title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=103 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Contrast in the density and biomass of fish in a reef system with different fishing intensity in the Mexican Caribbean link: https://peerj.com/articles/19031 last-modified: 2025-04-04 description: A wide range of fish species are caught in reef fisheries. However, fishing efforts tend to be highly selective in favor of large species, which generally have low population growth rates, making them more vulnerable to overfishing. When the decline of large predators occurs, fishing efforts start to focus on catching species from lower trophic levels, which can cause a trophic cascade effect. The objective of this research was to detect changes in the density and biomass of fish communities in areas with different fishing intensity in the study area. This study was carried out in the Banco Chinchorro Biosphere (BCBR) in the Mexican Caribbean and analyze the effect of fishing intensity on fish density and biomass, comparing data obtained from visual censuses with dependent information of the fishery. Evidence was found of a relationship between high fishing exploitation and low levels of density and biomass for Epinephelus striatus, E. guttatus and Lachnolaimus maximus. The decline of predators had no evident effect on the density and biomass of non-commercially important species. The density and biomass of commercially important fish species were influenced by the presence of algae, octocorals, hydrocorals and by variations in their catch per unit of effort (CPUE). This study detected that density and biomass have decreased in some species belonging to the Serranidae and Lutjanidae families in areas with high fishing intensity. On the other hand, little evidence was found that the density and total biomass of families of noncommercially important species increased through the decline of their predators. These results are consistent with previous work documenting how fishing activity affects fish species with high trophic levels. The information generated will help the Reserve’s managers make decisions towards better management and conservation of fishery resources. creator: José Manuel Castro-Pérez creator: Carmen Amelia Villegas-Sánchez creator: Alejandro Medina-Quej creator: Rigoberto Rosas-Luis creator: Jesús E. Arias-González uri: https://doi.org/10.7717/peerj.19031 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Castro-Pérez et al. title: Implications of high-dose vitamin D3 with and without vitamin C on bone mineralization and blood biochemical factors in broiler breeder hens and their offspring link: https://peerj.com/articles/18983 last-modified: 2025-04-04 description: As broiler breeder hens age, they often experience a decline in bone mineralization and calcium absorption, especially during the later stages of egg production. This issue not only affects the hens’ health, making them more prone to conditions like osteoporosis, but it also impacts the quality of their offspring. To tackle this problem, our study explores whether supplementing these hens with a combination of vitamins D3 and C could help improve their bone health and overall biochemical balance, both for them and their progeny. The goal of this research was to evaluate the effects of high doses of vitamin D3, with and without added vitamin C, on bone mineralization and key blood parameters in aging broiler breeder hens and their offspring. In this experiment, 240 hens and 24 roosters from the Ross 308 strain, aged between 49 and 61 weeks, were used, and a two-way ANOVA (2 × 2) design was applied. This involved two levels of vitamin D3 (3,500 IU and 5,500 IU) and two levels of vitamin C (0 and 150 mg/kg), with six replications of 10 hens and one rooster per group. At the end of the study, blood samples were collected from hens and their offspring for biochemical analysis, and tibia bones were taken for ash content and mineralization assessment. The findings showed that vitamin D3 supplementation significantly lowered blood cholesterol, alkaline phosphatase (ALP), and parathyroid hormone (PTH) levels (P < 0.05), while boosting calcium, 25-hydroxycholecalciferol (25(OH)D3), and 1,25-dihydroxycholecalciferol (1,25(OH)2D3) (P < 0.05). Higher doses of vitamin D3 also improved the strength, resistance, and ash content of the hens’ tibia bones, and increased calcium in the carcasses of their offspring. Adding 150 mg/kg of vitamin C to the diet also had a positive effect, reducing cholesterol, ALP, and PTH, while enhancing plasma calcium, total antioxidant capacity, and the active form of vitamin D3 (P < 0.05). Vitamin C supplementation significantly strengthened the tibial bones of the hens and improved plasma calcium and PTH levels in their offspring (P < 0.05). Interestingly, combining elevated doses of both vitamins D3 and C resulted in even greater improvements in tibial bone strength (P < 0.05). In conclusion, giving hens 150 mg of vitamin C along with 5,500 IU of vitamin D3 leads to substantial improvements in the calcium content and structural integrity of their bones, and also boosts calcium and ash content in the carcasses of their offspring. creator: Ruhollah Kianfar creator: Reza Kanani creator: Hossein Janmohammadi creator: Majid Olyaee creator: Maghsoud Besharati creator: Maximilian Lackner uri: https://doi.org/10.7717/peerj.18983 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kianfar et al. title: Saudi radiology trainees’ insights on safety and professionalism in the workplace link: https://peerj.com/articles/19257 last-modified: 2025-04-03 description: Introduction/PurposeIn the radiology department, where advanced technologies and multidisciplinary collaboration are crucial, establishing a strong safety culture is particularly challenging. The present cross-sectional study examines the challenges of establishing a safety culture in radiology, focusing on how Saudi radiology trainees perceive and respond to safety and unprofessional conduct. It evaluates their willingness to voice concerns and the influencing factors, including workplace culture, potential patient risks, and demographics.MethodsThe present study surveyed Saudi radiology residents and interns at two tertiary hospitals using a validated questionnaire. A non-probability total population purposive sampling method was employed. Descriptive statistics, Mann-Whitney U test, and Kruskal-Wallis H test were used to analyze differences in willingness to speak up across demographic groups.ResultsParticipants felt encouraged by colleagues to address patient safety and unprofessional behavior, with over 70% and 56% respectively agreeing. Residents demonstrated significantly greater support for raising concerns about safety and unprofessional conduct compared to interns (mean rank = 47.58 vs. 33.91, p = 0.009). Furthermore, residents expressed a stronger belief that speaking up leads to meaningful changes (mean rank = 46.24 vs. 35.36, p = 0.033) and reported observing others addressing these issues more frequently (mean rank = 46.98 vs. 34.56, p = 0.015). Trainees from different hospitals exhibited significantly varied perceptions regarding support from colleagues in addressing patient safety and unprofessional behavior (mean rank = KAMC 54.53 vs. KSMC 33.04, p < 0.0001), the perceived impact of raising concerns (mean rank = KAMC 50.50 vs. KSMC 35.41, p = 0.004), and the frequency of observing these concerns being addressed (mean rank = KAMC 55.28 vs. KSMC 32.60, p < 0.0001). Radiology trainees are particularly vigilant about unintentional breaches of sterile technique, often addressing these issues with nurses (66.7%).ConclusionThe clinical environment supports safety concerns but less so for unprofessional behavior, with residents being more proactive. Promoting open communication in radiology requires leadership education, multifaceted strategies, alternative channels for concerns, and future research to assess and track cultural attitudes. The findings highlight the need to cultivate a supportive culture for speaking up in clinical settings, particularly in radiology, where trainee involvement can enhance patient safety and professional conduct. The present study lays the groundwork for future research and interventions to strengthen safety and professionalism among medical trainees in Saudi Arabia. creator: Khalid M. Alshamrani creator: Elaf K. Basalamah creator: Ghadah M. AlQahtani creator: Manar M. Alwah creator: Rahaf H. Almutairi creator: Walaa Alsharif creator: Awadia Gareeballah creator: Adnan AS Alahmadi creator: Shrooq T. Aldahery creator: Sultan A. Alshoabi creator: Abdulaziz A. Qurashi uri: https://doi.org/10.7717/peerj.19257 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Alshamrani et al. title: Tumor marker elevations in chronic kidney disease: a retrospective study link: https://peerj.com/articles/19240 last-modified: 2025-04-03 description: AimTo investigate the changes in tumor markers such as carbohydrate antigen 125 (CA125), carbohydrate antigen 153 (CA15-3), carbohydrate antigen 19-9 (CA19-9), carbohydrate antigen 72-4 (CA72-4), pro-gastrin-releasing peptide (proGRP), and human epididymis protein 4 (HE4) in patients with chronic kidney disease (CKD) as compared to healthy individuals, and to analyze the potential indicators that can be utilized for monitoring early renal dysfunction, was the aim of this study.MethodsThis retrospective study involved 522 participants from our hospital, including 172 patients with CKD and 350 controls. CKD patients were divided into CKD1, CKD2, CKD3, CKD4, and CKD5 stages according to the estimated glomerular filtration rate (eGFR). Plasma creatinine and general clinical data were collected upon admission.ResultsThe level of tumor biomarkers, including carcinoembryonic antigen (CEA), CA125, CA15-3, CA19-9, NSE, proGRP, and HE4, were elevated in patients with CKD (p < 0.05). There were differences in CEA, CA125, CA19-9, NSE, proGRP, and HE4 between the control and CKD groups. The subgroup study showed that CEA, CA15-3, CA19-9, NSE, proGRP, and HE4 were elevated in patients with CKD having normal serum creatinine compared with those in the control group (p < 0.05). ProGRP and HE4 have high predictive values for early renal insufficiency with area under the curve of 0.736 and 0.931, respectively (p < 0.05). Furthermore, HE4 and proGRP were positively correlated with the stages of CKD, with correlation coefficients of 0.623 and 0.712, respectively.ConclusionsPatients with CKD have higher tumor markers, some of which are helpful for the early diagnosis of renal impairment. creator: Liuxia You creator: Zhongying Xu creator: Qiaoling Liu creator: Guoming Jin creator: Changting Wang uri: https://doi.org/10.7717/peerj.19240 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 You et al. title: A multi-center cross-sectional investigation of BRAF V600E mutation in Ameloblastoma link: https://peerj.com/articles/19137 last-modified: 2025-04-03 description: BackgroundB-Raf proto-oncogene, serine/threonine kinase (BRAF) V600E mutation stands as a pivotal genetic alteration strongly associated with several neoplasms and contributes significantly to their pathogenesis as well as potential targeted treatment strategies.ObjectiveThis cross-sectional study aimed to determine the frequency of BRAF V600E mutation in ameloblastoma in a multi-center of Thailand.MethodAnti-BRAF V600E (clone VE1) immunohistochemistry was performed on 227 conventional ameloblastoma (AM) and 113 unicystic ameloblastoma (UA) samples collected from four major dental schools located in the Central, North, South, and Northeast regions of Thailand. Tumor cells from randomly chosen AM cases were also micro-dissected from the FFPE sections and subjected to DNA sequencing to confirm the immunohistochemical results.ResultsBRAF V600E mutation was detected in 71.8% of the AM samples, while 65.5% of samples with UAs demonstrated BRAF V600E positivity. The BRAF V600E mutation was significantly different in the histological subtypes of AMs in the four centers (p = 0.012) and the location of UA in three centers (p = 0.013). There was no significant association between the BRAF V600E mutation and the location of ameloblastoma in the overall prevalence of our multi-center study; nonetheless, a statistically significant association was found between the BRAF V600E mutation and the mandible location of AMs from the Central Faculty of Dentistry, Mahidol University (MU) center (p = 0.033), as well as with the histological subtypes of AMs from the Southern Faculty of Dentistry, Prince of Songkla University (PSU) center (p = 0.009). No statistical association was observed between the BRAF V600E mutation and AM and UA recurrence (p = 0.920 and p = 0.312), respectively. The results of DNA sequencing performed in randomly selected 40 BRAF V600E-positive and 20 BRAF V600E-negative ameloblastoma tissues were in accordance with the immunohistochemical findings.ConclusionAs a result of a notable prevalence of BRAF V600E in Thai individuals diagnosed with ameloblastoma, they may benefit from the utilization of adjunctive anti-BRAF targeted therapy for treatment. creator: Khin Mya Tun creator: Puangwan Lapthanasupkul creator: Anak Iamaroon creator: Wacharaporn Thosaporn creator: Poramaporn Klanrit creator: Sompid Kintarak creator: Siwaporn Thanasan creator: Natchalee Srimaneekarn creator: Nakarin Kitkumthorn uri: https://doi.org/10.7717/peerj.19137 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tun et al. title: Advanced superimposition method to evaluate the marginal and internal fit of ceramic crowns fabricated using heat pressing techniques link: https://peerj.com/articles/19117 last-modified: 2025-04-03 description: BackgroundDigital technologies can enhance the success of permanent crowns. The present study aimed to evaluate marginal adaptation and internal fit of permanent crowns fabricated using stereolithography (SLA) and digital light processing (DLP) 3D printing technologies following scans using two different intraoral scanners (IOS) (Medit i700, shape (TRIOS 3)).MethodsThree typodont #14 teeth were prepared for full veneer all ceramic crowns with three types of margins—chamfer (CFL), rounded shoulder (RSFL) and rounded shoulder with bevel (RSBFL). A total of 360 study models were made and divided into two groups based on the type of intraoral scanner used for digital impressions. Group A in which the intraoral scanner MEDIT i700 was used, and Group B in which intraoral scanner TRIOS 3 was used (n = 360/group). The subgroups were made as Medit i700-SLA, Medit i700-DLP, TRIOS 3-SLA and TRIOS 3-DLP (n = 180/subgroup). These were further divided into three sub-subgroups based on the finish lines: CFL, RSFL, and RSBFL (n = 30 each sub-subgroups). All ceramic crowns were made on models and scanned to assess discrepancies (marginal adaptation and internal fit) at nine zones (Z1–Z9). Three-way analysis of variance and pairwise comparison was done (Tukey HSD test) (α = 0.05).ResultsThe mean marginal gap and internal fit values were lowest for Group A-1 with RSBFL in each zone. The intergroup comparison showed values for marginal gap and the internal fit were minimum for Group A-1 for each finish line design, with the lowest for RSBFL at zone Z2 0.04 ±0.001.ConclusionsRegardless of the IOS and 3D printing techniques, the smallest gap was observed in RSBFL, followed by RSFL and CFL. The all-ceramic crowns fabricated using a Medit intraoral scanner with an SLA 3DPrinter with a rounded shoulder finish line had the best marginal and internal fit. creator: Nasser M. Alqahtani creator: Saurabh Chaturvedi creator: Mohamed Khaled Addas creator: Manar Fahad A. AlQahtani creator: Arwa Ahmed M. Alhudiry creator: Shahrah H. Qahtani creator: Mohammad A. Zarbah creator: Asim Elsir Elmahdi creator: Marco Cicciù creator: Giuseppe Minervini uri: https://doi.org/10.7717/peerj.19117 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alqahtani et al. title: Evaluation of non-invasive hair snares for North American beavers (Castor canadensis): placement, efficiency, and beaver’s behavioral response link: https://peerj.com/articles/19080 last-modified: 2025-04-03 description: Although the commercial demand for North American beaver (Castor canadensis) hair shaped much of the socio-ecological landscape of North America, use of beaver hair in wildlife research has focused on the Eurasian beaver (Castor fiber) and collection methods have largely involved handling animals alive or sampling dead animals. In 2022 and 2023, we tested the utility of barbed-wire hair snares to non-invasively collect hair from beavers around ponds in Northern Minnesota. At 56 different beaver ponds, we deployed 64 hair snares with remote cameras. From these data, we determined the efficiency of hair snares to collect samples, from what side of the body samples are collected, the weight and dirtiness of samples collected, the potential for bycatch, and if snares impede beavers’ ability to travel on land. We collected beaver hair samples from 94% of snares deployed, with snares sampling beaver legs and back most often. Forty-two percent of samples collected had no dirt on them, and the most productive snare collected on average 3.4 mg of clean hair per day. Muskrats were the second most sampled animal, but only made up on average 16% of total samples recorded on video per snare. Snares inhibited beaver travel in 0.1% of videos (n = 5,627 videos of beavers recorded, n = 6 videos where beaver travel was inhibited). We did not find any predictive variable that influenced the collection of beaver hair (e.g., location of snare at pond, presence of wire brushes on snare, number of times beavers touched snares, or location on the beaver’s body that was sampled). Our study provides in depth evidence of passive hair snare methods used to collect North American beaver hair, and serves as a guide to non-invasive hair snaring for multiple objectives such as hormone, genetic, and stable-isotope sample collection. creator: Dani R. Freund creator: Joseph K. Bump uri: https://doi.org/10.7717/peerj.19080 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Freund and Bump title: A retrospective study on safety and clinical outcomes of unilateral biportal endoscopic technique for spinal degenerative diseases link: https://peerj.com/articles/19076 last-modified: 2025-04-03 description: Background and ObjectiveUnilateral biportal endoscopy (UBE) has been developing rapidly in coincidence with the popularization of minimally invasive spine surgery (MISS). However, the clinical outcome and invasiveness of UBE-assisted spinal surgery (UBESS) are undefined. The aim of the present study was to summarize the clinical outcome and surgical invasiveness of UBE for the treatment of various spinal degenerative diseases in a single center to validate the safety and application value of UBESS.MethodsIncluded in this study were 105 patients who received UBESS from November 2021 to June 2022 in our center. All patients were followed up postoperatively for at least 12 months. All basic information was recorded to depict the demographic and surgical variables. Clinical outcomes were assessed in terms of the operation time, complications, days of hospital stay, total blood loss, intraoperative blood loss, postoperative drainage volume, hidden blood loss, biochemical changes associated with surgical injury, comparison of the visual analogue scale (VAS) for back and leg pain, Japanese Orthopedic Association (JOA) scores for cervical diseases at preoperative and postoperative stage, as well as Oswetry Disability Index (ODI), and modified MacNab scores one year after treatment.ResultsOf the 105 included patients, 68 patients were with single-level lumbar degenerative diseases, 22 with two-level diseases, two with three-level diseases, 10 with single-level isthmic spondylolisthesis, and three with single-level cervical spondylotic radiculopathy. UBE was performed by using five surgical approaches. The operation time, days of hospital stay, blood loss, postoperative immobilization time and prognosis were all estimated in consideration of the surgical approaches and the number of operated segments. The mean operation time ranged from 80 min to 214 min for single-level spinal diseases, and 112 min to 330 min for two-level ones. Total blood loss was higher in multilevel spinal surgery and single-level UBE-assisted lumbar interbody fusion+discectomy (ULIFD). The postoperative immobilization duration was between 0.5 and 2 days for single level spinal diseases, 1 and 3 days for 2-level diseases, fewer than 2 days for three-level diseases, and 1.5–12 days for isthmic spondylolisthesis (IS). The VAS and ODI for lumbar diseases decreased significantly and the JOA scores for cervical diseases improved after operation. The satisfaction rate was 89.70%, 85.71%, 90.00%, 66.67%, and 90.00% for the five surgical approaches respectively.ConclusionsUBESS has proved to be a safe, reliable and minimally invasive option for spinal degenerative diseases, with significant benefits of pain control, rapid functional recovery, short hospitalization, and early rehabilitation. However, postoperative hidden blood loss should be put under the careful management when performing UBESS. creator: Haitao Sun creator: Qi Zhang creator: Kehan Xu creator: Zihuan Zhou creator: Dongjie Jiang creator: Shaohui He creator: Jilu Liu creator: Haifeng Wei uri: https://doi.org/10.7717/peerj.19076 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sun et al. title: Seasonal genetic variation and genetic structure of Spodoptera exigua in Liaoning Province, Northeast China: insights from 11 years of microsatellite data link: https://peerj.com/articles/19243 last-modified: 2025-04-02 description: BackgroundThe beet armyworm (BAW), Spodoptera exigua, is a destructive migratory pest worldwide that has caused severe economic losses in China’s major crop-producing regions. To control this pest effectively, it is crucial to investigate its seasonal genetic variation and population genetic structure in northern China.MethodsIn this study, we used eight nuclear microsatellite loci to investigate the seasonal genetic variation and genetic structure of BAW in Shenyang, Liaoning Province, Northeast China, from 2012–2022, collected from a single location on Welsh onion.ResultsMicrosatellite data revealed moderate levels of genetic variation among 50 seasonal populations of BAW sampled from 2012–2022, along with significant genetic differentiation among these populations. Neighbor-joining dendrograms, STRUCTURE analysis, and principal coordinate analysis (PCoA) revealed two genetically distinct groups: the SY2012–2018 group and the SY2019–2022 group. Our results revealed seasonal variation in the genetic subconstruction at this location, which may be related to the presence of different migratory individuals throughout the year. Accordingly, our unique insights into the population genetics of BAW will contribute to the development of effective management strategies for this migratory pest. creator: Ming-Li Yu creator: Xian-Zhi Xiu creator: Jin-Yang Wang creator: Xin-Yi Cao creator: Fa-Liang Qin creator: Xing-Ya Wang creator: Li-Hong Zhou uri: https://doi.org/10.7717/peerj.19243 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Yu et al. title: A new metriacanthosaurid theropod dinosaur from the Middle Jurassic of Yunnan Province, China link: https://peerj.com/articles/19218 last-modified: 2025-04-02 description: Metriacanthosaurid theropods represent a basal-branching lineage of tetanurans. Members of this clade are mainly medium to large-sized and lived in Laurasia during the Middle Jurassic to the Early Cretaceous. In this clade, Sinraptor dongi, Sinraptor hepingensis, and Yangchuanosarus shangyouensis from the Late Jurassic are well represented by the nearly complete specimens, but the incompleteness of Middle Jurassic taxa hinders our knowledge of the origin and early evolution of Metriacanthosauridae. This paper describes a new genus and species of metriacanthosaurids, Yuanmouraptor jinshajiangensis gen. et sp. nov, from the Middle Jurassic Zhanghe Formation of Yunnan Province, China. The new taxon is represented by a cranium and the anterior section of the vertebral column including the complete cervical series and the first dorsal vertebra. Yuanmouraptor jinshajiangensis can be diagnosed based on the following autapomorphies: the anterior process of postorbital sheet-shaped and keeping consistent depth; ventral ramus of postorbital bearing a laterally twisted trough running along its lateral surface; ventral surface of axial intercentrum parallel with that of axial centrum; discontinuity of inclination on anterodorsal margin of the third and fourth cervical vertebrae; strongly posteriorly elongated epipophyses of anterior cervical vertebrae; deeply excavated pneumatic foramina on the third cervical vertebra; sheet-shaped and subrectangular neural spines of posterior cervical vertebrae. Phylogenetic analysis recovers Yuanmouraptor as the most basal-branching member within Metriacanthosauridae and provides a new alternative phylogenetic topology of non-coelurosaurian tetanurans. creator: Yi Zou creator: Li Chen creator: Tao Wang creator: Guo-Fu Wang creator: Wei-Gang Zhang creator: Xiao-Qin Zhang creator: Zhen-Ji Wang creator: Xiao-Chun Wu creator: Hai-Lu You uri: https://doi.org/10.7717/peerj.19218 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zou et al.