PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Solubilization of skin collagen improves the accuracy and reliability of stable isotope measurements
items: Quality assessment from biobank plasma and serum specimens: a systematic review
items: Evaluation of NEUROG1 methylation status in stool specimens in the advanced adenomas and colorectal cancer
items: Optimal treatment options for acne scars in patients with historic acne: a systematic review and network meta-analysis
items: Unveiling water quality and health risks from groundwater chemicals in Poyang Lake basin of China: a sophisticated analysis
items: From lowlands to highlands: how elevation and habitat complexity drive anuran multidimensional diversity?
items: The safety and efficacy of phosphodiesterase type 5 inhibitors in the treatment of diabetic erectile dysfunction: a systematic review and meta-analysis
items: Comprehensive analysis of DNA methylation patterns in recurrent miscarriage: imprinted/non-imprinted genes and their regulation across sperm and fetal-maternal tissues
items: Sucking lice in bandicoot rats with first complete description of Hoplopleura malabarica nymphs
items: Transcriptome reveals differential expression of flavor and color in closely related strains of tomato (Solanum lycopersicum)

Solubilization of skin collagen improves the accuracy and reliability of stable isotope measurements
type: item
type: AcademicArticle
description: Stable isotope analysis of skin collagen is useful for detecting short-term or seasonal diet. Preparation of skin for stable isotope analysis varies across laboratories, and this may impact the comparability of data. It is important to understand the effects of different preparatory protocols on the stable isotopic and elemental compositions of skin samples. Using a Eurovector 3,300 elemental analyzer coupled to a Nu Horizon isotope ratio mass spectrometer, we tested the impact of three treatment variants (refluxing at three temperatures to remove non-collagenous proteins, treatment with sodium hydroxide (NaOH), and chemical lipid extraction using 2:1 chloroform:methanol) on the stable isotope (δ13carbon (C) and δ15nitrogen (N)) and elemental (wt% C, and wt% N) composition of pig (Sus scrofa domesticus) skin. The refluxing step produced pig skin with higher δ13C values, lower C:NAtomic ratios, less variable C:NAtomic ratios, wt% C, and wt% N. The chemical lipid extraction also produced higher, more reliable δ13C values and lower, less variable C:NAtomic ratios. The isotopic data in the lipid-extracted and refluxed samples were more consistent in the refluxed samples than the non-refluxed and non-lipid-extracted samples, as determined by the elemental compositions.
format: application/pdf
format: text/html
creator: Alexandra A.Y. Derian
creator: Ryan Pawlowski
creator: Paul Szpak
subject: Biochemistry
subject: Anatomy and Physiology
subject: Dermatology
description: doi:10.7717/peerj.20152
publisher: PeerJ Inc.
rights: © 2025 Derian et al.
abstract: Stable isotope analysis of skin collagen is useful for detecting short-term or seasonal diet. Preparation of skin for stable isotope analysis varies across laboratories, and this may impact the comparability of data. It is important to understand the effects of different preparatory protocols on the stable isotopic and elemental compositions of skin samples. Using a Eurovector 3,300 elemental analyzer coupled to a Nu Horizon isotope ratio mass spectrometer, we tested the impact of three treatment variants (refluxing at three temperatures to remove non-collagenous proteins, treatment with sodium hydroxide (NaOH), and chemical lipid extraction using 2:1 chloroform:methanol) on the stable isotope (δ13carbon (C) and δ15nitrogen (N)) and elemental (wt% C, and wt% N) composition of pig (Sus scrofa domesticus) skin. The refluxing step produced pig skin with higher δ13C values, lower C:NAtomic ratios, less variable C:NAtomic ratios, wt% C, and wt% N. The chemical lipid extraction also produced higher, more reliable δ13C values and lower, less variable C:NAtomic ratios. The isotopic data in the lipid-extracted and refluxed samples were more consistent in the refluxed samples than the non-refluxed and non-lipid-extracted samples, as determined by the elemental compositions.
bibliographic citation: Derian et al. (2025) Solubilization of skin collagen improves the accuracy and reliability of stable isotope measurements. PeerJ 13:e20152 https://doi.org/10.7717/peerj.20152
date submitted: 2025-04-10
date accepted: 2025-09-08
issued: 2025-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Derian
  given name: Alexandra A.Y.
author list: Agent
  family name: Pawlowski
  given name: Ryan
author list: Agent
  family name: Szpak
  given name: Paul
doi: 10.7717/peerj.20152
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-08
copyright: ©2025 Derian et al.
attribution name: Derian et al.

Quality assessment from biobank plasma and serum specimens: a systematic review
type: item
type: AcademicArticle
description: Accurate assessment of serum and plasma quality is essential for reliable biobanking and research. This systematic review synthesizes 46 studies and shows that current evaluation methods prioritize sample processing delays, freeze-thaw cycles, storage duration, and temperature variations, while neglecting preanalytical factors like medication and diet. Temperature critically affected stability: non-refrigerated samples (8–37 °C) showed 3.2 times more biomarker alterations than refrigerated samples after >24 h delays. Freeze-thaw cycles caused dose-dependent instability, with >10 cycles triggering severe degradation (70% altered biomarkers) and universal enzyme impairment. Even ≤5 cycles significantly altered enzymes (43% affected). Enzymes also degraded over time at <−20 °C, with alteration rates rising from 20% (1–5 years) to 55% (>10 years). The analysis consolidates stability data for enzymes, sterols, cytokines, and metabolites across conditions, providing an evidence-based foundation for quality control. Standardizing procedures to address these gaps will enhance sample integrity, research reliability, and clinical utility. Critically, this review underscores that preexisting biobank collections may have inherent limitations, necessitating careful evaluation of sample history when designing studies.
format: application/pdf
format: text/html
creator: Xiongshun Liang
creator: Wanna Xu
creator: Lin Chen
creator: Xiaoqian Liu
creator: Wenxu Hong
creator: Xuqiao Hu
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.20122
publisher: PeerJ Inc.
rights: © 2025 Liang et al.
abstract: Accurate assessment of serum and plasma quality is essential for reliable biobanking and research. This systematic review synthesizes 46 studies and shows that current evaluation methods prioritize sample processing delays, freeze-thaw cycles, storage duration, and temperature variations, while neglecting preanalytical factors like medication and diet. Temperature critically affected stability: non-refrigerated samples (8–37 °C) showed 3.2 times more biomarker alterations than refrigerated samples after >24 h delays. Freeze-thaw cycles caused dose-dependent instability, with >10 cycles triggering severe degradation (70% altered biomarkers) and universal enzyme impairment. Even ≤5 cycles significantly altered enzymes (43% affected). Enzymes also degraded over time at <−20 °C, with alteration rates rising from 20% (1–5 years) to 55% (>10 years). The analysis consolidates stability data for enzymes, sterols, cytokines, and metabolites across conditions, providing an evidence-based foundation for quality control. Standardizing procedures to address these gaps will enhance sample integrity, research reliability, and clinical utility. Critically, this review underscores that preexisting biobank collections may have inherent limitations, necessitating careful evaluation of sample history when designing studies.
bibliographic citation: Liang et al. (2025) Quality assessment from biobank plasma and serum specimens: a systematic review. PeerJ 13:e20122 https://doi.org/10.7717/peerj.20122
date submitted: 2025-04-01
date accepted: 2025-09-01
issued: 2025-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Xiongshun
author list: Agent
  family name: Xu
  given name: Wanna
author list: Agent
  family name: Chen
  given name: Lin
author list: Agent
  family name: Liu
  given name: Xiaoqian
author list: Agent
  family name: Hong
  given name: Wenxu
author list: Agent
  family name: Hu
  given name: Xuqiao
doi: 10.7717/peerj.20122
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-08
copyright: © 2025 Liang et al.
attribution name: Liang et al.

Evaluation of NEUROG1 methylation status in stool specimens in the advanced adenomas and colorectal cancer
type: item
type: AcademicArticle
description: Background To assess the status of NEUROG1 methylation in the advanced adenoma and colorectal cancer. Methods The NEUROG1 methylation in tissue and stool samples from patients with colorectal cancer (CRC), advanced adenoma (AA), and non-advanced adenoma (NAA) were evaluated using methylation-specific quantitative polymerase chain reaction (PCR). Results In tissue samples, the NEUROG1 methylation detection rates were 36% for CRC, 24% for NAA, and 88% for AA. In stool samples, the NEUROG1 methylation detection had a sensitivity of 63.46% for CRC with a positive predictive value (PPV) of 85.94%. The overall diagnostic specificity of the test for the NAA and the healthy control was 76.32%, with a negative predictive value (NPV) of 40.28%. Conclusion NEUROG1 methylation detection can potentially be used in the CRC and AA screening.
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creator: Lijin Zhang
creator: Aiping Lin
creator: Jie Lin
creator: Juan Chen
creator: Mengshi Chen
creator: Xunbin Yu
creator: Yijuan Wu
creator: Tao Wang
creator: Yan Lu
creator: Zhaofen Ba
creator: Xiaowei Cheng
creator: Tiantian Zhang
creator: Minghong Chen
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.19968
publisher: PeerJ Inc.
rights: © 2025 Zhang et al.
abstract: Background To assess the status of NEUROG1 methylation in the advanced adenoma and colorectal cancer. Methods The NEUROG1 methylation in tissue and stool samples from patients with colorectal cancer (CRC), advanced adenoma (AA), and non-advanced adenoma (NAA) were evaluated using methylation-specific quantitative polymerase chain reaction (PCR). Results In tissue samples, the NEUROG1 methylation detection rates were 36% for CRC, 24% for NAA, and 88% for AA. In stool samples, the NEUROG1 methylation detection had a sensitivity of 63.46% for CRC with a positive predictive value (PPV) of 85.94%. The overall diagnostic specificity of the test for the NAA and the healthy control was 76.32%, with a negative predictive value (NPV) of 40.28%. Conclusion NEUROG1 methylation detection can potentially be used in the CRC and AA screening.
bibliographic citation: Zhang et al. (2025) Evaluation of NEUROG1 methylation status in stool specimens in the advanced adenomas and colorectal cancer. PeerJ 13:e19968 https://doi.org/10.7717/peerj.19968
date submitted: 2024-11-22
date accepted: 2025-07-31
issued: 2025-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Lijin
author list: Agent
  family name: Lin
  given name: Aiping
author list: Agent
  family name: Lin
  given name: Jie
author list: Agent
  family name: Chen
  given name: Juan
author list: Agent
  family name: Chen
  given name: Mengshi
author list: Agent
  family name: Yu
  given name: Xunbin
author list: Agent
  family name: Wu
  given name: Yijuan
author list: Agent
  family name: Wang
  given name: Tao
author list: Agent
  family name: Lu
  given name: Yan
author list: Agent
  family name: Ba
  given name: Zhaofen
author list: Agent
  family name: Cheng
  given name: Xiaowei
author list: Agent
  family name: Zhang
  given name: Tiantian
author list: Agent
  family name: Chen
  given name: Minghong
doi: 10.7717/peerj.19968
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-08
copyright: ©2025 Zhang et al.
attribution name: Zhang et al.

Optimal treatment options for acne scars in patients with historic acne: a systematic review and network meta-analysis
type: item
type: AcademicArticle
description: Background Acne is a common skin condition that can cause permanent scarring and profoundly affect patients’ quality of life. Despite the increasing diversity of acne scar treatments, there is a dearth of comprehensive evidence-based guidelines to help clinicians and patients make the best choices. This study aimed to comprehensively assess the efficacy and safety of existing acne scar treatments through a network meta-analysis. Method PubMed, Embase, Cochrane Library, and Web of Science were thoroughly searched for relevant studies from database establishment to September 19, 2024. Outcome included Echelle d’evaluation clinique des cicatrices d’acne (ECCA), Goodman and Baron Scale (GBS), pain, patient satisfaction, and adverse events. Bayesian network meta-analyses were performed using the gemtc package in R. Risk of bias was assessed using Cochrane Risk of Bias (RoB 2) tool, while publication bias was assessed via funnel plots. The study protocol was registered with PROSPERO (CRD42024598780). Results A total of 68 randomized controlled trials were enrolled, comprising 4,480 patients with acne scarring. Laser + platelet-rich plasma (PRP) ranked best in reducing ECCA scores (surface under cumulative ranking curve to the total area (SUCRA): 98.4%), laser + filler injection ranked best in reducing GBS (SUCRA: 72.1%), and laser + chemical peels ranked the best in patient satisfaction (SUCRA: 89.6%). Microneedling was ranked as the most tolerable in terms of pain (SUCRA: 72.6%). In addition, no strong evidence suggesting a treatment reduced the risk of erythema nor post-inflammatory hyperpigmentation compared to the other treatments. Conclusions The evidence suggests laser combined with PRP or filler injections are the best options for reducing scar severity, while laser combined with chemical peeling yields the best patient satisfaction. Laser combined with other therapies should be considered to optimize treatment of acne scarring.
format: application/pdf
format: text/html
creator: Bingwei Wu
creator: Mingju Gao
creator: Yixuan Zhang
creator: Xinping Bai
subject: Dermatology
subject: Data Mining and Machine Learning
subject: Healthcare Services
description: doi:10.7717/peerj.19938
publisher: PeerJ Inc.
rights: © 2025 Wu et al.
abstract: Background Acne is a common skin condition that can cause permanent scarring and profoundly affect patients’ quality of life. Despite the increasing diversity of acne scar treatments, there is a dearth of comprehensive evidence-based guidelines to help clinicians and patients make the best choices. This study aimed to comprehensively assess the efficacy and safety of existing acne scar treatments through a network meta-analysis. Method PubMed, Embase, Cochrane Library, and Web of Science were thoroughly searched for relevant studies from database establishment to September 19, 2024. Outcome included Echelle d’evaluation clinique des cicatrices d’acne (ECCA), Goodman and Baron Scale (GBS), pain, patient satisfaction, and adverse events. Bayesian network meta-analyses were performed using the gemtc package in R. Risk of bias was assessed using Cochrane Risk of Bias (RoB 2) tool, while publication bias was assessed via funnel plots. The study protocol was registered with PROSPERO (CRD42024598780). Results A total of 68 randomized controlled trials were enrolled, comprising 4,480 patients with acne scarring. Laser + platelet-rich plasma (PRP) ranked best in reducing ECCA scores (surface under cumulative ranking curve to the total area (SUCRA): 98.4%), laser + filler injection ranked best in reducing GBS (SUCRA: 72.1%), and laser + chemical peels ranked the best in patient satisfaction (SUCRA: 89.6%). Microneedling was ranked as the most tolerable in terms of pain (SUCRA: 72.6%). In addition, no strong evidence suggesting a treatment reduced the risk of erythema nor post-inflammatory hyperpigmentation compared to the other treatments. Conclusions The evidence suggests laser combined with PRP or filler injections are the best options for reducing scar severity, while laser combined with chemical peeling yields the best patient satisfaction. Laser combined with other therapies should be considered to optimize treatment of acne scarring.
bibliographic citation: Wu et al. (2025) Optimal treatment options for acne scars in patients with historic acne: a systematic review and network meta-analysis. PeerJ 13:e19938 https://doi.org/10.7717/peerj.19938
date submitted: 2025-01-25
date accepted: 2025-07-27
issued: 2025-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Bingwei
author list: Agent
  family name: Gao
  given name: Mingju
author list: Agent
  family name: Zhang
  given name: Yixuan
author list: Agent
  family name: Bai
  given name: Xinping
doi: 10.7717/peerj.19938
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-08
copyright: ©2025 Wu et al.
attribution name: Wu et al.

Unveiling water quality and health risks from groundwater chemicals in Poyang Lake basin of China: a sophisticated analysis
type: item
type: AcademicArticle
description: Background Groundwater is a critical water resource in the Poyang Lake basin, especially given the increasing frequency of extreme drought events. However, comprehensive assessments of its chemical characteristics and associated health risks remain insufficient. This study aims to provide a comprehensive assessment of groundwater quality and associated health risks in the Poyang Lake basin, China. Methods This study collected 670 groundwater samples from domestic and agricultural wells across the basin during the 2022 dry season. Hydrochemical parameters, including manganese (Mn), ammonia nitrogen (NH4+), iron (Fe3+), aluminum (Al3+), chemical oxygen demand (COD), fluoride (F−), and nitrate (NO3−), were analyzed and compared against China’s Class III groundwater quality standards. Spatial variations in water quality were evaluated using the Entropically Weighted Water Quality Index (EWQI). Non-carcinogenic health risks via ingestion and dermal contact pathways were quantified through deterministic risk assessment models, with uncertainty and probability analyzed via Monte Carlo simulations (10,000 iterations). Sensitivity analysis was conducted to identify dominant factors influencing risk outcomes, ensuring a robust probabilistic interpretation of health hazards. Results The results unveils pronounced spatial variability across key hydrochemical parameters: pH ranges from 3.05 to 11.09, total dissolved solids (TDS) from 25.38 to 1,635.21 mg/L, Mn from below detection limits to 19.93 mg/L, COD from below detection limits to 8.57 mg/L, and TH from 9.47 to 905.78 mg/L. A notable proportion of samples breach the Class III groundwater quality standards, with 38% for Mn, 39% for COD, and 15% for NH4+. The Piper diagram analysis categorizes the primary groundwater type as HCO3− -Ca, with a secondary Cl-Ca-Mg type. Through the EWQI assessment, while the overall water quality is deemed acceptable, we identify 56 sites with EWQI values indicative of poor to very poor quality…
format: application/pdf
format: text/html
creator: Xiaodong Chu
creator: Jingyuan He
creator: Ting Chen
creator: Hailin You
creator: Xuhui Luo
creator: Shuping Liu
creator: Jinying Xu
creator: Zhifei Ma
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.19937
publisher: PeerJ Inc.
rights: © 2025 Chu et al.
abstract: Background Groundwater is a critical water resource in the Poyang Lake basin, especially given the increasing frequency of extreme drought events. However, comprehensive assessments of its chemical characteristics and associated health risks remain insufficient. This study aims to provide a comprehensive assessment of groundwater quality and associated health risks in the Poyang Lake basin, China. Methods This study collected 670 groundwater samples from domestic and agricultural wells across the basin during the 2022 dry season. Hydrochemical parameters, including manganese (Mn), ammonia nitrogen (NH4+), iron (Fe3+), aluminum (Al3+), chemical oxygen demand (COD), fluoride (F−), and nitrate (NO3−), were analyzed and compared against China’s Class III groundwater quality standards. Spatial variations in water quality were evaluated using the Entropically Weighted Water Quality Index (EWQI). Non-carcinogenic health risks via ingestion and dermal contact pathways were quantified through deterministic risk assessment models, with uncertainty and probability analyzed via Monte Carlo simulations (10,000 iterations). Sensitivity analysis was conducted to identify dominant factors influencing risk outcomes, ensuring a robust probabilistic interpretation of health hazards. Results The results unveils pronounced spatial variability across key hydrochemical parameters: pH ranges from 3.05 to 11.09, total dissolved solids (TDS) from 25.38 to 1,635.21 mg/L, Mn from below detection limits to 19.93 mg/L, COD from below detection limits to 8.57 mg/L, and TH from 9.47 to 905.78 mg/L. A notable proportion of samples breach the Class III groundwater quality standards, with 38% for Mn, 39% for COD, and 15% for NH4+. The Piper diagram analysis categorizes the primary groundwater type as HCO3− -Ca, with a secondary Cl-Ca-Mg type. Through the EWQI assessment, while the overall water quality is deemed acceptable, we identify 56 sites with EWQI values indicative of poor to very poor quality…
bibliographic citation: Chu et al. (2025) Unveiling water quality and health risks from groundwater chemicals in Poyang Lake basin of China: a sophisticated analysis. PeerJ 13:e19937 https://doi.org/10.7717/peerj.19937
date submitted: 2025-03-11
date accepted: 2025-07-27
issued: 2025-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Chu
  given name: Xiaodong
author list: Agent
  family name: He
  given name: Jingyuan
author list: Agent
  family name: Chen
  given name: Ting
author list: Agent
  family name: You
  given name: Hailin
author list: Agent
  family name: Luo
  given name: Xuhui
author list: Agent
  family name: Liu
  given name: Shuping
author list: Agent
  family name: Xu
  given name: Jinying
author list: Agent
  family name: Ma
  given name: Zhifei
doi: 10.7717/peerj.19937
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-08
copyright: ©2025 Chu et al.
attribution name: Chu et al.

From lowlands to highlands: how elevation and habitat complexity drive anuran multidimensional diversity?
type: item
type: AcademicArticle
description: Background Montane environments in Neotropical regions are known for their rich diversity of amphibians, but the ecological drivers behind this diversity along altitudinal gradients remain poorly understood. We investigated the effects of the altitudinal range and local environmental variables on the taxonomic, phylogenetic, and functional alpha and beta diversity of anuran assemblages along an altitudinal gradient in the Atlantic Forest of northeastern Brazil. Methods We characterized the richness, abundance, taxonomic, functional, and phylogenetic diversity of anurans in 24 transects within the interior of the forest along an altitudinal range of 200–950 m in the Private Reserve of Natural Heritage (RPPN) Serra Bonita, southern Bahia state, northeastern Brazil. For each transect, we measured the following environmental variables: altitude, leaf litter depth and cover, canopy opening, number of tank-bromeliads, number of trees, and mean air temperature. Results We found 36 anuran species distributed in 10 families. Altitudinal strata plays an important role in explaining anuran abundance, with direct-developing frogs being the most abundant species. The number of tank-bromeliads was interpreted as having the most substantial support to explain the anuran abundance, lineage richness and functional diversity, whereas leaf litter depth influenced the dominant lineages. Additionally, altitude significantly influenced taxonomic and phylogenetic dissimilarity. Lastly, we found an inverse pattern of altitudinal Rapoport’s rule, in which species with optimal altitudes in the highlands exhibit a lower range-size distribution, likely due to habitat specialization or micro-endemism at higher altitudes. Conclusion Altitude significantly influenced the abundance, taxonomic composition, and phylogenetic diversity of anuran communities, with higher elevations supporting a greater number of individuals and distinct evolutionary lineages. In contrast, functional diversity did not v…
format: application/pdf
format: text/html
creator: Iuri Ribeiro Dias
creator: Kássio de Castro Araújo
creator: Jorge Mario Herrera-Lopera
creator: Caio Vinícius de Mira-Mendes
creator: Tadeu Teixeira Medeiros
creator: Marcos Ferreira Vila Nova
creator: Marcelo Felgueiras Napoli
creator: Mirco Solé
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.19561
publisher: PeerJ Inc.
rights: © 2025 Dias et al.
abstract: Background Montane environments in Neotropical regions are known for their rich diversity of amphibians, but the ecological drivers behind this diversity along altitudinal gradients remain poorly understood. We investigated the effects of the altitudinal range and local environmental variables on the taxonomic, phylogenetic, and functional alpha and beta diversity of anuran assemblages along an altitudinal gradient in the Atlantic Forest of northeastern Brazil. Methods We characterized the richness, abundance, taxonomic, functional, and phylogenetic diversity of anurans in 24 transects within the interior of the forest along an altitudinal range of 200–950 m in the Private Reserve of Natural Heritage (RPPN) Serra Bonita, southern Bahia state, northeastern Brazil. For each transect, we measured the following environmental variables: altitude, leaf litter depth and cover, canopy opening, number of tank-bromeliads, number of trees, and mean air temperature. Results We found 36 anuran species distributed in 10 families. Altitudinal strata plays an important role in explaining anuran abundance, with direct-developing frogs being the most abundant species. The number of tank-bromeliads was interpreted as having the most substantial support to explain the anuran abundance, lineage richness and functional diversity, whereas leaf litter depth influenced the dominant lineages. Additionally, altitude significantly influenced taxonomic and phylogenetic dissimilarity. Lastly, we found an inverse pattern of altitudinal Rapoport’s rule, in which species with optimal altitudes in the highlands exhibit a lower range-size distribution, likely due to habitat specialization or micro-endemism at higher altitudes. Conclusion Altitude significantly influenced the abundance, taxonomic composition, and phylogenetic diversity of anuran communities, with higher elevations supporting a greater number of individuals and distinct evolutionary lineages. In contrast, functional diversity did not v…
bibliographic citation: Dias et al. (2025) From lowlands to highlands: how elevation and habitat complexity drive anuran multidimensional diversity?. PeerJ 13:e19561 https://doi.org/10.7717/peerj.19561
date submitted: 2024-08-26
date accepted: 2025-05-13
issued: 2025-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dias
  given name: Iuri Ribeiro
author list: Agent
  family name: Araújo
  given name: Kássio de Castro
author list: Agent
  family name: Herrera-Lopera
  given name: Jorge Mario
author list: Agent
  family name: Mira-Mendes
  given name: Caio Vinícius de
author list: Agent
  family name: Medeiros
  given name: Tadeu Teixeira
author list: Agent
  family name: Nova
  given name: Marcos Ferreira Vila
author list: Agent
  family name: Napoli
  given name: Marcelo Felgueiras
author list: Agent
  family name: Solé
  given name: Mirco
doi: 10.7717/peerj.19561
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-08
copyright: © 2025 Dias et al.
attribution name: Dias et al.

The safety and efficacy of phosphodiesterase type 5 inhibitors in the treatment of diabetic erectile dysfunction: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Previous studies have confirmed the efficacy of phosphodiesterase type 5 inhibitors (PDE-5 inhibitors) in treating diabetic erectile dysfunction (DED), but they still have research value in terms of efficacy comparison and individualized safety. This study, while evaluating safety and efficacy, also focused on the sources of heterogeneity and innovatively explored the nonlinear relationship between therapeutic effect and age. Aim This study aimed to systematically evaluate the safety and efficacy of PDE-5 inhibitors for the treatment of DED and the related application effects and to provide a clinical basis for its treatment. Methods By searching PubMed, Embase, Web Of Science, Cochrane Library, China Knowledge Network (CNKI), Wipro (VIP), Wanfang, and China Biomedical Literature Database (CBM) before December 31, 2024, and reading the retrieved articles and references, PDE-5 inhibitors for diabetic erectile dysfunction in randomized controlled trials (RCTs). The literature of the included studies was evaluated using the Cochrane Literature Quality Assessment Tool. The meta-analysis was registered to PROSPERO (CRD42025637725). Outcomes The International Index of Erectile Function (IIEF-5) overall and related evaluation questionnaires were used as the primary efficacy evaluation indicators, and adverse events were used as secondary indicators. Results Meta-analysis was performed using Rever Manager 5.3 and STATA18 software. A total of 10 studies were included, and random-effects model meta-analysis analyzed the post-treatment efficacy of the 10 articles with a combined RR = 2.91, 95% CI of [1.95–4.34], P < 0.001. Fixed-effects model meta-analysis investigated adverse effects with RR = 2.0, 95% CI of [1.53–2.61], P < 0.001. There was a non-linear relationship between age and PDE-5 inhibitors. Conclusion PDE-5 inhibitors can safely and effectively improve diabetic erectile dysfunction, but the degree of effectiveness of different types of drugs, the occurren…
format: application/pdf
format: text/html
creator: Zexin Zhu
creator: Jian Xu
creator: Bo Dai
creator: Minghao Lin
creator: Huhu Yang
creator: Shilin Liu
creator: Pengjie Bao
creator: Zheng Nan
subject: Andrology
subject: Diabetes and Endocrinology
subject: Internal Medicine
subject: Urology
description: doi:10.7717/peerj.20147
publisher: PeerJ Inc.
rights: © 2025 Zhu et al.
abstract: Background Previous studies have confirmed the efficacy of phosphodiesterase type 5 inhibitors (PDE-5 inhibitors) in treating diabetic erectile dysfunction (DED), but they still have research value in terms of efficacy comparison and individualized safety. This study, while evaluating safety and efficacy, also focused on the sources of heterogeneity and innovatively explored the nonlinear relationship between therapeutic effect and age. Aim This study aimed to systematically evaluate the safety and efficacy of PDE-5 inhibitors for the treatment of DED and the related application effects and to provide a clinical basis for its treatment. Methods By searching PubMed, Embase, Web Of Science, Cochrane Library, China Knowledge Network (CNKI), Wipro (VIP), Wanfang, and China Biomedical Literature Database (CBM) before December 31, 2024, and reading the retrieved articles and references, PDE-5 inhibitors for diabetic erectile dysfunction in randomized controlled trials (RCTs). The literature of the included studies was evaluated using the Cochrane Literature Quality Assessment Tool. The meta-analysis was registered to PROSPERO (CRD42025637725). Outcomes The International Index of Erectile Function (IIEF-5) overall and related evaluation questionnaires were used as the primary efficacy evaluation indicators, and adverse events were used as secondary indicators. Results Meta-analysis was performed using Rever Manager 5.3 and STATA18 software. A total of 10 studies were included, and random-effects model meta-analysis analyzed the post-treatment efficacy of the 10 articles with a combined RR = 2.91, 95% CI of [1.95–4.34], P < 0.001. Fixed-effects model meta-analysis investigated adverse effects with RR = 2.0, 95% CI of [1.53–2.61], P < 0.001. There was a non-linear relationship between age and PDE-5 inhibitors. Conclusion PDE-5 inhibitors can safely and effectively improve diabetic erectile dysfunction, but the degree of effectiveness of different types of drugs, the occurren…
bibliographic citation: Zhu et al. (2025) The safety and efficacy of phosphodiesterase type 5 inhibitors in the treatment of diabetic erectile dysfunction: a systematic review and meta-analysis. PeerJ 13:e20147 https://doi.org/10.7717/peerj.20147
date submitted: 2025-04-09
date accepted: 2025-09-05
issued: 2025-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Zexin
author list: Agent
  family name: Xu
  given name: Jian
author list: Agent
  family name: Dai
  given name: Bo
author list: Agent
  family name: Lin
  given name: Minghao
author list: Agent
  family name: Yang
  given name: Huhu
author list: Agent
  family name: Liu
  given name: Shilin
author list: Agent
  family name: Bao
  given name: Pengjie
author list: Agent
  family name: Nan
  given name: Zheng
doi: 10.7717/peerj.20147
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-07
copyright: © 2025 Zhu et al.
attribution name: Zhu et al.

Comprehensive analysis of DNA methylation patterns in recurrent miscarriage: imprinted/non-imprinted genes and their regulation across sperm and fetal-maternal tissues
type: item
type: AcademicArticle
description: Background Epigenetic regulation, including DNA methylation, is essential for normal embryonic development and maternal-fetal interactions. Recurrent miscarriage (RM), defined as the loss of two or more consecutive pregnancies, poses significant clinical and emotional challenges. However, the role of epigenetic alterations in RM, particularly in gametes and placental tissues, remains underexplored. This study aims to investigate global DNA methylation profiles and imprinting gene expression in the context of RM, providing insights into epigenetic mechanisms that contribute to pregnancy failure. Methods Genome-wide DNA methylation profiling was performed on sperm and chorionic villi from RM patients and control couples undergoing artificial abortion using the Illumina HumanMethylation 450 BeadChip platform. Genes related to differentially methylated probes (DMPs) in functionally critical genomic regions, including enhancers, promoters, and DNase hypersensitive sites (DHS), were identified and submitted to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Key imprinting genes (CPA4 and PRDM16) were validated at the protein level using Western blotting. Results RM samples exhibited a significant increase in hypermethylated DMPs across all analyzed tissues, with villi and decidua showing the highest numbers of epigenetic changes. Enrichment analyses highlighted pathways implicated in tissue morphogenesis, immune regulation, and cell signaling, including the PI3K-Akt, TGF-beta, and Wnt signaling pathways. Among imprinting genes, CPA4 and PRDM16 showed distinct hypomethylation at enhancer regions, corresponding to elevated protein expression in RM villi tissues. Conclusions This study identifies profound epigenetic dysregulation in RM-associated tissues, emphasizing the contribution of imprinting gene methylation abnormalities to pregnancy loss. Future studies incorporating functional assays and animal models are essential to eluci…
format: application/pdf
format: text/html
creator: Yanru Niu
creator: Lanlan Yin
creator: Yulan Zhou
creator: Xiaoyan Pang
creator: Yunqinq Li
creator: Cailing Peng
creator: Meihua Yao
creator: Guoling Zhang
creator: Kaijie Yang
creator: Tianzhong Ma
subject: Genetics
subject: Molecular Biology
subject: Gynecology and Obstetrics
description: doi:10.7717/peerj.20125
publisher: PeerJ Inc.
rights: © 2025 Niu et al.
abstract: Background Epigenetic regulation, including DNA methylation, is essential for normal embryonic development and maternal-fetal interactions. Recurrent miscarriage (RM), defined as the loss of two or more consecutive pregnancies, poses significant clinical and emotional challenges. However, the role of epigenetic alterations in RM, particularly in gametes and placental tissues, remains underexplored. This study aims to investigate global DNA methylation profiles and imprinting gene expression in the context of RM, providing insights into epigenetic mechanisms that contribute to pregnancy failure. Methods Genome-wide DNA methylation profiling was performed on sperm and chorionic villi from RM patients and control couples undergoing artificial abortion using the Illumina HumanMethylation 450 BeadChip platform. Genes related to differentially methylated probes (DMPs) in functionally critical genomic regions, including enhancers, promoters, and DNase hypersensitive sites (DHS), were identified and submitted to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Key imprinting genes (CPA4 and PRDM16) were validated at the protein level using Western blotting. Results RM samples exhibited a significant increase in hypermethylated DMPs across all analyzed tissues, with villi and decidua showing the highest numbers of epigenetic changes. Enrichment analyses highlighted pathways implicated in tissue morphogenesis, immune regulation, and cell signaling, including the PI3K-Akt, TGF-beta, and Wnt signaling pathways. Among imprinting genes, CPA4 and PRDM16 showed distinct hypomethylation at enhancer regions, corresponding to elevated protein expression in RM villi tissues. Conclusions This study identifies profound epigenetic dysregulation in RM-associated tissues, emphasizing the contribution of imprinting gene methylation abnormalities to pregnancy loss. Future studies incorporating functional assays and animal models are essential to eluci…
bibliographic citation: Niu et al. (2025) Comprehensive analysis of DNA methylation patterns in recurrent miscarriage: imprinted/non-imprinted genes and their regulation across sperm and fetal-maternal tissues. PeerJ 13:e20125 https://doi.org/10.7717/peerj.20125
date submitted: 2025-02-20
date accepted: 2025-09-01
issued: 2025-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niu
  given name: Yanru
author list: Agent
  family name: Yin
  given name: Lanlan
author list: Agent
  family name: Zhou
  given name: Yulan
author list: Agent
  family name: Pang
  given name: Xiaoyan
author list: Agent
  family name: Li
  given name: Yunqinq
author list: Agent
  family name: Peng
  given name: Cailing
author list: Agent
  family name: Yao
  given name: Meihua
author list: Agent
  family name: Zhang
  given name: Guoling
author list: Agent
  family name: Yang
  given name: Kaijie
author list: Agent
  family name: Ma
  given name: Tianzhong
doi: 10.7717/peerj.20125
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-07
copyright: ©2025 Niu et al.
attribution name: Niu et al.

Sucking lice in bandicoot rats with first complete description of Hoplopleura malabarica nymphs
type: item
type: AcademicArticle
description: Background Studies of insect biodiversity and parasitism are often based on adult stages, as immature stages are poorly known and often cannot be identified to species level. However, sucking lice (Anoplura) are permanent, hematophagous parasites with single-host life cycles, making it possible to track the occurrence of all life stages. Only the complete identification of all life stages provides a full picture of parasitism, including infestation levels, parasite topography preferences on the host, and host specificity. The detection of different development stages on a host provides strong evidence that lice of a particular species are actively reproducing and completing their life cycle on that host, making full use of its resources. Conversely, the presence of adult lice alone, particularly when found sporadically, may suggest a failed or incidental attempt at host colonization rather than an established parasitic association. Methodology The description of the nymphal stages of Hoplopleura malabarica is based on specimens of sucking lice from the greater bandicoot rat Bandicota indica from Southeast Asia, specifically from the Vientiane area of Lao PDR. The study used morphometric analysis and scanning microscopy techniques. Results This study presents the first description of the nymphal stages of Hoplopleura malabarica, an oligoxenous parasite of rodents of the genus Bandicota. In addition, a global checklist of Anoplura parasitizing rodents of the genus Bandicota was provided. Conclusions The detection of different life stages of lice within the host confirms that they reproduce and develop on a given host species, fully utilizing its resources.
format: application/pdf
format: text/html
creator: Paulina Kozina
creator: Joanna N. Izdebska
creator: Serge Morand
creator: Alexis Ribas
subject: Entomology
subject: Parasitology
subject: Taxonomy
description: doi:10.7717/peerj.20115
publisher: PeerJ Inc.
rights: © 2025 Kozina et al.
abstract: Background Studies of insect biodiversity and parasitism are often based on adult stages, as immature stages are poorly known and often cannot be identified to species level. However, sucking lice (Anoplura) are permanent, hematophagous parasites with single-host life cycles, making it possible to track the occurrence of all life stages. Only the complete identification of all life stages provides a full picture of parasitism, including infestation levels, parasite topography preferences on the host, and host specificity. The detection of different development stages on a host provides strong evidence that lice of a particular species are actively reproducing and completing their life cycle on that host, making full use of its resources. Conversely, the presence of adult lice alone, particularly when found sporadically, may suggest a failed or incidental attempt at host colonization rather than an established parasitic association. Methodology The description of the nymphal stages of Hoplopleura malabarica is based on specimens of sucking lice from the greater bandicoot rat Bandicota indica from Southeast Asia, specifically from the Vientiane area of Lao PDR. The study used morphometric analysis and scanning microscopy techniques. Results This study presents the first description of the nymphal stages of Hoplopleura malabarica, an oligoxenous parasite of rodents of the genus Bandicota. In addition, a global checklist of Anoplura parasitizing rodents of the genus Bandicota was provided. Conclusions The detection of different life stages of lice within the host confirms that they reproduce and develop on a given host species, fully utilizing its resources.
bibliographic citation: Kozina et al. (2025) Sucking lice in bandicoot rats with first complete description of Hoplopleura malabarica nymphs. PeerJ 13:e20115 https://doi.org/10.7717/peerj.20115
date submitted: 2025-04-22
date accepted: 2025-08-29
issued: 2025-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kozina
  given name: Paulina
author list: Agent
  family name: Izdebska
  given name: Joanna N.
author list: Agent
  family name: Morand
  given name: Serge
author list: Agent
  family name: Ribas
  given name: Alexis
doi: 10.7717/peerj.20115
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-07
copyright: © 2025 Kozina et al.
attribution name: Kozina et al.

Transcriptome reveals differential expression of flavor and color in closely related strains of tomato (Solanum lycopersicum)
type: item
type: AcademicArticle
description: Fruit flavor and color are critical quality characteristics of tomatoes (Solanum lycopersicum). Numerous studies have demonstrated that tomato flavor is primarily linked to the sugar-acid content and its ratio, while fruit color is predominantly determined by the composition and concentration of carotenoids and flavonoids. To elucidate the regulatory mechanisms underlying the differences in sugar-acid and color formation during fruit ripening, transcriptome analysis was conducted for the first time on the breaker stage (Br) and mature fruit stage (MF) of the closely related strains yellow-fruited tomato (No. 19) and red-fruited tomato (No. 20). This analysis aimed to identify key regulatory genes and biosynthetic pathways associated with the formation of flavor and color in tomato fruits. The transcriptome analysis revealed that 1,546 differentially expressed genes (DEGs) were identified in the Br19_vs_Br20 comparison, of which 507 were up-regulated and 1,039 were down-regulated. In the MF19_vs_MF20 comparison, 2,178 DEGs were detected, with 1,235 up-regulated and 943 down-regulated. Upon further analysis of the DEGs, we identified several key genes in the sugar-acid metabolic pathway, including sucrose synthase (SUS), phosphofructokinase (PFK), fructose-bisphosphate aldolase (FBA), citrate synthase (CS), and succinate dehydrogenase (SuDH), which may significantly influence tomato flavor. Additionally, differential genes related to carotenoid and flavonoid metabolism, such as cytochrome P450 98A (CYP98A), caffeoyl-CoA3-O-methyltransferase (CCoAMT), carotenoid isomerase (CRTISO), lycopene beta cyclase (LCYB), zeaxanthin epoxidase (ZEP), violaxanthin deepoxidase (VDE), and 9-cis-epoxycarotenoid dioxygenase (NCED), as well as genes linked to ethylene synthesis, such as 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), may play a role in the color changes observed in tomatoes. The findings of this study provide ins…
format: application/pdf
format: text/html
creator: Chunmei Guo
creator: Xiuyuan Liu
creator: Yingfeng Ding
creator: Zhaoyilan He
creator: Songmei Shi
creator: Yumei Ding
creator: Hui Shen
creator: Zhengan Yang
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.20113
publisher: PeerJ Inc.
rights: © 2025 Guo et al.
abstract: Fruit flavor and color are critical quality characteristics of tomatoes (Solanum lycopersicum). Numerous studies have demonstrated that tomato flavor is primarily linked to the sugar-acid content and its ratio, while fruit color is predominantly determined by the composition and concentration of carotenoids and flavonoids. To elucidate the regulatory mechanisms underlying the differences in sugar-acid and color formation during fruit ripening, transcriptome analysis was conducted for the first time on the breaker stage (Br) and mature fruit stage (MF) of the closely related strains yellow-fruited tomato (No. 19) and red-fruited tomato (No. 20). This analysis aimed to identify key regulatory genes and biosynthetic pathways associated with the formation of flavor and color in tomato fruits. The transcriptome analysis revealed that 1,546 differentially expressed genes (DEGs) were identified in the Br19_vs_Br20 comparison, of which 507 were up-regulated and 1,039 were down-regulated. In the MF19_vs_MF20 comparison, 2,178 DEGs were detected, with 1,235 up-regulated and 943 down-regulated. Upon further analysis of the DEGs, we identified several key genes in the sugar-acid metabolic pathway, including sucrose synthase (SUS), phosphofructokinase (PFK), fructose-bisphosphate aldolase (FBA), citrate synthase (CS), and succinate dehydrogenase (SuDH), which may significantly influence tomato flavor. Additionally, differential genes related to carotenoid and flavonoid metabolism, such as cytochrome P450 98A (CYP98A), caffeoyl-CoA3-O-methyltransferase (CCoAMT), carotenoid isomerase (CRTISO), lycopene beta cyclase (LCYB), zeaxanthin epoxidase (ZEP), violaxanthin deepoxidase (VDE), and 9-cis-epoxycarotenoid dioxygenase (NCED), as well as genes linked to ethylene synthesis, such as 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), may play a role in the color changes observed in tomatoes. The findings of this study provide ins…
bibliographic citation: Guo et al. (2025) Transcriptome reveals differential expression of flavor and color in closely related strains of tomato (Solanum lycopersicum). PeerJ 13:e20113 https://doi.org/10.7717/peerj.20113
date submitted: 2025-02-14
date accepted: 2025-08-29
issued: 2025-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Chunmei
author list: Agent
  family name: Liu
  given name: Xiuyuan
author list: Agent
  family name: Ding
  given name: Yingfeng
author list: Agent
  family name: He
  given name: Zhaoyilan
author list: Agent
  family name: Shi
  given name: Songmei
author list: Agent
  family name: Ding
  given name: Yumei
author list: Agent
  family name: Shen
  given name: Hui
author list: Agent
  family name: Yang
  given name: Zhengan
doi: 10.7717/peerj.20113
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-07
copyright: © 2025 Guo et al.
attribution name: Guo et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359