title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=118 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Leveraging diverse cell-death patterns in diagnosis of sepsis by integrating bioinformatics and machine learning link: https://peerj.com/articles/19077 last-modified: 2025-02-26 description: BackgroundSepsis is a life-threatening disease causing millions of deaths every year. It has been reported that programmed cell death (PCD) plays a critical role in the development and progression of sepsis, which has the potential to be a diagnosis and prognosis indicator for patient with sepsis.MethodsFourteen PCD patterns were analyzed for model construction. Seven transcriptome datasets and a single cell sequencing dataset were collected from the Gene Expression Omnibus database.ResultsA total of 289 PCD-related differentially expressed genes were identified between sepsis patients and healthy individuals. The machine learning algorithm screened three PCD-related genes, NLRC4, TXN and S100A9, as potential biomarkers for sepsis. The area under curve of the diagnostic model reached 100.0% in the training set and 100.0%, 99.9%, 98.9%, 99.5% and 98.6% in five validation sets. Furthermore, we verified the diagnostic genes in sepsis patients from our center via qPCR experiment. Single cell sequencing analysis revealed that NLRC4, TXN and S100A9 were mainly expressed on myeloid/monocytes and dendritic cells. Immune infiltration analysis revealed that multiple immune cells involved in the development of sepsis. Correlation and gene set enrichment analysis (GSEA) analysis revealed that the three biomarkers were significantly associated with immune cells infiltration.ConclusionsWe developed and validated a diagnostic model for sepsis based on three PCD-related genes. Our study might provide potential peripheral blood diagnostic candidate biomarkers for patients with sepsis. creator: Mi Liu creator: Xingxing Gao creator: Hongfa Wang creator: Yiping Zhang creator: Xiaojun Li creator: Renlai Zhu creator: Yunru Sheng uri: https://doi.org/10.7717/peerj.19077 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al. title: Trueness and precision of complete denture digital impression compared to conventional impression: an in vitro study link: https://peerj.com/articles/19075 last-modified: 2025-02-26 description: BackgroundThis study aimed to compare the precision and trueness of digital impressions of the edentulous arch made with different scanners to conventional physical impressions.MethodsA total of 40 impressions of a completely edentulous maxillary arch model (n = 10) were made using different digital impressions with an extraoral scanner, E3 3Shape desktop scanner, as the reference scan, intraoral scanner (TRIOS IOS, and Medit IOS) and Vinyl Polysiloxane impressions (VPS) impression using a Computer-Aided Design and Computer-Aided Manufacturing (CAD-CAM) custom tray. The VPS impression was scanned with the desktop scanner to produce standard tessellation language (STL) files for comparison with the digital impressions made by the Desktop and intraoral scanners. The STL files were super-imposed to a desktop scan and to each other with the same group using Geomagic Control X Software to assess the trueness and precision, respectively. A t-test was conducted for statistical analysis with a significance level of 0.05.ResultsThe overall trueness, Medit had the highest deviation compared to the VPS and TRIOS groups with a P value of 0.0013 and <0.0001, respectively. In terms of overall precision, TRIOS had a lower deviation than the VPS group, with a P value of 0.0002. The TRIOS and Medit groups had statistically comparable results. The desktop scanner showed the highest precision in digitizing completely edentulous cases, followed by the TRIOS scanner. The Medit scanner’s trueness had the highest deviation compared to the VPS and TRIOS groups. creator: Yousif A. Al-Dulaijan creator: Haidar Alalawi creator: Mohammed M. Gad creator: Faisal D. Al-Qarni creator: Shaimaa M. Fouda creator: Passent Ellakany uri: https://doi.org/10.7717/peerj.19075 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Al-Dulaijan et al. title: Impact of online support of physical activity management using a wearable device on renal function in patients with acute coronary syndrome: a randomized controlled trial protocol link: https://peerj.com/articles/19067 last-modified: 2025-02-26 description: BackgroundAcute coronary syndromes (ACS) often cause rapid decline in renal and cardiac function. In patients with ACS, combined renal dysfunction is associated with increased overall mortality and cardiovascular events. Physical activity (PA) management may crucially contribute towards protection of renal function in patients with ACS. This article describes the study protocol of a randomized controlled trial (RCT) assessing whether online support for PA management using wearable devices and information communication technology for patients with ACS facing difficulties in participating in outpatient cardiac rehabilitation after discharge can protect renal function following disease onset.MethodsWe have designed a two-arm RCT with a 3-month follow-up period. The online support intervention incorporates monitoring of PA, pulse rate, and blood pressure using a wearable device with an accelerometer and a web application system, as well as periodic educational feedback and goal setting. The primary study endpoint is the estimated glomerular filtration rate based on serum cystatin C (eGFRcys). The intervention effect will be assessed using the eGFRcys at 3 months adjusted for baseline values. The secondary endpoints are the urine albumin/creatinine ratio, brain natriuretic peptide levels, average step count, peak oxygen uptake, quality of life, and incidence of adverse events.DiscussionThis RCT will provide evidence regarding the effectiveness of online support for PA management as a renal protection strategy following ACS onset. This novel strategy not only mitigates barriers impeding participation in outpatient cardiac rehabilitation and protects cardiac and renal function in patients with ACS, but also may contribute towards improving survival and recurrence rates, preventing dialysis, and reducing medical and long-term care costs.Trial registration:The trial was registered in the Japan Registry of Clinical Trials on July 5, 2024. The registration number is jRCT1022240014 (Impact of Online Support of Physical Activity Management Using a Wearable Device on Renal Function in Patients with Acute Coronary Syndrome). creator: Toshimi Sato creator: Daisuke Suzuki creator: Yuichiro Sasamoto creator: Masahiro Ono creator: Namiko Shishito creator: Kohko Kanazawa creator: Akihito Watanabe creator: Koichi Naito creator: Shinichiro Morishita creator: Masahiro Kohzuki uri: https://doi.org/10.7717/peerj.19067 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Sato et al. title: Exploratory analyses of the associations between Ki-67 expression, lymph node metastasis, and prognosis in patients with esophageal squamous cell cancer link: https://peerj.com/articles/19062 last-modified: 2025-02-26 description: BackgroundThe relationships between Ki-67/MKI67 expression, lymph node metastasis (LNM), vascular invasion (VI), and perineural invasion (PI) in esophageal squamous cell cancer (ESCC) remain unclear. This retrospective cohort study was performed to evaluate the prognostic value of Ki-67 expression and its association with LNM in patients with resected ESCC.MethodsThe analysis included 168 patients with ESCC with available Ki-67 protein expression data. The patients were divided into Ki-67 high-expression group (Ki-67 High, 93 cases) and Ki-67 low-expression (Ki-67 Low, 75 cases) groups. Associations between Ki-67 expression and ESCC pathological features was assessed using chi-square test. Overall survival (OS) was compared between the two groups using Kaplan–Meier survival analysis and Cox proportional hazards model.ResultsMedian follow-up duration was 33.5 months (range 3.0–60.0 months). High Ki-67 expression was significantly associated with poor OS in patients with ESCC compared to that of the low-expression in both univariate (hazard ratios (HR) = 3.42, 95% CI [2.22–5.27], P < 0.001) and multivariate analyses (HR = 1.98, 95% CI [1.33–2.94], P < 0.001). Furthermore, high Ki-67 expression was significantly associated with an increased risk of LNM (χ2 = 11.219, P = 0.011), VI (χ2 = 6.359, P = 0.012), and PI (χ2 = 8.877, P = 0.003).ConclusionsHigh Ki-67 protein expression is associated with poor prognosis in ESCC. Increased Ki-67 expression significantly increases the risk of LNM, VI, and PI in ESCC, and thus may serve as an indication for adjuvant therapy in ESCC management. creator: Jianqing Zheng creator: Bifen Huang creator: Ying Chen creator: Bingwei Zeng creator: Lihua Xiao creator: Min Wu uri: https://doi.org/10.7717/peerj.19062 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Zheng et al. 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