Diagnostic accuracy of the atherogenic index of plasma in metabolic syndrome: a diagnostic meta-analysis
Objective This study aims to assess the diagnostic performance of the atherogenic index of plasma (AIP) in estimating the risk of metabolic syndrome (MetS) among adults across various geographic regions. Methods A comprehensive search was conducted across EMBASE, Web of Science, PubMed, and the Cochrane Library from their inception until September 29, 2024. Eligible studies were selected and evaluated for methodological quality using the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) framework. Statistical analyses were performed using STATA 15.1. Sensitivity, specificity, diagnostic odds ratio, positive and negative likelihood ratios, the summary receiver operating characteristic (SROC), curve, and 95% confidence intervals (CI) were calculated to assess the diagnostic accuracy of AIP for MetS. Statistical significance was defined as a p-value < 0.05. Results Eleven observational studies involving 36,463 participants were included. The analysis showed that AIP is an effective biomarker for identifying the risk of MetS, with an area under the curve (AUC) of 0.84 (95% CI [0.81–0.87]). AIP demonstrated comparable diagnostic value in both males and females, with an AUC of 0.82, highlighting its potential utility in sex-specific assessments. Geographic region, diagnostic reference standards, and publication year were identified as potential sources of heterogeneity. Conclusions This study demonstrates that AIP is a relatively accurate tool for detecting MetS, supporting its role in prevention and in reducing the risk of associated chronic diseases. Further research with larger sample sizes and multi-center designs is needed to explore the combined use of AIP with other biomarkers to enhance diagnostic accuracy for MetS.
Gao et al. (2025) Diagnostic accuracy of the atherogenic index of plasma in metabolic syndrome: a diagnostic meta-analysis. PeerJ 13:e20074 https://doi.org/10.7717/peerj.20074
Genetic modifiers of response to thalidomide in transfusion-dependent beta-thalassemia patients: a whole-exome sequence analysis
Background Thalidomide induces fetal hemoglobin and renders most thalassemia patients transfusion-independent. Some patients, however, do not respond. Underlying genetic variations responsible for variable responses to thalidomide are unexplored. Aims and objectives To discover genetic variations that influence response to thalidomide in transfusion-dependent beta-thalassemia patients. Methods Twenty beta-thalassemia patients (14 excellent responders and six non-responders) who had received thalidomide were included in the study by a non-probability purposive sampling technique. Patients who showed a rise of >2 mg/dl in hemoglobin level and/or whose hemoglobin levels reached 9 gm/dl without blood transfusions were designated as excellent responders. Patients whose hemoglobin levels did not show an increment rise of >2 and/or whose hemoglobin levels did not rise above 5.9 gm/dl and needed blood transfusions to maintain optimal hemoglobin levels were designated as non-responders. DNA was extracted, and whole-exome sequencing was performed on an Illumina HiSeq System. Aligning and variant calling were done by the Sentieon software. Annotation was done by Annovar. Results The age of study participants ranged from 1–12 years, with a mean of 5.45 ± 3.81 years. There were 17 (85%) males and three (15%) females. A total of 222,180 germline variants were identified across 20 subjects, from which 24 candidate variants across 24 genes were identified. The three most common polymorphisms in the excellent responder group were found in the exon region of CHI3L1 (rs880633), NPNT (rs35132891), and ZNF 208 (rs10425763), which were found in 92%, 85%, and 71% cases, respectively. The commonest polymorphisms in the non-responder group were found in the PM20D1 gene (rs7518979), LGR6 (rs75658797), MYH15 (rs4299484), and RESF1 (rs3207618), each of which was found in 66.6% cases. Conclusion This study shows a significant association of single-nucleotide polymorphisms rs880633, rs35132891, and rs10425763 with excellent response status, while rs7518979, rs75658797, rs4299484, and rs3207618 are associated with non-response status.
Bawazir et al. (2025) Genetic modifiers of response to thalidomide in transfusion-dependent beta-thalassemia patients: a whole-exome sequence analysis. PeerJ 13:e20038 https://doi.org/10.7717/peerj.20038
Soil storage temperature and air-drying did not significantly change bacterial taxa in the short-term
Analysing soil microbial communities is vital for understanding ecosystem health, but samples from remote locations often require preservation before DNA can be extracted. In this study, we used the 16S rRNA amplicon sequencing to investigate how different storage methods affect soil microbial diversity over 4 weeks. We implemented storage temperature and moisture as two experimental factors. Three topsoils (sandy, silty loam, and clay loam) were collected and stored under four conditions: frozen at −20 °C, refrigerated at 4 °C, room temperature, and air-dried. DNA extractions and sequencing were performed at 1, 3, 7, 14, and 28 days. Our results revealed that storage temperature and moisture did not substantially change bacterial diversity and composition across all three soil types. Rare taxa showed a similar pattern to abundant taxa but were more variable in beta diversity. Overall, all tested methods effectively preserved both abundant and rare taxa in the short term. However, the long-term impacts of the sample storage, particularly on rare taxa, need further exploration.
Du et al. (2025) Soil storage temperature and air-drying did not significantly change bacterial taxa in the short-term. PeerJ 13:e20162 https://doi.org/10.7717/peerj.20162
Bioinformatic analysis and experimental validation of hub autophagy-related genes as novel biomarkers for type 2 diabetes mellitus and Alzheimer’s disease
Background & Objectives Alzheimer’s disease (AD) and type 2 diabetes mellitus (T2DM) share considerable similarities in their proposed patho mechanisms. Autophagy, an intrinsic cellular process involved in the degradation of dysfunctional organelles and abnormal proteins, has been implicated in the pathogenesis of both AD and T2DM. This study aims to identify potential shared biomarkers related to autophagy in AD and T2DM by analyzing hub differentially expressed autophagy-related genes (DEARGs) and examining their potential functions. Methods Gene expression profiles for AD and T2DM were acquired from the Gene Expression Omnibus (GEO) database (training sets: GSE109887 for AD and GSE104674 for T2DM; validation sets: GSE122063 for AD and GSE64998 for T2DM). Autophagy-related genes (ARGs) were extracted from multiple databases. DEARGs were identified and integrated with module genes derived from weighted gene co-expression network analysis (WGCNA) to determine key shared ARGs. Then, the STRING database was used to construct a protein-protein interaction (PPI) network, from which hub genes were identified. These hub genes were validated using independent microarray datasets through differential expression analysis, and ROC curves were generated to assess their diagnostic value. Moreover, the expression of the hub genes was validated in brain tissues of T2DM mouse models using qRT-PCR. Results A total of 33 shared DEARGs were identified, among which 12 were designated as hub genes (ANXA5, CCND1, MAP2K1, HSPB1, BNIP3, BAG3, YAP1, MET, FBXW7, CCL2, PFKFB3, CDKN1A) in both AD and T2DM patients. Validation using other datasets confirmed that ANXA5, BAG3, and CDKN1A remained significantly upregulated, while MET remained downregulated in both AD and T2DM patients. Additionally, PFKFB3 showed an inverse expression pattern between the two diseases. The diagnostic performance of these five hub genes was assessed using ROC curves, with all five exhibiting values of area under the curve (AUC) exceeding 0.7 for T2DM in both training and validation sets. However, only MET and PFKFB3 demonstrated good diagnostic efficacy in AD patients. In animal models, qRT-PCR analysis revealed that the expression of ANXA5, BAG3, and MET was consistent with the bioinformatics results. In contrast, the expression of PFKFB3 and CDKN1A did not differ significantly between db/db model mice and db/m control mice. Conclusions Our integrated bioinformatics analyses, supported by preliminary experimental validations, identified several hub ARGs shared between AD and T2DM. Among these, ANXA5, BAG3, and MET exhibited consistent expression trends across datasets and experimental models, while CDKN1A and PFKFB3 showed inconsistent expression patterns. These findings underscore the complexity of autophagy-related crosstalk in AD-T2DM comorbidity and highlight the need for further research to clarify their diagnostic and therapeutic potential.
Zhang et al. (2025) Bioinformatic analysis and experimental validation of hub autophagy-related genes as novel biomarkers for type 2 diabetes mellitus and Alzheimer’s disease. PeerJ 13:e20143 https://doi.org/10.7717/peerj.20143
Factors influencing compliance with endoscopy final rinsing water standards: a study in a tertiary hospital setting
Background Maintaining a high compliance rate for final rinsing water is essential for patient safety and infection control in healthcare facilities. This study aims to investigate the causes of fluctuations in compliance rates at a tertiary hospital and evaluate the effectiveness of preventive measures. Methods Monitoring data from October 2022 to December 2023 were analyzed to assess microbial contamination in final rinse water. Environmental assessments and literature reviews were conducted to identify potential contributing factors. Strategic interventions were implemented, and their impact on water quality and infection control was systematically evaluated. Findings Initial assessments revealed fluctuating compliance rates, with faucet aerators identified as a potential source of contamination. Water samples collected before the aerator showed 100% compliance (6/6 samples), while colonies of Cupriavidus pauculus and Stenotrophomonas maltophilia were detected on aerator surfaces and in final rinse water. After removing the aerators and enhancing disinfection protocols, compliance improved significantly, with subsequent samples meeting infection control standards (≤10 CFU/100 mL). Conclusion This study suggests a potential link between fluctuations in endoscopy final rinsing water quality and the presence of faucet aerators. These findings support further research and the development of guidelines for the appropriate use of aerators in healthcare settings.
Environmental Contamination and Remediation
Yuan et al. (2025) Factors influencing compliance with endoscopy final rinsing water standards: a study in a tertiary hospital setting. PeerJ 13:e20134 https://doi.org/10.7717/peerj.20134
Knowledge and attitudes of university staff toward organ donation: a cross-sectional study in Oman
Background Organ donation remains low when it is not accompanied by a good knowledge and positive attitude. Most published articles have evaluated organ donation knowledge and attitudes within single categories such as healthcare workers, students, or patients. Few studies have assessed these factors across various job categories. Therefore, this study aimed to fill that gap by evaluating knowledge and attitudes about organ donation among university staff from various job categories. Methods A cross-sectional study was conducted among university staff between June 2023 and January 2024 using an online validated self-designed questionnaire. University employees were divided into academic, medical, technical and administrative staff. The survey instrument included five distinct sections: study information, informed consent, demographic data, knowledge about organ donation, and attitudes toward organ donation. Analyses included descriptive statistics, Chi-square tests, and binary logistic regression. Results The study included 385 staff. 64.4% were females, and 52.2% were in the age group between 30–41 years old. The majority of participants demonstrated good knowledge about organ donation (67.5%) and brain death (63.9%), while a significant proportion (67.5%) exhibited a negative attitude toward organ donation. Medical staff have the highest knowledge and attitude with 94.7% and 60.5%, respectively. Multivariate analysis revealed that medical and academic staff were more likely than administrative staff to have good knowledge (AOR 9.244, 95% CI [2.143–39.871]; AOR 2.300, 95% CI [1.126–4.696], respectively) and a positive attitude (AOR 3.444, 95% CI [1.633–7.262]; AOR 2.636, 95% CI [1.266–5.491], respectively), while females were 2.026 times more likely (95% CI [1.246–3.295]) to have good knowledge compared to males. The most cited organ for organ donation was kidneys (94.5%). The most common reason for supporting donating organs among university students was to save a life (67.3%) and the most common reason for refusing organs was hesitation (45.7%). Conclusions The study revealed moderate knowledge about organ donation among university staff, with medical and academic staff showing higher levels. However, overall attitudes were less positive, and there was significant reliance on the internet for information. These findings emphasize the need for targeted awareness campaigns and educational programs to improve knowledge and attitudes, promoting a cultural shift towards increased organ donation.
Alwahaibi et al. (2025) Knowledge and attitudes of university staff toward organ donation: a cross-sectional study in Oman. PeerJ 13:e20133 https://doi.org/10.7717/peerj.20133
Trade-offs between aquatic and terrestrial locomotion and functional parallelism in Desmognathus salamanders
A trade-off between aquatic and terrestrial locomotion is self-evident at broad phylogenetic scales. While the effects of more subtle trade-offs in the evolution of closely related species are less clear, they are hypothesized to drive ecological speciation and adaptive radiation. Amphibious animals strike a balance between aquatic and terrestrial activity, and the need to maintain performance in one medium is hypothesized to constrain evolution of high performance in the other (the running-swimming dilemma). Closely related species of Desmognathus salamanders partition local habitats along a gradient from mid-stream to stream edge to completely terrestrial. The trade-off hypothesis predicts that these species will differ in relative running vs. swimming performance depending on the relative importance of each mode of locomotion in their niches. Here, I show that primarily aquatic Desmognathus ecomorphs are superior swimmers and inferior runners relative to semi-aquatic ecomorphs using paired escape performance trials in aquatic and terrestrial arenas. I measured performance as the velocity of the fast-start response to simulated predator attack. I tested two species of each ecomorph, representing two divergent clades with parallel evolution of aquatic and semi-aquatic species. Notably, the different southern clade ecomorphs have been genetically isolated for millions of years, whereas the northern clade ecomorphs share a recent common ancestor and interbreed regularly. My results showed a negative correlation between aquatic and terrestrial performance, with aquatic ecomorphs being faster swimmers and semi-aquatic ecomorphs being faster runners. While there was a possible trend consistent with faster swimming speeds of northern forms relative to their southern counterparts, the functional differences between ecomorphs were similar in both clades. These results are consistent with the hypothesis that trade-offs between aquatic and terrestrial locomotion have contributed to a consistent pattern of habitat partitioning during parallel speciation.
Fitzpatrick (2025) Trade-offs between aquatic and terrestrial locomotion and functional parallelism in Desmognathus salamanders. PeerJ 13:e20111 https://doi.org/10.7717/peerj.20111
Predictive role of systemic immune-inflammation index in the prognosis of patients with advanced left-sided colorectal cancer: a retrospective study
Purpose This study aimed to evaluate the prognostic value of the systemic immune-inflammation index (SII) in patients with advanced left-sided colorectal cancer (CRC) receiving CAPEOX ± bevacizumab as first-line chemotherapy. Methods A total of 231 patients with advanced left-sided CRC who received first-line CAPEOX ± bevacizumab therapy were included. Patients’ blood cell counts, clinical, and pathological data were collected before treatment, and systemic inflammatory indices were calculated, including neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), monocyte-to-lymphocyte ratio (MLR), and SII. Optimal cutoffs for NLR, PLR, MLR, SII, and age were determined using X-Tile software, categorizing patients in to high- or low-value groups; clinicopathological characteristics were then compared between the high- and low-value groups within each systemic inflammatory index using chi-square tests. Survival curves were estimated using the Kaplan–Meier method, with log-rank tests applied to compare differences between groups. The Shapiro–Wilk test for normality and Spearman correlation analysis were used to evaluate the correlations among SII, NLR, PLR, and MLR. Univariable and multivariable analyses were performed with the Cox proportional hazards regression model. The prognostic value of systemic inflammatory indices was compared using the concordance index (C-index) and 5-fold cross-validation. The stability and generalizability of the C-index under varying data partitions were evaluated using mean square error (MSE). Interaction effects between treatment regimens and SII were further explored using multivariable Cox regression analysis. Results Univariable and multivariable Cox regression analyses identified age, primary tumor resection, SII, NLR, PLR, and MLR as independent prognostic factors for overall survival (OS). Comparative analysis of the C-index and MSE in the training and validation datasets demonstrated that SII outperformed NLR, PLR, and MLR, exhibiting the highest average C-index and the lowest MSE across 5-fold cross-validation. Patients with elevated pre-treatment SII had significantly worse OS compared to those with lower values. Conclusion SII is a robust prognostic marker in patients with advanced left-sided CRC receiving CAPEOX ± bevacizumab as first-line chemotherapy, demonstrating superior prognostic value compared to NLR, PLR, and MLR. Higher pre-treatment SII values were associated with worse OS, underscoring its clinical utility in prognostic stratification.
Su et al. (2025) Predictive role of systemic immune-inflammation index in the prognosis of patients with advanced left-sided colorectal cancer: a retrospective study. PeerJ 13:e20095 https://doi.org/10.7717/peerj.20095
cpSNP discovery and genotyping for a Pinus taeda breeding population with targeted comparison to related conifers
Pinus taeda (Loblolly pine) is the most important commercial tree species in the southern United States and a significant non-native plantation species in China. Its genetic improvement program has been implemented in South China for 30 years. In this study, the chloroplast (cp) genome of P. taeda was sequenced, assembled, and compared with other available chloroplast genomes of Pin aceae using BLAST. Codon usage among 33 species of Pinaceae was analyzed using the relative synonymous codon usage (RSCU) value. The results were then visualized using the pheatmap v1.0.10 in R. The rates of nonsynonymous (Ka) and synonymous (Ks) substitutions in the chloroplast genomes among five species of Pinus were estimated using the seqinr package in R. Additionally, selected single nucleotide polymorphisms (SNPs) were used to genotype 33 individuals from the P. taeda breeding population. The P. taeda cp genome is 121,530 bp, with certain regions (e.g., ycf1 and ycf2) showing lower sequence conservation compared to other Pinaceae species. Codon usage analysis revealed that codons ending in G or C were not prevalently used, with significant differences in natural selection pressure on chloroplast genes between three species (P. taiwanensis, P. thunbergii, and P. koraiensis) and the other 30 species. Phylogenomic analysis using 36 cp genomes (representing 25 species) resolved Pinus into two subgenera, with P. taeda clustered with P. rigida within the diploxylon pines. Notably, ycf1-based phylogenetic analysis recovered a topology highly congruent (normalized RF = 0.15) with whole-plastome phylogenies. This study validates the single-copy gene ycf1 as a robust and low-cost phylogenetic marker for conifer genus-level reconstruction. The identified SNPs provide valuable molecular markers for genotyping individuals in P. taeda breeding programs, supporting germplasm characterization and management.
Wang et al. (2025) cpSNP discovery and genotyping for a Pinus taeda breeding population with targeted comparison to related conifers. PeerJ 13:e20092 https://doi.org/10.7717/peerj.20092
Eyestalk transcriptome analysis reveals sexually dimorphic host-parasite interactions: divergent molecular strategies of Polyascus sp. for reproductive and growth regulation in Eriocheir sinensis
Background The Chinese mitten crab (Eriocheir sinensis), an economically critical migratory species inhabiting both freshwater and marine environments, is susceptible to parasitization by the rhizocephalan barnacle Polyascus sp. in estuarine ecosystems. In this study, E. sinensis was found to be parasitized by Polyascus sp. in the freshwater waters of the Anqing section of the Yangtze River, which manifested itself as restricted growth and development, hindered gonadal development, and apparent changes in sexual characteristics. Methods Morphological analysis, serological testing, and eyestalk transcriptome analysis were conducted on male and female parasitized and non-parasitized crabs to investigate the molecular mechanisms by which Polyascus sp. affects host growth and reproduction. Results The study revealed that parasitized hosts of both sexes were significantly smaller than normal individuals and exhibited gonadal atrophy. Male hosts displayed feminization of secondary sexual characteristics, whereas females showed no significant alterations. Testosterone and ecdysterone levels decreased in male hosts, whereas estradiol levels declined in female hosts. Transcriptomic profiling revealed differentially expressed genes predominantly associated with metabolic processes, stimulus response, signal transduction, and reproduction. Thirteen key candidate genes related to parasite-induced suppression of host molting and growth, fourteen key candidate genes involved in male reproductive regulation, and ten candidate genes affecting female gonadal development were identified. Key genes involved in gonadal development—including 5-HT1B, CHH, MIH, JHE1, Dmrt family, cytochrome P450 family, Abd-A, and Antp exhibited sex-specific expression patterns. Additionally, critical growth-related genes such as Dib, HR38, and Cht3 exhibited significant alterations in hosts of both sexes. Polyascus sp. parasitism suppresses gonadal development and growth in both sexes, employing distinct regulatory strategies. It uses a “neuroendocrine disruption and reproductive gene regulation” strategy to regulate reproductive development in male hosts, while influencing female reproductive metabolism through a “Nutrient Hijacking-Hormonal Suppression” mechanism. Additionally, the parasitism disrupts host growth via “molting inhibition”. These findings elucidate the sex-specific metabolic, reproductive, and growth disruption strategies of Polyascus sp., providing new insights into host-parasite interactions in decapod crustaceans.
Xie et al. (2025) Eyestalk transcriptome analysis reveals sexually dimorphic host-parasite interactions: divergent molecular strategies of Polyascus sp. for reproductive and growth regulation in Eriocheir sinensis. PeerJ 13:e20089 https://doi.org/10.7717/peerj.20089