title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=105 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Association of chromosomal aberrations in chromosomes 3 and 7, and P16 mutations with malignancy in salivary gland tumors link: https://peerj.com/articles/19217 last-modified: 2025-03-31 description: BackgroundSalivary gland tumors, a prevalent type of head and neck neoplasm, exhibit significant morphological diversity and overlapping features, complicating pathological diagnosis. Although fluorescence in situ hybridization (FISH) is widely used for tumor detection, its diagnostic utility in salivary gland tumors remains unclear. This study aimed to explore a novel FISH-based approach to differentiate benign from malignant salivary gland tumors.MethodsGene probes (CSP3, CSP7, and GSP P16) were designed to detect P16 gene deletion, and polysomies of chromosomes 3 and 7. The FISH analysis was conducted on 22 malignant and 12 benign salivary gland tumor samples with complete clinical data. The study was expanded to 78 samples for further validation.ResultsThe CSP3, CSP7, and GSP P16 probes exhibited high specificity for salivary gland tumors, though CSP7 exhibited lower sensitivity. The combination of CSP3 and GSP P16 probes outperformed single-probe analysis or other probe combinations.ConclusionThe CSP3 and GSP P16 probe combination provides a highly sensitive and specific method for distinguishing malignant from benign salivary gland tumors. creator: Yanxia Wu creator: Zhiyue Xie creator: Nan Peng creator: Rui Zhou creator: Liang Zhao uri: https://doi.org/10.7717/peerj.19217 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wu et al. title: Effectiveness of dexmedetomidine as a premedication for pediatric patients undergoing outpatient dental surgery under general anesthesia-systematic review and meta-analysis link: https://peerj.com/articles/19216 last-modified: 2025-03-31 description: Pediatric patients undergoing outpatient dental surgery often exhibit instinctive resistance and fear in face of the unknown, which in turn creates obstacles to subsequent treatment. Appropriate sedation can increase compliance, decrease the incidence of adverse events, and lead to improved treatment outcomes. To evaluate the effectiveness of dexmedetomidine as pre-medication in children undergoing tooth extraction with general anesthesia, we searched databases including the Medline, Embase and Cochrane library for eligible trials. Randomized controlled trials of dexmedetomidine for premedication vs. placebo or midazolam in pediatric patients were included, while trials involving children having dental treatment under local anesthesia were excluded. Two review authors independently participated in the inclusion of trials and assessment of bias. Decisions were made based on group discussion. We finally included seven trials in this review, with a total of 496 pediatric patients. Three of the included trials compared dexmedetomidine with placebo. A meta-analysis indicated that dexmedetomidine was effective for preoperative sedation and for preventing emergence delirium; two of these studies reported no incidences of bradycardia and hypoxemia during study observation period. Four trials compared dexmedetomidine with midazolam, meta-analysis of these four trials gave risk ratios (RR) for successful parental separation, satisfactory mask acceptance and emergence delirium rate of 1.26 (95% CI [0.86–1.84]); 1.07(95% CI [0.94–1.22]); −0.18(95% CI [−0.29 to −0.07]), respectively. Only one study reported complications arising from administration of premedication. Based on the current evidence, we can conclude that the dexmedetomidine appears to be an effective premedication, offering the advantage of reducing the incidence of postoperative delirium compared to midazolam. However, high-quality clinical trials with larger sample sizes are needed to determine the selection of different medication modes and doses, as well as to study perioperative adverse reactions. creator: Xiao Zhang creator: Ze Fan creator: Danyi He creator: Yang Liu creator: Xiaotong Shi creator: Haopeng Zhang uri: https://doi.org/10.7717/peerj.19216 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Temporal and spatial distribution of histone acetylation in mouse molar development link: https://peerj.com/articles/19215 last-modified: 2025-03-31 description: Histone acetylation is one of the most widely studied histone modification, regulating a variety of biological activities like organ development and tumorigenesis. However, the role of histone acetylation in tooth development is poorly understood. Using the mouse molar as a model, we mapped the distribution patterns of histone H3 and H4, as well as their corresponding acetylation sites during tooth formation in order to unveil the connection between histone acetylation modification and tooth development. Moreover, key histone acetyltransferases and histone deacetylases were detected in both epithelial and mesenchymal cells during tooth development by scRNA-seq and immunohistochemistry. These results suggest that histone acetylation modification functions as an important mechanism in tooth development at different stages. creator: Wen Du creator: Wanyi Luo creator: Liwei Zheng creator: Xuedong Zhou creator: Wei Du uri: https://doi.org/10.7717/peerj.19215 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Du et al. title: A novel simple immunoassay for quantification of blood anti-NMDAR1 autoantibodies link: https://peerj.com/articles/19212 last-modified: 2025-03-31 description: Low titers of blood circulating anti-NMDAR1 autoantibodies have been reported in a significant subset of the general human population. Currently, immunohistochemical staining and cell-based assays are the standard methods for their detection and semi-quantification. However, detection and quantification of these low titers of blood circulating anti-NMDAR1 autoantibodies are problematic because of high non-specific background. Development of a new method to more accurately quantify these low titers of blood anti-NMDAR1 autoantibodies will facilitate studies on their potential impacts on psychiatric symptoms and cognition. We previously reported a robust production of anti-NMDAR1 autoantibodies against the ligand binding domain of NMDAR1. As a proof of principle, we report the development of a novel simple immunoassay for quantification of cross-species blood anti-NMDAR1 autoantibodies and its validation with immunohistochemistry and cell-based assays in both humans and mice. Specificity of our quantification was also investigated. creator: Melonie Vaughn creator: Susan Powell creator: Victoria Risbrough creator: Xianjin Zhou uri: https://doi.org/10.7717/peerj.19212 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Vaughn et al. title: Microecological recombination of Angelica sinensis driven by the transplanting of “alpine seedling–cellar planting–dam cultivation” link: https://peerj.com/articles/19208 last-modified: 2025-03-31 description: Transplanting is important for obtaining and maintaining excellent germplasm of cultivated plants. During plant transplantation, the endophytic microbial community regularly reorganizes, which may be crucial for plant germplasm rejuvenation. Angelica sinensis, a widely used medicinal and edible plant, relies on transplanting for its exceptional quality. To explore the microecological recombination of A. sinensis during the transplanting process of “alpine seedling–cellar planting–dam cultivation”, this study analyzed shifts in endophytic and soil microbial communities across the three transplanting stages in Min County, Gansu Province, China. High-throughput sequencing revealed significant changes, with 82.27% to 84.65% of bacteria and 93.19% to 93.49% of fungi species altering in transplanted Angelica. Main findings indicate that Mortierellomycota, Actinobacteriota, and Myxococcota were dominant in cellar planting root and cellar rhizosphere soil, contrasting with Firmicutes predominance in alpine and dam areas. Notably, potentially pathogenic endophytes like Fusarium and Xanthomonas decreased post-alpine seedling and cellar planting, favoring a healthier plant environment. Cellar planting root exhibited a rich accumulation of psychrophilic flora, including Tetracladium, Pseudomonas, and Flavobacterium, alongside a unique dominance of Mortierella fungi. Microbial co-occurrence network analysis highlighted cellar planting root as pivotal, suggesting its importance in microbial interactions. In conclusion, transplanting significantly reshaped A. sinensis’s endophytic flora, with fungi showing more pronounced recombination than bacteria. Soil microbial communities emerged as crucial drivers of this recombination, facilitating the overwintering of A. sinensis, reducing diseases, and rejuvenating the germplasm. Transplanting-driven microecological reorganization is an important scientific mechanism for the high-quality production of cultivated medicinal plants. creator: Dongmei He creator: Weiping Gao creator: Zhanling Zhang creator: Jinniu Xing creator: Guiqi Han creator: Hai Wang creator: Zhuyun Yan uri: https://doi.org/10.7717/peerj.19208 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 He et al. title: Predictive factors associated with acute radiation dermatitis in patients with breast cancer: a retrospective cohort study link: https://peerj.com/articles/19202 last-modified: 2025-03-31 description: BackgroundRadiation therapy (RT) is a primary postsurgical treatment for breast cancer; however, it can cause acute radiation dermatitis (ARD), which can severely impair quality of life. The aim of this study was to identify predictive factors associated with moderate to severe ARD.Materials and MethodsIn this retrospective analysis, we utilized data from Chulabhorn Hospital’s Health Information System that was collected between January 2017 and December 2022. A radiation oncology specialist assessed ARD in a cohort of 635 patients using the Radiation Therapy Oncology Group (RTOG) ARD grading scale. The patients were classified into two groups based on the maximum grade recorded: mild (grade < 2) and moderate to severe (grade ≥ 2). Various factors were examined, including demographic characteristics (age, body mass index (BMI), comorbidities) and treatment-related variables (surgical history, adjuvant chemotherapy, hormone therapy, targeted therapy, fractionation, boost treatments, and bolus application). Logistic regression was used to perform the statistical analysis.ResultsAmong the 635 patients, the average age was 54.2 ± 10.9 years, and 32% were classified as having moderate to severe ARD. Multiple logistic regression analysis identified BMI ≥ 30 kg/m2 (adjusted odds ratio (AOR) = 2.33; 95% confidence interval (CI) [1.36–3.98]; p-value = 0.002), localized boost treatments (AOR = 2.09; 95% CI [1.08–4.06]; p-value = 0.029), and bolus application (AOR = 2.08; 95% CI [1.02–4.24]; p-value = 0.044) as significant risk factors for moderate to severe ARD. Conversely, hypofractionated RT (AOR = 0.31; 95% CI [0.16–0.57]; p < 0.001) and hormonal therapy (AOR = 0.60; 95% CI [0.42–0.86]; p-value = 0.005) were associated with a decreased risk. However, radiation to both the primary site and regional lymph nodes (AOR = 0.81; 95% CI [0.41–1.59]; p-value = 0.538) and targeted therapy (AOR = 0.72; 95% CI [0.43–1.20]; p-value = 0.210) did not significantly affect the risk of moderate to severe ARD.ConclusionsWe have identified key risk factors for moderate to severe ARD, including obesity and treatment modalities such as localized boost treatments and bolus application. Hormone therapy and hypofractionated RT appear to reduce ARD severity. These findings have implications for the development of treatment plans and the mitigation of the risk of ARD in patients undergoing RT. creator: Rattanaporn Nanthong creator: Sunanta Tungfung creator: Kamonwan Soonklang creator: Wiriya Mahikul uri: https://doi.org/10.7717/peerj.19202 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Nanthong et al. title: Evaluation of optic nerve sheath diameter in acute stroke: pre- and post-thrombolytic assessment link: https://peerj.com/articles/19197 last-modified: 2025-03-31 description: BackgroundIntracranial pressure increases due to ischemic infarction caused by stroke. This study aimed to evaluate the pre-thrombolytic and post-thrombolytic optic nerve sheath diameter (ONSD) measurements in predicting clinical outcomes and complications for stroke patients.MethodsONSD was measured on computed tomography (CT) scans. The average ONSD (aONSD) was calculated from the right and left eyes. Pre-thrombolytic (ONSD-0) and post-thrombolytic (ONSD-24) values were compared according to right vs left eye, stroke-affected side of the brain, presence of complications, and mortality.ResultsNinety-three patients were enrolled; 52.7% were female, and the mean age of all participants was 76 years. The aONSD-24 values were higher than the aONSD-0 values (5.5 ± 0.7 mm and 5.3 ± 0.7 mm, respectively, p < 0.001). There was no significant difference between right and left measurements (right ONSD-0 5.3 mm vs. left ONSD-0 5.3 mm, p = 0.257; right ONSD-24 5.6 mm vs. left ONSD-24 5.5 mm, p = 0.146; and ∆right ONSD 0.23 mm vs. ∆left ONSD 0.22, p = 0.717) and between the stroke-affected side and non-stroke-affected side measurements (stroke-affected ONSD-0 5.2 mm vs. non-stroke-affected ONSD-0 5.2 mm, p = 0.292; stroke-affected ONSD-24 5.5 mm vs. non-stroke-affected ONSD-24 5.4 mm, p = 0.124; and ∆stroke-affected ONSD 0.23 mm vs. non-∆stroke-affected ONSD 0.23 mm, p = 0.569). Intracranial complications occurred in 14 (15%) patients. There was no difference in ONSD values between patients with and without complications (p = 0.338 for aONSD-0, p = 0.216 for aONSD-24, and p = 0.902 for ∆a ONSD). There was no significant difference between the aONSD-0 and aONSD-24 values of surviving and non-surviving patients (aONSD-0: 5.3 ± 0.7 vs. 5.0 ± 0.5, p = 0.345; aONSD-24: 5.5 ± 0.7 vs. 5.3 ± 0.4, p = 0.522; and p = 0.386 for ∆ aONSD).ConclusionsONSD values on 24-h brain CT scans were higher than admission values in acute stroke patients receiving thrombolytic therapy, irrespective of the right or left side, stroke-affected side, presence of complications, and mortality. However, ONSD is not a sufficient parameter for predicting complications and death. creator: Erdem Sivas creator: Nese Colak creator: Basak Bayram creator: Muhammet Kursat Simsek creator: Nuri Karabay creator: Vesile Ozturk uri: https://doi.org/10.7717/peerj.19197 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sivas et al. title: Rapid detection and quantification of Nile Red-stained microplastic particles in sediment samples link: https://peerj.com/articles/19196 last-modified: 2025-03-31 description: The distribution and migration processes of microplastics (MPs) in the marine sediments have yet to be fully elucidated. To estimate the contamination levels and distribution patterns, and develop countermeasures, the amount of MPs must be understood. Rapid and efficient processing of numerous samples is also needed to detect and determine MP contamination. However, whatever the sample of interest, MP analysis is time consuming. This is especially the case for deep-sea sediments, where the particle sizes are small and pretreatment processes are complex and time-consuming. To address the need for rapid and efficient detection of MPs, we propose a novel method for automatically identifying and counting Nile Red (NR)-stained sedimentary MP particles captured under a stereoscopic fluorescence microscope. In this study, we demonstrated the utility of the developed system by comparing its recovery rate and analysis time with those of the conventional methods used for manual processing. The developed method can efficiently detect MPs of sizes between 18 and 500 µm and classify them as fibers or grains (or fragments). This means that our method can efficiently detect MPs as small as 100 µm found in deep-sea sediments. The semi-automated MP detection system gave a counting time of 4.2–8.8 s per particle—as the number of particles increases, the analysis time per particle decreases. Similarly, when the number of particles counted using a stereomicroscope and image analysis software was set at 100, the automatic measurement method using a flow cell could measure 50−80% of the total number of particles, depending on the type of MPs. By using artificial particulate and fibrous MPs as training data and combining them with a machine learning system, we were able to build a system that can classify both types with 98% accuracy (100% for fibers and 96% for grains). In natural samples, approximately 150 µm (20–350 µm in range) MPs were detected, and the number was consistent with previous studies. This demonstrates the effectiveness of the method we developed. We established a rapid detection method for the number and form of MPs using a continuous semi-automated method, combining NR staining and artificial intelligence. Although this method does not allow the identification of polymer types, it enables that rapid and reliable quantification of MPs numbers. The new method established in this study is expected to improve the accuracy of information on the distribution, destination, and quantity of MPs. It is also relatively easy to use and can transfer technology in various fields, from citizen science to rapid diagnosis on research vessels in the open ocean. creator: Masashi Tsuchiya creator: Tomo Kitahashi creator: Yosuke Taira creator: Hitoshi Saito creator: Kazumasa Oguri creator: Ryota Nakajima creator: Dhugal J. Lindsay creator: Katsunori Fujikura uri: https://doi.org/10.7717/peerj.19196 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Tsuchiya et al. title: Performance comparison of QuantiFERON-TB Gold In-Tube and QuantiFERON-TB Gold Plus in detecting Mycobacterium tuberculosis infection among HIV patients in China link: https://peerj.com/articles/19195 last-modified: 2025-03-31 description: IntroductionNo direct comparative study assessing QuantiFERON-TB Gold In-Tube (QFT-GIT) and QuantiFERON-TB Gold Plus (QFT-Plus) for Mycobacterium tuberculosis infection among persons living with HIV (PLHIV) in China has been conducted.MethodsSimultaneous QFT-GIT and QFT-Plus tests were conducted on PLHIV in a prison hospital. Positivity and negativity results from both assays were compared, and their diagnostic agreement was assessed.ResultsA total of 232 PLHIV individuals were included in this study. Among them, 57 patients (24.6%) and 56 patients (24.1%) were diagnosed with Mycobacterium tuberculosis infection based on QFT-GIT results and QFT-Plus, respectively. The overall agreement between the two assays was 98.3%, with a Cohen’s kappa value of 0.954. Consistency rates were observed between QFT-GIT plus, QFT-Plus TB1 and TB2 with QFT-GIT were 98.3%, 97.4% and 97.8%. The IFN-γ levels measured in QFT-GIT were found to surpass those in QFT-Plus TB1 (P = 0.04), while the difference compared to QFT-Plus TB2 exhibited a marginal trend (P = 0.134). Among the subgroup of 52 individuals who underwent dual QFT-GIT tests, a significant proportion of 23.1% (12 individuals) experienced a change in their QFT-GIT results, transitioning from a positive to a negative outcome.ConclusionsThe diagnostic performance of QFT-GIT and QFT-Plus for Mycobacterium tuberculosis infection among PLHIV with relatively higher CD4 counts was found to be comparable. Additionally, our investigation revealed that irrespective of the treatment regimen, whether it involved chemotherapy or immunotherapy, preventive Mycobacterium tuberculosis infection interventions among PLHIV consistently led to a reduction in IFN-γ levels. creator: Peng Lu creator: Haitao Yang creator: Fang Ge creator: Kai Wu creator: Yilin Lian creator: Xiaoyan Ding creator: Jingjing Pan creator: Hui Ding creator: Wei Lu creator: Qiao Liu creator: Limei Zhu uri: https://doi.org/10.7717/peerj.19195 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lu et al. title: The relationship between MAPK signaling pathways and osteogenic differentiation of periodontal ligament stem cells: a literature review link: https://peerj.com/articles/19193 last-modified: 2025-03-31 description: Periodontitis is a common oral disease that can lead to gingival inflammation, development of periodontal pockets, resorption of the alveolar bone, and the loosening and eventual loss of teeth. The optimal outcome of periodontitis treatment is maximum regeneration and functional reconstruction of periodontal tissues after control of infection and elimination of inflammation. Since both the self-healing ability of alveolar bone and the efficacy of traditional treatment methods are very limited, stem cell-based tissue regeneration engineering has received more and more attention from scholars. The best cells for periodontal tissue regeneration have been well examined, and these are called periodontal ligament stem cells (PDLSCs). The MAPK signaling pathways, including the ERK1/2, p38 MAPK, JNK, and ERK5 signaling pathways, are very complex and highly conserved tertiary kinase signaling pathways. These pathways are closely related to the osteogenic differentiation of PDLSCs, and this paper provides an overview of the research on the MAPK signaling pathways and the osteogenic differentiation of PDLSCs. creator: Xuanning Liu creator: Wanqing Zhao creator: Yanhui Peng creator: Na Liu creator: Qing Liu uri: https://doi.org/10.7717/peerj.19193 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liu et al.