title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=99 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics link: https://peerj.com/articles/19158 last-modified: 2025-04-14 description: DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, and their implementation as standardized monitoring methods is approaching. Evaluating the efficacy and reliability of these technological developments is crucial for macrobenthos biodiversity assessments. In this study, we compared three DNA-based techniques for assessing the diversity of bulk macrobenthos samples from the Belgian North Sea. Specifically, we compared amplicon sequencing using Illumina MiSeq and portable real-time sequencing of Oxford Nanopore versus shotgun sequencing using Illumina NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served as the target region for the metabarcoding analysis. Our results indicate that Oxford Nanopore and MiSeq metabarcoding had similar performances in terms of alpha and beta diversity, revealing highly similar location-specific community compositions. The NovaSeq metagenomics method also resulted in similar alpha diversity, but slightly different community compositions compared to the metabarcoding approach. Despite these differences, location-specific community compositions were maintained across all platforms. Notably, read counts from the NovaSeq metagenomic analysis showed the weakest correlation to size corrected morphological abundance and there were mismatches between morphological identification and all DNA based findings which are likely caused by a combination of factors such as primer efficiency and an incomplete reference database. Our findings underscore the critical importance of database completeness prior to implementing DNA-based techniques as standardized monitoring method, especially for metagenomics. Nevertheless, our findings emphasize that Oxford Nanopore metabarcoding proves to be a viable alternative to the conventional Illumina MiSeq metabarcoding platform for macrobenthos biodiversity monitoring. creator: Karlijn Doorenspleet creator: Amalia Aikaterini Mailli creator: Berry B. van der Hoorn creator: Kevin K. Beentjes creator: Annelies De Backer creator: Sofie Derycke creator: Albertinka J. Murk creator: Henning Reiss creator: Reindert Nijland uri: https://doi.org/10.7717/peerj.19158 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Doorenspleet et al. title: LASSO-derived nomogram prediction model for lymph node metastasis in colorectal cancer: a retrospective analysis link: https://peerj.com/articles/19148 last-modified: 2025-04-14 description: ObjectiveThis study aims to develop a prediction model for lymph node metastasis (LNM) in colorectal cancer (CRC) patients using common clinicopathologic data and a nomogram. The model seeks to uncover correlations between LNM and clinical indicators, providing an effective tool to identify high-risk patients, aiding clinical decision-making, and enhancing patient prognosis.MethodsWe conducted a retrospective analysis of CRC patients diagnosed between January 2021 and December 2023 at Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University. Risk predictors for LNM were identified through comparative analysis and Least Absolute Shrinkage and Selection Operator (LASSO) logistic regression. Nomograms were then utilized to predict the probability of metastasis, and their performance was assessed using calibration curves, receiver operating characteristic (ROC) curves, and decision curve analysis.ResultsThe study comprised 869 CRC patients, with 435 cases allocated to the training set and 434 cases to the validation set. First, 12 potential risk factors for LNM in CRC patients were identified through comparative analysis in the training set. Next, nine independent predictors (T stage, vascular tumor thrombus, PMS2, MSH2, KRAS, BRAF, PIK3CA, leukocyte, and neutrophil) of LNM occurrence were refined using LASSO regression and multivariate logistic regression models. Subsequently, a clinical nomogram was developed based on these independent predictors of LNM. The nomogram exhibited a C-index of 0.751 (95% CI [0.728–0.774]), indicating its robust predictive value, which was further validated in the independent validation set.ConclusionT stage, vascular tumor thrombus, PMS2, MSH2, KRAS, BRAF, and neutrophil emerged as significant risk factors for LNM in CRC, while leukocytes appeared to be protective. These findings emphasize the importance of comprehensive risk assessment and personalized therapeutic strategies in CRC management. creator: Xiyun Quan creator: Yi Deng creator: Zhimin Liu creator: Zhenqin Gao creator: Huimei Yi creator: Ming Li uri: https://doi.org/10.7717/peerj.19148 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Quan et al. title: A retrospective study using machine learning to develop predictive model to identify rotavirus-associated acute gastroenteritis in children link: https://peerj.com/articles/19025 last-modified: 2025-04-14 description: BackgroundRotavirus is the leading cause of severe dehydrating diarrhea in children under 5 years worldwide. Timely diagnosis is critical, but access to confirmatory testing is limited in hospital settings. Machine learning (ML) models have shown promising potential in supporting symptom-based diagnosis of several diseases in resource-limited settings.ObjectivesThis study aims to develop a machine-learning predictive model integrated with multiple sources of clinical parameters specific to rotavirus infection without relying on laboratory tests.MethodsA clinical dataset of 509 children was collected in collaboration with the Regional Institute of Medical Sciences, Imphal, India. The clinical symptoms included diarrhea and its duration, number of stool episodes per day, fever, vomiting and its duration, number of vomiting episodes per day, temperature and dehydration. Correlation analysis is performed to check the feature-feature and feature-outcome collinearity. Feature selection using ANOVA F test is carried out to find the feature importance values and finally obtain the reduced feature subset. Seven supervised learning models were tested and compared viz., support vector machine (SVM), K-nearest neighbor (KNN), naive Bayes (NB), logistic regression (Log_R) , random forest (RF), decision tree (DT), and XGBoost (XGB). A comparison of the performances of the seven models using the classification results obtained. The performance of the models was evaluated based on accuracy, precision, recall, specificity, F1 score, macro F1, F2, and receiver operator characteristic curve.ResultsThe seven ML models were exhaustively experimented on our dataset and compared based on eight evaluation scores which are accuracy, precision, recall, specificity, F1 score, F2 score, macro F1 score, and AUC values computed. We observed that when the seven ML models were applied, RF performed the best with an accuracy of 81.4%, F1 score of 86.9%, macro F1-score of 77.3%, F2 score of 86.5% and area under the curve (AUC) of 89%.ConclusionsThe machine learning models can contribute to predicting symptom-based diagnosis of rotavirus-associated acute gastroenteritis in children, especially in resource-limited settings. Further validation of the models using a large dataset is needed for predicting pediatric diarrheic populations with optimum sensitivity and specificity. creator: Sourav Paul creator: Minhazur Rahman creator: Anutee Dolley creator: Kasturi Saikia creator: Chongtham Shyamsunder Singh creator: Arifullah Mohammed creator: Ghazala Muteeb creator: Rosy Sarmah creator: Nima D. Namsa uri: https://doi.org/10.7717/peerj.19025 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Paul et al. title: Genetic assessment of farmed Oreochromis mossambicus populations in South Africa link: https://peerj.com/articles/18877 last-modified: 2025-04-14 description: The global utilisation of Oreochromis spp. in freshwater aquaculture extends to South Africa. Here the native Mozambique tilapia (Oreochromis mossambicus) has been proposed as a priority species for regional aquaculture projects, although it is still not preferred over the non-native O. niloticus. There is limited understanding of the genetic diversity, and genetic differentiation of farmed O. mossambicus in South Africa. Using a suite of 14 microsatellite markers, the present study aimed to determine the origin and genetic diversity of four farmed O. mossambicus populations in KwaZulu-Natal and Mpumalanga provinces. Wild O. mossambicus from rivers surrounding the farms were included to trace the origin of farmed populations. Results revealed lower genetic diversity in farmed populations compared to wild populations. In particular, the University of Zululand population exhibited lower genetic diversity compared to the rest of the farmed populations. While most farmed populations closely resembled their local wild counterparts, the uMphafa ponds exhibited distinct genetic characteristics. Notably, some individuals from uMphafa shared genetic affinities with those from the Thukela River, suggesting that the Thukela River could be the source of this farmed population, or that farmed fish may have been introduced or escaped into the river. The study suggests that select farmed populations may have the potential for use in breeding and broodstock supplementation programs but emphasizes the importance of thorough genetic monitoring. However, before these populations can be considered for broodstock supplementation, further investigation is required to confirm their genetic integrity and rule out potential contamination from invasive species. creator: Mahlatse Fortunate Mashaphu creator: Gordon Craig O’Brien creator: Colleen Thelma Downs creator: Sandi Willows-Munro uri: https://doi.org/10.7717/peerj.18877 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mashaphu et al. title: Diversity and distribution of the caddisfly genus Atopsyche Banks, 1905 in Ecuador, with the description of seven new species (Trichoptera: Hydrobiosidae) link: https://peerj.com/articles/18769 last-modified: 2025-04-14 description: Atopsyche is the largest Hydrobiosidae genus on the South American continent. The genus previously included 27 species in Ecuador. In this work, we describe and illustrate seven new species of Atopsyche from the Andes of Ecuador: Atopsyche andinasp. nov., Atopsyche azuayanasp. nov., Atopsyche chocoandinasp. nov., Atopsyche jocotocosp. nov., Atopsyche papallactasp. nov., Atopsyche piburjasp. nov., and Atopsyche tapichalacasp. nov. Additionally, we provide distributional information for all Ecuadorian Atopsyche, including three new country records: A. kingi, A. mayucapac, and A. neotropicalis. With these additions, there are now 37 species of Atopsyche in Ecuador, or about 75% of species in the country, according to the CHAO 2 species estimator. Finally, we provide new and more detailed illustrations for A. bolivari, A. bravoi, and A. davidsoni. creator: Ernesto Rázuri-Gonzales creator: Ralph Holzenthal creator: Blanca Ríos-Touma uri: https://doi.org/10.7717/peerj.18769 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Rázuri-Gonzales et al. title: Assessing reliability and accuracy of qPCR, dPCR and ddPCR for estimating mitochondrial DNA copy number in songbird blood and sperm cells link: https://peerj.com/articles/19278 last-modified: 2025-04-11 description: Mitochondrial DNA (mtDNA) copy number varies across species, individuals, and cell types. In birds, there are two types of cells with a relatively low number of mitochondria: red blood cells and spermatozoa. Previous studies investigating variation of mitochondrial abundance in animal sperm have generally used quantitative PCR (qPCR), but this method shows potential limitations when quantifying targets at low abundance. To mitigate such issues, we investigated and compared the reliability and accuracy of qPCR, digital PCR (dPCR) and droplet digital PCR (ddPCR) to quantify high and low concentration DNA. We used synthetic DNA targets, to calculate the limit of detection and the limit of quantification and found that with both dPCR and ddPCR, these limits were lower than with qPCR. Then, to compare quantification accuracy and repeatability, we used DNA extracted from blood and sperm cells of Eurasian siskin. We found that qPCR, dPCR and ddPCR all reliably quantified mitochondrial DNA in sperm samples but showed significant differences when analyzing the typically lower levels of mtDNA in blood, with ddPCR consistently showing lower variation among replicates. Our study provides critical insights and recommendations for future studies aiming to quantify target mtDNA and indicates that dPCR and ddPCR are the preferred methods when working with samples with low abundance of mtDNA. creator: Laima Bagdonaitė creator: Erica H. Leder creator: Jan T. Lifjeld creator: Arild Johnsen creator: Quentin Mauvisseau uri: https://doi.org/10.7717/peerj.19278 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Bagdonaitė et al. title: Association between polymorphisms of the adenylate cyclase 3 gene rs2241759 and the effect of high-intensity interval training on blood lipid profiles link: https://peerj.com/articles/19271 last-modified: 2025-04-11 description: BackgroundOne of the recognized effects of systematic physical activity is the improvement of physical fitness, with a negative correlation found between physical fitness and cardiovascular and cardiometabolic risk. The purpose of this study is to analyze the influence of single nucleotide polymorphisms (SNPs) of the adenylate cyclase 3 (ADCY3) gene on the effect of high-intensity interval training (HIIT) on blood lipids, and simultaneously screen out the genetic markers sensitive to HIIT in Chinese Han youth.MethodsIn the 12-week HIIT program, a total of 237 Chinese Han college students with non-regular exercise habits were recruited, and these volunteers participated in the training three times a week. Baseline and after the HIIT program, total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) were measured, respectively. DNA was extracted from the white blood cells of volunteers and genotyping was carried out. The PLINK v1.09 software was used to conduct quality control screening on the obtained SNPs, and a linear regression model was constructed to analyze the association between ADCY3 gene SNPs and the effect of HIIT on blood lipids. ANOVA multiple comparison (LSD) was performed to test the difference between groups (P < 0.05).Results(1) Through the analysis of Illumina CGA chip scanning, a total of 22 SNPs of the ADCY3 gene were identified. Following rigorous quality control screening, 15 SNPs were included in the subsequent analysis. Notably, it was found that the rs2241759 locus is associated with the effect of HIIT on blood lipid profiles. (2) Among male volunteers, significant differences in the baseline HDL-C values were observed among the three genotypes at the rs2241759 locus of the ADCY3 gene (β =  − 0.019, P = 0.040). The baseline value for the GG genotype was higher than that AA/AG genotypes. (3) After HIIT, the total levels of TC and HDL-C in volunteers increased significantly (P < 0.05). In contrast, the total levels of TG and LDL-C decreased significantly (P < 0.05). Further statistical analysis categorized by gender revealed that, with the exception of TC values in men, significant changes were observed for TC, TG, HDL-C, and LDL-C across both genders (P < 0.05). (4) Compared to male volunteers with the GG genotype, male volunteers carrying the A allele exhibited a more pronounced change in TC values following training (β = 0.044, P = 0.038). (5) The rs2241759 locus demonstrated a significant association with the effect of HIIT on LDL-C (β =  − 0.065, P = 0.04363).Conclusion(1) The implementation of a 12-week HIIT regimen can significantly enhance the blood lipid status of college students. (2) The locus rs2241759 of the ADCY3 gene is significantly associated with the sensitivity of LDL-C to HIIT. creator: Junren Lai creator: Li Gong creator: Yan Liu creator: Yanchun Li creator: Jing Ni creator: Duoqi Zhou uri: https://doi.org/10.7717/peerj.19271 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Lai et al. title: Circulating microRNAs demonstrate limited diagnostic potential for diabetic retinopathy in the population of Kazakhstan link: https://peerj.com/articles/19259 last-modified: 2025-04-11 description: BackgroundDiabetic retinopathy (DR) is the most common complication of diabetes, leading to blindness. The asymptomatic onset and the existing difficulties in diagnosing warrant the search for biomarkers that can facilitate the early diagnosis of DR. The aim of this study was to evaluate the potential of plasma microRNAs (miRNAs), which have previously been shown to be involved in the pathogenesis of DR and differentially expressed in plasma/serum of patients, as biomarkers for DR in the Kazakhstani population.Materials and MethodsUsing quantitative RT-PCR, we compared the levels of ten candidate miRNAs in plasma among three groups: type 2 diabetes mellitus (T2DM) patients with DR (DR patients, N = 100), T2DM patients without DR (noDR patients, N = 98), and healthy controls (N = 30).ResultsLevel of miR-423-3p was significantly reduced in DR patients compared to noDR patients (pFDR = 5.4 × 10−3). Levels of miR-423-3p and miR-221-3p were significantly reduced in DR patients compared to controls (pFDR = 5.4 × 10−3 and 0.024, respectively ), level of miR-23a-3p was significantly reduced in noDR patients compared to controls (pFDR = 0.047), levels of miR-221-3p and miR-23a-3p were significantly reduced in T2DM patients (combined group) compared to controls (pFDR = 0.047, and 0.049, respectively). Also, there were several significant differences between groups formed based on clinical-pathological characteristics, but none of these results remained significant after adjustment for multiple comparisons. Correlation analysis revealed weak associations between the levels of miR-423 and miR-221-3p and DR staging (pFDR = 1.3 × 10−3 and 0.026, respectively), and fair associations between the levels of miR-29b-3p and miR-328-3p and diabetes duration in noDR patients (pFDR = 8.8 × 10−3 and 0.016, respectively). According to receiver operating characteristic (ROC) analysis, only miR-23a-3p can be considered a potential biomarker with moderate informativeness for diagnosing proliferative DR (PDR); however, a larger sample size is needed to verify this finding. Furthermore, the small magnitude of observed changes in miRNA levels between groups significantly complicates classification.ConclusionsDue to the low specificity and small magnitude of deviations from the norm, the studied miRNAs have low potential in the diagnosis of DR. creator: Aizhan Magazova creator: Yeldar Ashirbekov creator: Arman Abaildayev creator: Kantemir Satken creator: Gulzhakhan Utegenova creator: Ayaz Belkozhayev creator: Altynay Balmukhanova creator: Zaure Dzhumatayeva creator: Ainagul Beissova creator: Iryna Shargorodska creator: Aigul Balmukhanova creator: Kamalidin Sharipov uri: https://doi.org/10.7717/peerj.19259 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Magazova et al. title: Differences in depression prevalence among older adults in China before and during the COVID-19 pandemic: a systematic review and meta-analysis link: https://peerj.com/articles/19251 last-modified: 2025-04-11 description: ObjectiveChanges in the prevalence of depression during the COVID-19 (Coronavirus disease 2019) pandemic among older adults in China have not been systematically evaluated. We aimed to systematically summarize existing evidence to conduct a meta-analysis to quantify changes in the prevalence of depression before and during the COVID-19 pandemic.MethodsThe PubMed, Web of Science, Scopus, Embase, PsycINFO, China National Knowledge Infrastructure (CNKI), WangFang Data, CQVIP, and China Biology Medicine disc (CBMdisc) databases were searched from January 1, 2017, to November 20, 2024. Studies reporting the prevalence of depression among Chinese individuals aged 60 or older using validated diagnostic tools were included. A random-effects model was applied to estimate pooled prevalence, with subgroup analyses performed by demographic and socio-economic factors. Relative risks (RR) were calculated to compare prevalence across different pandemic stages.ResultsA total of 101 studies involving 264,758 participants were included. The pooled prevalence of depression among older adults was 25.8% (95% CI [21.7–29.9]) from 2017–2019 and 23.8% (95% CI [19.8–27.8]) from 2020–2023. During the early pandemic stage (January–April 2020), prevalence significantly decreased (RR = 0.849, P < .001) but increased in later stages, reaching 24.4% by 2021–2023. The prevalence of depression among older adults during the COVID-19 pandemic showed a significant increasing trend (Ptrend < .001). Subgroup analyses revealed higher prevalence among females, rural residents, individuals with lower education levels, and those living alone.ConclusionDepression prevalence among older adults in China decreased during the early pandemic response but showed an increasing trend over time, reflecting the complex mental health impact of prolonged public health measures. Effective interventions are needed to address the specific needs of vulnerable subgroups during and beyond public health crises. creator: Xin Zhao creator: Xiaojing Du creator: Shuliang Bai creator: Pianpian Zheng creator: Xun Zhou creator: Zhenjie Wang uri: https://doi.org/10.7717/peerj.19251 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhao et al. title: Effects of gait speed on paraspinal muscle activation: an sEMG analysis of the multifidus and erector spinae link: https://peerj.com/articles/19244 last-modified: 2025-04-11 description: BackgroundThe paraspinal muscles, such as the multifidus muscles and erector spinae muscles, play an important role in trunk stabilization and pelvic mobility during gait. Understanding how they are activated according to the speed of locomotion can facilitate the diagnosis and treatment of patients with these conditions. This study aimed to comprehensively analyze the activity of postural muscles (multifidus and erector spinae) using surface electromyography (sEMG) across a range of gait speeds.MethodsThe study group consisted of 31 students of physiotherapy at the Pomeranian University in Słupsk, including 20 women (64.51%) and 11 men (35.48%). The research process included an interview and participation in the sEMG survey. The sEMG examination of the musculus erector spinae (MES) and musculus multifidus (MM) was carried out in the supine, standing position, while walking on a treadmill, maintaining speeds: 1 km/h, 3 km/h, 5 km/h and 6 km/h, for 60 s at each stage and at maximum voluntary isometric contraction (MVIC). The percentage value of the amplitude of the sEMG recording in relation to maximum voluntary isometric contraction (%MVIC) was determined. The average rate of change in muscle activity was also assessed in relation to the respective changes in locomotion speed for MES and MM.ResultsThe results show significant differences in the %MVIC parameter between sides (left vs right) for both muscle groups (MES and MM) in the supine position and in the standing position for the multifidus muscles. At the set speeds of 1 km/h, 3 km/h, 5 km/h and 6 km/h, the differences are not statistically significant. A decreasing trend in the rate of change in muscle activity was also observed for both muscle groups as gait speed increased. The most significant decrease is observed at average gait speeds of 3–5 km/h.ConclusionsIn the sEMG examination during rest, standing and walking, the activity of the right and left MES and MM muscles examined is not always equal. The activity of the muscles studied (MES and MM) increases with increasing gait speed. The rate of change in muscle activity decreases as gait speed increases. creator: Aleksandra Bryndal creator: Wojciech Nawos-Wysocki creator: Agnieszka Grochulska creator: Karol Łosiński creator: Sebastian Glowinski uri: https://doi.org/10.7717/peerj.19244 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Bryndal et al.