PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: AIMP1: multifunctional regulator in physiology and pathology with therapeutic implications
items: Machine learning classification of mango maturity based on carotene content from Raman spectra
items: Identification of mitochondrial-related genes to evaluate the immune infiltration and prognosis of lung adenocarcinoma
items: Acute effect of short foot exercise on dynamic stability and foot kinematic in trail runners: a proof-of-concept study

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…
format: application/pdf
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.

AIMP1: multifunctional regulator in physiology and pathology with therapeutic implications
type: item
type: AcademicArticle
description: Aminoacyl tRNA synthetase complex interacting multifunctional protein 1 (AIMP1), also referred to as p43, serves as an auxiliary factor of the macromolecular aminoacyl tRNA synthetase complex. Beyond its classical role in the assembling the multisynthetase complex (MSC) for protein translation, growing evidence has elucidated that AIMP1 plays a pivotal role in regulating immune response, brain function and angiogenesis. Furthermore, accumulating studies have demonstrated that AIMP1 is involved in a spectrum of pathological processes, including cancer, immunity associated disorders, and neurological diseases. Herein, we summarize the current research regarding the functions of AIMP1 under both physiological and pathological conditions, with a particular focus on its therapeutic potential in these diseases.
format: application/pdf
format: text/html
creator: Xunan Yuan
creator: Xinmiao Wang
creator: Xiaodan Ma
creator: Yaping Mao
creator: Qinqin Wang
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Immunology
subject: Neurology
description: doi:10.7717/peerj.20334
publisher: PeerJ Inc.
rights: © 2025 Yuan et al.
abstract: Aminoacyl tRNA synthetase complex interacting multifunctional protein 1 (AIMP1), also referred to as p43, serves as an auxiliary factor of the macromolecular aminoacyl tRNA synthetase complex. Beyond its classical role in the assembling the multisynthetase complex (MSC) for protein translation, growing evidence has elucidated that AIMP1 plays a pivotal role in regulating immune response, brain function and angiogenesis. Furthermore, accumulating studies have demonstrated that AIMP1 is involved in a spectrum of pathological processes, including cancer, immunity associated disorders, and neurological diseases. Herein, we summarize the current research regarding the functions of AIMP1 under both physiological and pathological conditions, with a particular focus on its therapeutic potential in these diseases.
bibliographic citation: Yuan et al. (2025) AIMP1: multifunctional regulator in physiology and pathology with therapeutic implications. PeerJ 13:e20334 https://doi.org/10.7717/peerj.20334
date submitted: 2025-05-30
date accepted: 2025-10-13
issued: 2025-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Yuan
  given name: Xunan
author list: Agent
  family name: Wang
  given name: Xinmiao
author list: Agent
  family name: Ma
  given name: Xiaodan
author list: Agent
  family name: Mao
  given name: Yaping
author list: Agent
  family name: Wang
  given name: Qinqin
doi: 10.7717/peerj.20334
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-18
copyright: © 2025 Yuan et al.
attribution name: Yuan et al.

Machine learning classification of mango maturity based on carotene content from Raman spectra
type: item
type: AcademicArticle
description: Determining mango ripeness is essential for ensuring its delicious taste, enticing aroma, and rich nutritional value. For farmers, harvesting mangoes too early can result in stunted fruit and lower yields compared to those harvested at a ripe stage. This study aims to develop a potentially non-invasive and efficient method for detecting mango ripeness using Raman spectroscopy. Traditional methods, which rely on human assessment and color evaluation with image processing, are inconsistent, inaccurate, and time-consuming due to variations in mango color and individual differences in vision and perception. To address these limitations, this study pursued three main objectives: extracting data characteristics of organic compounds in mangoes based on raw Raman spectrum data, identifying the correlation between carotene characteristics and mango ripeness levels, and evaluating the performance of machine learning models in classifying mango ripeness levels. A total of 29 mango fruit spectra were analyzed, with 13 samples selected to represent three ripeness categories: underripe, ripe, and overripe. Raman spectra peak signal analysis revealed that mango peel contains lycopene, β-carotene, lutein, and neoxanthin, all of which are derived from carotenoid molecules in the range of 1,480 cm−1 to 1,550 cm−1. Statistical analysis confirmed the significance (p < 0.05) of extracted Raman Peak Intensity features in distinguishing ripeness levels, supported by high correlation coefficients between carotenoid peak intensity and mango maturity. This study achieved 100% accuracy in classifying mango ripeness levels using three classifier models: the Medium Gaussian Support Vector Machine, the Cubic Support Vector Machine, and the Weighted K-Nearest Neighbors. Raman spectroscopy has proven to be a reliable and robust method, immune to external factors such as light, humidity, and noise, which makes it a promising approach for assessing mango ripeness.
format: application/pdf
format: text/html
creator: Ji Loun Tan
creator: Fazida Hanim Hashim
creator: Jahariah Sampe
creator: Aqilah Baseri Huddin
creator: Ghassan Maan Salim
creator: Sawal Hamid Md Ali
subject: Biochemistry
subject: Plant Science
subject: Computational Science
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.20288
publisher: PeerJ Inc.
rights: © 2025 Tan et al.
abstract: Determining mango ripeness is essential for ensuring its delicious taste, enticing aroma, and rich nutritional value. For farmers, harvesting mangoes too early can result in stunted fruit and lower yields compared to those harvested at a ripe stage. This study aims to develop a potentially non-invasive and efficient method for detecting mango ripeness using Raman spectroscopy. Traditional methods, which rely on human assessment and color evaluation with image processing, are inconsistent, inaccurate, and time-consuming due to variations in mango color and individual differences in vision and perception. To address these limitations, this study pursued three main objectives: extracting data characteristics of organic compounds in mangoes based on raw Raman spectrum data, identifying the correlation between carotene characteristics and mango ripeness levels, and evaluating the performance of machine learning models in classifying mango ripeness levels. A total of 29 mango fruit spectra were analyzed, with 13 samples selected to represent three ripeness categories: underripe, ripe, and overripe. Raman spectra peak signal analysis revealed that mango peel contains lycopene, β-carotene, lutein, and neoxanthin, all of which are derived from carotenoid molecules in the range of 1,480 cm−1 to 1,550 cm−1. Statistical analysis confirmed the significance (p < 0.05) of extracted Raman Peak Intensity features in distinguishing ripeness levels, supported by high correlation coefficients between carotenoid peak intensity and mango maturity. This study achieved 100% accuracy in classifying mango ripeness levels using three classifier models: the Medium Gaussian Support Vector Machine, the Cubic Support Vector Machine, and the Weighted K-Nearest Neighbors. Raman spectroscopy has proven to be a reliable and robust method, immune to external factors such as light, humidity, and noise, which makes it a promising approach for assessing mango ripeness.
bibliographic citation: Tan et al. (2025) Machine learning classification of mango maturity based on carotene content from Raman spectra. PeerJ 13:e20288 https://doi.org/10.7717/peerj.20288
date submitted: 2025-05-05
date accepted: 2025-10-03
issued: 2025-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tan
  given name: Ji Loun
author list: Agent
  family name: Hashim
  given name: Fazida Hanim
author list: Agent
  family name: Sampe
  given name: Jahariah
author list: Agent
  family name: Baseri Huddin
  given name: Aqilah
author list: Agent
  family name: Salim
  given name: Ghassan Maan
author list: Agent
  family name: Md Ali
  given name: Sawal Hamid
doi: 10.7717/peerj.20288
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-18
copyright: ©2025 Tan et al.
attribution name: Tan et al.

Identification of mitochondrial-related genes to evaluate the immune infiltration and prognosis of lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Mitochondrial dysfunction critically impacts lung adenocarcinoma (LUAD) progression and tumor microenvironment (TME) remodeling, highlighting the urgent need to identify predictive biomarkers with clinical utility. Methods RNA-seq data sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to identify mitochondrial-related (MTR) genes associated with LUAD progression. A three-gene prognostic signature, consisting of SFXN1, CPS1, and MTFR2, was developed through univariate, Least Absolute Shrinkage and Selection Operator (LASSO), and multivariate Cox regression analyses. Functional enrichment, immune infiltration, and tumor mutation burden (TMB) analyses were performed to characterize the TME. Experimental studies were conducted in LUAD cell lines via siRNA-mediated knockdown, assessing mitochondrial dynamics, mitochondrial membrane potential (ΔΨm), reactive oxygen species (ROS) levels, and mitochondrial DNA (mtDNA) stability. Results The signature stratified patients into high-risk and low-risk groups with significant survival differences (TCGA: HR = 1.476, P < 0.001; GSE31210: P < 0.001; GSE30219: P = 0.001). High-risk patients exhibited features of immunosuppressive TME, including elevated tumor purity, higher TIDE scores, increased TMB, and immune checkpoint expression (CD274, CD276, PDCD1, RELT). Functional analyses revealed that siRNA-mediated knockdown of CPS1 triggered mitochondrial fission, as evidenced by ΔΨm↓/ROS↑. Conversely, SFXN1 knockdown induced mitochondrial fusion accompanied by hyperpolarization (ΔΨm↑/ROS↓). Notably, MTFR2 knockdown promoted mitochondrial fusion, contributing to ΔΨm↑/ROS↓. All three siRNA treatments compromised mtDNA integrity, with CPS1 knockdown uniquely inducing the release of cytosolic mtDNA. Conclusion This study has successfully established a mitochondrial-related prognostic signature that predicts survival outcomes and immune phenotypes of LUAD patients, providing a clinically …
format: application/pdf
format: text/html
creator: Yutong Ge
creator: Ao Sun
creator: Tao Yu
creator: Shaokun Yu
creator: Kaihua Lu
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.20262
publisher: PeerJ Inc.
rights: © 2025 Ge et al.
abstract: Background Mitochondrial dysfunction critically impacts lung adenocarcinoma (LUAD) progression and tumor microenvironment (TME) remodeling, highlighting the urgent need to identify predictive biomarkers with clinical utility. Methods RNA-seq data sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to identify mitochondrial-related (MTR) genes associated with LUAD progression. A three-gene prognostic signature, consisting of SFXN1, CPS1, and MTFR2, was developed through univariate, Least Absolute Shrinkage and Selection Operator (LASSO), and multivariate Cox regression analyses. Functional enrichment, immune infiltration, and tumor mutation burden (TMB) analyses were performed to characterize the TME. Experimental studies were conducted in LUAD cell lines via siRNA-mediated knockdown, assessing mitochondrial dynamics, mitochondrial membrane potential (ΔΨm), reactive oxygen species (ROS) levels, and mitochondrial DNA (mtDNA) stability. Results The signature stratified patients into high-risk and low-risk groups with significant survival differences (TCGA: HR = 1.476, P < 0.001; GSE31210: P < 0.001; GSE30219: P = 0.001). High-risk patients exhibited features of immunosuppressive TME, including elevated tumor purity, higher TIDE scores, increased TMB, and immune checkpoint expression (CD274, CD276, PDCD1, RELT). Functional analyses revealed that siRNA-mediated knockdown of CPS1 triggered mitochondrial fission, as evidenced by ΔΨm↓/ROS↑. Conversely, SFXN1 knockdown induced mitochondrial fusion accompanied by hyperpolarization (ΔΨm↑/ROS↓). Notably, MTFR2 knockdown promoted mitochondrial fusion, contributing to ΔΨm↑/ROS↓. All three siRNA treatments compromised mtDNA integrity, with CPS1 knockdown uniquely inducing the release of cytosolic mtDNA. Conclusion This study has successfully established a mitochondrial-related prognostic signature that predicts survival outcomes and immune phenotypes of LUAD patients, providing a clinically …
bibliographic citation: Ge et al. (2025) Identification of mitochondrial-related genes to evaluate the immune infiltration and prognosis of lung adenocarcinoma. PeerJ 13:e20262 https://doi.org/10.7717/peerj.20262
date submitted: 2025-04-23
date accepted: 2025-09-29
issued: 2025-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Ge
  given name: Yutong
author list: Agent
  family name: Sun
  given name: Ao
author list: Agent
  family name: Yu
  given name: Tao
author list: Agent
  family name: Yu
  given name: Shaokun
author list: Agent
  family name: Lu
  given name: Kaihua
doi: 10.7717/peerj.20262
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-18
copyright: © 2025 Ge et al.
attribution name: Ge et al.

Acute effect of short foot exercise on dynamic stability and foot kinematic in trail runners: a proof-of-concept study
type: item
type: AcademicArticle
description: Background Trail runners face uneven terrains requiring optimal foot stability and postural control. The short foot exercise (SFE) may acutely enhance dynamic balance and foot arch height, potentially mitigating injury risk. This study aimed to evaluate the acute effects of the SFE on postural control and kinematics during a dynamic balance test in trail runners, considering the variations in the weekly training volumes of the participants. Methods Sixteen adult trail runners (mean age 36 ± 8.4 years; 50% male) with at least one year of trail running experience were evaluated. Dynamic balance was assessed using the Y-Balance Test (YBT), and kinematics of the foot arch were measured via the Arch Height Index (AHI) using a 3D motion capture system. Baseline measurements were taken, followed by an SFE protocol: the participants had to perform 12 repetitions of 5-second contractions, which they did in three sets with 2 minutes of rest between sets. Immediately afterward, YBT and AHI were reassessed. Results YBT showed significant improvements in all reach directions after the application of the SFE (p < 0.05). In contrast, no significant changes were observed in the AHI across reach directions (p > 0.05). Yet, subgroup analysis by weekly training volume revealed that participants with higher weekly volumes experienced a significant increase in anterior AHI (mean difference = −0.54 mm; 95% CI [−1.09 to 0.01]; p = 0.027; effect size = 0.13). The SFE may acutely improve foot kinematics and dynamic balance in trail runners; however, these effects are influenced by the weekly training volume of the participants. Conclusion This study suggests that a single session of the SFE may induce acute improvements in arch height and dynamic balance in trail runners, with differential responses depending on training volume. These preliminary results highlight the potential of the SFE as an acute activation strategy for the intrinsic foot muscles, but caution should be exercised when ex…
format: application/pdf
format: text/html
creator: Claudio Aguilar-Risco
creator: Mauricio San Martín-Correa
creator: Felipe Araya-Quintanilla
creator: Joaquín Calatayud
creator: Guillermo Mendez-Rebolledo
subject: Kinesiology
description: doi:10.7717/peerj.20364
publisher: PeerJ Inc.
rights: © 2025 Aguilar-Risco et al.
abstract: Background Trail runners face uneven terrains requiring optimal foot stability and postural control. The short foot exercise (SFE) may acutely enhance dynamic balance and foot arch height, potentially mitigating injury risk. This study aimed to evaluate the acute effects of the SFE on postural control and kinematics during a dynamic balance test in trail runners, considering the variations in the weekly training volumes of the participants. Methods Sixteen adult trail runners (mean age 36 ± 8.4 years; 50% male) with at least one year of trail running experience were evaluated. Dynamic balance was assessed using the Y-Balance Test (YBT), and kinematics of the foot arch were measured via the Arch Height Index (AHI) using a 3D motion capture system. Baseline measurements were taken, followed by an SFE protocol: the participants had to perform 12 repetitions of 5-second contractions, which they did in three sets with 2 minutes of rest between sets. Immediately afterward, YBT and AHI were reassessed. Results YBT showed significant improvements in all reach directions after the application of the SFE (p < 0.05). In contrast, no significant changes were observed in the AHI across reach directions (p > 0.05). Yet, subgroup analysis by weekly training volume revealed that participants with higher weekly volumes experienced a significant increase in anterior AHI (mean difference = −0.54 mm; 95% CI [−1.09 to 0.01]; p = 0.027; effect size = 0.13). The SFE may acutely improve foot kinematics and dynamic balance in trail runners; however, these effects are influenced by the weekly training volume of the participants. Conclusion This study suggests that a single session of the SFE may induce acute improvements in arch height and dynamic balance in trail runners, with differential responses depending on training volume. These preliminary results highlight the potential of the SFE as an acute activation strategy for the intrinsic foot muscles, but caution should be exercised when ex…
bibliographic citation: Aguilar-Risco et al. (2025) Acute effect of short foot exercise on dynamic stability and foot kinematic in trail runners: a proof-of-concept study. PeerJ 13:e20364 https://doi.org/10.7717/peerj.20364
date submitted: 2025-03-14
date accepted: 2025-10-17
issued: 2025-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aguilar-Risco
  given name: Claudio
author list: Agent
  family name: San Martín-Correa
  given name: Mauricio
author list: Agent
  family name: Araya-Quintanilla
  given name: Felipe
author list: Agent
  family name: Calatayud
  given name: Joaquín
author list: Agent
  family name: Mendez-Rebolledo
  given name: Guillermo
doi: 10.7717/peerj.20364
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-11-17
copyright: ©2025 Aguilar-Risco et al.
attribution name: Aguilar-Risco et al.

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