title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=12 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Mandibular form and function is more disparate in amniotes than in non-amniote tetrapods from the late Palaeozoic link: https://peerj.com/articles/20243 last-modified: 2025-11-26 description: Terrestrial tetrapods originated during the Middle Devonian, and the group rapidly diversified throughout the subsequent Carboniferous and Permian periods. Feeding in air rather than water is expected to require changes to tetrapod mandibular form and function. Previous biomechanical studies on jaw evolution, however, found that the increase in functional disparity lagged behind terrestrialisation by approximately 70 Myr, coinciding with the origin of amniotes and herbivory. We expand on a previous dataset composed primarily of non-amniote tetrapods to identify the drivers of this diversification, including representatives of all major amniote clades from the Permo-Carboniferous. First, we measured nine biomechanical traits from 111 tetrapod jaws in medial view. Second, we performed an Elliptical Fourier Analysis on 198 jaws in lateral view and 73 jaws in occlusal view. The first peak in jaw disparity, during the Pennsylvanian, occurs in carnivorous non-amniote tetrapods. However, the jaws of amniotes, particularly those inferred as herbivorous, are consistently more disparate than non-amniote tetrapods from the early Permian, especially in terms of jaw depth, symphysial length and force transmission. Functional and shape disparity of Palaeozoic tetrapod jaws follow a similar pattern that is explained by large-scale faunal turnovers and ecosystem structures. creator: Jasper Ponstein creator: Mark J. MacDougall creator: Joep Schaeffer creator: Christian F. Kammerer creator: Jörg Fröbisch uri: https://doi.org/10.7717/peerj.20243 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ponstein et al. title: Overexpression of ORAOV1 and its association with immunotherapy resistance in hepatocellular carcinoma link: https://peerj.com/articles/20390 last-modified: 2025-11-25 description: Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality globally. Previous studies have reported that oral cancer overexpression 1 (ORAOV1) is overexpressed in HCC and correlated with poor prognosis, yet its molecular mechanisms remain incompletely understood. In this study, ORAOV1 overexpression was confirmed in HCC tissues via tissue microarray analysis and functionally linked to tumor cell proliferation through a positive correlation with Ki-67 expression in the human HCC cell line MHCC-97L. Bioinformatics analyses using The Cancer Genome Atlas (TCGA) and three Gene Expression Omnibus (GEO) HCC datasets further supported these findings. Multiple mechanisms appear to drive ORAOV1 upregulation, including promoter hypomethylation, amplification of the 11q13 region, and a putative ceRNA network involving AC005332.1, AC012615.1, and hsa-miR-100-5p. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses implicated ORAOV1 in various cellular processes, such as abnormal membrane channel function, extracellular matrix–receptor interactions, IL-17 signaling, and peroxisome proliferator-activated receptor (PPAR) signaling. Co-expression analysis identified significant associations between ORAOV1 and the oncogenes TPCN2 and CCND1. Additionally, ORAOV1 expression correlated with enhanced infiltration of immunosuppressive cells, including regulatory T cells, myeloid-derived suppressor cells, and cancer-associated fibroblasts, as well as upregulation of immune checkpoint markers (PD-1, PD-L1, and CTLA-4). These results indicate that ORAOV1 may modulate the immunosuppressive tumor microenvironment and contribute to resistance against immunotherapy, highlighting its potential as a therapeutic target in HCC. creator: Yuzhen Huang creator: Ni Yang creator: Su Wen creator: Ziwei Fang creator: Yucong Zhang creator: Zonghao Qian creator: Yi Huang creator: Tiejun Yin creator: Cuntai Zhang creator: Le Zhang uri: https://doi.org/10.7717/peerj.20390 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Huang et al. title: Resistance of cervical vertebrae in response to muscular stresses in pterosaurs: implications for foraging habits and skeletal pneumatization link: https://peerj.com/articles/20388 last-modified: 2025-11-25 description: The necks of pterosaurs were flexible and provided mobility for a relatively long skull. The varied morphologies and levels of pneumatization of their cervical vertebrae reflected differences in biomechanical behavior. Here, we examined the structural resistance of the cervical vertebrae to infer the most advantageous movements during the foraging behaviors of two pterodactyloid pterosaurs. We also examined the relationship between vertebral resistance and the presence of pneumatic foramina on the bone cortex. For this purpose, we analyzed three-dimensional models of the cervical vertebrae of Anhanguera piscator and Azhdarcho lancicollis, which are hypothesized to be aquatic and terrestrial predators, respectively, and employed Finite Element Analysis (FEA) to assess and quantify the stresses experienced by the vertebrae due to the performance of six different movement scenarios. We observed that the shorter vertebrae at the ends of the neck of both species favored the proliferation of larger stresses in these regions, especially in the posterior cervicals of Anhanguera piscator and in the atlas-axis of Azhdarcho lancicollis, and that their taller neural arches aided in absorbing stress. Larger stresses at the ends of the neck are consistent with the interior trabecular reinforcement of the atlas-axis and posterior cervical vertebrae, suggesting a link between biomechanical behavior and the level of pneumatization. Additionally, mechanical requirements may have also influenced the presence, size, and number of pneumatic foramina on the vertebral cortex, as evidenced by the large lateral foramen in Anhanguera piscator and the smaller and more numerous ones bordering the neural canal in Azhdarcho lancicollis. Our inferences corroborate the differences in foraging strategies hypothesized for anhanguerids and azhdarchids. The absorption of stresses resulting from ventral pitching of the head and neck indicates that the cervical vertebrae were well-adapted for making rapid movements during predatory hunting. However, variations in the height of the neural spine indicate different mechanical behaviors between these species when raising the skull and neck, which could be faster in Anhanguera piscator while more vigorous in Azhdarcho lancicollis. creator: Richard Buchmann creator: Taissa Rodrigues uri: https://doi.org/10.7717/peerj.20388 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Buchmann and Rodrigues title: Microbiome shifts during Fusarium oxysporum and F. solani (syn. Neocosmospora solani)—induced Ligusticum chuanxiong root rot: endophtic bacterial protective responses and fungal pathogenic tendencies link: https://peerj.com/articles/20369 last-modified: 2025-11-25 description: Root rot disease is a globally significant threat to the health of diverse economically important crops. Understanding shifts in the plant microbiome during disease progression can aid in identifying beneficial microbes with disease-resistant potential and developing ecofriendly biocontrol strategies. However, microbiome changes during root rot progression in the medicinal plant Ligusticum chuanxiong remain poorly understood. This study aimed to investigate the response of host-associated microbiomes to pathogen stress (Fusarium oxysporum and F. solani syn. Neocosmospora solani) during L. chuanxiong root rot. The diversity, composition, function, and network interactions of bacterial and fungal communities were examined using high-throughput sequencing and network analysis in healthy rhizomes, healthy layers of diseased rhizomes, rotten layers of diseased rhizomes, and rhizosphere and non-rhizosphere soils. The bacterial diversity decreased as root rot progressed in end ophytic (from 0.72 to 0.38) and rhizosphere soils (from 0.80 to 0.68), whereas the fungal diversity showed no significant changes. The diseased samples were enriched with root rot pathogens and other potential pathogens, such as the soil bacterium Pectobacterium and the soil fungus Gibberella, whereas beneficial taxa, including endophytic Bacillus and Trichoderma, and soil-dwelling Candidatus_Solibacter and Beauveria, were significantly reduced. Notably, in the healthy layers of diseased rhizomes, which represent a “transitional phase”, fungal communities resembled those in rotten tissues with increased pathogenic taxa (e.g., Ceratocystis and Plectosphaerella), whereas bacterial communities were more similar to healthy rhizomes and enriched in beneficial genera (e.g., Microbacterium and Variovorax). Functional prediction indicated suppressed bacterial activity and enhanced fungal saprotrophy in rotten rhizomes. The cross-kingdom network complexity decreased in both endophytic and soil microbial communities during root rot, while positive correlations within endophytic networks increased. Overall, as root rot progresses, the stability and competitive interactions within endophytic and soil microbiomes of L. chuanxiong weaken. Early in infection, endophytic bacterial and fungal communities exhibit divergent responses: bacteria likely contribute to disease resistance, whereas fungi may promote pathogenesis. This findings suggest that a more beneficial role for endophytic bacteria in controlling L. chuanxiong root rot. Restoring microbial community complexity may offer a viable biocontrol strategy. Our findings provide a theoretical foundation for future identification of specific beneficial microbes and the development of safe biocontrol approaches. creator: Weiping Gao creator: Hai Wang creator: Hongmei Jia creator: Jianyun Zhang creator: Zhuyun Yan creator: Dongmei He creator: Chuan Zheng uri: https://doi.org/10.7717/peerj.20369 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Gao et al. title: Comparative efficacy of different exercise interventions in patients with ankylosing spondylitis: a systematic review and network meta-analysis link: https://peerj.com/articles/20336 last-modified: 2025-11-25 description: BackgroundExercise interventions have been widely applied as an adjunctive treatment for ankylosing spondylitis (AS), effectively alleviating pain, improving function, and enhancing quality of life. However, the efficacy of different exercise modalities remains inconclusive. This study aims to systematically compare the effects of various exercise interventions on clinical outcomes in AS patients using a network meta-analysis (NMA) to determine the optimal exercise regimen.MethodsA comprehensive search was performed across six databases to identify studies assessing the impact of exercise interventions on AS. The primary outcomes analyzed included the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Bath Ankylosing Spondylitis Functional Index (BASFI), Bath Ankylosing Spondylitis Metrology Index (BASMI), and Ankylosing Spondylitis Quality of Life (ASQoL). A network meta-analysis was conducted using the frequentist approach in STATA 18.0, while effect publication bias analysis used Review Manager 5.4.ResultsForty-eight studies involving 3,140 participants were included, published between 2002 and 2024. Compared to the control group, all exercise interventions demonstrated varying degrees of benefit in improving BASDAI, BASFI, BASMI, and ASQoL scores. For BASDAI, the Aquatic Stretching Exercise (ASE) (−1.42, 95% CI [−2.51 to −0.33]), Land Aerobic Exercise (LAE) (−0.94, 95% CI [−1.41 to −0.47]), and Land Stretching Exercise (LSE) (−0.49, 95% CI [−0.94 to −0.04]) exhibited significant symptom relief, with ASE ranking highest (surface under the cumulative ranking curve (SUCRA) = 85.5). For BASFI, statistically significant improvements were observed with the Aquatic Aerobic Exercise (AAE) (−0.90, 95% CI [−1.50 to −0.29]), ASE (−1.74, 95% CI [−2.45 to −1.04]), LAE (−0.74, 95% CI [−1.05 to −0.43]), LSE (−0.54, 95% CI [−0.81 to −0.27]), and Muscle Exercise (ME) (−0.48, 95% CI [−0.83 to −0.13]). ASE had the highest SUCRA ranking (99.6). For BASMI, ASE (−1.06, 95% CI [−2.10 to −0.02]), LAE (−0.51, 95% CI [−1.01 to −0.01]), and the China Health Campaign (CHC) (−1.15, 95% CI [−2.18 to −0.13]) showed significant improvements, with CHC ranking highest (SUCRA = 78.7). For ASQoL, ASE (−3.67, 95% CI [−6.17 to −1.18]) and LAE (−2.64, 95% CI [−4.50 to −0.79]) demonstrated statistical significance, with ASE achieving the highest ranking (SUCRA = 88.4).ConclusionThis NMA systematically evaluated the effectiveness of different exercise interventions on clinical outcomes in AS patients. All exercise modalities provided varying degrees of benefit compared to the control group. ASE exhibited the most significant improvements in BASDAI, BASFI, and ASQoL, suggesting its superiority as an intervention. Additionally, CHC demonstrated the most significant potential for BASMI improvement. ASE is the most effective exercise modality for symptom relief, functional enhancement, and quality-of-life improvement, warranting further promotion in clinical practice. Registration PROSPERO (No. CRD42025639115). creator: Lingkui Kong creator: Chuanwen Yu creator: Chaoxin Wang creator: Zhanpeng Meng uri: https://doi.org/10.7717/peerj.20336 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kong et al. title: Coral reefs in the Mahafaly Seascape (SW Madagascar) as potential climate refugia following the 2024 mass bleaching event link: https://peerj.com/articles/20319 last-modified: 2025-11-25 description: The southwesternmost coast of Madagascar, including the Mahafaly seascape, is home to some of the country’s most ecologically and culturally important coral reefs, which remain largely understudied. These ecosystems are facing growing pressure from a panel of disturbances, with climate-induced events such as marine heatwaves being among of the causes of coral bleaching. The decline of these reefs can directly threaten the livelihoods of the local communities, who depend heavily on the resources they provide. In this context, understanding how different disturbances impact coral reef condition and recovery is critical for developing effective management strategies and conservation for this vulnerable region. This study investigates coral bleaching dynamics in the Mahafaly seascape during and after the fourth mass coral bleaching event in 2024. Six reef locations within locally managed marine areas were surveyed, comprising a total of 11 stations, with 20 one-square-meter quadrats randomly deployed at each station during each sampling period. Average hard coral densities of 18.3 and 19.3 colonies m−2 were recorded during and after the event, respectively. Bleaching prevalence peaked during the event, affecting 38.8% of coral colonies, with a marked decrease to 6.0% afterward. However, coral mortality remained relatively low across the entire seascape, with a slight post-bleaching increase in dead colonies (+3.5%). Northern sites experienced the highest thermal stress, with Beheloke and Besambay reefs being the most susceptible to bleaching, whereas Ambola exhibited remarkable resilience. In the south, Ambohibola showed low vulnerability, Lembehitake moderate susceptibility, and Itampolo the highest bleaching prevalence despite lower thermal stress. Taxa-specific patterns were also evident, with thermally sensitive branching genera being most affected, contrasting with the relative tolerance of massive and encrusting corals. The heterogeneous coral bleaching patterns observed across the seascape emphasize the importance of site- and taxa-specific monitoring to prioritize management actions where reef resilience is highest or degradation most severe. Despite bleaching severity, the results suggest that coral assemblages in the seascape have a strong capacity to recover following the event. The Mahafaly seascape reefs could serve as vital refugia in the face of climate change, underscoring the need for ongoing conservation efforts. creator: Mahery Randrianarivo creator: Solotahiana Rakotomanga creator: Fanja Razafindramasy creator: Danny Kornelio Ravelojaona creator: Tahiry Ranaivoson creator: Domoina Rakotomalala creator: Rémi Ratsimbazafy uri: https://doi.org/10.7717/peerj.20319 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Randrianarivo et al. title: Feasibility of a pulsed multiphase contrast media injection protocol in head and neck computed tomography angiography: a systematic retrospective study link: https://peerj.com/articles/20216 last-modified: 2025-11-25 description: BackgroundThis study aimed to evaluate the efficacy and value of a pulsed multiphase contrast media injection protocol in head and neck computed tomographic angiography (CTA).Information and MethodologyA total of 522 patients who underwent head and neck CTA at the Second Hospital of Qiqihar Medical University between March 1, 2022, and March 31, 2024, were reviewed. After excluding 174 patients, 348 were included in the analysis. All scans were performed using a GE Revolution computed tomography (CT) scanner (256-row detector). In the conventional group (n = 179), patients received 60 mL of contrast agent followed by 40 mL of saline. In the pulse group (n = 169), patients received an initial 35 mL of contrast agent, followed by alternating injections of five mL contrast agent and five mL saline across four additional stages, and concluded with 40 mL of saline. Images were post-processed using a GE workstation with curved planar reformation (CPR), maximum intensity projection (MIP), and volume rendering (VR). CT values, contrast-to-noise ratio (CNR), and signal-to-noise ratio (SNR) were measured for target arteries and veins. Subjective image quality was assessed using a five-point scale.ResultsThere were no significant differences in CT values, CNR, or SNR between the conventional and pulse groups. However, the pulse group showed significantly lower CT values in the subclavian vein (SCV) and superior vena cava (SVC) compared to the conventional group (P < 0.001). Both groups achieved image quality scores of three or higher, but a statistically significant difference in subjective image quality was observed (P < 0.001). Inter-rater agreement was moderate in the conventional group (Kappa = 0.573) and substantial in the pulse group (Kappa = 0.684). Radiation dose analysis revealed a significant reduction in the pulse group (P < 0.001), with mean dose-length product (DLP) and effective dose (ED) reduced by 67.58 mGy cm and 0.16 mSv, respectively.ConclusionThe pulsed multiphase contrast agent injection protocol improves image quality by reducing venous contrast residue while simultaneously lowering radiation exposure and contrast agent usage. creator: Xinghao Yang creator: Zheng Li creator: Junyao Cai creator: Lei Wu creator: Jingyue Zhang creator: Yihong Wu creator: Hua Yao creator: Shengkun Yuan creator: Yantong Tao creator: Kunrong Yu creator: Shufeng Zhu creator: Yuan Fang creator: Dongxu Wang uri: https://doi.org/10.7717/peerj.20216 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang et al. title: Microgreens: nutritional properties, health benefits, production techniques, and food safety risks link: https://peerj.com/articles/17938 last-modified: 2025-11-25 description: “Microgreens” is a hypothetical name given to a new class of edible plants that have become popular in recent years. Microgreens are plants that are larger than sprouts and smaller than baby greens, with an average height of 2–8 cm. They have some advantages, such as the microgreens are better than mature greens in terms of vitamins, minerals, antioxidants and phenolic compounds and the dense and digestible nutrient profile they contain. Microgreens appeal to vegan and vegetarian individuals and simple cultivation in a home environment. Industrial cultivation techniques are being developed under different environmental conditions to ensure that microgreens have a superior nutritional profile. Also, the current health benefits of microgreens are noteworthy. On the other hand, they may pose some food safety risks, especially due to cross-contamination which has created the need to establish suitable decontamination methods for microgreens. Microgreens have become a great topic of interest in the last 10 years, and studies in areas such as nutritional properties and health benefits, production techniques and food safety risks are increasing in the existing literature. This creates the need to bring together existing knowledge about microgreens. Therefore, the aim of this study is to conduct a very detailed literature review about microgreens. creator: Seyda Kaya creator: Hülya Yardımcı uri: https://doi.org/10.7717/peerj.17938 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kaya and Yardımcı title: Elemental pollution and risk assessment of soils and Gundelia tournefortii in a multi-sector industrial zone with a history of agricultural use link: https://peerj.com/articles/20374 last-modified: 2025-11-24 description: The study provides new insights into elemental enrichments in soil and Gundelia tournefortii (GT) parts in a complex land use region where intensive agricultural activities were carried out in the past and 343 industrial facilities from various sectors have been operating for the last 32 years. The levels of crustal elements (aluminum (Al), iron (Fe), potassium (K), sodium (Na), titanium (T)), heavy metals (cadmium (Cd), chromium (Cr), copper (Cu), manganese (Mn), nickel (Ni), lead (Pb), zinc (Zn)), sulfer (S) and phosphorus (P) were determined in the sample matrices, their possible sources and the health risks associated with their human consumption were investigated. Significant enrichments in Cr, Ni, Pb, and Zn were observed in the soils, with the exceptionally high Pb enrichment (EF: 81.34) being noteworthy. The soil pollution index values (PI:2.06–6.82) confirm significant anthropogenic contamination. Bioconcentration factors (BCF) for Cu, K, Na, Mg, P and S were found to be >1 in all roots and stems, Zn showed high accumulation in all roots and most stems, while Cd, Cr, Pb and Mn accumulated in a more limited number of samples. Principal component analysis (PCA) showed that the elements found in the geochemical composition of the region and those representing agricultural chemicals used throughout the long agricultural history overlap and form clusters that cannot be fully separated, while the analysis of the datasets from GT parts yielded similar results. However, the effects of industrial emissions and solid fuel use were clearly evident in the GT root and stem samples. High Nemerow Compound Pollution Index values (NCPIs) indicated contamination in plant parts. Estimated daily intake (EDI) values for Cu and Mn exceeded the tolerable upper intake level (TUIL) for children in many root and stem samples, while EDI values for Cr, Fe, and Zn also exceeded the limit value in several samples. Risk assessments for non-carcinogenic effects showed that numerous samples surpassed the safety limit for children as a result of elevated levels of Cr, Cu, Pb, Zn, Fe and Mn. Estimates for carcinogenic risk (CR) suggested that Cd and Cr in the majority of samples, along with Ni in some samples, could pose a lifetime cancer risk for children. The results reveal that geogenic influences, as well as pressures from past agricultural production and current industrial and fossil fuel-related pressures, are evident on the region’s soils and GT crops. The accumulation of toxic elements in edible plant parts poses a risk to food security, necessitating detailed risk assessments. The findings provide a scientific basis for land-use planning and agricultural management, emphasizing the importance of effective emissions monitoring, agricultural production in areas away from polluting sources, and implementing stricter land-use policies for protecting the environment and public health. creator: Ayşenur Özuysal creator: Fariborz Fadaeivash creator: Görkem Akıncı uri: https://doi.org/10.7717/peerj.20374 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Özuysal et al. title: Bioinformatics-based identification of RAS disequilibrium involved in post-hemorrhagic shock mesenteric lymph return-mediated acute kidney injury in mice link: https://peerj.com/articles/20359 last-modified: 2025-11-24 description: Post-hemorrhagic shock mesenteric lymph (PHSML) return plays a critical role in the development of acute kidney injury (AKI). However, the molecular mechanism underlying PHSML-mediated AKI remains unclear. In this study, bioinformatics analysis identified key common targets of hemorrhagic shock and AKI, revealing significant enrichment in the renin-angiotensin system (RAS). To further investigate the role of RAS in PHSML-mediated AKI, we established mesenteric lymph duct ligation (MLDL) technology in mice and confirmed that MLDL alleviated hemorrhagic shock-induced AKI. Subsequently, male C57BL/6 mice subjected to hemorrhagic shock were treated with the angiotensin converting enzyme (ACE) inhibitor enalapril, angiotensin (1-7) (Ang (1-7)), and angiotensin II (Ang II) type 1 receptor (AT1R) inhibitor losartan. Additionally, mice with hemorrhage and MLDL were treated with Ang II, the Mas receptor (MasR) inhibitor A-779, or subjected to Ace2 knockout. Renal histomorphology, expression of ACE, ACE2, AT1R, and MasR, and levels of Ang II and Ang (1-7) were assessed 4 h after resuscitation. The results demonstrated that hemorrhagic shock upregulated ACE and AT1R, while downregulating ACE2 and MasR, accompanied by elevated Ang II and reduced Ang (1-7). These adverse effects were partially reversed by MLDL, enalapril, Ang-(1-7), or losartan. Conversely, the beneficial role of MLDL was abolished by Ace2 deficiency and the administration of Ang II and A-779. Collectively, these findings indicate that disequilibrium between the ACE-AngII-AT1R and ACE2-Ang (1-7)-MasR axes is implicated in PHSML-mediated AKI. creator: Yujie Jin creator: Jing Wang creator: Shaoxuan Wang creator: Yuting Li creator: Kun Su creator: Niuniu Feng creator: Huibo Du creator: Limin Zhang creator: Xiuhong Yang creator: Chun-Yu Niu creator: Zi-Gang Zhao uri: https://doi.org/10.7717/peerj.20359 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Jin et al.