance is present amongst eponyms honouring scientists, contrary to previous findings our results detect no actual bias in naming practices, instead indicating that female scientists have been honoured in proportion to their collective presence in the field. Though previous studies have flagged a significant proportion of eponyms named for colonialist figures, these were found in relatively small numbers among Decapoda. creator: Sammy De Grave creator: Elizabeth Cole creator: Sancia E. T. van der Meij uri: https://doi.org/10.7717/peerj.20337 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 De Grave et al. title: Geographical and seasonal distribution of the Short-crested Coquette hummingbird: a microendemic and endangered species link: https://peerj.com/articles/20312 last-modified: 2025-11-11 description: Species movements along elevational or latitudinal gradients occur primarily due to climatic variations and food resource availability. However, the role of seasonal climatic conditions in species with highly restricted distributions has been poorly addressed. In this study, we analyzed the geographic distribution and seasonal climatic niche during the dry and rainy seasons of the Short-crested Coquette hummingbird (SCCH; Lophornis brachylophus), a species with high conservation priority at the global scale. We generated ecological niche and species distribution models for both seasons and used niche similarity tests to represent and compare their climatic differences. We recorded the availability of flowering and fruiting plants that the SCCH feeds on within its distribution area during both seasons and performed a kernel density analysis to evaluate the main peaks in food availability. Our results revealed that the potential distribution of the SCCH is larger (642 pixels) in the dry season than in the rainy season (487 pixels). In the dry season, the distribution of this hummingbird includes sites at lower elevations (reaching 780 m above sea level [masl]). In contrast, in the rainy season, it extends to higher elevations (up to 1,450 masl). This seasonal shift between the two seasons coincides with the availability of flowers and fruits along the elevational gradient. The climatic niche similarity between the dry and rainy seasons shows moderate overlap (Schoener’s D = 0.50) and is higher than expected by chance. Our results suggest that the SCCH moderate changes in its climatic niche throughout the year, with plant phenology being a primary driver of changes in its elevational range between seasons. creator: Pablo Sierra-Morales creator: Octavio R. Rojas-Soto creator: Luis A. Sánchez-González creator: Carina Gutiérrez-Flores creator: R. Carlos Almazán-Núñez uri: https://doi.org/10.7717/peerj.20312 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sierra-Morales et al.