PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Exploring phytochemicals as potential pharmacological inhibitors for NS1 protein of Kyasanur forest disease virus using virtual screening, molecular docking, and molecular simulation approach
items: Scanning electron microscopy (SEM) reveals high diversity of setae on the hind tibiae and basitarsi of Peruvian Stingless Bees (Apidae: Meliponini)
items: Retrospective study: anthropometric and metabolic characteristics of patients with metabolic syndrome–a gender-specific analysis of clinical and correlation patterns
items: Barriers to care and the need for dental educational materials for the Lowe syndrome community: a survey of dentists
items: Impact of two field preservation methods on genotyping success of feces
items: Solubilization of skin collagen improves the accuracy and reliability of stable isotope measurements
items: Quality assessment from biobank plasma and serum specimens: a systematic review
items: Evaluation of NEUROG1 methylation status in stool specimens in the advanced adenomas and colorectal cancer
items: Optimal treatment options for acne scars in patients with historic acne: a systematic review and network meta-analysis
items: Unveiling water quality and health risks from groundwater chemicals in Poyang Lake basin of China: a sophisticated analysis

Exploring phytochemicals as potential pharmacological inhibitors for NS1 protein of Kyasanur forest disease virus using virtual screening, molecular docking, and molecular simulation approach
type: item
type: AcademicArticle
description: Background Kyasanur forest disease virus (KFDV) remains a significant public health challenge due to the limitations of existing vaccines, creating a critical need for effective antiviral treatments. KFDV is a tick-borne virus responsible for 400–500 new cases annually, with a mortality rate of 3–5%. The nonstructural protein 1 (NS1), which plays crucial roles in host cell interactions, immune evasion, and viral replication, represents a promising target for antiviral drug development. Objective This study aims to identify potential antiviral compounds that inhibit the activity of KFDV NS1 protein using a computational pharmacological drug design approach. The objectives include determining the 3D structure of the NS1 protein through homology modeling, conducting virtual screening of phytochemicals to identify potential inhibitors, and performing molecular dynamics simulations to assess the stability and binding free energies of the selected compounds. Methods The 3D structure of KFDV NS1 protein was predicted using homology modeling and validated using Ramachandran plot analysis. Virtual screening of phytochemicals from the Indian Medicinal Plants, Phytochemistry And Therapeutics (IMPPAT) database was performed to identify potential NS1 inhibitors. The top 15 compounds with the highest binding affinities were selected and subjected to absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Molecular dynamics simulations were conducted in duplicates for 200 ns to evaluate the stability of the ligand-NS1 complexes, and an additional independent simulation with randomized initial velocities was performed to ensure statistical robustness. Binding free energies were calculated using the molecular mechanics-generalized born surface area (MM-GBSA) method to determine the binding strength of each compound. Results The 3D structure of the KFDV NS1 protein was determined using I-Tasser-MTD, Robetta, and Swiss Model servers, and a minimized model of I-…
format: application/pdf
format: text/html
creator: Sharanappa Achappa
creator: Nayef Abdulaziz Aldabaan
creator: Ibrahim Ahmed Shaikh
creator: Mater H. Mahnashi
creator: Shivalingsarj V. Desai
creator: Mufarreh Asmari
creator: Mohammed Alasmary
creator: Uday M. Muddapur
creator: Basheerahmed Abdulaziz Mannasaheb
creator: Aejaz Abdullatif Khan
subject: Bioinformatics
subject: Infectious Diseases
subject: Pharmacology
subject: Computational Science
description: doi:10.7717/peerj.19954
publisher: PeerJ Inc.
rights: © 2025 Achappa et al.
abstract: Background Kyasanur forest disease virus (KFDV) remains a significant public health challenge due to the limitations of existing vaccines, creating a critical need for effective antiviral treatments. KFDV is a tick-borne virus responsible for 400–500 new cases annually, with a mortality rate of 3–5%. The nonstructural protein 1 (NS1), which plays crucial roles in host cell interactions, immune evasion, and viral replication, represents a promising target for antiviral drug development. Objective This study aims to identify potential antiviral compounds that inhibit the activity of KFDV NS1 protein using a computational pharmacological drug design approach. The objectives include determining the 3D structure of the NS1 protein through homology modeling, conducting virtual screening of phytochemicals to identify potential inhibitors, and performing molecular dynamics simulations to assess the stability and binding free energies of the selected compounds. Methods The 3D structure of KFDV NS1 protein was predicted using homology modeling and validated using Ramachandran plot analysis. Virtual screening of phytochemicals from the Indian Medicinal Plants, Phytochemistry And Therapeutics (IMPPAT) database was performed to identify potential NS1 inhibitors. The top 15 compounds with the highest binding affinities were selected and subjected to absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Molecular dynamics simulations were conducted in duplicates for 200 ns to evaluate the stability of the ligand-NS1 complexes, and an additional independent simulation with randomized initial velocities was performed to ensure statistical robustness. Binding free energies were calculated using the molecular mechanics-generalized born surface area (MM-GBSA) method to determine the binding strength of each compound. Results The 3D structure of the KFDV NS1 protein was determined using I-Tasser-MTD, Robetta, and Swiss Model servers, and a minimized model of I-…
bibliographic citation: Achappa et al. (2025) Exploring phytochemicals as potential pharmacological inhibitors for NS1 protein of Kyasanur forest disease virus using virtual screening, molecular docking, and molecular simulation approach. PeerJ 13:e19954 https://doi.org/10.7717/peerj.19954
date submitted: 2024-11-18
date accepted: 2025-07-29
issued: 2025-10-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Achappa
  given name: Sharanappa
author list: Agent
  family name: Aldabaan
  given name: Nayef Abdulaziz
author list: Agent
  family name: Shaikh
  given name: Ibrahim Ahmed
author list: Agent
  family name: Mahnashi
  given name: Mater H.
author list: Agent
  family name: Desai
  given name: Shivalingsarj V.
author list: Agent
  family name: Asmari
  given name: Mufarreh
author list: Agent
  family name: Alasmary
  given name: Mohammed
author list: Agent
  family name: Muddapur
  given name: Uday M.
author list: Agent
  family name: Mannasaheb
  given name: Basheerahmed Abdulaziz
author list: Agent
  family name: Khan
  given name: Aejaz Abdullatif
doi: 10.7717/peerj.19954
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-09
copyright: ©2025 Achappa et al.
attribution name: Achappa et al.

Scanning electron microscopy (SEM) reveals high diversity of setae on the hind tibiae and basitarsi of Peruvian Stingless Bees (Apidae: Meliponini)
type: item
type: AcademicArticle
description: Stingless bees belong to the group of corbiculate bees, all characterized by the presence of a corbicula, a specialized structure of the hind tibia used for pollen collection. This group exhibits significant variation in foraging behavior, from flower-visiting foragers to kleptoparasites and obligate necrophagous. So far, scanning electron microscopy (SEM) studies have been mainly focused on the hind leg setae of Apis spp. and Bombus spp. Here, we performed a comparative morphological analysis of the setae and the pollen handling structures in the hind tibiae and basitarsi of seven stingless bee species: the floral pollen collector bees Melipona cf. eburnea, Partamona testacea, Scaura cf. latitarsis, Trigonisca cf. atomaria, Trigona dallatorreana, the robber bee Lestrimelitta sp. and the obligate necrophagous Trigona cf. hypogea, collected in Peruvian forests in 2020. The setae were classified into simple and branched types, subdivided into five and seven subtypes, respectively. In addition, we described three types of penicillum, five types of rastellum, three types of pollen brush, two types of setae covering the auricular area, and show the setae forming the sericeous area of Trigona spp. Finally, seven types of keirotrichia are described. We highlight that certain types of setae show a high degree of conservation across species, while others are unique and potentially indicative of adaptive specialization. Among species that have abandoned pollen foraging on flowers, we observed a simplification in the number of setal types and the absence of pollen handling structures in Lestrimelitta sp., whereas T. cf. hypogea exhibits the highest diversity of setae and retains most of these structures. Finally, based on these two species, we reflect on the link between reduced corbicula and functional corbicula. The study highlights the importance of further exploring the mechanical and sensory roles of setae and expanding this research in Meliponini. Such investigations can…
format: application/pdf
format: text/html
creator: Marilena Marconi
creator: Carlos Daniel Vecco-Giove
creator: Javier Ormeño Luna
creator: Agustín Cerna Mendoza
creator: Emiliano Mancini
creator: Andrea Di Giulio
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.19749
publisher: PeerJ Inc.
rights: © 2025 Marconi et al.
abstract: Stingless bees belong to the group of corbiculate bees, all characterized by the presence of a corbicula, a specialized structure of the hind tibia used for pollen collection. This group exhibits significant variation in foraging behavior, from flower-visiting foragers to kleptoparasites and obligate necrophagous. So far, scanning electron microscopy (SEM) studies have been mainly focused on the hind leg setae of Apis spp. and Bombus spp. Here, we performed a comparative morphological analysis of the setae and the pollen handling structures in the hind tibiae and basitarsi of seven stingless bee species: the floral pollen collector bees Melipona cf. eburnea, Partamona testacea, Scaura cf. latitarsis, Trigonisca cf. atomaria, Trigona dallatorreana, the robber bee Lestrimelitta sp. and the obligate necrophagous Trigona cf. hypogea, collected in Peruvian forests in 2020. The setae were classified into simple and branched types, subdivided into five and seven subtypes, respectively. In addition, we described three types of penicillum, five types of rastellum, three types of pollen brush, two types of setae covering the auricular area, and show the setae forming the sericeous area of Trigona spp. Finally, seven types of keirotrichia are described. We highlight that certain types of setae show a high degree of conservation across species, while others are unique and potentially indicative of adaptive specialization. Among species that have abandoned pollen foraging on flowers, we observed a simplification in the number of setal types and the absence of pollen handling structures in Lestrimelitta sp., whereas T. cf. hypogea exhibits the highest diversity of setae and retains most of these structures. Finally, based on these two species, we reflect on the link between reduced corbicula and functional corbicula. The study highlights the importance of further exploring the mechanical and sensory roles of setae and expanding this research in Meliponini. Such investigations can…
bibliographic citation: Marconi et al. (2025) Scanning electron microscopy (SEM) reveals high diversity of setae on the hind tibiae and basitarsi of Peruvian Stingless Bees (Apidae: Meliponini). PeerJ 13:e19749 https://doi.org/10.7717/peerj.19749
date submitted: 2024-12-13
date accepted: 2025-06-24
issued: 2025-10-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marconi
  given name: Marilena
author list: Agent
  family name: Vecco-Giove
  given name: Carlos Daniel
author list: Agent
  family name: Ormeño Luna
  given name: Javier
author list: Agent
  family name: Cerna Mendoza
  given name: Agustín
author list: Agent
  family name: Mancini
  given name: Emiliano
author list: Agent
  family name: Di Giulio
  given name: Andrea
doi: 10.7717/peerj.19749
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-09
copyright: ©2025 Marconi et al.
attribution name: Marconi et al.

Retrospective study: anthropometric and metabolic characteristics of patients with metabolic syndrome–a gender-specific analysis of clinical and correlation patterns
type: item
type: AcademicArticle
description: Background Metabolic syndrome (MetS) is a prevalent condition associated with increased cardiometabolic risk. Despite its clinical significance, the relationships between anthropometric indices and metabolic markers—particularly in a gender-specific context—remain inadequately explored. Methods This retrospective study included 104 patients diagnosed with MetS between 2016 and 2022. Anthropometric indices, including body roundness index (BRI), body mass index (BMI), waist-to-height ratio (WHtR), and weight-to-waist index (WWI), were analyzed for their associations with metabolic markers reflecting insulin resistance and glucose metabolism: fasting blood glucose (FBG), fasting insulin (FIns), and homeostatic model assessment of insulin resistance (HOMA-IR). These markers represent key components of MetS, although other diagnostic elements such as dyslipidemia and hypertension were beyond the scope of this analysis. Gender-specific subgroup analyses were conducted for 57 female and 47 male patients. Results Significant differences in anthropometric and metabolic characteristics were observed between genders. Male patients exhibited higher BMI (40.4 [37.5, 44.2] vs. 37.2 [33.6, 40.3], p = 0.022), waist circumference (128.0 [120.2, 137.5] cm vs. 115.0 [106.0, 120.0] cm, p < 0.001), and FIns levels (22.8 [16.4, 29.5] μIU/mL vs. 17.8 [15.0, 23.4] μIU/mL, p = 0.107). Correlation analyses revealed that BMI and BRI were strongly associated with HOMA-IR and FIns in both genders, with stronger associations observed in males (e.g., BMI vs. FIns, r = 0.60, p < 0.001). WHtR was significantly correlated with metabolic markers in males but not in females. WWI showed limited correlations across both genders. Discussion This study highlights distinct gender-specific patterns in the relationships between anthropometric indices and metabolic markers in MetS patients. These findings underscore the importance of tailored strategies in managing MetS, particularly considering gender-based …
format: application/pdf
format: text/html
creator: Yingxin Li
creator: Huanhua Wu
creator: Yingtong Lu
creator: Jingjie Shang
creator: Yong Cheng
creator: Xiaozheng Cao
creator: Zhiqiang Tan
creator: Qijun Cai
creator: Hao Xu
creator: Bin Guo
subject: Diabetes and Endocrinology
subject: Obesity
description: doi:10.7717/peerj.20183
publisher: PeerJ Inc.
rights: © 2025 Li et al.
abstract: Background Metabolic syndrome (MetS) is a prevalent condition associated with increased cardiometabolic risk. Despite its clinical significance, the relationships between anthropometric indices and metabolic markers—particularly in a gender-specific context—remain inadequately explored. Methods This retrospective study included 104 patients diagnosed with MetS between 2016 and 2022. Anthropometric indices, including body roundness index (BRI), body mass index (BMI), waist-to-height ratio (WHtR), and weight-to-waist index (WWI), were analyzed for their associations with metabolic markers reflecting insulin resistance and glucose metabolism: fasting blood glucose (FBG), fasting insulin (FIns), and homeostatic model assessment of insulin resistance (HOMA-IR). These markers represent key components of MetS, although other diagnostic elements such as dyslipidemia and hypertension were beyond the scope of this analysis. Gender-specific subgroup analyses were conducted for 57 female and 47 male patients. Results Significant differences in anthropometric and metabolic characteristics were observed between genders. Male patients exhibited higher BMI (40.4 [37.5, 44.2] vs. 37.2 [33.6, 40.3], p = 0.022), waist circumference (128.0 [120.2, 137.5] cm vs. 115.0 [106.0, 120.0] cm, p < 0.001), and FIns levels (22.8 [16.4, 29.5] μIU/mL vs. 17.8 [15.0, 23.4] μIU/mL, p = 0.107). Correlation analyses revealed that BMI and BRI were strongly associated with HOMA-IR and FIns in both genders, with stronger associations observed in males (e.g., BMI vs. FIns, r = 0.60, p < 0.001). WHtR was significantly correlated with metabolic markers in males but not in females. WWI showed limited correlations across both genders. Discussion This study highlights distinct gender-specific patterns in the relationships between anthropometric indices and metabolic markers in MetS patients. These findings underscore the importance of tailored strategies in managing MetS, particularly considering gender-based …
bibliographic citation: Li et al. (2025) Retrospective study: anthropometric and metabolic characteristics of patients with metabolic syndrome–a gender-specific analysis of clinical and correlation patterns. PeerJ 13:e20183 https://doi.org/10.7717/peerj.20183
date submitted: 2025-05-16
date accepted: 2025-09-15
issued: 2025-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yingxin
author list: Agent
  family name: Wu
  given name: Huanhua
author list: Agent
  family name: Lu
  given name: Yingtong
author list: Agent
  family name: Shang
  given name: Jingjie
author list: Agent
  family name: Cheng
  given name: Yong
author list: Agent
  family name: Cao
  given name: Xiaozheng
author list: Agent
  family name: Tan
  given name: Zhiqiang
author list: Agent
  family name: Cai
  given name: Qijun
author list: Agent
  family name: Xu
  given name: Hao
author list: Agent
  family name: Guo
  given name: Bin
doi: 10.7717/peerj.20183
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-08
copyright: © 2025 Li et al.
attribution name: Li et al.

Barriers to care and the need for dental educational materials for the Lowe syndrome community: a survey of dentists
type: item
type: AcademicArticle
description: Background This study aimed to assess dentists’ experience in treating individuals with Lowe syndrome (LS), reasons they may be unable to provide dental care for individuals with LS, and perceptions of the need for educational materials tailored to the LS community regarding the dental setting. Methods A link to an electronic Qualtrics survey addressing these topics was emailed to the Tufts University School of Dental Medicine Alumni Network listserv. Results Data from 73 respondents were analyzed. Of the 57 who answered the question about having treated a patient with LS, three (5.3%) responded affirmatively. Among the 61 who answered why they might not be able to treat an individual with LS, the most common reasons were lack of experience treating children with special needs and not accepting medical assistance such as Medicaid/Medicare (both 31.1%). Of the 58 who responded to the item regarding the need for educational materials to support patients with LS in the dental setting, 47 (81.0%) agreed or strongly agreed. Conclusion Substantial barriers to dental care exist for individuals with LS. Educational materials about the dental setting should be developed for the LS community.
format: application/pdf
format: text/html
creator: Adam Lowenstein
creator: Matthew Finkelman
creator: Jay Dalal
creator: Crystal Smith
creator: Glory Ogunyinka
creator: David Tesini
creator: Carlos Fernando Mourão
subject: Dentistry
subject: Epidemiology
subject: Global Health
subject: Healthcare Services
description: doi:10.7717/peerj.20174
publisher: PeerJ Inc.
rights: © 2025 Lowenstein et al.
abstract: Background This study aimed to assess dentists’ experience in treating individuals with Lowe syndrome (LS), reasons they may be unable to provide dental care for individuals with LS, and perceptions of the need for educational materials tailored to the LS community regarding the dental setting. Methods A link to an electronic Qualtrics survey addressing these topics was emailed to the Tufts University School of Dental Medicine Alumni Network listserv. Results Data from 73 respondents were analyzed. Of the 57 who answered the question about having treated a patient with LS, three (5.3%) responded affirmatively. Among the 61 who answered why they might not be able to treat an individual with LS, the most common reasons were lack of experience treating children with special needs and not accepting medical assistance such as Medicaid/Medicare (both 31.1%). Of the 58 who responded to the item regarding the need for educational materials to support patients with LS in the dental setting, 47 (81.0%) agreed or strongly agreed. Conclusion Substantial barriers to dental care exist for individuals with LS. Educational materials about the dental setting should be developed for the LS community.
bibliographic citation: Lowenstein et al. (2025) Barriers to care and the need for dental educational materials for the Lowe syndrome community: a survey of dentists. PeerJ 13:e20174 https://doi.org/10.7717/peerj.20174
date submitted: 2025-02-05
date accepted: 2025-09-11
issued: 2025-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lowenstein
  given name: Adam
author list: Agent
  family name: Finkelman
  given name: Matthew
author list: Agent
  family name: Dalal
  given name: Jay
author list: Agent
  family name: Smith
  given name: Crystal
author list: Agent
  family name: Ogunyinka
  given name: Glory
author list: Agent
  family name: Tesini
  given name: David
author list: Agent
  family name: Mourão
  given name: Carlos Fernando
doi: 10.7717/peerj.20174
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-08
copyright: © 2025 Lowenstein et al.
attribution name: Lowenstein et al.

Impact of two field preservation methods on genotyping success of feces
type: item
type: AcademicArticle
description: Non-invasive samples, such as feces, remain an important source of DNA for genetic analyses in molecular ecology and conservation genetics, especially when working with elusive or endangered species. However, as labs transition to higher throughput and genomic-based technologies, many protocols that have been used for decades are becoming obsolete. New approaches have been developed for high-quality samples, now low-quality samples require further technical advances. Fecal samples obtained for non-invasive wildlife studies are typically of very low quality and sampling methods need to be optimized to reduce work and costs per sample. Preservation methods in the field affect the workload in the lab required to obtain genetic data, as well as the final genotype quality. Liquid preservation methods, such as nucleic acid preservation (NAP) buffer and ethanol, have been used during sampling to maintain DNA quality at room temperature until samples can reach the lab. NAP buffer is a non-hazardous, non-flammable solution (easy to send through post), and avoids having to dry the feces before DNA extraction (saving time and increasing safety). Here we compare two different liquid preservation methods (NAP buffer and 96% ethanol) for microsatellite genotyping by next generation sequencing of wolf fecal samples collected in the field and shipped at ambient temperature. Samples preserved in ethanol showed a higher rate of amplification and genotyping success than in NAP buffer, especially due to a higher rate of allelic dropout in NAP. Consequently, the number of replicates required to achieve high quality genotypes was slightly higher for fecal samples preserved in NAP buffer than for those preserved in ethanol. These results are important for the planning and optimization of projects that involve microsatellite genotyping from feces using high throughput technologies.
format: application/pdf
format: text/html
creator: Valentina Valencia-Montoya
creator: Isabel Salado
creator: Ines Sanchez-Donoso
creator: Alberto Fernández-Gil
creator: Carles Vilà
creator: Jennifer A. Leonard
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.20154
publisher: PeerJ Inc.
rights: © 2025 Valencia-Montoya et al.
abstract: Non-invasive samples, such as feces, remain an important source of DNA for genetic analyses in molecular ecology and conservation genetics, especially when working with elusive or endangered species. However, as labs transition to higher throughput and genomic-based technologies, many protocols that have been used for decades are becoming obsolete. New approaches have been developed for high-quality samples, now low-quality samples require further technical advances. Fecal samples obtained for non-invasive wildlife studies are typically of very low quality and sampling methods need to be optimized to reduce work and costs per sample. Preservation methods in the field affect the workload in the lab required to obtain genetic data, as well as the final genotype quality. Liquid preservation methods, such as nucleic acid preservation (NAP) buffer and ethanol, have been used during sampling to maintain DNA quality at room temperature until samples can reach the lab. NAP buffer is a non-hazardous, non-flammable solution (easy to send through post), and avoids having to dry the feces before DNA extraction (saving time and increasing safety). Here we compare two different liquid preservation methods (NAP buffer and 96% ethanol) for microsatellite genotyping by next generation sequencing of wolf fecal samples collected in the field and shipped at ambient temperature. Samples preserved in ethanol showed a higher rate of amplification and genotyping success than in NAP buffer, especially due to a higher rate of allelic dropout in NAP. Consequently, the number of replicates required to achieve high quality genotypes was slightly higher for fecal samples preserved in NAP buffer than for those preserved in ethanol. These results are important for the planning and optimization of projects that involve microsatellite genotyping from feces using high throughput technologies.
bibliographic citation: Valencia-Montoya et al. (2025) Impact of two field preservation methods on genotyping success of feces. PeerJ 13:e20154 https://doi.org/10.7717/peerj.20154
date submitted: 2025-04-15
date accepted: 2025-09-08
issued: 2025-10-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valencia-Montoya
  given name: Valentina
author list: Agent
  family name: Salado
  given name: Isabel
author list: Agent
  family name: Sanchez-Donoso
  given name: Ines
author list: Agent
  family name: Fernández-Gil
  given name: Alberto
author list: Agent
  family name: Vilà
  given name: Carles
author list: Agent
  family name: Leonard
  given name: Jennifer A.
doi: 10.7717/peerj.20154
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-10-08
copyright: ©2025 Valencia-Montoya et al.
attribution name: Valencia-Montoya et al.

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

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

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

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

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

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