title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=22 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Carbon capture, photosynthesis, and leaf gas exchange of shade tree species and Arabica coffee varieties in coffee agroforestry systems in Veracruz state, Mexico link: https://peerj.com/articles/20255 last-modified: 2025-11-21 description: Agroforestry systems with native vegetation enhance climate adaptation and mitigation by improving coffee farm resilience, carbon storage, and income diversification. Seven native tree species were pre-selected as shade providers for Veracruz coffee agroforestry systems based on ecological, cultural, and economic criteria. The present study evaluated their physiological performance through above-ground biomass, carbon stocks, and in-situ chlorophyll fluorescence and gas exchange measurements under controlled light and temperature conditions. Five Coffea arabica varieties were also assessed under these shade canopies using the same leaf-level parameters, and leaf nitrogen and moisture content. Erythrina americana and Persea schiedeana had the highest carbon sequestration per tree. E. americana showed the highest water-use efficiency, whereas P. schiedeana showed the lowest transpiration and stomatal conductance, indicating a water-saving strategy via stomatal restriction. These traits reflect their ecological adaptations to shade and microclimate conditions in agroforestry systems. Inga inicuil achieved the highest carbon capture per hectare due to high tree density, despite lower individual performance. Species-specific strategies were identified: Psidium guajava and P. schiedeana exhibited high transpiration but limited carbon gain. E. americana and Inga punctata formed a drought-resilient group, having a high carbon assimilation and low water loss. Intermediate species (Heliocarpus appendiculatus, Inga vera, I. inicuil) balanced moderate CO2 assimilation rates with adaptable stomatal response. Photochemical efficiency remained stable across species. Shaded Coffea arabica var. Oro Azteca had significantly higher leaf nitrogen, moisture, and water-use efficiency than unshaded ones. These differences coincided with lower PAR under shade, aligning with known variations in shaded versus unshaded coffee plants. Principal component analysis showed that PC1 correlated strongly with stomatal conductance and transpiration, driven by P. guajava and P. schiedeana. PC2 showed a carbon economy trade-off between CO2 assimilation and internal concentration, dominated by E. americana. Collectively, these components highlight stomatal regulation and carbon management as adaptive strategies. Coffee PCA revealed contrasting water-use strategies: PC1 showed inverse stomatal regulation (especially in shaded varieties), and PC2 an energy allocation trade-off between photochemical efficiency and carbon assimilation, with shaded plants maintaining stable CO2 assimilation regarding unshaded ones. These results demonstrate notable interspecific variation in carbon storage, water-use efficiency, and light conditions among shade trees, offering empirical support for species selection in Veracruz coffee agroforestry. creator: Daniel Cabrera-Santos creator: Patricia Dávila creator: Isela Rodríguez-Arévalo creator: Anabel Ruiz-Flores creator: Josefina Vázquez-Medrano creator: Salvador Sampayo-Maldonado creator: Cesar Ordoñez-Salanueva creator: Maraeva Gianella creator: Elizabeth Bell creator: María Toledo-Garibaldi creator: Robert Manson creator: Flor G. Vázquez-Corzas creator: Jazmin Cobos-Silva creator: Cesar Mateo Flores Ortiz creator: Tiziana Ulian uri: https://doi.org/10.7717/peerj.20255 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Cabrera-Santos et al. title: Utilization of soft pistachio hulls in Japanese quail diets for enhanced egg quality and yolk pigmentation link: https://peerj.com/articles/20204 last-modified: 2025-11-21 description: BackgroundJapanese quail (Coturnix coturnix japonica) offer rapid growth, early maturity and excellent feed conversion, but feed cost accounts for ∼70% of production expenses. This study evaluated soft pistachio hull (PH), an abundant agro-industrial by-product, as a low-cost dietary ingredient in laying quails.MethodsNinety-six female quails, seven weeks old age, were randomly distributed to four dietary groups (24 birds each; three replicates of eight birds). The treatment diets were based on a standard layer feed, with graded PH inclusion of 0%, 2%, 4%, and 6%, administered over a for five-week period. Parameters measured included live weight, feed intake, egg production rate, egg weight, feed conversion ratio, and a range of egg quality indicators, such as shape index, shell thickness, Haugh unit, albumen and yolk indices, and yolk color score, assessed at weeks 7 and 11.ResultsFinal live weight followed a cubic trend (P = 0.05), with the 2% and 6% PH groups (356.5 g and 350.6 g, respectively) exceeding the control (333.9 g), while 4% PH yielded intermediate values. Although differences in egg production were not statistically conclusive, the 4% PH group showed the highest output (76.4%). Feed intake increased by 7.3% in birds fed 4% PH group (P < 0.05), with feed conversion efficiency slightly reduced in noth 2% and 6% PH treatments. Egg shape index improved significantly at 4% PH (+3.3%, P < 0.01), whereas shell thickness, albumen index and Haugh unit remained unchanged (P > 0.05). Yolk color score exhibited strong linear, quadratic and cubic increases (P < 0.01), with the 6% PH group scoring 11.43 (+38.9% vs. 8.23 control).ConclusionPistachio hulls can be incorporated into laying quail diets up to 6% without adverse effects on egg quality. The 4% inclusion level appears optimal for egg shape and pruductivity, while 6% maximizes yolk coloration. Nonetheless, the observed decline in feed efficiency at some levels suggests that careful ration balancing is essential. The use of PH represents a promising route for upcycling agro-residues into functional feed components with added economic and nutritional value. creator: Mehmet Çetin uri: https://doi.org/10.7717/peerj.20204 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Çetin title: Evaluation study of effect of virtual care education on healthcare providers’ knowledge, confidence, and satisfaction link: https://peerj.com/articles/20414 last-modified: 2025-11-20 description: BackgroundVirtual care can increase access to healthcare and improve provider efficiency; however, many healthcare providers lack formal education in virtual care delivery, including skills in virtual communication, physical examination adaptations, confidentiality, and billing procedures. This training gap can result in reduced confidence and suboptimal patient care. To address this, an asynchronous continuing professional development (CPD) module was developed. The objective of this study was to evaluate the module’s efficacy regarding satisfaction and changes in knowledge and confidence.MethodsThe module covered key topics such as virtual visit etiquette, technology troubleshooting, adapted physical examinations, documentation, and remuneration processes. Interactive features included embedded videos, knowledge-check quizzes, and reflective questions. A single-group pre-post quasi-experimental design was used to evaluate its impact. Data were collected via electronic surveys administered at three time points (before, during, and post-module). Surveys included multiple choice questions assessing objective knowledge, and Likert-scale questions assessing confidence levels in virtual care delivery. Open-ended short answer questions captured qualitative feedback. Quantitative data were analyzed using descriptive statistics and paired t-tests or Wilcoxon signed-rank tests where appropriate. Qualitative data were analyzed thematically to identify learner-reported strengths and areas for improvement.ResultsA total of nine to 22 learners responded at each time point. Respondents were heterogeneous, with most identifying as male (66.7%), general practitioners (55.6%), practicing in hospital settings (55.6%), and in communities of 2,000 to 10,000 people (55.6%). Learners reported high satisfaction with the module’s content relevance, navigation, and interactive components, but requested more interactive components (e.g., case-based learning). Statistically significant improvements were observed in confidence levels (n = 20–21; p < 0.001 to 0.009) and objective knowledge scores (n = 20–22; p = 0.046).ConclusionThis evaluation study demonstrated that the asynchronous virtual care module had a statistically significant impact on objective knowledge and confidence, in addition to having positive satisfaction ratings. Limitations include the small sample size and lack of long-term follow-up to assess sustained practice change. However, these findings support the incorporation of asynchronous, virtual modules into CPD curricula to enhance provider competencies in virtual care delivery. Future directions include integrating additional case-based and specialty-specific content, as well as exploring the module’s scalability for other health professions to promote interprofessional virtual care training. creator: Megan Clemens creator: Josheil Boparai creator: Robert Glynn creator: Gerry White creator: Vernon Curran uri: https://doi.org/10.7717/peerj.20414 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Clemens et al. title: MAFF inhibits angiogenesis in non-small cell lung cancer by suppressing YAP1 nuclear translocation link: https://peerj.com/articles/20395 last-modified: 2025-11-20 description: ObjectiveTo investigate the roles of MAFF and Yes-associated protein 1 (YAP1) in regulating angiogenesis in non-small cell lung cancer (NSCLC) and to explore the mechanism through which MAFF inhibits angiogenesis by suppressing YAP1 nuclear translocation.MethodsBioinformatics analysis was used to assess MAFF expression and its associated regulatory pathways. Clinical samples from NSCLC patients were analyzed by immunohistochemistry (IHC) to evaluate the correlation between MAFF expression and microvessel density (MVD). Cellular experiments were conducted to examine the effects of MAFF overexpression on proliferation, migration, and angiogenesis. Western blot (WB) and immunofluorescence (IF) analyses were performed to assess the expression of YAP1, vascular endothelial growth factor (VEGF), and connective tissue growth factor (CTGF). Tumor growth suppression was evaluated using nude mouse xenograft models.ResultsMAFF was significantly downregulated in NSCLC tissues and correlated with advanced T stage and higher MVD. Overexpression of MAFF inhibited NSCLC cell proliferation, migration, and angiogenesis, and downregulated the expression of YAP1, VEGF, and CTGF. IF confirmed that MAFF suppressed nuclear translocation of YAP1. In vivo, MAFF overexpression reduced tumor volume and weight, which was accompanied by inhibition of the YAP1 signaling pathway.ConclusionMAFF suppresses angiogenesis in NSCLC by blocking YAP1 nuclear translocation and downregulating VEGF and CTGF, highlighting its potential as a therapeutic target. creator: Yao Ding creator: Shizi Wang creator: Rui Hu creator: ZiYi Cao creator: Yuting Zou creator: Wei-ling Yang creator: Weihang Ji creator: Lin Liu creator: Na Xiao creator: Xiao lei Li creator: Yi Zeng uri: https://doi.org/10.7717/peerj.20395 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Ding et al. title: Efficacy and safety of rivaroxaban in neonatal catheter-related thrombosis: a single-center retrospective study of 122 cases link: https://peerj.com/articles/20375 last-modified: 2025-11-20 description: BackgroundTo systematically evaluate the clinical efficacy of rivaroxaban in treating neonatal catheter-related thrombosis (CRT) and analyze risk factors affecting treatment outcomes.MethodsClinical data of 122 neonatal CRT patients treated with rivaroxaban from March 2022 to October 2024 at Fujian Provincial Maternal and Child Health Hospital were retrospectively analyzed. The primary outcome was the complete thrombus resolution rate. Multivariate logistic regression was used to analyze risk factors affecting treatment efficacy.ResultsAmong 122 patients, the complete thrombus resolution rate was 71.31% (87/122) after 6 weeks of anticoagulation, which significantly increased to 88.52% (108/122) after extending to 3 months (p < 0.01). Multivariate logistic regression analysis showed that chemotherapy (OR = 5.48, 95% CI [1.04–28.73], P < 0.05) and difficult catheter placement (OR = 12.53, 95% CI [3.13–50.22], P < 0.05) were independent risk factors reducing the likelihood of complete thrombus resolution at 3 months. No anticoagulation-related bleeding or other complications were observed during the study period, though the sample size and follow-up period may limit the detection of rare events.ConclusionRetrospective data suggest that rivaroxaban is safe and effective in treating neonatal catheter-related thrombosis, with a higher complete thrombus resolution rate observed at 3 months compared to 6 weeks of anticoagulation therapy. Chemotherapy and difficult catheter placement were identified as independent risk factors affecting treatment efficacy. These findings, derived from a single-center retrospective study, require validation through multi-center, prospective, randomized controlled trials. creator: Rong Zhang creator: Gang Chen creator: Wen Hong Cai creator: Bin Yang creator: Yun Feng Lin creator: Teng Hui Zhan uri: https://doi.org/10.7717/peerj.20375 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: The bee bread of honey bees is characterized by a core microbiota despite the application of miticide treatments and variation across space and time link: https://peerj.com/articles/20366 last-modified: 2025-11-20 description: BackgroundBee bread is composed of a mixture of pollen and nectar used as the main source of proteins and lipids for the development of bee larvae. Despite its important role in honey bee food preservation, relatively little is known about the composition of bee bread microbiota and the potential impact of beekeeping management of hives on these microbial systems.MethodsHere, we evaluated whether (1) the bee bread of honey bees is characterized by a core microbiota and (2) miticide applications (formic acid and amitraz) affect the diversity and composition of the bee bread microbiota. We collected a total of 36 samples from six sites across two distinct geographic locations and sequenced the bee bread bacterial communities before and after miticide applications.ResultsOur results revealed a conserved bee bread core microbiota comprised of 15 taxa belonging to the phyla Proteobacteria (11 taxa), Firmicutes (two taxa), Actinobacteriota (one taxon), and Bacteroidota (one taxon). In addition, we found weak evidence of miticide treatments impacting the diversity of the bee bread microbiota, with a general trend of a decrease in the diversity of non-core taxa following the application of organic miticides.ConclusionTaken together, our results demonstrate that the bee bread of honey bees is characterized by a core microbiota despite variations associated with geographic location, sampling period, and miticide applications. creator: Brooke L. Lawrence creator: Gordon F. Custer creator: Robyn M. Underwood creator: Robert R. Dunn creator: Francisco Dini-Andreote creator: Margarita M. López-Uribe uri: https://doi.org/10.7717/peerj.20366 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Lawrence et al. title: Assessment of healing dynamics in dental extraction sockets among non-diabetic, prediabetic, and type 2 diabetic patients: a comparative clinical investigation link: https://peerj.com/articles/20361 last-modified: 2025-11-20 description: BackgroundDiabetes mellitus is a chronic metabolic disorder characterized by persistent hyperglycaemia, affecting various metabolic processes and leading to multiple complications, particularly in wound healing. This study aims to evaluate the impact of diabetes on the healing of extraction sockets in non-diabetic, prediabetic, and type 2 diabetic patients in Saudi Arabia.MethodologyA prospective observational study was conducted with 72 participants who were divided equally (n = 24 for each group) into three groups, viz. non-diabetic, prediabetic, and diabetic groups based on glycated hemoglobin (HbA1c) and random blood glucose levels. Tooth extractions were performed by an experienced maxillofacial surgeon. Healing outcomes were assessed by measuring extraction socket size, post-operative pain, discharge, swelling, infection, erythema, dry socket occurrence, and analgesic consumption over one week. Initially descriptive statistics were calculated and one way Analysis of Variance (ANOVA) test was done to compare the reduction in socket size between groups. The level of statistical significance was set at P ≤ 0.05.ResultsOut of 275 screened participants, 104 provided informed consent, and 72 completed the study. Significant differences were found in socket size reduction, with non-diabetic patients showing a 62.5% reduction, prediabetic 56.4%, and diabetic 48.6% (p < 0.001). Diabetic patients experienced more post-operative pain (p = 0.039) and a higher incidence of complications such as swelling, infection, and discharge, although not statistically significant (p = 0.141).ConclusionDiabetes significantly affects post-operative healing in dental extractions, leading to less socket size reduction, higher pain levels, and increased complications. These findings underscore the necessity for specialized post-operative care for diabetic patients, including stringent infection control and pain management strategies. Further research with larger sample sizes and extended follow-up periods is recommended to better understand the long-term impacts of diabetes on oral health. creator: Mohammed Saad Alqarni uri: https://doi.org/10.7717/peerj.20361 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Alqarni title: Hybrid contour and geometric partitioning for accurate plantar foot region segmentation link: https://peerj.com/articles/20352 last-modified: 2025-11-20 description: BackgroundPrecise segmentation of plantar foot regions is crucial for analyzing foot structure and pressure distribution, aiding in the diagnosis of pathologies and enabling preventive interventions. However, conventional segmentation approaches often struggle to accurately delineate key anatomical regions and detect their boundaries, particularly in the presence of foot abnormalities.MethodsWe created a dataset of plantar pressure images and proposed a hybrid algorithm that integrates edge contour detection techniques with dynamic geometric partitioning to address persistent challenges in plantar region segmentation. Our method first determines the lengths of the left and right feet using precise contour detection, then partitions the plantar surface into primary anatomical regions (forefoot, midfoot, and heel) based on standardized geometric proportions. Additionally, the methodology allows for finer subdivisions (e.g., inner/outer forefoot) that adapt to the unique morphology of each foot. This algorithm accommodates five foot types, including normal, low arch, high arch, inward heel tilt, and outward heel tilt.ResultsA comparative evaluation of three edge detection methods revealed that the Canny algorithm, when combined with geometric partitioning, yielded superior performance. On a dataset of 200 plantar pressure footprints encompassing both normal and abnormal feet, this hybrid approach achieved Intersection over Union (IoU) and mean Average Precision (mAP) scores exceeding 0.90 across all segmented regions (forefoot, midfoot, and heel). Furthermore, the results indicate that the proposed hybrid algorithm performs comparably across both normal and abnormal foot types, with no significant differences observed.ConclusionsOur synergistic integration of contour detection and geometric partitioning yields an efficient technique for segmenting plantar regions from static plantar pressure images. Validation on a diverse dataset shows that the proposed approach accurately distinguishes foot-specific regions across five different foot types, including both normal and pathological cases. creator: Shumei Zhang creator: Xi Liang creator: Minmin Wu creator: Weiming Gu uri: https://doi.org/10.7717/peerj.20352 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: DHCR7: from sterol biosynthesis to oncogenic role in colorectal cancer link: https://peerj.com/articles/20323 last-modified: 2025-11-20 description: Objective7-Dehydrocholesterol reductase (DHCR7) is an enzyme that plays a crucial regulatory role in sterol biosynthesis and has been implicated in tumorigenesis and progression. This study aims to elucidate the biological function of DHCR7 in the pathogenesis of colorectal cancer (CRC).MethodsBy integrating multi-omics data (including public genomic databases and mass spectrometry data from clinical samples) and establishing in vivo and in vitro experimental systems (encompassing animal models and CRC cell lines with gene overexpression and knockdown), we systematically investigated the functional role of DHCR7 in CRC. A multimodal research strategy combining bioinformatics analysis with molecular biology experiments (Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), western blotting, immunohistochemistry, etc.), proteomics analysis (liquid chromatography–mass spectrometry), and cellular functional assays (proliferation, apoptosis, migration, and invasion) was employed.ResultsElevated levels of sterols were observed in CRC tumor tissues, and high cholesterol levels were found to promote the malignant phenotype of tumor cells. Mass spectrometry revealed that DHCR7 was significantly upregulated in CRC tissues and correlated with poor clinical prognosis. DHCR7 could modulate the cholesterol levels in CRC cells; overexpression of this gene enhanced cell proliferation, inhibited apoptosis, and promoted invasion and migration. Conversely, inhibition of DHCR7 expression abrogated these pro-tumorigenic effects, which was consistent with the inactivation of the PI3K/AKT/mTOR signaling pathway and confirmed by pathway reactivation experiments. DHCR7 deficiency significantly reduced tumorigenicity in vivo.ConclusionDHCR7 regulates the progression of CRC both in vitro and in vivo through the PI3K/AKT/mTOR signaling axis and affects the cholesterol levels in CRC. creator: Chuan Zhou creator: Jia Wang creator: Han He creator: Chao Wang creator: YunFeng Zhang creator: Wenbo Zhang creator: Bin Wei creator: Mingxu Da creator: Minghui Pang uri: https://doi.org/10.7717/peerj.20323 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Zhou et al. title: Unveiling the clinical profiles of critically ill COVID-19 patients: insights from Ezhou during the early spread link: https://peerj.com/articles/20318 last-modified: 2025-11-20 description: The coronavirus disease 2019 (COVID-19) started in December 2019 in Wuhan. This article evaluated clinical characteristics, and imaging manifestations in Ezhou, an early locked-down city, 80 kilometers east of Wuhan. We analyzed data from 98 confirmed severe COVID-19 patients in Ezhou Central Hospital between February 1st and March 22nd, 2020. We compared patients’ laboratory results, imaging manifestations, and treatments between survival and death groups. Of these 98 confirmed COVID-19 patients, 24 individuals (24.6%) had chronic diseases. The main symptoms of critically ill patients were fever (86.7%), cough (83.7%), and dyspnea (59.1%). Common complications were acute respiratory distress syndrome (ARDS; 49%), acute kidney injury (37.7%), and multiple organ dysfunction syndrome (MODS; 32.6%). Computed tomography (CT) scans displayed ground-glass opacity at subpleural regions that were associated with interlobular septal thickening. Within 28 days, 39 (39.8%) patients died. Compared to survivors, the death group had a higher median age (69.8 vs. 61.3, p < 0.05), and were more prone to ARDS (100% vs. 15.2%) and MODS (76% vs. 3.4%). Our report showed that in the early days of the COVID-19 outbreak, there was a high mortality rate in critically ill patients. Elderly patients (>65 years) normally have an increased risk of complications and ARDS. Most non-survivors were highly dependent upon mechanical ventilation. CT scans with imaging manifestations showed abnormal conditions in the lower multiple bilateral lung lobes, which provides a useful characterization of this fatal disease by recognizing COVID-19 pneumonia and assessing its evolution for the target for intervention of the patient recovery. creator: Guohui Yang creator: Zewen Liu creator: Tabitha Abraham creator: Linwei Li creator: Tingyang Zhou creator: Qing Zhang creator: Li Zuo uri: https://doi.org/10.7717/peerj.20318 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yang et al.