PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Outcomes and safety of colonoscopy in elderly patients aged 80 years and older: a retrospective cohort study
items: Risk factors and predictive model for intrapartum cesarean delivery in women with epidural analgesia: a retrospective cohort study
items: Effect of quality sleep on basketball three-point shooting outcomes: the mediating role of athletic mental energy in a cross-sectional study of collegiate athletes
items: Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments
items: Cross-cultural adaptation and psychometric validation of the Chinese quality-of-life questionnaire for patients with systemic sclerosis
items: Dissecting antibody-dependent enhancement modulation by Fc-modified cross-neutralizing human monoclonal antibody
items: Comparison of anti-PD-1/PD-L1-based regimens in relapsed/refractory diffuse large B-cell lymphoma: a meta-analysis
items: Deciphering the role of Hat1 in spermatogenesis: Chromatin organization and beyond
items: A Bayesian model for assessing organic matter supply in complex marine food webs using amino acid stable isotope analysis
items: Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province

Outcomes and safety of colonoscopy in elderly patients aged 80 years and older: a retrospective cohort study
type: item
type: AcademicArticle
description: Background The incidence of colorectal tumors increases with age. Colonoscopy is crucial for early detection, yet performing it on patients aged 80 and older poses challenges due to their complex health conditions. Methods This retrospective study included 447 elderly patients aged 80 years and older who underwent colorectal examinations at Peking University International Hospital from November 2015 to June 2024. Data on demographics, comorbidities, smoking and drinking history, and colonoscopy indications were collected. Risk factors for non-colorectal malignant tumors, colorectal malignant tumors, and colorectal advanced-stage tumors were compared. All patients received standard bowel preparation, and procedures were conducted by experienced endoscopists. Results A total of 364 patients (81.4%) completed the procedure successfully. The main reasons for failure were inadequate intestinal preparation and intestinal stenosis. A total of 37 (8.3%) had no significant abnormalities, 315 (70.5%) were diagnosed with colorectal polyps, and 110 (24.6%) had malignant tumors. The complication rate was 0.67%. Univariate analysis showed that patients with colorectal malignant tumors were older (P = 0.000) and had a higher prevalence of alcohol consumption history (P = 0.014). For advanced tumors, patients were also older (P = 0.000). Discussion Age is a significant risk factor for colorectal malignancies and advanced tumors. Although colonoscopy in elderly patients has acceptable safety, they face challenges in bowel preparation and examination techniques. The incidence of polyps and malignant tumors in this population is high. However, the study has limitations, such as its retrospective nature and reliance on incomplete electronic medical records. Conclusion Colonoscopy is effective and safe for elderly patients aged 80 and older. It is essential for detecting colorectal malignancies and polyps. Age-related risk factors highlight the importance of this procedure in this high-…
format: application/pdf
format: text/html
creator: Yiming Ding
creator: Xiangchun Lin
subject: Gastroenterology and Hepatology
subject: Geriatrics
subject: Internal Medicine
description: doi:10.7717/peerj.20404
publisher: PeerJ Inc.
rights: © 2025 Ding and Lin
abstract: Background The incidence of colorectal tumors increases with age. Colonoscopy is crucial for early detection, yet performing it on patients aged 80 and older poses challenges due to their complex health conditions. Methods This retrospective study included 447 elderly patients aged 80 years and older who underwent colorectal examinations at Peking University International Hospital from November 2015 to June 2024. Data on demographics, comorbidities, smoking and drinking history, and colonoscopy indications were collected. Risk factors for non-colorectal malignant tumors, colorectal malignant tumors, and colorectal advanced-stage tumors were compared. All patients received standard bowel preparation, and procedures were conducted by experienced endoscopists. Results A total of 364 patients (81.4%) completed the procedure successfully. The main reasons for failure were inadequate intestinal preparation and intestinal stenosis. A total of 37 (8.3%) had no significant abnormalities, 315 (70.5%) were diagnosed with colorectal polyps, and 110 (24.6%) had malignant tumors. The complication rate was 0.67%. Univariate analysis showed that patients with colorectal malignant tumors were older (P = 0.000) and had a higher prevalence of alcohol consumption history (P = 0.014). For advanced tumors, patients were also older (P = 0.000). Discussion Age is a significant risk factor for colorectal malignancies and advanced tumors. Although colonoscopy in elderly patients has acceptable safety, they face challenges in bowel preparation and examination techniques. The incidence of polyps and malignant tumors in this population is high. However, the study has limitations, such as its retrospective nature and reliance on incomplete electronic medical records. Conclusion Colonoscopy is effective and safe for elderly patients aged 80 and older. It is essential for detecting colorectal malignancies and polyps. Age-related risk factors highlight the importance of this procedure in this high-…
bibliographic citation: Ding et al. (2025) Outcomes and safety of colonoscopy in elderly patients aged 80 years and older: a retrospective cohort study. PeerJ 13:e20404 https://doi.org/10.7717/peerj.20404
date submitted: 2025-02-26
date accepted: 2025-10-27
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ding
  given name: Yiming
author list: Agent
  family name: Lin
  given name: Xiangchun
doi: 10.7717/peerj.20404
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: © 2025 Ding and Lin
attribution name: Ding and Lin

Risk factors and predictive model for intrapartum cesarean delivery in women with epidural analgesia: a retrospective cohort study
type: item
type: AcademicArticle
description: Background Labor epidural analgesia (LEA) is the gold standard for labor pain management, yet its association with intrapartum cesarean delivery (CD) remains controversial. This study aimed to identify risk factors and develop a predictive model for CD conversion in parturients receiving LEA. Methods A retrospective cohort study analyzed 1,896 parturients receiving LEA at Zhengzhou Central Hospital (2022–2023). Participants were categorized into vaginal delivery group (n = 1, 541) and cesarean delivery group (n = 355). The original dataset was randomly split into training/testing sets (7:3 ratio) for analytical purposes. Univariate analysis identified significant variables, followed by Least Absolute Shrinkage and Selection Operator (LASSO) regression and multivariate logistic regression to construct a predictive nomogram. Model performance was evaluated by area under the receiver operating characteristic curve (AUC), calibration curves, and decision curve analysis (DCA). Results The CD conversion rate was 18.7%. Eight independent predictors were identified: height, pre-pregnancy body mass index (BMI), gestational age ≥ 40 weeks, hypertension, meperidine use, cervical dilation at analgesia initiation, intrapartum fever (≥ 38.0 °C), and estimated fetal weight. The nomogram demonstrated good discrimination (training set area under the curve (AUC) = 0.729, 95% confidence interval (CI) [0.695–0.763]; testing set AUC = 0.722, 95% CI [0.670–0.774]) and calibration (Hosmer-Lemeshow P > 0.05). DCA confirmed clinical utility. Conclusions This model provides a tool for individualized labor management that aims to reduce unnecessary cesarean deliveries.
format: application/pdf
format: text/html
creator: Yu Feng
creator: Yili Zhao
creator: Rui Shao
creator: Yan Wang
creator: Pin Zhang
subject: Anesthesiology and Pain Management
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.20358
publisher: PeerJ Inc.
rights: © 2025 Feng et al.
abstract: Background Labor epidural analgesia (LEA) is the gold standard for labor pain management, yet its association with intrapartum cesarean delivery (CD) remains controversial. This study aimed to identify risk factors and develop a predictive model for CD conversion in parturients receiving LEA. Methods A retrospective cohort study analyzed 1,896 parturients receiving LEA at Zhengzhou Central Hospital (2022–2023). Participants were categorized into vaginal delivery group (n = 1, 541) and cesarean delivery group (n = 355). The original dataset was randomly split into training/testing sets (7:3 ratio) for analytical purposes. Univariate analysis identified significant variables, followed by Least Absolute Shrinkage and Selection Operator (LASSO) regression and multivariate logistic regression to construct a predictive nomogram. Model performance was evaluated by area under the receiver operating characteristic curve (AUC), calibration curves, and decision curve analysis (DCA). Results The CD conversion rate was 18.7%. Eight independent predictors were identified: height, pre-pregnancy body mass index (BMI), gestational age ≥ 40 weeks, hypertension, meperidine use, cervical dilation at analgesia initiation, intrapartum fever (≥ 38.0 °C), and estimated fetal weight. The nomogram demonstrated good discrimination (training set area under the curve (AUC) = 0.729, 95% confidence interval (CI) [0.695–0.763]; testing set AUC = 0.722, 95% CI [0.670–0.774]) and calibration (Hosmer-Lemeshow P > 0.05). DCA confirmed clinical utility. Conclusions This model provides a tool for individualized labor management that aims to reduce unnecessary cesarean deliveries.
bibliographic citation: Feng et al. (2025) Risk factors and predictive model for intrapartum cesarean delivery in women with epidural analgesia: a retrospective cohort study. PeerJ 13:e20358 https://doi.org/10.7717/peerj.20358
date submitted: 2025-06-20
date accepted: 2025-10-16
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feng
  given name: Yu
author list: Agent
  family name: Zhao
  given name: Yili
author list: Agent
  family name: Shao
  given name: Rui
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Zhang
  given name: Pin
doi: 10.7717/peerj.20358
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Feng et al.
attribution name: Feng et al.

Effect of quality sleep on basketball three-point shooting outcomes: the mediating role of athletic mental energy in a cross-sectional study of collegiate athletes
type: item
type: AcademicArticle
description: Introduction Quality sleep is crucial for optimal sports performance, yet the psychological mechanisms underpinning the sleep-sports performance relationship require further examination. Methods This cross-sectional study explored the effects of athletic mental energy (AME) and sleep quality on basketball three-point shooting outcomes with a particular emphasis on the mediating role of AME. One hundred and forty-five collegiate basketball athletes (71 males and 74 females; Mage = 19.62 ± 1.35) with highly trained levels were recruited to evaluate sleep quality, AME, and basketball three-point shooting performance and percentage. Data were collected through validated questionnaires and a standardized three-point shooting test, and analyzed using structural equation modeling (SEM) with bootstrapping. Results Sleep quality was positively associated with basketball three-point shooting performance (r = 0.22, p = 0.007) and shooting percentage (r = 0.22, p = 0.009). AME partially and fully mediated these associations (indirect effect = 0.18, p = 0.031, 95% bias-corrected CI [0.02–0.42] for shooting performance; indirect effect = 0.27, p = 0.019, 95% bias-corrected CI [0.04–0.60] for shooting percentage). Conclusions The findings contribute to the literature on the relationship between sleep and competition-relevant sports performance and suggest AME as one of the potential psychological mechanisms underlying these associations. These results highlight the importance of considering athletes’ sleep quality and AME in performance contexts, while further research is needed to strengthen and generalize these conclusions.
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format: text/html
creator: Shu-Yueh Chan
creator: Wei-Jiun Shen
creator: Shin-Liang Lo
creator: Yun Che Hsieh
creator: Frank J.H. Lu
creator: Garry Kuan
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.20355
publisher: PeerJ Inc.
rights: © 2025 Chan et al.
abstract: Introduction Quality sleep is crucial for optimal sports performance, yet the psychological mechanisms underpinning the sleep-sports performance relationship require further examination. Methods This cross-sectional study explored the effects of athletic mental energy (AME) and sleep quality on basketball three-point shooting outcomes with a particular emphasis on the mediating role of AME. One hundred and forty-five collegiate basketball athletes (71 males and 74 females; Mage = 19.62 ± 1.35) with highly trained levels were recruited to evaluate sleep quality, AME, and basketball three-point shooting performance and percentage. Data were collected through validated questionnaires and a standardized three-point shooting test, and analyzed using structural equation modeling (SEM) with bootstrapping. Results Sleep quality was positively associated with basketball three-point shooting performance (r = 0.22, p = 0.007) and shooting percentage (r = 0.22, p = 0.009). AME partially and fully mediated these associations (indirect effect = 0.18, p = 0.031, 95% bias-corrected CI [0.02–0.42] for shooting performance; indirect effect = 0.27, p = 0.019, 95% bias-corrected CI [0.04–0.60] for shooting percentage). Conclusions The findings contribute to the literature on the relationship between sleep and competition-relevant sports performance and suggest AME as one of the potential psychological mechanisms underlying these associations. These results highlight the importance of considering athletes’ sleep quality and AME in performance contexts, while further research is needed to strengthen and generalize these conclusions.
bibliographic citation: Chan et al. (2025) Effect of quality sleep on basketball three-point shooting outcomes: the mediating role of athletic mental energy in a cross-sectional study of collegiate athletes. PeerJ 13:e20355 https://doi.org/10.7717/peerj.20355
date submitted: 2025-05-14
date accepted: 2025-10-16
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chan
  given name: Shu-Yueh
author list: Agent
  family name: Shen
  given name: Wei-Jiun
author list: Agent
  family name: Lo
  given name: Shin-Liang
author list: Agent
  family name: Hsieh
  given name: Yun Che
author list: Agent
  family name: Lu
  given name: Frank J.H.
author list: Agent
  family name: Kuan
  given name: Garry
doi: 10.7717/peerj.20355
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Chan et al.
attribution name: Chan et al.

Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments
type: item
type: AcademicArticle
description: Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces—Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance.
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creator: Xuemei Han
creator: Huan Liu
creator: Xue Bai
creator: Diyan Li
creator: Tao Wang
creator: Hang Zhong
creator: Yongfang Yao
creator: Jing Sun
subject: Bioinformatics
subject: Ecology
subject: Genomics
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.20348
publisher: PeerJ Inc.
rights: © 2025 Han et al.
abstract: Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces—Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance.
bibliographic citation: Han et al. (2025) Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments. PeerJ 13:e20348 https://doi.org/10.7717/peerj.20348
date submitted: 2025-08-05
date accepted: 2025-10-15
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Xuemei
author list: Agent
  family name: Liu
  given name: Huan
author list: Agent
  family name: Bai
  given name: Xue
author list: Agent
  family name: Li
  given name: Diyan
author list: Agent
  family name: Wang
  given name: Tao
author list: Agent
  family name: Zhong
  given name: Hang
author list: Agent
  family name: Yao
  given name: Yongfang
author list: Agent
  family name: Sun
  given name: Jing
doi: 10.7717/peerj.20348
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Han et al.
attribution name: Han et al.

Cross-cultural adaptation and psychometric validation of the Chinese quality-of-life questionnaire for patients with systemic sclerosis
type: item
type: AcademicArticle
description: Background Patients with systemic sclerosis (SSc) frequently experience symptoms such as pain, fatigue, and functional impairments, leading to a significant decline in their quality of life (QoL). Accurately evaluating the QoL of SSc patients is crucial for developing personalized treatment plans and enhancing prognosis. The Systemic Sclerosis Quality of Life Questionnaire (SScQoL), an internationally recognized SSc-specific tool, is commonly used for QoL assessment. However, this questionnaire has not undergone cross-cultural adaptation in China, and its reliability and validity require further validation. Objectives To localize the Systemic Sclerosis Quality of Life Questionnaire (SScQoL) into Chinese and assess its reliability and validity. Methods Following the principles of scale introduction, the Beaton model was employed to translate and back-translate the English version. The scale underwent cross-cultural adaptation through expert consultation, resulting in the Chinese version of the SScQoL test. From August 2023 to December 2024, a convenience sampling method was used to recruit 160 patients with systemic sclerosis from two hospitals for questionnaire surveys to evaluate questionnaire reliability and validity. Results SScQoL comprises five dimensions and 29 items. The content validity index (CVI) at the item level ranges from 0.83 to 1.00, and the CVI at the scale level is 0.97. Exploratory factor analysis identified five common factors, with a cumulative variance contribution rate of 65.761%. The Cronbach’s α coefficient for the total scale is 0.922, and the Cronbach’s α coefficients for the five dimensions range from 0.756 to 0.942. The test-retest reliability for the total scale is 0.969; for the five dimensions, it ranges from 0.710 to 0.961. Conclusions SScQoL is a reliable and effective tool for evaluating patients’ quality of life with systemic sclerosis. This tool can support nurses and researchers and help them formulate targeted strategies, there…
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format: text/html
creator: Yinfeng Hu
creator: Wenjie Zhong
creator: Liqiong Zhou
subject: Global Health
subject: Nursing
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.20331
publisher: PeerJ Inc.
rights: © 2025 Hu et al.
abstract: Background Patients with systemic sclerosis (SSc) frequently experience symptoms such as pain, fatigue, and functional impairments, leading to a significant decline in their quality of life (QoL). Accurately evaluating the QoL of SSc patients is crucial for developing personalized treatment plans and enhancing prognosis. The Systemic Sclerosis Quality of Life Questionnaire (SScQoL), an internationally recognized SSc-specific tool, is commonly used for QoL assessment. However, this questionnaire has not undergone cross-cultural adaptation in China, and its reliability and validity require further validation. Objectives To localize the Systemic Sclerosis Quality of Life Questionnaire (SScQoL) into Chinese and assess its reliability and validity. Methods Following the principles of scale introduction, the Beaton model was employed to translate and back-translate the English version. The scale underwent cross-cultural adaptation through expert consultation, resulting in the Chinese version of the SScQoL test. From August 2023 to December 2024, a convenience sampling method was used to recruit 160 patients with systemic sclerosis from two hospitals for questionnaire surveys to evaluate questionnaire reliability and validity. Results SScQoL comprises five dimensions and 29 items. The content validity index (CVI) at the item level ranges from 0.83 to 1.00, and the CVI at the scale level is 0.97. Exploratory factor analysis identified five common factors, with a cumulative variance contribution rate of 65.761%. The Cronbach’s α coefficient for the total scale is 0.922, and the Cronbach’s α coefficients for the five dimensions range from 0.756 to 0.942. The test-retest reliability for the total scale is 0.969; for the five dimensions, it ranges from 0.710 to 0.961. Conclusions SScQoL is a reliable and effective tool for evaluating patients’ quality of life with systemic sclerosis. This tool can support nurses and researchers and help them formulate targeted strategies, there…
bibliographic citation: Hu et al. (2025) Cross-cultural adaptation and psychometric validation of the Chinese quality-of-life questionnaire for patients with systemic sclerosis. PeerJ 13:e20331 https://doi.org/10.7717/peerj.20331
date submitted: 2025-04-23
date accepted: 2025-10-13
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Yinfeng
author list: Agent
  family name: Zhong
  given name: Wenjie
author list: Agent
  family name: Zhou
  given name: Liqiong
doi: 10.7717/peerj.20331
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: © 2025 Hu et al.
attribution name: Hu et al.

Dissecting antibody-dependent enhancement modulation by Fc-modified cross-neutralizing human monoclonal antibody
type: item
type: AcademicArticle
description: Background Dengue is a mosquito-borne disease caused by four dengue virus serotypes (DENV1 to DENV4). Secondary infections can generate flavivirus cross-reactive antibodies at sub-neutralizing levels. This phenomenon can significantly increase the severity of secondary infections through antibody-dependent enhancement (ADE). ADE is associated with a high risk of viral infection in immune effector cells, triggering cytokine cascades and activating the complement system, which can lead to severe symptoms. Despite extensive studies, therapeutic antibodies, particularly fully human monoclonal antibodies, which could serve as candidates for immune passive therapy, have not yet been discovered. Methodology This study generated LALA-mutated human monoclonal antibody clone B3B9 (LALA-B3B9 HuMAb) which can neutralize all four DENV serotypes without enhancing viral activity. The number of infected cells in the ADE assay was compared among the wild-type antibody (B3B9), LALA-B3B9 HuMAb, and an Fc modified variant at position N297Q (N297Q-B3B9), with or without complement proteins. Moreover, the therapeutic efficacy of these HuMAbs against ADE infection by competing with natural antibodies in patients with acute dengue was evaluated using the in vitro suppression-of-enhancement assay in K562 cells. Result Our novel Fc-modified antibody LALA-B3B9 (Leu234Ala/Leu235Ala mutations), exhibited neutralizing activity against all dengue virus serotypes without triggering ADE activity at any antibody concentration. This outcome was similar to that observed with the previously developed Fc-modified N297Q-B3B9 antibody (N297Q mutation). We further evaluated the effect of complement protein on the enhancing and neutralizing activities of our Fc-modified antibodies. The results showed that LALA-B3B9 and N297Q-B3B9 HuMAbs were complement-independent, meaning that the reduced binding between complement protein (C1q) and the Fc portion of the antibody left the neutralizing and enhancing activit…
format: application/pdf
format: text/html
creator: Subenya Injampa
creator: Surachet Benjathummarak
creator: Sujitra Keadsanti
creator: Rochanawan Sootichote
creator: Wilarat Puangmanee
creator: Atsushi Yamanaka
creator: Tadahiro Sasaki
creator: Pongrama Ramasoota
creator: Pannamthip Pitaksajjakul
subject: Biotechnology
subject: Virology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.20329
publisher: PeerJ Inc.
rights: © 2025 Injampa et al.
abstract: Background Dengue is a mosquito-borne disease caused by four dengue virus serotypes (DENV1 to DENV4). Secondary infections can generate flavivirus cross-reactive antibodies at sub-neutralizing levels. This phenomenon can significantly increase the severity of secondary infections through antibody-dependent enhancement (ADE). ADE is associated with a high risk of viral infection in immune effector cells, triggering cytokine cascades and activating the complement system, which can lead to severe symptoms. Despite extensive studies, therapeutic antibodies, particularly fully human monoclonal antibodies, which could serve as candidates for immune passive therapy, have not yet been discovered. Methodology This study generated LALA-mutated human monoclonal antibody clone B3B9 (LALA-B3B9 HuMAb) which can neutralize all four DENV serotypes without enhancing viral activity. The number of infected cells in the ADE assay was compared among the wild-type antibody (B3B9), LALA-B3B9 HuMAb, and an Fc modified variant at position N297Q (N297Q-B3B9), with or without complement proteins. Moreover, the therapeutic efficacy of these HuMAbs against ADE infection by competing with natural antibodies in patients with acute dengue was evaluated using the in vitro suppression-of-enhancement assay in K562 cells. Result Our novel Fc-modified antibody LALA-B3B9 (Leu234Ala/Leu235Ala mutations), exhibited neutralizing activity against all dengue virus serotypes without triggering ADE activity at any antibody concentration. This outcome was similar to that observed with the previously developed Fc-modified N297Q-B3B9 antibody (N297Q mutation). We further evaluated the effect of complement protein on the enhancing and neutralizing activities of our Fc-modified antibodies. The results showed that LALA-B3B9 and N297Q-B3B9 HuMAbs were complement-independent, meaning that the reduced binding between complement protein (C1q) and the Fc portion of the antibody left the neutralizing and enhancing activit…
bibliographic citation: Injampa et al. (2025) Dissecting antibody-dependent enhancement modulation by Fc-modified cross-neutralizing human monoclonal antibody. PeerJ 13:e20329 https://doi.org/10.7717/peerj.20329
date submitted: 2025-06-03
date accepted: 2025-10-13
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Injampa
  given name: Subenya
author list: Agent
  family name: Benjathummarak
  given name: Surachet
author list: Agent
  family name: Keadsanti
  given name: Sujitra
author list: Agent
  family name: Sootichote
  given name: Rochanawan
author list: Agent
  family name: Puangmanee
  given name: Wilarat
author list: Agent
  family name: Yamanaka
  given name: Atsushi
author list: Agent
  family name: Sasaki
  given name: Tadahiro
author list: Agent
  family name: Ramasoota
  given name: Pongrama
author list: Agent
  family name: Pitaksajjakul
  given name: Pannamthip
doi: 10.7717/peerj.20329
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Injampa et al.
attribution name: Injampa et al.

Comparison of anti-PD-1/PD-L1-based regimens in relapsed/refractory diffuse large B-cell lymphoma: a meta-analysis
type: item
type: AcademicArticle
description: Aim To evaluate the therapeutic value and find out potential combination agents of programmed death 1/programmed death-ligand 1 (PD-1/PD-L1) monoclonal antibody (mAb) in relapsed/refractory (r/r) diffuse large B-cell lymphoma (DLBCL). Methods We conducted a meta-analysis to assess the efficacy and safety of PD-1/PD-L1 mAb in r/r DLBCL, potential qualified studies were searched in PubMed, Embase, Web of Science, and ClinicalTrials.gov. This meta-analysis had been registered on the PROSPERO platform (CRD42023340031). Results After systematic screening, a total of 32 records involving 29 studies were included, pooled survival curves indicated better progression-free survival (PFS) (p < 0.0001; HR = 0.51, 95% CI [0.42–0.62]) and overall survival (OS) (p = 0.013; HR = 0.71, 95% CI [0.57–0.88]) for combination therapy compared with monotherapy. Combination therapy group also achieved a better pooled complete response rate (CRR) (14.6% vs. 3.0%; p < 0.001) and overall response rate (ORR) (30.5% vs. 10.3%; p < 0.001). Analysis of the incidence of adverse events (AEs) did not demonstrate additional toxicities of combination therapy. The limitation was the predominance of single-arm trials, precluding the direct comparison of combination versus partner agents alone. Conclusions These findings support further exploration of PD-1/PD-L1-mAb-based combination therapy to identify long-term survival benefits, while application of monotherapy in unselected DLBCL patients is not recommended.
format: application/pdf
format: text/html
creator: Wenxin Jiang
creator: Tingyu Wen
creator: Peng Liu
subject: Hematology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.20314
publisher: PeerJ Inc.
rights: © 2025 Jiang et al.
abstract: Aim To evaluate the therapeutic value and find out potential combination agents of programmed death 1/programmed death-ligand 1 (PD-1/PD-L1) monoclonal antibody (mAb) in relapsed/refractory (r/r) diffuse large B-cell lymphoma (DLBCL). Methods We conducted a meta-analysis to assess the efficacy and safety of PD-1/PD-L1 mAb in r/r DLBCL, potential qualified studies were searched in PubMed, Embase, Web of Science, and ClinicalTrials.gov. This meta-analysis had been registered on the PROSPERO platform (CRD42023340031). Results After systematic screening, a total of 32 records involving 29 studies were included, pooled survival curves indicated better progression-free survival (PFS) (p < 0.0001; HR = 0.51, 95% CI [0.42–0.62]) and overall survival (OS) (p = 0.013; HR = 0.71, 95% CI [0.57–0.88]) for combination therapy compared with monotherapy. Combination therapy group also achieved a better pooled complete response rate (CRR) (14.6% vs. 3.0%; p < 0.001) and overall response rate (ORR) (30.5% vs. 10.3%; p < 0.001). Analysis of the incidence of adverse events (AEs) did not demonstrate additional toxicities of combination therapy. The limitation was the predominance of single-arm trials, precluding the direct comparison of combination versus partner agents alone. Conclusions These findings support further exploration of PD-1/PD-L1-mAb-based combination therapy to identify long-term survival benefits, while application of monotherapy in unselected DLBCL patients is not recommended.
bibliographic citation: Jiang et al. (2025) Comparison of anti-PD-1/PD-L1-based regimens in relapsed/refractory diffuse large B-cell lymphoma: a meta-analysis. PeerJ 13:e20314 https://doi.org/10.7717/peerj.20314
date submitted: 2025-07-16
date accepted: 2025-10-08
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Wenxin
author list: Agent
  family name: Wen
  given name: Tingyu
author list: Agent
  family name: Liu
  given name: Peng
doi: 10.7717/peerj.20314
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Jiang et al.
attribution name: Jiang et al.

Deciphering the role of Hat1 in spermatogenesis: Chromatin organization and beyond
type: item
type: AcademicArticle
description: Spermatogenesis, a core process for male fertility, relies heavily on chromatin organization regulated by histone acetyltransferases (HATs). However, the spatiotemporal expression pattern of histone acetyltransferase 1 (Hat1) in mouse testes and its specific role in spermatogenesis via chromatin organization remain unclear. This study employed RT-qPCR, Western blot, immunofluorescence localization, and bioinformatics to explore Hat1’s dynamic expression and regulatory mechanisms during mouse spermatogenesis. Results showed that both Hat1 mRNA and protein were significantly upregulated in the testes of 8-week-old (mature) mice compared to 3-week-old (immature) mice. Immunofluorescence revealed Hat1 was predominantly localized in the nuclei of male germ cells, with stage-specific expression: highest in spermatogonia and sperm, intermediate in primary spermatocytes, and lowest in secondary spermatocytes. Bioinformatics analysis (based on single-cell sequencing data GSE214315) identified 246 differentially expressed genes (DEGs) related to chromatin organization—these DEGs were screened between adjacent stages of male germ cell development during spermatogenesis, including comparisons of leptotene-zygotene vs. pachytene-diplotene cells, pachytene-diplotene vs. round spermatids, round spermatids vs. early elongating spermatids, and early elongating vs. late elongating spermatids (screening criteria: FDR < 0.05, |log2(FC)| ≥ 1). Additionally, 41 Hat1-interacting proteins encoded by these DEGs were identified. Functional enrichment indicated stage-specific roles of Hat1: in the leptotene-zygotene phase, it participated in transcription regulation to initiate meiosis; in round spermatids, it shifted to refined epigenetic regulation and chromatin assembly for subsequent spermiogenesis; in late spermiogenesis and sperm, it was involved in DNA repair and ATP-dependent chromatin remodeling to protect sperm genetic material. In summary, the stage-specific expression patterns of …
format: application/pdf
format: text/html
creator: Shenni Peng
creator: Yulian Tang
creator: Ruiqun Lu
creator: Shi Huang
creator: Yinyin Mo
creator: Hailing Huang
creator: Genliang Li
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.20240
publisher: PeerJ Inc.
rights: © 2025 Peng et al.
abstract: Spermatogenesis, a core process for male fertility, relies heavily on chromatin organization regulated by histone acetyltransferases (HATs). However, the spatiotemporal expression pattern of histone acetyltransferase 1 (Hat1) in mouse testes and its specific role in spermatogenesis via chromatin organization remain unclear. This study employed RT-qPCR, Western blot, immunofluorescence localization, and bioinformatics to explore Hat1’s dynamic expression and regulatory mechanisms during mouse spermatogenesis. Results showed that both Hat1 mRNA and protein were significantly upregulated in the testes of 8-week-old (mature) mice compared to 3-week-old (immature) mice. Immunofluorescence revealed Hat1 was predominantly localized in the nuclei of male germ cells, with stage-specific expression: highest in spermatogonia and sperm, intermediate in primary spermatocytes, and lowest in secondary spermatocytes. Bioinformatics analysis (based on single-cell sequencing data GSE214315) identified 246 differentially expressed genes (DEGs) related to chromatin organization—these DEGs were screened between adjacent stages of male germ cell development during spermatogenesis, including comparisons of leptotene-zygotene vs. pachytene-diplotene cells, pachytene-diplotene vs. round spermatids, round spermatids vs. early elongating spermatids, and early elongating vs. late elongating spermatids (screening criteria: FDR < 0.05, |log2(FC)| ≥ 1). Additionally, 41 Hat1-interacting proteins encoded by these DEGs were identified. Functional enrichment indicated stage-specific roles of Hat1: in the leptotene-zygotene phase, it participated in transcription regulation to initiate meiosis; in round spermatids, it shifted to refined epigenetic regulation and chromatin assembly for subsequent spermiogenesis; in late spermiogenesis and sperm, it was involved in DNA repair and ATP-dependent chromatin remodeling to protect sperm genetic material. In summary, the stage-specific expression patterns of …
bibliographic citation: Peng et al. (2025) Deciphering the role of Hat1 in spermatogenesis: Chromatin organization and beyond. PeerJ 13:e20240 https://doi.org/10.7717/peerj.20240
date submitted: 2025-06-04
date accepted: 2025-09-24
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peng
  given name: Shenni
author list: Agent
  family name: Tang
  given name: Yulian
author list: Agent
  family name: Lu
  given name: Ruiqun
author list: Agent
  family name: Huang
  given name: Shi
author list: Agent
  family name: Mo
  given name: Yinyin
author list: Agent
  family name: Huang
  given name: Hailing
author list: Agent
  family name: Li
  given name: Genliang
doi: 10.7717/peerj.20240
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Peng et al.
attribution name: Peng et al.

A Bayesian model for assessing organic matter supply in complex marine food webs using amino acid stable isotope analysis
type: item
type: AcademicArticle
description: While several software packages have been developed to solve stable isotope mixing models, none are currently equipped to trace the flow of organic matter through the lower trophic levels of planktonic food webs. To address this gap, we have developed a new Bayesian mixing model tailored for use with δ15N values of individual amino acids. This model simultaneously estimates trophic relationships between consumers and organic matter sources at the base of the food web, determines the relative contributions of these basal organic matter sources to consumers, and accounts for trophic discrimination affecting amino acid δ15N values during protozoan and metazoan trophic steps. This “Organic Matter Supply Model” is uniquely suited for applications where food web structure is unknown and trophic intermediaries, such as protozoan and metazoan grazers with distinct amino acid trophic discrimination factors, play a critical role in nutrient transfer. In this paper, we describe the model’s basic structure, outline key considerations for adapting it to specific applications, evaluate its performance using simulated zooplankton data, discuss its strengths and limitations, and offer recommendations for its further development. By testing the model on simulated zooplankton amino acid δ15N data, we demonstrate that the Organic Matter Supply Model can enhance our understanding of the roles of small particles and diel vertical migration in deep-sea organic matter supply pathways. Furthermore, it provides a new framework for exploring the foundational role of heterotrophic protists in marine ecosystems. We find specific subsets of amino acids to be most useful as markers of trophic ecology (in this case including glutamic acid and proline) and to identify supply from basal organic matter sources (phenylalanine, lysine, and threonine). Other amino acids may be more ideal source tracers in other settings, although amino acids with inconsistent or poorly constrained isotope fractionation…
format: application/pdf
format: text/html
creator: Connor H.H. Shea
creator: Jeffrey C. Drazen
creator: Brian N. Popp
subject: Ecology
subject: Ecosystem Science
subject: Statistics
subject: Biogeochemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.20220
publisher: PeerJ Inc.
rights: © 2025 Shea et al.
abstract: While several software packages have been developed to solve stable isotope mixing models, none are currently equipped to trace the flow of organic matter through the lower trophic levels of planktonic food webs. To address this gap, we have developed a new Bayesian mixing model tailored for use with δ15N values of individual amino acids. This model simultaneously estimates trophic relationships between consumers and organic matter sources at the base of the food web, determines the relative contributions of these basal organic matter sources to consumers, and accounts for trophic discrimination affecting amino acid δ15N values during protozoan and metazoan trophic steps. This “Organic Matter Supply Model” is uniquely suited for applications where food web structure is unknown and trophic intermediaries, such as protozoan and metazoan grazers with distinct amino acid trophic discrimination factors, play a critical role in nutrient transfer. In this paper, we describe the model’s basic structure, outline key considerations for adapting it to specific applications, evaluate its performance using simulated zooplankton data, discuss its strengths and limitations, and offer recommendations for its further development. By testing the model on simulated zooplankton amino acid δ15N data, we demonstrate that the Organic Matter Supply Model can enhance our understanding of the roles of small particles and diel vertical migration in deep-sea organic matter supply pathways. Furthermore, it provides a new framework for exploring the foundational role of heterotrophic protists in marine ecosystems. We find specific subsets of amino acids to be most useful as markers of trophic ecology (in this case including glutamic acid and proline) and to identify supply from basal organic matter sources (phenylalanine, lysine, and threonine). Other amino acids may be more ideal source tracers in other settings, although amino acids with inconsistent or poorly constrained isotope fractionation…
bibliographic citation: Shea et al. (2025) A Bayesian model for assessing organic matter supply in complex marine food webs using amino acid stable isotope analysis. PeerJ 13:e20220 https://doi.org/10.7717/peerj.20220
date submitted: 2025-05-30
date accepted: 2025-09-21
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shea
  given name: Connor H.H.
author list: Agent
  family name: Drazen
  given name: Jeffrey C.
author list: Agent
  family name: Popp
  given name: Brian N.
doi: 10.7717/peerj.20220
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Shea et al.
attribution name: Shea et al.

Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province
type: item
type: AcademicArticle
description: Background Hongta District of Yuxi city is located in the central region of Yunnan Province, Southwest China. Previous studies have shown a high prevalence of enteric infectious diseases in the area, which may be related to sewage discharge. However, there has been no systematic analysis of the microbiome in sewage in this area. In this study, we investigated environmental sewage in Hongta District, Yuxi city, Yunnan Province. Methods Surveillance was conducted in Hongta District, Yuxi city, for a period of one year. At both its urban and rural sites, sewage samples were collected for metagenomic sequencing. Results The results revealed that in the sewage samples, bacteria accounted for 98.31% of the total microbiome, followed by Archaea (1.05%), Viruses (0.30%) and Eukaryota (0.34%). At the phylum level, Proteobacteria was the taxon with the highest relative abundance, accounting for 57.57% of all samples, followed by Firmicutes (17.17%), Bacteroidetes (12.23%), Actinobacteria (7.10%), and Synergistetes (1.45%). At the genus level, the taxa with the highest relative abundances of all the microbiomes were Acidovorax (6.63%), Pseudomonas (4.98%), Acinetobacter (4.23%), Comamonas (3.85%), and Aliarcobacter (2.78%). The diversity of the samples grouped by site and rainfall formed their own clusters, but only the compositions of different taxa grouped by rainfall significantly differed (P = 0.038 at the family, P = 0.019 at the genus and P = 0.005 at the species level). In general, the abundance of several taxa at the family, genus and species levels in the dry season group was higher (P < 0.05) than that in the rainy season group according to the Kruskal–Wallis test. The relative abundance s of most virulence genes were higher at urban sites than at rural sites, while those in the rainy season was higher than those in the dry season. The distribution of antibiotic resistance genes (ARGs) in urban and rural sewage was significantly different (P = 0.018). The relative ab…
format: application/pdf
format: text/html
creator: Senquan Jia
creator: Wenpeng Gu
creator: Lili Jiang
creator: Yong Zhang
creator: Xiaoqing Fu
creator: Jianwen Yin
creator: Yongming Zhou
subject: Microbiology
subject: Global Health
subject: Public Health
subject: Environmental Contamination and Remediation
subject: Environmental Health
description: doi:10.7717/peerj.20199
publisher: PeerJ Inc.
rights: © 2025 Jia et al.
abstract: Background Hongta District of Yuxi city is located in the central region of Yunnan Province, Southwest China. Previous studies have shown a high prevalence of enteric infectious diseases in the area, which may be related to sewage discharge. However, there has been no systematic analysis of the microbiome in sewage in this area. In this study, we investigated environmental sewage in Hongta District, Yuxi city, Yunnan Province. Methods Surveillance was conducted in Hongta District, Yuxi city, for a period of one year. At both its urban and rural sites, sewage samples were collected for metagenomic sequencing. Results The results revealed that in the sewage samples, bacteria accounted for 98.31% of the total microbiome, followed by Archaea (1.05%), Viruses (0.30%) and Eukaryota (0.34%). At the phylum level, Proteobacteria was the taxon with the highest relative abundance, accounting for 57.57% of all samples, followed by Firmicutes (17.17%), Bacteroidetes (12.23%), Actinobacteria (7.10%), and Synergistetes (1.45%). At the genus level, the taxa with the highest relative abundances of all the microbiomes were Acidovorax (6.63%), Pseudomonas (4.98%), Acinetobacter (4.23%), Comamonas (3.85%), and Aliarcobacter (2.78%). The diversity of the samples grouped by site and rainfall formed their own clusters, but only the compositions of different taxa grouped by rainfall significantly differed (P = 0.038 at the family, P = 0.019 at the genus and P = 0.005 at the species level). In general, the abundance of several taxa at the family, genus and species levels in the dry season group was higher (P < 0.05) than that in the rainy season group according to the Kruskal–Wallis test. The relative abundance s of most virulence genes were higher at urban sites than at rural sites, while those in the rainy season was higher than those in the dry season. The distribution of antibiotic resistance genes (ARGs) in urban and rural sewage was significantly different (P = 0.018). The relative ab…
bibliographic citation: Jia et al. (2025) Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province. PeerJ 13:e20199 https://doi.org/10.7717/peerj.20199
date submitted: 2025-03-04
date accepted: 2025-09-16
issued: 2025-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jia
  given name: Senquan
author list: Agent
  family name: Gu
  given name: Wenpeng
author list: Agent
  family name: Jiang
  given name: Lili
author list: Agent
  family name: Zhang
  given name: Yong
author list: Agent
  family name: Fu
  given name: Xiaoqing
author list: Agent
  family name: Yin
  given name: Jianwen
author list: Agent
  family name: Zhou
  given name: Yongming
doi: 10.7717/peerj.20199
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-19
copyright: ©2025 Jia et al.
attribution name: Jia et al.

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