title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=120 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: LTR retrotransposon-derived novel lncRNA2 enhances cold tolerance in Moso bamboo by modulating antioxidant activity and photosynthetic efficiency link: https://peerj.com/articles/19056 last-modified: 2025-02-26 description: In Moso bamboo, the mechanism of long terminal repeat (LTR) retrotransposon-derived long non-coding RNA (TElncRNA) in response to cold stress remains unclear. In this study, several Pe-TElncRNAs were identified from Moso bamboo transcriptome data. qRT-PCR analysis showed that the expression of a novel Pe-TElncRNA2 in Moso bamboo seedlings reached its highest level at 8 hours of cold treatment at 4 °C and was significantly higher in the stems compared to the leaves, roots, and buds. Furthermore, cellular localization analysis revealed that Pe-TElncRNA2 expression was significantly higher in the cytoplasm than in the nucleus. Pe-TElncRNA2 overexpression in Moso bamboo protoplasts showed that Pe-TElncRNA2 positively regulated the expression of FZR2, NOT3, ABCG44 and AGD6 genes. Further validation of this lncRNA in Arabidopsis thaliana enhanced antioxidant activities, as evidenced by increased superoxide dismutase (SOD) activity and proline content, as well as maximum photochemical efficiency PS II in dark-adapted leaves (Fv/Fm), in the transgenic plants compared to the wild-type controls. Conversely, malondialdehyde (MDA) content, a lipid peroxidation marker (a marker of oxidative stress), was significantly reduced in the transgenic plants. Notably, the expression levels of both Pe-TElncRNA2 and the genes that were regulated by this lncRNA were upregulated in the transgenic plants after two days of cold stress treatment. These findings elucidate the critical role of LTR retrotransposon-derived lncRNAs in mediating cold stress responses in Moso bamboo. creator: Jiamin Zhao creator: Yiqian Ding creator: Muthusamy Ramakrishnan creator: Long-Hai Zou creator: Yujing Chen creator: Mingbing Zhou uri: https://doi.org/10.7717/peerj.19056 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Zhao et al. title: Optimal input DNA thresholds for genome skimming in marine crustacean zooplankton link: https://peerj.com/articles/19054 last-modified: 2025-02-26 description: Crustacean zooplanktons are key secondary and tertiary producers in marine ecosystems, yet their genomic resources remain poorly understood. To advance biodiversity research on crustacean zooplankton, this study evaluated the effectiveness of genome skimming, a method that assembles genetic regions, including mitogenome, from shotgun genome sequencing data. Because the small amount of DNA available is a limitation in zooplankton genetics, different input DNA amounts (1 pg–10 ng) were prepared for library construction for genome skimming using two large species: Euphausia pacifica (Euphausiacea) and Calanus glacialis (Copepoda). Additionally, de novo assembly was used to obtain long contigs from short reads because reference-guided assembly can not be applied to all crustacean zooplankton. Evaluation of the raw sequence reads showed increased proportions of high-quality and distinct reads (low duplication levels) for large DNA inputs. By contrast, low sequence quality and high sequence duplication were observed for ≤ 10 pg DNA samples, owing to increased DNA amplification cycles. Complete mitogenomes, including all 37 genes, were successfully retrieved for ≥ 10 pg (E. pacifica) and ≥ 100 pg (C. glacialis) of DNA. Despite the large estimated genome sizes of these zooplankton species, only ≥ 1 and ≥ 3 M reads were sufficient for mitogenome assembly for E. pacifica and C. glacialis, respectively. Nuclear ribosomal repeats and histone 3 were identified in the assembled contigs. As obtaining sufficient DNA amounts (≥ 100 pg) is feasible even from small crustacean zooplankton, genome skimming is a powerful approach for robust phylogenetics and population genetics in marine zooplankton. creator: Junya Hirai uri: https://doi.org/10.7717/peerj.19054 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Hirai title: Assessment of urinary oxidative stress biomarkers associated with fine particulate matter (PM2.5) exposure in Chiang Mai, Thailand link: https://peerj.com/articles/19047 last-modified: 2025-02-26 description: BackgroundExposure to fine particulate matter (PM2.5) is known to increase oxidative stress, impacting health adversely. This study examines the relationship between PM2.5 exposure and oxidative stress biomarkers in Chiang Mai, Thailand.MethodsA pilot prospective observational study was conducted in Samoeng District, Chiang Mai, including 25 healthy participants (age 25–60 years). Urine samples were collected during high (March–April 2023) and low (May–July 2023) PM2.5 seasons. PM2.5 concentrations were monitored daily from the Northern Thailand Air Quality Health Index (NTAQHI) system. Biomarkers analyzed included 1-hydroxypyrene (1-OHP) using high-performance liquid chromatography (HPLC), malondialdehyde (MDA) via Spectrophotometry, and 8-epi-prostaglandin F2α (8-epi-PGF2α) with Enzyme-linked Immunosorbent Assay (ELISA). Statistical analysis was performed using IBM SPSS Statistics 22.0.ResultsSignificant increases in urinary 1-OHP, MDA, and 8-epi-PGF2α were observed during the high PM2.5 season compared to the low season. The mean concentration of PM2.5 was 67 µg/m3 during high pollution and 7 µg/m3 during low pollution. Elevated levels of these biomarkers indicate increased oxidative stress associated with higher PM2.5 exposure.ConclusionsThis study highlights a significant association between elevated PM2.5 levels and increased oxidative stress biomarkers in Chiang Mai, Thailand. The findings suggest that exposure to higher concentrations of PM2.5 contributes to oxidative stress, potentially leading to adverse health outcomes. creator: Shamsa Sabir creator: Surat Hongsibsong creator: Hataichanok Chuljerm creator: Wason Parklak creator: Sakaewan Ounjaijean creator: Puriwat Fakfum creator: Sobia Kausar creator: Kanokwan Kulprachakarn uri: https://doi.org/10.7717/peerj.19047 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sabir et al. title: Association of Chinese visceral adiposity index with asymptomatic hyperuricemia incidence in type 2 diabetes: a cross-sectional study link: https://peerj.com/articles/19045 last-modified: 2025-02-26 description: BackgroundPrevious research has shown a correlation between high visceral fat levels and hyperuricemia incidence. The Chinese Visceral Adiposity Index (CVAI) assessed visceral fat status in the Chinese population. Our study investigates the correlation between CVAI and asymptomatic hyperuricemia in type 2 diabetes patients.MethodsThis cross-sectional study analyzed 1,588 hospitalized type 2 diabetes patients to investigate the association between CVAI and hyperuricemia. CVAI was included in the logistic regression analysis as both a continuous and categorical variable, and restricted cubic splines were used to assess the dose-response relationship. Additionally, subgroup analyses were performed to investigate potential interactions among variables. The predictive capability of CVAI was assessed using the receiver operating characteristic (ROC) curve based on the basic model.ResultsThe CVAI quartile group analysis revealed a higher prevalence of hyperuricemia with increasing CVAI levels. CVAI is significantly associated with hyperuricemia, as identified through multifactorial logistic regression analysis. After adjusting for all covariates, the odds ratios for CVAI in the second, third, and fourth quartiles were significantly higher than in the lowest quartile, with values of 2.688 (95% CI [1.301–5.554], p = 0.008), 2.752 (95% CI [1.320–5.739], p = 0.007), and 4.990 (95% CI [2.392–10.409], p < 0.001), respectively. No significant interactions were observed in the subgroup analysis. Incorporating CVAI into the basic model increased the ROC curve’s area under the curve to 0.714.ConclusionThis study found a positive correlation between CVAI and hyperuricemia incidence in type 2 diabetes patients. Consequently, CVAI may reliably indicate hyperuricemia in this patient population. creator: Qing Wang creator: Tian Liu creator: Changxin Jia creator: Ping Wang creator: Yangang Wang creator: Qing He uri: https://doi.org/10.7717/peerj.19045 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 Wang et al. title: Prognostic nutritional index (PNI) as an influencing factor for in-hospital mortality in patients with stroke-associated pneumonia: a retrospective study link: https://peerj.com/articles/19028 last-modified: 2025-02-26 description: BackgroundStroke-associated pneumonia (SAP) significantly increases patients’ risk of death after stroke. The identification of patients at high risk for SAP remains difficult. Nutritional assessment is valuable for risk identification in stroke patients. The aim of this study was to evaluate the relationship between prognostic nutritional index (PNI) levels and in-hospital mortality in SAP patients.MethodsA total of 336 SAP patients who visited the Third People’s Hospital of Chengdu from January 2019 to December 2023 were included in this study, and PNI were calculated based on the results of admission examinations. Linear regression was used to analyze the influencing factors of baseline PNI in SAP patients. Logistic regression as well as restricted cubic splines (RCS) were used to analyze the relationship between baseline PNI levels and hospital mortality events in SAP patients. Receiver operating characteristic (ROC) curves were plotted to assess the predictive value of PNI for in-hospital mortality by area under the curve (AUC).ResultsThirty out of 336 SAP patients presented with in-hospital mortality and these patients had significantly lower PNI levels. In our study, PNI levels were influenced by age, body mass index, and total cholesterol. Increased PNI levels are an independent protective factor for the risk of in-hospital mortality in SAP patients (OR: 0.232, 95% CI [0.096–0.561], P = 0.001). There was a nonlinear correlation between PNI and in-hospital mortality events (P for nonlinear <0.001). In terms of predictive effect, PNI levels were more efficacious in predicting in-hospital mortality in SAP patients with higher sensitivity and/or specificity compared to individual indicators (AUC = 0.750, 95% CI [0.641–0.860], P < 0.001).ConclusionPNI levels in SAP patients were associated with the short-term prognosis of patients, and SAP patients with elevated PNI levels had a reduced risk of in-hospital mortality. creator: Ke Xie creator: Chuan Zhang creator: Shiyu Nie creator: Shengnan Kang creator: Zhong Wang creator: Xuehe Zhang uri: https://doi.org/10.7717/peerj.19028 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Xie et al. title: Effects of larval foam-making and prolonged terrestriality on morphology, nitrogen excretion and development to metamorphosis in a Leptodactylid frog link: https://peerj.com/articles/18990 last-modified: 2025-02-26 description: At ontogenetic transitions, animals often exhibit plastic variation in development, behavior and physiology in response to environmental conditions. Most terrestrial-breeding frogs have aquatic larval periods. Some species can extend their initial terrestrial period, as either a plastic embryonic response to balance trade-offs across environments or an enforced wait for rain that allows larvae to access aquatic habitats. Terrestrial larvae of the foam-nesting frog, Leptodactylus fragilis, can arrest development, make their own nest foam to prevent dehydration, and synthesize urea to avoid ammonia toxicity. These plastic responses enable survival during unpredictably long periods in underground nest chambers, waiting for floods to enable exit and continued development in water. However, such physiological and behavioral responses may have immediate and long-term carry-over effects across subsequent ecological and developmental transitions. We examined effects of prolonged terrestriality and larval foam-making activity on larval physiology, development, and metamorphosis in L. fragilis. We tested for changes in foam-making ability by measuring the nests larvae produced following complete removal of parental foam at different ages. We measured ammonia and urea levels in larval foam nests to assess nitrogen excretion patterns, testing for effects of larval age, soil hydration around parental nests, and repeated nest construction. We also assessed immediate and long-term effects of larval foam-making and prolonged terrestriality on larval morphology at water entry and development to metamorphosis. We found that larvae arrested development during prolonged time on land and even young larvae were able to effectively produce multiple foam nests. We found high ammonia concentrations in larval nests, very high urea excretion by developmentally arrested older larvae, and faster growth of larvae in water than while constructing nests. Nonetheless, sibling larvae had a similar aquatic larval period and size at metamorphosis, regardless of their nest-making activity and timing of water entry. Sibship size increased the size of larval foam nests, but reduced per-capita foam production and increased size at metamorphosis, suggesting maternal effects in cooperative groups. Metamorph size also decreased with aquatic larval period. Our results highlight the extent of larval ability to maintain and construct a suitable developmental environment and excrete N-waste as urea, which are both crucial for survival during enforced extensions of terrestriality. Our results suggest that the energetic reserves in large eggs are sufficient to meet metabolic costs of urea synthesis and foam production during developmental arrest over an extended period on land, with no apparent carry-over effects on fitness-relevant traits at metamorphosis. creator: Javier Méndez-Narváez creator: Karen M. Warkentin uri: https://doi.org/10.7717/peerj.18990 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Méndez-Narváez and Warkentin title: Shoe configuration effects on equine forelimb gait kinetics at a walk link: https://peerj.com/articles/18940 last-modified: 2025-02-26 description: The shift in vertical forces on the equine hoof surface by heart-bar, egg-bar, and wooden clog shoes can significantly impact gait kinetics. Hypotheses tested in this study were that vertical, braking, and propulsion peak force (PF) and impulse (IMP) are different while shod with heart-bar, egg-bar, open-heel, and wooden clog shoes, or while unshod, and the resultant ground reaction force vector (GRFYZ) has the longest duration of cranial angulation with open-heel shoes followed by unshod, then egg-bar and heart-bar shoes, and the shortest with wooden clog shoes. Forelimb GRFs were recorded as six non-lame, light-breed horses walked across a force platform (four trials/side) while unshod or with egg-bar, heart-bar, open-heel, or wooden clog shoes. Outcomes included vertical, braking, and propulsive peak forces (PFV, PFB, PFP) and impulses (IMPV, IMPB, IMPP), percent stance time to each PF, braking to vertical PF ratio (PFB/PFV), walking speed (m s−1), total stance time (ST) and percent of stance in braking and propulsion. The magnitude and direction of the resultant GRFYZ vectors were quantified at 5% stance increments. Kinetic measures were compared among shoeing conditions with a mixed effects model (p-value < 0.05). A random forest classifier algorithm was used to predict shoeing condition from kinetic outcome measures. All results are reported as mean ± SEM. Trial speed, 1.51 ± 0.02 m s−1, was not different among shoeing conditions. The PFV was lower with wooden clog (6.13 ± 0.1 N kg−1) versus egg-bar (6.35 ± 0.1 N kg−1) shoes or unshod (6.32 ± 0.1 N kg−1); the PFP was higher with wooden clog (0.81 ± 0.03 N kg−1) versus open-heel (0.71 ± 0.03 N kg−1) or egg-bar (0.75 ± 0.03 N kg−1) shoes or unshod (0.74 ± 0.03 N kg−1), and lower with open-heel compared to heart-bar shoes (0.77 ± 0.03 N kg−1). Both IMP B and IMPV were higher with open-heel shoes (−0.19 ± 0.008 N s kg−1, 3.28 ± 0.09 N s kg−1) versus unshod (−0.17 ± 0.008 N s kg−1, 3.16 ± 0.09 N s kg−1), and IMPV was higher with wooden clog shoes (3.26 ± 0.09 N s kg−1) versus unshod. With wooden clog shoes, PFB/PFV (0.12 ± 0.004) was higher than unshod (0.11 ± 0.004). Percent time to peak PFV, PFB, and PFP, and percent braking time were highest and percent propulsion time lowest with wooden clog shoes. The magnitude of the GRFYZ vector with the wooden clog shoe was the highest among shoeing conditions during the first stance half, lowest during the second stance half, highest during late propulsion, and had the most gradual braking to propulsion transition. Vectors were angled cranially with wooden clog shoes slightly longer than the others. Wooden clog shoes was the only shoeing condition accurately predicted from kinetic measures. Distinct, predictable changes in gait kinetics with wooden clog shoes may reduce stresses on hoof structures. Study results enhance knowledge about shoe effects on equine gait kinetics and cutting-edge measures to quantify them. creator: Rita Aoun creator: Zaneta Ogunmola creator: Anaïs Musso creator: Takashi Taguchi creator: Catherine Takawira creator: Mandi J. Lopez uri: https://doi.org/10.7717/peerj.18940 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Aoun et al. title: Development and validation of a prognostic nomogram for predicting poor outcomes following intravenous rt-PA in patients with acute ischemic stroke link: https://peerj.com/articles/18937 last-modified: 2025-02-26 description: BackgroundIntravenous administration of recombinant tissue plasminogen activator (rt-PA) within 4.5 h of symptom onset is a standard treatment for acute ischemic stroke (AIS). However, certain patients continue to develop unfavorable outcomes despite timely rt-PA therapy. Identifying those at high risk is essential for developing individualized care plans and establishing appropriate follow-up.MethodsThis retrospective study included AIS patients treated with intravenous rt-PA at 0.9 mg/kg at our center. Outcomes at three months were evaluated using the modified Rankin Scale (mRS). Patients with mRS scores ≤2 were considered to have favorable outcomes, and those with scores >2 were considered to have poor outcomes. Univariable analysis and stepwise logistic regression were used to identify independent predictors of poor prognosis, and a nomogram was subsequently developed. The model’s discriminative power was assessed with area under the receiver operating characteristic curves (AUC-ROC), and its calibration was examined using calibration plots. Decision curves and clinical impact curves were applied to determine clinical utility.ResultsAmong 392 enrolled patients, 77 had poor outcomes three months after rt-PA therapy. Fibrinogen (Fg), baseline NIHSS, and a history of hypertension emerged as independent predictors of poor prognosis. The nomogram achieved an AUC of 0.948 (95% CI [0.910–0.985]), with sensitivity of 0.900 and specificity of 0.916 in the training dataset, and an AUC of 0.959 (95% CI [0.907–1.000]), with sensitivity of 0.943 and specificity of 0.947 in the validation dataset. Calibration plots demonstrated close agreement between predicted and observed probabilities, and decision curves indicated a wide range of net benefit threshold probabilities.ConclusionsThis nomogram, incorporating baseline NIHSS, Fg, and a history of hypertension, accurately predicts poor three-month outcomes in AIS patients treated with intravenous rt-PA. Its ease of use may facilitate early risk stratification and assist clinicians in formulating more targeted management strategies and follow-up protocols for patients likely to experience unfavorable outcomes. creator: Fengjiao Zhang creator: Dan Zhao creator: Jing Zhang uri: https://doi.org/10.7717/peerj.18937 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zhang et al. title: Deep-learning tool for early identification of non-traumatic intracranial hemorrhage etiology and application in clinical diagnostics based on computed tomography (CT) scans link: https://peerj.com/articles/18850 last-modified: 2025-02-26 description: BackgroundTo develop an artificial intelligence system that can accurately identify acute non-traumatic intracranial hemorrhage (ICH) etiology (aneurysms, hypertensive hemorrhage, arteriovenous malformation (AVM), Moyamoya disease (MMD), cavernous malformation (CM), or other causes) based on non-contrast computed tomography (NCCT) scans and investigate whether clinicians can benefit from it in a diagnostic setting.MethodsThe deep learning model was developed with 1,868 eligible NCCT scans with non-traumatic ICH collected between January 2011 and April 2018. We tested the model on two independent datasets (TT200 and SD 98) collected after April 2018. The model’s diagnostic performance was compared with clinicians’ performance. We further designed a simulated study to compare the clinicians’ performance with and without the deep learning system complements.ResultsThe proposed deep learning system achieved area under the receiver operating curve of 0.986 (95% CI [0.967–1.000]) on aneurysms, 0.952 (0.917–0.987) on hypertensive hemorrhage, 0.950 (0.860–1.000) on arteriovenous malformation (AVM), 0.749 (0.586–0.912) on Moyamoya disease (MMD), 0.837 (0.704–0.969) on cavernous malformation (CM), and 0.839 (0.722–0.959) on other causes in TT200 dataset. Given a 90% specificity level, the sensitivities of our model were 97.1% and 90.9% for aneurysm and AVM diagnosis, respectively. On the test dataset SD98, the model achieved AUCs on aneurysms and hypertensive hemorrhage of 0.945 (95% CI [0.882–1.000]) and 0.883 (95% CI [0.818–0.948]), respectively. The clinicians achieve significant improvements in the sensitivity, specificity, and accuracy of diagnoses of certain hemorrhage etiologies with proposed system complements.ConclusionsThe proposed deep learning tool can be an accuracy tool for early identification of hemorrhage etiologies based on NCCT scans. It may also provide more information for clinicians for triage and further imaging examination selection. creator: Meng Zhao creator: Wenjie Li creator: Yifan Hu creator: Ruixuan Jiang creator: Yuanli Zhao creator: Dong Zhang creator: Yan Zhang creator: Rong Wang creator: Yong Cao creator: Qian Zhang creator: Yonggang Ma creator: Jiaxi Li creator: Shaochen Yu creator: Ran Zhang creator: Yefeng Zheng creator: Shuo Wang creator: Jizong Zhao uri: https://doi.org/10.7717/peerj.18850 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhao et al. title: Diversity and efficacy of insect sampling methods in an urban tropical dry forest of the Colombian Caribbean link: https://peerj.com/articles/18262 last-modified: 2025-02-26 description: Tropical dry forests (TDFs) are among the most threatened ecosystems in Colombia and globally. Characterized by distinct dry and wet seasons, TDFs support a rich diversity of flora and fauna and offer crucial ecosystem services, despite facing significant threats such as deforestation, urbanization and climate change. This study provides a comprehensive assessment of insect diversity within an urban TDF area in Puerto Colombia, Atlántico and in the Colombian Caribbean, by comparing three traditional sampling methods: Malaise traps, pitfall traps, and canopy fogging. In total, 3,135 insects were collected, representing 413 morphospecies across various trophic guilds. Our findings indicate that Malaise traps were the most effective in capturing a diverse range of species, followed by pitfall traps, while canopy fogging yielded the lowest species richness. Each method captured unique species, demonstrating that these methods are complementary in capturing the full spectrum of insect diversity in TDFs. Additionally, our study contributes valuable data on the taxonomic and functional diversity of insects in this continuously threatened ecosystem, underscoring the need for conservation efforts in urban and peri-urban TDFs. creator: Rodrigo Sarmiento-Garcés creator: Daniel Posada-Echeverría creator: Rafik Neme uri: https://doi.org/10.7717/peerj.18262 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sarmiento-Garcés et al.