title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=137 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: In-vitro comparative thermo-chemical aging and penetration analyses of bioactive glass-based dental resin infiltrates link: https://peerj.com/articles/18831 last-modified: 2025-01-28 description: BackgroundTeeth with small to moderate cavities can be repaired with enamel resin infiltrants, a form of dental restorative material. In dental materials, it is standard practice to include several filler particles for experimental use in dental resin infiltrates. The resin’s BG particles penetrate the lesion and release ions that combine with saliva to provide a mineral-rich environment that can strengthen enamel and heal. This study aimed to compare resin infiltrants based on three types of bioactive glass materials and investigate the penetration depth, microleakage, and the effect of thermal and chemical aging.MethodologyA triethylene glycol dimethacrylate (TEGDMA) and urethane dimethacrylate (UDMA)-based experimental resin infiltrate was prepared. Initial mixing was done manually for 1 h at room temperature, followed by another mix for 30 min on a magnetic stirrer. This prepared resin, called “PURE RESIN” was then further incorporated with three different types of bioactive glasses, i.e., Bioglass (45S5), boron-substituted (B-BG), and fluoride-substituted (F-BG). Initial manual mixing for 1 h, followed by ultrasonic mixing for 3 min and then proceeded for the final mixing on a magnetic stirrer for 24 h in a dark room at ambient temperature. Human-extracted teeth were demineralized, and the experimental resins were infiltrated on the demineralized surface. The surface area, pore size, and volume of the demineralized surface were measured. The microleakage and penetration depth were analyzed with the stereomicroscope and micro-CT, respectively. The samples were challenged with the pH cycle for 14 days, followed by a scanning electron microscope (SEM). Thermocycling (5,000 cycles) and chemical aging (4 weeks) were conducted, followed by microhardness, surface roughness, and SEM analyses. Statistical analyses were conducted after each test.ResultsThe F-BG group achieved the highest initial and day 14 penetration coefficients. There was a superior dye penetration with the microleakage analysis in the F-BG group. The 45S5 group had the highest average penetration depth via micro-CT analysis. After thermocycling and chemical aging, the micro-hardness was reduced (non-significantly) among all samples except the F-BG group in post-chemical aging analysis, whereas the surface roughness was significantly increased. SEM images showed the presence of micro-pits on the surfaces after the thermal and chemical aging.ConclusionThe F-BG group achieved the highest initial and day 14 penetration coefficients. There was a superior dye penetration with the microleakage analysis in the F-BG group. The 45S5 group had the highest average penetration depth via micro-CT analysis. After thermocycling and chemical aging, the micro-hardness was reduced (non-significantly) among all samples except the F-BG group in post-chemical aging analysis, whereas the surface roughness was significantly increased. SEM images showed the presence of micro-pits on the surfaces after the thermal and chemical aging. creator: Syed Zubairuddin Ahmed creator: Abdul Samad Khan creator: Maram Alshehri creator: Fatimah Alsebaa creator: Fadak Almutawah creator: Moayad Mohammed Aljeshi creator: Asma Tufail Shah creator: Budi Aslinie Md Sabri creator: Sultan Akhtar creator: Mohamed Ibrahim Abu Hassan uri: https://doi.org/10.7717/peerj.18831 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ahmed et al. title: Clinical considerations on antimicrobial resistance potential of complex microbiological samples link: https://peerj.com/articles/18802 last-modified: 2025-01-28 description: Antimicrobial resistance (AMR) is one of our greatest public health challenges. Targeted use of antibiotics (ABs) can reduce the occurrence and spread of AMR and boost the effectiveness of treatment. This requires knowledge of the AB susceptibility of the pathogens involved in the disease. Therapeutic recommendations based on classical AB susceptibility testing (AST) are based on the analysis of only a fraction of the bacteria present in the disease process. Next and third generation sequencing technologies allow the identification of antimicrobial resistance genes (ARGs) present in a bacterial community. Using this metagenomic approach, we can map the antimicrobial resistance potential (AMRP) of a complex, multi-bacterial microbial sample. To understand the interpretiveness of AMRP, the concordance between phenotypic AMR properties and ARGs was investigated by analyzing data from 574 Escherichia coli strains of five different studies. The overall results show that for 44% of the studied ABs, phenotypically resistant strains are genotypically associated with a 90% probability of resistance, while for 92% of the ABs, the phenotypically susceptible strains are genotypically susceptible with a 90% probability. ARG detection showed a phenotypic prediction with at least 90% confidence in 67% of ABs. The probability of detecting a phenotypically susceptible strain as resistant based on genotype is below 5% for 92% of ABs. While the probability of detecting a phenotypically resistant strain as susceptible based on genotype is below 5% for 44% of ABs. We can assume that these strain-by-strain concordance results are also true for bacteria in complex microbial samples, and conclude that AMRP obtained from metagenomic ARG analysis can help choose efficient ABs. This is illustrated using AMRP by a canine external otitis sample. creator: Norbert Solymosi creator: Adrienn Gréta Tóth creator: Sára Ágnes Nagy creator: István Csabai creator: Csongor Feczkó creator: Tamás Reibling creator: Tibor Németh uri: https://doi.org/10.7717/peerj.18802 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Solymosi et al. title: Correction factors for prey size estimation from PenguCams link: https://peerj.com/articles/18598 last-modified: 2025-01-28 description: The use of animal-borne cameras enables scientists to observe behaviours and interactions that have until now, gone unseen or rarely documented. Researchers can now analyse prey preferences and predator-prey interactions with a new level of detail. New technology allows researchers to analyse prey features before they are captured, adding a new dimension to existing prey analysis techniques, which have primarily relied on examining partially or fully digested prey through stomach flushing. To determine prey size, the video footage captured needs a correction factor (pixel:mm ratio) that allows researchers to measure prey dimensions using image measuring software and convert the pixels to actual measurements. This in turn will help estimating the prey energy content. This method requires a reference object with known dimensions (such as beak measurements) to ground truth your distance. Using PenguCams we determined the correction factor by measuring a 2 cm section of 1 mm grid paper from video footage taken at known distances (10, 20, 30, 40, 50, 60 cm) in different salinities ranging from air and fresh water, up to 35 psu in 5 psu increments while controlling for temperature and pressure. We found no significant difference between correction factors of water at different salinities. However, due to their considerable differences in refraction index, correction factors contrast between water and air. Linear equations modelled from correction factors at tested distances help predict correction factors between tested distances and, therefore, enable a wider application of this research. We provide examples from PenguCam footage taken of Humboldt (Spheniscus humboldti), Tawaki (Eudyptes pachyrhynchus) and King (Aptenodytes patagonicus) penguins to illustrate the use of identified correction factors. This study provides a tool for researchers to further enhance their understanding of predator-prey interactions. creator: Owen Dabkowski creator: Ursula Ellenberg creator: Thomas Mattern creator: Klemens Pütz creator: Pablo Garcia Borboroglu uri: https://doi.org/10.7717/peerj.18598 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Dabkowski et al. title: Surgical outcomes in patients with Achilles tendon rupture—a retrospective study link: https://peerj.com/articles/18890 last-modified: 2025-01-27 description: BackgroundThere are two main methods used to treat Achilles tendon rupture (ATR): conservative treatment and surgical intervention. Surgical techniques are divided into three main categories: open surgical repair, mini-open surgical repair, and percutaneous repair (PR). We aimed to compare clinical outcomes in individuals with ATR who were treated with PR, primary repair, and flexor hallucis longus augmentation (FHL-A) with those treated with V-Y plasty and FHL-A.MethodsThe study involved 54 patients who underwent ATR surgical intervention retrospectively. Thirty-two of these were identified as acute and 22 were chronic rupture patients. PR was performed in 32 patients, primary repair and FHL-A in 14 patients, and V-Y plasty and FHL-A in eight patients.ResultsThe mean forward jump was 142.69 ± 7.14 cm in individuals who received PR, 137.71 ± 4.51 cm in those who received primary repair + FHL-A, and 123.88 ± 3.09 cm in those who received V-Y plasty + FHL-A (p < 0.001). The decrease in the mean vertical jump distance on the operated side compared to the contralateral extremity was 0.97 ± 0.93, 2.07 ± 0.99, and 3.00 ± 1.69 cm in individuals who underwent PR, primary repair + FHL-A, and V-Y plasty + FHL-A, respectively (p < 0.001). The decrease in the mean dorsiflexion of the operated side ankle compared to the contralateral extremity was found to be 4.34 ± 1.18, 1.93 ± 1.07, and 2.38 ± 0.92 degrees in individuals who underwent PR, primary repair + FHL-A, and V-Y plasty + FHL-A, respectively (p < 0.001).ConclusionAlthough no surgical technique is completely superior to another, better performance tests were observed after PR repair compared to open surgery in individuals involved in sports, but rerupture, dorsiflexion restriction, and painful ankle were disadvantages. FHL-A, which has gained popularity in recent years, showed better performance in tests by contributing to more stable and stronger ankles in sporting individuals with chronic ruptures who had undergone open surgery. FHL-A can be utilized in addition to primary surgical intervention in individuals with high performance expectations before and after injury. creator: Hüseyin Kürüm creator: Hacı Bayram Tosun creator: Faruk Aydemir creator: Orhan Ayas creator: Kübra Orhan Kürüm creator: Funda İpekten uri: https://doi.org/10.7717/peerj.18890 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Kürüm et al. title: Safety profile of EZH2 inhibitors for cancer: a systematic review and meta-analysis link: https://peerj.com/articles/18871 last-modified: 2025-01-27 description: ObjectiveTo evaluate the safety profiles of EZH2-targeted inhibitors in cancer treatment, focusing on treatment-related adverse events (TRAEs) across various clinical trials.MethodsWe conducted a systematic review and meta-analysis using data from clinical trials involving EZH2 inhibitors reported up to May 31, 2024. Databases searched included PubMed, Embase, CENTRAL (Cochrane Central Register of Controlled Trials), and ClinicalTrials.gov. Studies included were those involving patients treated with EZH2 inhibitors as monotherapy or in combination, specifically detailing the incidence of TRAEs. Data on all-grade TRAEs, grade 3 or higher TRAEs, and severe TRAEs were extracted and analyzed using random-effects models.ResultsOur systematic review and meta-analysis included 22 studies encompassing 1,002 patients who met the inclusion criteria. TRAEs were commonly observed during EZH2 inhibitor therapy, affecting 86% of patients (95% CI [79–94%]%; I2 = 89.5%). The incidence of grade 3 or higher TRAEs was 33% (95% CI [21–44%]; I2 = 93.5%), while severe TRAEs occurred in 15% of the cases (95% CI [9–22%]; I2 = 87.5%). The most frequently reported grade 3 or higher TRAEs in the pooled analysis were neutropenia (8%), thrombocytopenia (8%), and anemia (6%). Specifically, for tazemetostat, the most common grade 3 or higher TRAE was neutropenia (5%). For SHR2554, the most prevalent grade 3 or higher TRAEs were thrombocytopenia (17%), neutropenia (8%), and anemia (7%). Notably, treatment-related fatalities were rare, with only 0.9% of patients experiencing potentially fatal outcomes due to therapy.ConclusionEZH2 inhibitors demonstrate a manageable safety profile with a low incidence of severe TRAEs, emphasizing their potential as safe therapeutic options in cancer treatment. The low rate of severe TRAEs and the rare occurrences of treatment-related deaths support the continued clinical use and further investigation of EZH2 inhibitors. creator: Zhou Zhao creator: Xiufeng Chen creator: Huayang Pang creator: Yan Shi creator: Hao Sun uri: https://doi.org/10.7717/peerj.18871 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Zhao et al. title: Correlation of diabetes and adverse outcomes in hospitalized COVID-19 patients admitted to a tertiary hospital in China during a small-scale COVID-19 outbreak link: https://peerj.com/articles/18865 last-modified: 2025-01-27 description: BackgroundThe aim of this study was to investigate the impact of diabetes on mortality and adverse outcomes in COVID-19 patients and to analyse the associated risk factors.MethodsThis is a retrospective cohort study in 500 hospitalized patients with COVID-19 infection (214 with diabetes and 286 without diabetes) admitted to a tertiary hospital in China from December 2022 to February 2023. Demographic information, clinical characteristics and outcomes were collected. Survival status was investigated at discharge and at 6 months after discharge.ResultsThe mortality rate of COVID-19 patients with diabetes was higher than the rate of non-diabetic COVID-19 patients, both at discharge, and at 6 months after discharge. Body mass index (BMI), C-reactive protein (CRP), pH, D-dimer, blood osmotic pressure, serum creatinine, white blood cell count, creatine kinase and hospitalization expenses were significantly different between diabetic group and non-diabetic group (p < 0.05). Compared with the survivors, non-survived COVID-19 patients with diabetes had worse diabetes control indicators, with random blood glucose increased by 3.58 mmol/L (p < 0.05), and fasting blood glucose increased by 2.77 mmol/L (p < 0.01). In addition, there were significant differences in age, heart rate, CRP, pH, potassium (K+), serum creatinine, white blood cell count, creatine kinase, the proportion with diabetic complications, treatment in ICU and mechanical ventilation between survivors and non-survivors of COVID-19 patients with diabetes. By multivariate logistic regression analysis, the death of COVID-19 patients with diabetes is positively correlated with age and CRP (p < 0.05), and has a trend towards significance with fasting blood glucose (p < 0.1).ConclusionInfection with COVID-19 on the basis of diabetes can significantly increase mortality, which was further associated with diabetes control indicators. creator: Yu Li creator: Guanni Li creator: Jiahong Li creator: Zirui Luo creator: Yaxuan Lin creator: Ning Lan creator: Xiaodan Zhang uri: https://doi.org/10.7717/peerj.18865 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Li et al. title: Clusters explaining the relation between menopause and self-reported periodontal disease: a cross-sectional study link: https://peerj.com/articles/18861 last-modified: 2025-01-27 description: BackgroundMenopause is an important milestone in the women’s life continuum and is associated with potentially adverse effects, including those related to oral health. This study assessed self-reported periodontal disease in relation to menopausal status.MethodsA cross-sectional study involving a convenience sample of female university dental hospital attendees was conducted using a validated, self-administered, self-reported periodontal disease questionnaire. A two-step cluster analysis was used to categorize the participants based on menstrual period (MP) continuity, systemic diseases and age. Differences between clusters were analyzed using chi-square test.ResultsFrom 112 included participants, three clusters resulted from the analysis: Cluster #1 (37 ± 8 years, no systemic diseases and continued MP), Cluster #2 (40 ± 10, with systemic diseases and continued MP) and Cluster #3 (54 ± 9, with systemic diseases and discontinued MP). Cluster #3 tended to have less optimal oral hygiene habits and more missing teeth (p > 0.05). Clusters #1 and #2 insignificantly reported more gingival bleeding, tooth sensitivity and calculus (p > 0.05). Cluster #3, on the other hand, presented with more self-reported oral dryness (p ≤ 0.05).ConclusionsWithin study limits, clusters of menopausal women with systemic diseases reported high symptoms of periodontal disease that were not significantly different from younger individuals, with the exception of oral dryness. creator: Hani T. Fadel creator: Lujain A. Qarah creator: Manal O. Alharbi creator: Alla Al-Sharif creator: Doaa S. Al-Harkan creator: Saba Kassim creator: Osama Abu-Hammad creator: Najla Dar-Odeh uri: https://doi.org/10.7717/peerj.18861 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Fadel et al. title: A novel ddPCR™ assay for eDNA detection and quantification of Greater Amberjack Seriola dumerilli and three congeners in US waters: challenges and application to fisheries independent surveys link: https://peerj.com/articles/18778 last-modified: 2025-01-27 description: BackgroundFour Seriola species support recreational and commercial fisheries along the U.S. Atlantic Ocean and the Gulf of Mexico, with the S. dumerili Gulf of Mexico stock being overfished for over three decades. The study presented here is part of a fisheries-independent project initiated to determine an absolute abundance of S. dumerili, to expand biological knowledge of the species and to develop novel tools for fisheries management. Environmental DNA (eDNA) tools aimed at the detection and quantification of target species are starting to emerge in support of marine fisheries surveys. Key to progressing the field is Droplet Digital™ PCR (ddPCR™), a highly sensitive technique with advanced multiplexing and direct quantification capabilities that can provide fisheries scientists with improved interpretation of eDNA data.MethodsWe developed and validated a novel tetraplex ddPCR™ assay able to detect and distinguish between S. dumerili, S. fasciata, S. rivoliana, and S. zonata from seawater eDNA samples. In order to groundtruth ddPCR™ data, and explore its capacity to provide abundance estimates, we compared ddPCR™ detections and quantifications to abundance data inferred from multiple camera (ROV, S-BRUV, chevron trap) and acoustic (VPS array) gears deployed during a fisheries research gear-calibration cruise.ResultsWe demonstrated that with eDNA contamination controls and best practice protocols, it is viable to conduct eDNA research as part of a fisheries survey cruise. eDNA sampling was completed in less time than camera gears (15 min vs 2 h). Both eDNA and camera gears detected the presence of S. dumerili and S. rivoliana at both sites and all sampling days, but not S. fasciata and S. zonata. eDNA concentration data was higher for S. dumerili than S. rivoliana at both sites for all sampling days, in line with abundance patterns obtained from camera gears. The highest correlation (r = 0.97) was obtained between the measures of eDNA between gear deployments and ROV.DiscussionIncorporating eDNA in fisheries surveys would not require additional days at sea and could improve precision in fish detection and abundance. eDNA can be a valuable complement to camera gears deployed in geographic areas or seasons with poor visibility conditions, where fish may be present but cannot be confidently identified to the species level. The high correlation obtained between ROV and eDNA data collected between gear deployments adds to a growing number of studies demonstrating the potential of eDNA as an indicator of abundance for fisheries stock assessments. Time-series data from a carefully designed eDNA survey, that estimates relative abundance, could be used as an index of relative abundance for the S. dumerili stock assessment. To achieve this, investment into follow-up studies with increased sample sizes and spatial and temporal replication would be necessary to allow for year-to-year comparisons and validate the robustness of the correlation observed. creator: P. Joana Dias creator: Ryan Lehman creator: Bryan L. Huerta-Beltrán creator: Ana Wheeler creator: Crystal L. Hightower creator: Jessica Heise creator: Theodore Switzer creator: Clint Rhode creator: J. Marcus Drymon creator: Lynne Stokes creator: Mark A. Albins creator: Sean Powers creator: Nicole Phillips uri: https://doi.org/10.7717/peerj.18778 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Dias et al. title: Super Partition: fast, flexible, and interpretable large-scale data reduction in R link: https://peerj.com/articles/18580 last-modified: 2025-01-27 description: MotivationAs data sets increase in size and complexity with advancing technology, flexible and interpretable data reduction methods that quantify information preservation become increasingly important.ResultsSuper Partition is a large-scale approximation of the original Partition data reduction algorithm that allows the user to flexibly specify the minimum amount of information captured for each input feature. In an initial step, Genie, a fast, hierarchical clustering algorithm, forms a super-partition, thereby increasing the computational tractability by allowing Partition to be applied to the subsets. Applications to high dimensional data sets show scalability to hundreds of thousands of features with reasonable computation times.Availability and implementationSuper Partition is a new function within the partition R package, available on the CRAN repository (https://cran.r-project.org/web/packages/partition/index.html). creator: Katelyn J. Queen creator: Malcolm Barrett creator: Joshua Millstein uri: https://doi.org/10.7717/peerj.18580 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Queen et al. title: Beyond support: exploring the dynamic and static biomechanical changes induced by preventive ankle taping: a novel cross-sectional study link: https://peerj.com/articles/18472 last-modified: 2025-01-27 description: IntroductionIn sports, 80% of all ankle injuries are sprains of the external compartment. Functional bandages are usually used preventively, specially in individuals with a history of lateral ankle injuries. To this day, the actual benefits of such taping remain unknown as important modifications are introduced in the ankle biomechanics.ObjectiveThe aim of the present study is to describe the biomechanical processes underlying these effects, such as modification during stance times, balance, contact surface and maximum and average pressures in the rearfoot, forefoot and midfoot, using a sprain preventive taping for the external ankle compartment.MethodsAn observational, analytic, cross-sectional study was designed. Data from static and dynamic plantar pressures with a pressure platform and balance data assessed with the Y Balance Test (YBT) were analysed in 50 participants (age = 21.00 ± 2.34 years, weight = 71.11 ± 13.12 kg, height = 1.75 ± 00.9 m, BMI = 22.94 ± 2.50 kg/m2, foot size = 41.60 ± 3.00) with and without preventive functional taping for lateral ankle sprain (LAS).ResultsA statistically significant decrease in YBT was observed in the taped participants toward anterior (p = 0.001) and posterolateral (p = 0.005) motion. On the static measures at the pressure platform, an increase in peak pressure at the midfoot (p = 0.001), a decrease in the maximum pressure in the forefoot (p = 0.003) and a decrease in the contact surface in the rearfoot (p = 0.003) were recorded. Dynamic measures at the pressure platform analysis showed a statistically significant decrease in contact surface at the rearfoot (p = 0.001), an increase in mean pressure in both the midfoot (p = 0.044) and forefoot (p = 0.001) and a significant decrease in velocity in the forefoot (p = 0.003).ConclusionsIn conclusion, we observed that ankle taping led to increased peak pressures in the midfoot and decreased maximum pressures in the forefoot, indicating a shift in load distribution within the plantar surface. Simultaneously, a significant reduction in the velocity at the forefoot during dynamic tasks suggests that taping may alter natural gait dynamics, potentially affecting movement efficiency and stride characteristics. In addition, the application of ankle taping significantly altered balance, as evidenced by a decrease of YBT scores anterior and posterolateral directions. Prophylactic taping in patients with no prior history of LAS is not recommended. creator: María Bravo-Aguilar creator: Vanesa Abuín-Porras creator: María Blanco-Morales creator: Carlos Romero Morales creator: Jaime Almazán-Polo creator: Jorge Hugo Villafañe creator: Lorena Canosa-Carro uri: https://doi.org/10.7717/peerj.18472 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Bravo-Aguilar et al.