title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=131 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The association between serum lipids at diagnosis and renal outcome in microscopic polyangiitis patients link: https://peerj.com/articles/18839 last-modified: 2025-02-10 description: ObjectivesMicroscopic polyangiitis (MPA) is a subgroup of ANCA-associated vasculitis (AAV), which is characterized by vascular endothelial cell damage caused by abnormally activated neutrophils. Dyslipidemia is associated with vascular endothelial cell injury, and the relationship between blood lipid levels and renal prognosis in MPA patients is not clear. We aim to investigate the correlation between blood lipid levels at diagnosis and renal prognosis in MPA patients.MethodsFirstly, we retrospectively included 110 patients diagnosed with MPA and the primary endpoint was the occurrence of end stage renal disease (ESRD). The association between blood lipids at diagnosis and renal outcome was evaluated with Cox regression analysis and survival analysis. Secondly, we explored the potential underlying mechanism of poor renal prognosis in patients with high triglycerides (TG) levels at diagnosis using data independent acquisition (DIA) quantitative proteomics.ResultsDuring a median follow-up period of 23 months, 44 out of 110 patients (40%) developed ESRD. High serum TG at diagnosis was associated with ESRD development after adjusting for several confounding factors including age, gender, body mass index (BMI), hypertension, diabetes mellitus, estimated glomerular filtration rate (eGFR) and Birmingham Vasculitis Activity Score (BVAS). Serum very low-density lipoprotein (VLDL) demonstrated a marginal trend towards association with ESRD development. MPA patients with TG >1.45 mmol/L or VLDL > 0.66 mmol/L had significantly higher risk of ESRD development than those with TG ≤ 1.45 mmol/L or VLDL ≤ 0.66 mmol/L. DIA quantitative proteomics analysis suggested that patients with elevated TG levels and severe MPA had an upregulation of profibrotic pathways, inflammatory signaling, and complement and coagulation cascades, in contrast to those with lower TG levels and milder disease severity.ConclusionsIn MPA patients, high TG or VLDL at diagnosis is associated with an increased risk of ESRD development. The potential mechanisms may be associated with the upregulation of profibrotic and inflammatory signaling pathways, and the activation of complement and coagulation cascades. creator: Zigui Zheng creator: Yujia Wang creator: Jingzhi Xie creator: Zhimin Chen creator: Bingjing Jiang creator: Yanfang Xu uri: https://doi.org/10.7717/peerj.18839 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zheng et al. title: Genome-wide survey and expression analysis of the OMT gene family in Stephania japonica link: https://peerj.com/articles/18600 last-modified: 2025-02-10 description: BackgroundO-methyltransferase (OMT) is an important rate-limiting enzyme that plays a vital role in synthesizing various key metabolites, such as benzylisoquinoline alkaloids (BIA). Nevertheless, there is a dearth of extensive research on the analysis of the OMT gene family in Stephania japonica, a main source of cepharanthine with an anti-coronavirus effect.MethodsTwo OMT family genes, SjCCoAOMT and SjCOMT, were identified from the high-quality genome of S. japonica during this investigation. Further analysis of SjCCoAOMT and SjCOMT genes involved chromosome distribution, gene structure, phylogenetic relationship, conserved motif, expression profile, quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) experiments an d cis-acting elements analysis.ResultsThere are six SjCCoAOMT members and fifty-two SjCOMT members in the genome of S. japonica, which are unevenly distributed on 11 chromosomes. OMTs could be clustered into SjCCoAOMT and SjCOMT subfamilies through phylogenetic relationship, consistent with the conserved motif and gene structure analysis results. The expression profile revealed SjCOMT11 and SjCOMT13 showed specific expression levels mainly in root. SjCOMT21, SjCOMT33 and SjCOMT37 were significantly expressed in the root and slightly expressed in the stem, bud and leaf. SjCOMT15 and SjCOMT45 were not only significantly expressed in root, but also expressed highly in leaf. Significantly enhanced expression of SjCOMT11, SjCOMT13, SjCOMT15, SjCOMT21, SjCOMT33, SjCOMT37, and SjCOMT45 suggested these OMTs are essential for cepharanthine synthesis in the S. japonica roots. Cis-acting element analysis revealed the potential roles of OMTs in S. japonica in growth, development, and resistance to stress. These findings provide insight into understanding the functions and characterization of OMTs from S. japonica and lay a foundation for further revealing the role of the OMT genes in the biosynthesis of cepharanthine. creator: Zenghao Bi creator: Tianxing He creator: Yuting Liang creator: Changqing Zhou creator: Yuetong Yu creator: Liang Leng uri: https://doi.org/10.7717/peerj.18600 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Bi et al. title: New record of Frilled shark Chlamydoselachus anguineus Garman, 1884 (Chondrichthyes: Hexanchiformes) in the South Pacific Ocean link: https://peerj.com/articles/18992 last-modified: 2025-02-07 description: Frilled sharks are rarely observed and limited information is available regarding their life history. The global number of records for these sharks does not exceed 40, with most sightings reported in the Western Pacific Ocean. In 1976, one specimen was recorded for the first time in the South East Pacific Ocean; however, this study provides new evidence for the presence of Chlamydoselachus anguineus in Chilean waters, extending its distribution range 850 km south of the previous record. The morphological features of all specimens from Chile are discussed, supplementing previous observations and adding to the existing knowledge on this species in the Pacific Ocean. creator: Maria J. Indurain creator: Angel Mancilla creator: Leandro Brizuela creator: Carolina Vargas-Caro creator: Carlos Bustamante uri: https://doi.org/10.7717/peerj.18992 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Indurain et al. title: Berberine-induced browning and energy metabolism: mechanisms and implications link: https://peerj.com/articles/18924 last-modified: 2025-02-07 description: Obesity has become a global pandemic. The approaches researched to prevent it include decreasing energy intake and/or enhancing energy expenditure. Therefore, research on brown adipose tissue is of great importance. Brown adipose tissue is characterized by its high mitochondrial content. Mitochondrial uncoupling protein 1 (UCP1) releases energy as heat instead of chemical energy. Thermogenesis increases energy expenditure. Berberine, a phytochemical widely used in Asian countries, has positive effects on body weight control. While the precise mechanisms behind this effect remain unclear, the adenosine monophosphate-activated protein kinase (AMPK) pathway is known to play a crucial role. Berberine activates AMPK through phosphorylation, significantly impacting brown adipose tissue by enhancing lipolytic activity and increasing the expression of UCP1, peroxisome proliferator-activated receptor γ-co-activator-1α (PGC1α), and PR domain containing 16 (PRDM16). While investigating the mechanism of action of berberine, both the AMPK pathway is being examined in more detail and alternative pathways are being explored. One such pathway is growth differentiation factor 15 (GDF15), known for its appetite-suppressing effect. Berberine’s low stability and bioavailability, which are the main obstacles to its clinical use, have been improved through the development of nanotechnological methods. This review examines the potential mechanisms of berberine on browning and summarizes the methods developed to enhance its effect. creator: Aslıhan Alpaslan Ağaçdiken creator: Zeynep Göktaş uri: https://doi.org/10.7717/peerj.18924 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Alpaslan Ağaçdiken and Göktaş title: Assessing the quality of life among African medical and health science students using the WHOQOL-BREF tool link: https://peerj.com/articles/18809 last-modified: 2025-02-07 description: BackgroundThe quality of life (QoL) among health professional students is available in the literature, yet there is a paucity of information concerning QoL among African students. The study aimed to measure the QoL with the World Health Organization Quality of Life-BREF (WHOQOL-BREF) tool among African medical and health science students.MethodsA cross-sectional study was conducted involving 349 African medical and health science students from various disciplines at the International African University in May 2024. A purposive sampling method was used to recruit participants from five different faculties. Data were collected using the WHOQOL-BREF tool, and analyzed using descriptive statistics, chi-square test and multiple linear regression to determine the predictors of QoL among students.ResultsThe overall QoL among 349 African medical and health science students was moderate, with a mean score of 67.5% ± 10.8%. The highest mean scores were observed in the physical health domain (69.3% ± 12.0%), while the lowest scores were in the environmental domain (62.9% ± 12.0%). The multiple regression analysis using demographic data as predictors of QoL revealed that dentistry students were significant predictors of higher overall QoL scores compared to other student groups (β = 7.059, p < 0.05), as well as specific QoL domains including physical health (β = 6.328), psychological health (β = 8.415), social relationships (β = 7.823), and environment (β = 7.017). Furthermore, students from the fields of laboratory sciences and medicine significantly predicted higher scores in the physical health domain (β = 5.223) and the psychological health domain (β = 4.433), respectively. Age was also a significant predictor; students aged between 20 and 23 years showed a positive impact on social relationship domain of QoL (β = 10.296). However, second year (β = −11.146), third year (β = −13.629), and fourth-year students (β = −10.144) exhibited lower social relationship domain of QoL scores.ConclusionStudents of medical and health sciences in Africa exhibited moderate quality of life (QoL). The findings indicate that dentistry students generally experience higher QoL across multiple domains, which contrasts with students from other disciplines, such as pharmacy and nursing. Age and academic year were also significant predictors of QoL, with younger students and those in their initial years of study reporting lower scores. These results align with existing literature and underscore the need for targeted interventions to support students, particularly those in high-stress disciplines or at earlier stages of their education. creator: Fatima Alzahra Galgam creator: Adil Abdalla creator: Mahmoud Shahin creator: Magda Yousif creator: Nahla Abdulrahman creator: Fatmah Alamoudi creator: Mehrunnisha Ahmad creator: Amira Yahia creator: Mohammad Sidiq creator: Aksh Chahal creator: Fuzail Ahmad creator: Mohammad Abu Shaphe creator: Gopal Nambi creator: Moattar Raza Rizvi creator: Faizan Kashoo uri: https://doi.org/10.7717/peerj.18809 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Galgam et al. title: Effect of intercropping Lolium perenne in Ziziphus jujuba orchards on soil quality in the canopy link: https://peerj.com/articles/18710 last-modified: 2025-02-07 description: The cultivation of Lingwu jujube traditionally employs clean tillage, leaving substantial gaps between rows and exposing almost 60% of the orchard to the elements. This method promotes rapid soil moisture evaporation, exacerbates soil erosion, and deteriorates the soil’s physicochemical properties. Consequently, there is a critical need for a more sustainable planting approach that optimally utilizes land resources. A pertinent question is whether varying densities of ryegrass intercropping can improve the uptake of nutrients and water by the jujube tree, the primary species in this ecosystem. In this context, a 2-year field experiment was conducted with three densities of perennial ryegrass intercropped with Lingwu jujube. The experiment assessed the impact on soil’s physical and chemical attributes beneath the jujube canopy, with a focus on correlating soil moisture, enzyme activity, and physical properties. The findings reveal that intercropping at a medium density most effectively enhanced the soil’s physical characteristics. Relative to monoculture, this approach increased the proportion of water-stable aggregates (0.5–0.25 mm) by 4.16%, decreased the soil’s fractal dimension by 0.46%, augmented the field water holding capacity by 14.78%, and significantly boosted soil enzyme activity. Furthermore, high-density ryegrass intercropping elevated the soil’s organic matter content by 36.09% and ameliorated both the pH and cation exchange capacity. Conversely, low-density intercropping raised soil moisture levels by 40.18% in the top 20 cm of the soil. Collectively, these results suggest that an optimal density of ryegrass in intercropping not only bolsters the moisture retention capabilities of soil in Lingwu jujube orchards but also enhances overall soil fertility. Therefore, the adoption of ryegrass and jujube tree intercropping is highly advisable in the ecologically sensitive and resource-constrained arid sandy regions of northern China, offering substantial practical benefits. creator: Yao Ma creator: Bin Cao creator: Xiaojia Wang creator: Weijun Chen uri: https://doi.org/10.7717/peerj.18710 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ma et al. title: Sex differences in anaerobic performance in CrossFit® athletes: a comparison of three different all-out tests link: https://peerj.com/articles/18930 last-modified: 2025-02-05 description: BackgroundAthletic performance can be influenced by various factors, including those related to biological sex. Various scientific disciplines have studied the observed differences in athletic performance between men and women. Moreover, anaerobic performance refers to the capacity of the human body to generate energy quickly and efficiently during high-intensity and short-duration activities. It is associated with the ability to perform explosive actions and the capacity for rapid recovery between repeated efforts. Anaerobic performance is a determining factor for performance in high-intensity sports and those with predominantly lower intensity but intermittent peaks of higher intensity. One high-intensity sport that has experienced exponential growth and attracts increasing numbers of participants yearly is commercially known as CrossFit® (CF). Therefore, the primary purpose of this study was to determine the anaerobic performance differences between sexes in CF athletes in terms of absolute and relative values.MethodsA cross-sectional study was conducted over 2 weeks. Fifty CrossFit® athletes (25 men and 25 women) voluntarily participated in the study. They were subjected to body composition analysis and three maximal effort tests to measure anaerobic performance: a cycle ergometer test, a continuous jump test and a squat test.ResultsSignificant differences were found in all the variables of absolute peak power and relative to body mass in the three tests. In values adjusted to lean and muscle mass, significant differences were only found in the cycle ergometer test but not in the other two. In mean power variables, significant differences were found in all the variables studied, except for the mean power adjusted to muscle mass in the squat test. In conclusion, this study’s results indicate that differences between sexes in absolute and relative peak powers measured in all tests evaluated are explained by the amount of lean and muscle mass. However, mean powers show significant differences in all variables except for the one related to muscle mass in the squat test. creator: Tomás Ponce-García creator: Jerónimo García-Romero creator: Laura Carrasco-Fernández creator: Alejandro Castillo-Domínguez creator: Javier Benítez-Porres uri: https://doi.org/10.7717/peerj.18930 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Ponce-García et al. title: PyBootNet: a python package for bootstrapping and network construction link: https://peerj.com/articles/18915 last-modified: 2025-02-05 description: BackgroundNetwork analysis has emerged as a tool for investigating interactions among species in a community, interactions among genes or proteins within cells, or interactions across different types of data (e.g., genes and metabolites). Two aspects of networks that are difficult to assess are the statistical robustness of the network and whether networks from two different biological systems or experimental conditions differ.MethodsPyBootNet is a user-friendly Python package that integrates bootstrapping analysis and correlation network construction. The package offers functions for generating bootstrapped network metrics, statistically comparing network metrics among datasets, and visualizing bootstrapped networks. PyBootNet is designed to be accessible and efficient with minimal dependencies and straightforward input requirements. To demonstrate its functionality, we applied PyBootNet to compare correlation networks derived from study using a mouse model to investigate the impacts of Polycystic Ovary Syndrome (PCOS) on the gut microbiome. PyBootNet includes functions for data preprocessing, bootstrapping, correlation matrix calculation, network statistics computation, and network visualization.ResultsWe show that PyBootNet generates robust bootstrapped network metrics and identifies significant differences in one or more network metrics between pairs of networks. Our analysis of the previously published PCOS gut microbiome data also showed that our network analysis uncovered patterns and treatment effects missed in the original study. PyBootNet provides a powerful and extendible Python bioinformatics solution for bootstrapping analysis and network construction that can be applied to microbes, genes, metabolites and other biological data appropriate for network correlation comparison and analysis. creator: Shayan R. Akhavan creator: Scott T. Kelley uri: https://doi.org/10.7717/peerj.18915 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Akhavan and Kelley title: The effects of gluteal stretching vs. Lightback® on hip rotation range of motion and posterior chain flexibility in healthy subjects: a cross-over clinical trial link: https://peerj.com/articles/18523 last-modified: 2025-02-05 description: IntroductionHip range of motion (ROM) across various planes is necessary in sport-related activities. Static stretching was commonly used to improve hip ROM. The Lightback system, a novel compression device, has been developed to enhance hip mobility by applying controlled axial forces on the femur. This study aimed to evaluate the effectiveness of the Lightback system in improving hip ROM and posterior chain flexibility compared to conventional static stretching.MethodsA randomized cross-over trial was carried out in 31 physically active participants (62 lower limbs; n = 31 Lightback group (LBG) and n = 31 stretching group (SG)). Hip rotation at two positions of hip flexion (active and passive external (ER) and internal rotation (IR) at 0–90° hip flexion), total rotation ROM (TRROM), and the flexibility of the posterior chain (active knee extension test (AKE) and active straight leg raise (ASLR)) were measured before and after the stretching session.ResultsLBG demonstrated significantly greater improvements in hip ER and IR compared to the SG. Specifically, the LBG showed significant increases in active ER at 0° (p = 0.002) and 90° (p < 0.001) of hip flexion, as well as IR at 0° (p = 0.007) and 90° (p < 0.001). TRROM in neutral and at 90° of hip flexion also improved significantly in the LBG (p < 0.001). In passive ROM, the LBG exhibited significant increases in ER at 0° (p < 0.001), IR at 90° (p = 0.001), and TRROM at both positions (p < 0.001), compared to the SG. Regarding posterior chain flexibility, both groups improved in AKE and ASLR (p < 0.001), but the LBG showed a significantly larger effect in ASLR (p < 0.001), with no significant difference between groups in AKE.ConclusionThis study demonstrated that both the Lightback system and static gluteal stretching improved passive hip ROM. However, the Lightback system showed greater improvements in active ROM, particularly in external and internal rotation at various degrees of hip flexion, as well as in posterior chain flexibility. Notably, the Lightback system significantly enhanced large improvement in the ASLR test. creator: Charles Cotteret creator: Jaime Almazán-Polo creator: Fabien Guérineau creator: Ángel González de-la-Flor uri: https://doi.org/10.7717/peerj.18523 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Cotteret et al. title: Closing the gap while standing still: clinimetric properties of a low-cost balance platform and a user-friendly app for posturography link: https://peerj.com/articles/18299 last-modified: 2025-02-04 description: BackgroundThe Wii Balance Board (WBB) is used as a rehabilitation tool for balance or strength interventions and posturography in balance tasks. Nonetheless, implementation of posturography using the WBB in a clinical setting is hampered by required technical skills for signal processing to obtain meaningful balance measures. Therefore, this study aims to evaluate the concurrent validity and test–retest reliability of a WBB to measure center of pressure (COP) parameters and to provide an easy-to-use web application to improve implementation of posturography in clinical practice.MethodsA cross-sectional study was carried out including 30 healthy adults who performed repeated balance tasks including single and double leg standing still with eyes open or eyes closed. A WBB on top of a laboratory-grade force plate synchronously measured COP. Parameters based on COP displacement were calculated, including standard deviation of displacement, velocity, pathlength and 95% predicted ellipse area.ResultsThe concurrent validity of the WBB to measure COP in quiet standing still tasks was excellent for all parameters (Intraclass Correlation Coefficient (ICC) > 0.900, p < 0.001), apart from medio-lateral velocity (ICC = 0.571, p = 0.090 to ICC = 0.711, p = 0.057). For the single leg balance tasks, across the two measurements, all WBB COP derived parameters showed excellent correlations with COP parameters derived from a laboratory-grade force plate (ICC > 0.95, p < 0.001). Test–retest reliability of the WBB was poor (ICC below 0.5) to occasionally good (ICC between 0.75 to 0.90) for the COP parameters from quiet standing balance tasks. Comparable reliability was found for the repeated measurements of single leg standing still. Power spectra analysis of both force plates revealed larger measurement error by the WBB in medio-lateral direction in tasks requiring minimal postural adjustments.ConclusionThe WBB revealed excellent concurrent validity with a laboratory-grade force plate for balance tasks on a single leg or two legs for most COP parameters. The reliability was poor to moderate for most tasks, however comparable to the findings from the laboratory grade force plate. An open-source web application, employing R Shiny, was created to provide a tool to analyse COP parameters. Hereby, it was demonstrated that open-source scientific tools may help researchers to bridge the gap between scientific findings and clinical use of posturography. creator: Tom Vredeveld creator: John F. Stins creator: Annelies J. van Vliet creator: Vincent C.M. Tuinder creator: Stephan P.J. Ramaekers creator: Michel W. Coppieters creator: Annelies L. Pool-Goudzwaard uri: https://doi.org/10.7717/peerj.18299 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Vredeveld et al.