Morpho-physiological traits and yield quality for cassava genotypes planted under drought during canopy establishment
Growth analysis provides better insight into the adaptability of cassava genotypes grown under drought conditions during canopy establishment and full irrigation. This study is intended to determine the growth rate and starch yield of different cassava genotypes grown under irrigation and drought treatments during canopy establishment. The experiment was conducted in two growing seasons at Khon Kaen University, Thailand, from August 2021 to August 2022 (2021/2022) and from August 2022 to August 2023 (2022/2023) using six cassava genotypes. A 2 × 6 split-plot design with four replications was used. The main plots were full irrigation and drought conditions during canopy establishment (90 to 150 days after planting (DAP)), and the cassava genotypes were assigned as subplots. The results showed that drought treatment applied during 90 to 150 DAP reduced relative water content (RWC) in cassava leaves for both growing seasons, storage root growth rate (SRGR) in the 2021/2022 growing season, and stem growth rate (SGR) and crop growth rate (CGR) in the 2022/2023 growing season. Re-watering after a drought supported cassava’s growth rate, resulting in desirable yield and biomass at final harvest. The Rayong 72 and CMR38-125-77 produced significantly higher storage root dry weight, harvest index (HI), and starch yield than the other tested genotypes. Growing under drought treatment, the best performance in storage root dry weight with statistical significance for both years was recorded for CMR38-125-77 (11.2 and 11.4 t ha−1 for the 2021/2022 and 2022/2023 growing seasons, respectively), and this was associated with a high crop growth rate (CGR, 12.3 g m−2 day−1 for the 2021/2022 growing season) and relative growth rate (RGR, 1.11 × 10−2 g g−1 day−1 for the 2022/2023 growing season) during 180 to 360 DAP. These favorable cassava genotypes should be utilized for future plant breeding programs and cultivation to achieve the desired productivity in the growing areas with drought during canopy establishment.
Ittipong et al. (2025) Morpho-physiological traits and yield quality for cassava genotypes planted under drought during canopy establishment. PeerJ 13:e20440 https://doi.org/10.7717/peerj.20440
Retrospective study on the clinical outcomes and characteristics of acute myeloid leukemia: different outcomes in the same risk group
Background Acute myeloid leukemia (AML) remains a prognostically heterogeneous malignancy despite advances in molecular risk stratification. While the 2022 European Leukemia Network (ELN) guidelines refine risk classification, their accuracy in predicting survival outcomes across genetic requires validation. Methods We conducted a retrospective analysis of 154 newly diagnosed AML patients at Daping Hospital, integrating next-generation sequencing (NGS)-based genetic profiling, 2022 ELN risk classification, and clinical outcomes. Results The most frequent mutations were FLT3 (26.6%), DNMT3A (21.4%), NPM1 (18.2%), CEBPA (17.5%), and TET2 (15.6%). Median overall survival (OS) and progression-free survival (PFS) were 22.9 months and 14.1 months, respectively. Hematopoietic stem cell transplantation (HSCT), female sex, age < 60 years, and normal karyotype emerged as favorable prognostic factors. No significant differences were observed between allogeneic (allo-HSCT) and autologous HSCT (ASCT). Idarubicin, cytarabine, etoposide (IA ± E) chemotherapy yielded superior survival, while azacitidine+venetoclax (AZA+VEN) regimens underperformed. Conversely, TP53 and KIT mutations correlated with inferior survival, while NPM1, CEBPA mutations predicted longer survival. Notably, significant survival heterogeneity existed within 2022 ELN risk groups, particularly among patients with FLT3, CEBPA, or TET2 mutations. Conclusions The ELN risk classification demonstrate limitations in prognostication, particularly for patients with FLT3, CEBPA, or TET2 mutations. Our findings highlight the necessity for refined risk models incorporating additional molecular markers (KIT) and mutation interactions to enhance personalized prognostication. Gene coexistence is also a factor that needs to be considered when determining patient prognosis. Trial registration The study was registered on the Chinese clinical trial registry (ChiCTR) platform (No. ChiCTR2500096484).
Meng et al. (2025) Retrospective study on the clinical outcomes and characteristics of acute myeloid leukemia: different outcomes in the same risk group. PeerJ 13:e20436 https://doi.org/10.7717/peerj.20436
Paw-spective shift: how our mood alters the way we read dog emotions
This study explored the influence of people’s mood on their perception of dog emotions in order to expand our understanding of how mood biases may shape emotional interpretation. Across two experiments, participants were primed into positive, neutral, or negative moods using validated visual stimuli before they evaluated video clips of dogs displaying positive, neutral, or negative emotional states. Participants were asked to rate valence and arousal of the dogs in the videos. Experiment 1 utilized visual primes unrelated to animals, while Experiment 2 employed dog-specific primes. Although mood priming significantly influenced participants’ self-reported emotions in Experiment 1, it did not affect their interpretation of the dogs’ emotional states. Dog-specific primes influenced participants’ interpretation of dog emotions in Experiment 2; however, the effect was a contrasting one, in that participants in the positively induced group rated dogs as sadder and those in the negative group rated dogs as happier. These findings challenge previous assumptions about mood-congruence effects in cross-species emotional perception, suggesting a more complex interplay of factors than anticipated. The study underscores the need for further research to disentangle the mechanisms governing how humans perceive and respond to animals’ emotional cues, with implications for improving animal welfare and human-animal interactions.
Molinaro et al. (2025) Paw-spective shift: how our mood alters the way we read dog emotions. PeerJ 13:e20411 https://doi.org/10.7717/peerj.20411
Biomarkers of mitochondrial permeability transition-driven necrosis in the regulation of ulcerative colitis
Background Ulcerative colitis (UC) is a gastrointestinal condition characterized by chronic intestinal inflammation and damage to the mucosal barrier, with regulated cell death (RCD) playing a pivotal role in its pathogenesis. Among the various forms of RCD, mitochondrial permeability transition-driven necrosis (MPTDN) has not been thoroughly investigated in relation to UC in the current literature. Objective The objective of this study was to identify genes associated with MPTDN that are relevant to UC and to explore their potential implications in the disease process. Methods Data were obtained from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were utilized to identify differentially expressed MPTD-related genes (MPTDEGs). Machine learning techniques, including Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine-Recursive Feature Elimination (SVM-RFE), and Random Forest (RF), were employed to isolate key hub genes. The diagnostic potential of these genes was evaluated through receiver operating characteristic (ROC) curve analysis, and their expression was validated using an external dataset. Additionally, immunoinfiltration analysis was conducted to investigate the relationship between differentially expressed immune cells and the identified diagnostic genes. The correlation between gene expression and response to anti-TNF therapy was also assessed. Finally, the differential expression of these genes was confirmed in a mouse model of UC induced by 2.5% dextran sulfate sodium (DSS). Results A total of six MPTDEGs were identified. The genes CASP1 and CASP4, which were identified through machine learning algorithms, exhibited strong diagnostic performance, with area under the curve (AUC) values exceeding 0.7, indicating the effectiveness of the model. Immunoinfiltration analysis demonstrated a significant correlation between the expression of CASP1 and CASP4 and the presence of macrophages and neutrophils. Importantly, low expression levels of CASP1 were associated with a favorable response to infliximab treatment. Furthermore, the expression levels of CASP1 and CASP4 were significantly increased in UC mouse models (p < 0.05). Conclusions The MPTDN-related genes CASP1 and CASP4 have been identified as potential biomarkers for the diagnosis of UC and are associated with abnormal immune cell infiltration in UC patients. Additionally, CASP1 may serve as a predictor of sensitivity to infliximab therapy.
Sun et al. (2025) Biomarkers of mitochondrial permeability transition-driven necrosis in the regulation of ulcerative colitis. PeerJ 13:e20345 https://doi.org/10.7717/peerj.20345
The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more
Metatranscriptomics–the sequencing of community RNA–has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation.
Di Leo et al. (2025) The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more. PeerJ 13:e20328 https://doi.org/10.7717/peerj.20328
Association between bone marrow adipose tissue, abdominal adipose tissue distribution, and volumetric bone mineral density in the Chinese adult population: a retrospective cohort study
Background Increasing studies have suggested that bone closely interacts with bone marrow adipose tissue (BMAT) and abdominal adipose tissue. However, this relationship remains debated. This study aimed to explore the association among BMAT, abdominal adipose tissue, and lumbar volumetric bone mineral density (vBMD). Methods A total of 306 Chinese adult living liver transplant donors were enrolled in this cross-sectional study. vBMD and abdominal adipose tissue in terms of total adipose tissue (TAT), visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT), were derived using quantitative computed tomography (QCT). Chemical shift encoded magnetic resonance imaging (MRI) of the lumbar spine was performed, and proton density fat fraction (PDFF) maps were calculated. Correlation analysis and multiple linear regression were used to assess the associations among BMAT, abdominal adipose tissue distribution, and vBMD. Results The mean age of the participants was 38.1 ± 9.5 years (range: 19–66 years). The vBMD was significantly negatively associated with age (r = −0.508, p < 0.001), VAT (r = −0.235, p < 0.001), TAT (r = −0.127, p = 0.03), and BMAT measured by PDFF (r = −0.642, p < 0.001). After adjusting for age, gender, and BMI, multiple linear regression analysis showed BMAT (β = −0.523, p < 0.001), SAT (β = 0.116, p = 0.045) and VAT (β = −0.108, p = 0.037) to be independent factors influencing vBMD. Conclusion Our results indicated a negative association between BMAT and BMD. The association between abdominal adipose tissue distribution and BMD was dual; there was a positive association between SAT and BMD and a negative association between VAT and BMD. These findings suggest that the distribution of abdominal adipose tissue, particularly visceral adipose tissue accumulation, should be prioritized over total body weight in considerations of bone health.
Zhu et al. (2025) Association between bone marrow adipose tissue, abdominal adipose tissue distribution, and volumetric bone mineral density in the Chinese adult population: a retrospective cohort study. PeerJ 13:e20446 https://doi.org/10.7717/peerj.20446
Exploring the impact of visual stimuli on taste expectations and the role of pull-tab position in food packaging
Background Preference for an image is often associated with the perceived ease of use of the depicted object. Aim This study investigated the impact of visual stimuli on taste expectations, focusing on the presentation of food in images. Specifically, it explored how the presence of a pull-tab—perceived by participants as a tool that makes the product easy to use or open—influences these expectations. Methods A sample of 42 right-handed university students (30 women, 12 men; mean age = 20.4 years) evaluated perceived taste expectations of food presented under different conditions using a 9-point Likert scale. The conditions included images of canned food (“Can condition”) with varying pull-tab positions (0°, 90°, 180°, 270°, and Down), as well as images of actual food (“Pineapple condition”). Each participant was shown 12 images per trial in a randomized order and rated their taste expectations immediately after viewing each image. Statistical analyses were conducted using linear mixed models and ANOVA using the Kenward-Roger method. Results Taste expectations were significantly lower in the Can condition compared with the Pineapple condition (mean difference = 3.14, SE = 0.23, p < 0.001). Within the Can condition, pull-tab positions had a significant effect on taste expectation ratings (F = 116.94, p < 0.001). The 0° position (pull-tab facing the viewer) received the highest rating (M = 4.87, SD = 1.86), while the 180° position (pull-tab facing away) received the lowest (M = 3.95, SD = 1.73). Conclusion These findings underscore the complex relationship between visual presentation and taste expectations, providing valuable insights for optimizing product presentation in marketing strategies.
Shibuya et al. (2025) Exploring the impact of visual stimuli on taste expectations and the role of pull-tab position in food packaging. PeerJ 13:e20417 https://doi.org/10.7717/peerj.20417
Metabolites of traffic-related volatile organic compounds in age-related macular degeneration
Background Volatile organic compounds (VOCs), commonly emitted from vehicle exhaust and industrial activities, are prevalent air pollutants in urban environments. These compounds have been reported to cause various health effects through mechanisms such as oxidative stress and neurotoxicity. Recently, air pollution has attracted attention as a potential risk factor for age-related macular degeneration (AMD); however, the association between VOC exposure and AMD remains unclear. Objective This study aimed to assess VOC exposure levels among urban-dwelling AMD patients by quantifying urinary metabolites and investigating the association between VOCs and AMD. Methods This cross-sectional study included 40 untreated AMD patients (AMD group), 10 cataract patients (Cataract group), and 10 healthy controls (Healthy group). Representative urinary metabolites of VOCs—2-methylhippuric acid, 3-methylhippuric acid, mandelic acid, phenylglyoxylic acid, and trans,trans-muconic acid—were measured using gas chromatography-mass spectrometry (GC/MS), with concentrations corrected for urinary creatinine. Group comparisons were performed based on creatinine-adjusted metabolite levels. Results The AMD group exhibited elevated urinary VOC metabolite levels compared to both control groups. The ratios of mean concentrations in the AMD group versus the Healthy and Cataract groups, respectively, were: 2-methylhippuric acid (201% and 181%), 3-methylhippuric acid (190% and 139%), mandelic acid (304% and 198%), phenylglyoxylic acid (118% and 90%), and trans,trans-muconic acid (214% and 92%). Among these, 2-methylhippuric acid and mandelic acid were significantly higher in the AMD group than in both controls (p < 0.001 and p = 0.042; p < 0.001, respectively). Trans,trans-muconic acid also showed a significant increase compared to the Healthy group (p < 0.001). Correlation analysis within the AMD group revealed moderate but significant associations for 2-methylhippuric acid (r = 0.29, p = 0.011), mandelic acid (r = 0.47, p < 0.001), and trans,trans-muconic acid (r = 0.27, p = 0.020). Multivariate logistic regression identified mandelic acid as an independent factor significantly associated with AMD (odds ratio = 17.20, p < 0.001). Subgroup analysis categorized the AMD group into drusenoid AMD, typical AMD (t-AMD), polypoidal choroidal vasculopathy (PCV), and retinal angiomatous proliferation (RAP). No significant differences in urinary VOC metabolite levels were observed among the four subtypes after multiple comparison adjustment. Conclusions These findings indicate that AMD patients are exposed to higher levels of traffic-related VOCs. While mandelic acid—a styrene metabolite—was independently associated with AMD, its role should be interpreted as a potential exposure marker rather than a definitive disease biomarker. Further longitudinal studies are warranted to clarify causal relationships between VOC exposure and AMD development.
Mimura et al. (2025) Metabolites of traffic-related volatile organic compounds in age-related macular degeneration. PeerJ 13:e20405 https://doi.org/10.7717/peerj.20405
Virtual reality technology for upper and lower limb motor function, daily function, and balance in stroke patients: a meta-analysis of randomized controlled trials
Background Stroke is a common neurological disorder that often results in motor dysfunction, significantly impairing patients’ quality of life and increasing the economic burden on healthcare systems. Virtual reality (VR) technology has emerged as an innovative approach in stroke rehabilitation. This meta-analysis aimed to comprehensively evaluate the effects of VR-based interventions on motor function, daily function, and balance in stroke patients. Methods We systematically searched PubMed, Embase, the Cochrane Library, Web of Science, and China National Knowledge Infrastructure (CNKI) databases from inception to October 2025 for randomized controlled trials (RCTs) investigating VR technology in stroke rehabilitation. Study quality was assessed using the Cochrane Risk of Bias 2.0 tool. Data synthesis involved pooling effect sizes, conducting subgroup analyses, and assessing publication bias using Stata 17. Results A total of 27 RCTs involving 877 stroke patients were included in the meta-analysis. VR technology demonstrated statistically significant improvements across multiple functional domains: lower limb motor function (Cohen’s d = 0.41, 95% CI [0.25–0.57], P < 0.001), upper limb motor function (Cohen’s d = 0.25, 95% CI [0.03–0.48], P = 0.03), daily function (Cohen’s d = 0.24, 95% CI [0.07–0.42], P = 0.01), and balance (Cohen’s d = 0.31, 95% CI [0.09–0.52], P < 0.001). The effects ranged from small to moderate across domains, with lower limb function showing the most substantial improvement. Sensitivity analyses confirmed the robustness of these findings, and subgroup analyses revealed that factors such as training cycle influenced treatment effects. Conclusion VR technology demonstrates significant potential as an effective complementary intervention for improving motor function, daily function, and balance in stroke patients. The small to moderate effect sizes across domains support its integration into conventional rehabilitation protocols. Future research should focus on optimizing VR parameters, investigating different VR technology types, and evaluating long-term sustainability to further establish its efficacy in stroke rehabilitation.
Zhang et al. (2025) Virtual reality technology for upper and lower limb motor function, daily function, and balance in stroke patients: a meta-analysis of randomized controlled trials. PeerJ 13:e20402 https://doi.org/10.7717/peerj.20402
Metabolite profiling from the fermentation of marine-derived extracts by Lactobacillus acidophilus LB
Background Lactobacillus acidophilus LB is a probiotic strain with the ability to produce valuable bioactive metabolites through fermentation. Sustainable biomass sources such as Spirulina platensis, Ulva reticulata, and Caulerpa lentillifera, which can also be obtained from agricultural or aquacultural by-products, offer a promising alternative for microbial cultivation, but their effects on the metabolic profile of L. acidophilus LB are still unclear. Methods The study utilized L. acidophilus LB (GenBank accession OK398226) cultivated in media containing Spirulina platensis, Ulva reticulata, and Caulerpa lentillifera extracts. High-resolution mass spectrometry (liquid chromatography-high resolution mass spectrometry-quadrupole-time-of-flight, LC-HRMS QTOF) was employed for compound profiling. Principal component analysis (PCA) and Pearson correlation were used to analyze metabolic variations across different culture conditions. The Kruskal-Wallis test assessed statistical differences in metabolite concentrations. Results Methyl lucidenate Q and 6-Gingerol were the most abundant bioactive compounds detected across samples. PCA revealed that L. acidophilus LB in media supplemented with different preparations of Spirulina platensis, Ulva reticulata, and Caulerpa lentillifera was associated with distinct differences in metabolite profiles, leading to clustering patterns. K-means clustering identified three metabolomic groups, with the pellet obtained from L. acidophilus LB cultured in medium supplemented with U. reticulata seaweed showing a unique chemical profile. Pearson correlation analysis suggested possible biochemical interactions among metabolites, with Auraptenol and Daturametelin B exhibiting a strong positive correlation (r = 0.99). The absence of Methyl lucidenate Q in this sample indicates potential enzymatic degradation or metabolic inhibition. Conclusion This study highlights the impact of L. acidophilus LB on metabolite diversity in substrate-driven fermentation systems. The findings suggest microbial interactions modulate metabolite patterns in the fermented supernatants, potentially enhancing pharmacological properties. Future research should focus on optimizing culture conditions to maximize yield and functional validation of identified compounds for therapeutic applications. These insights contribute to the broader field of natural product discovery and marine biotechnology.
Hoang et al. (2025) Metabolite profiling from the fermentation of marine-derived extracts by Lactobacillus acidophilus LB. PeerJ 13:e20399 https://doi.org/10.7717/peerj.20399