PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Molecular identification of critically endangered European eels (Anguilla anguilla) in US retail outlets
items: Remote sensing technology for rapid extraction of burned areas and ecosystem environmental assessment
items: Putative source and niche shift pattern of a new alien ant species (Odontomachus troglodytes) in Taiwan
items: Cross-sectional associations between body mass index, waist circumference, and multimorbidity: Pró-Saúde study
items: Efficacy of Saccharothrix algeriensis NRRL B-24137 to suppress Fusarium oxysporum f.sp. vasinfectum induced wilt disease in cotton
items: Prohexadione calcium enhances rice growth and tillering under NaCl stress
items: Influence of resin modified glass ionomer cement incorporating protein-repellent and antimicrobial agents on supragingival microbiome around brackets: an in-vivo split-mouth 3-month study
items: Construction and validation of a fatty acid metabolism-related gene signature for predicting prognosis and therapeutic response in patients with prostate cancer
items: Elevated serum FGF21 levels predict heart failure during hospitalization of STEMI patients after emergency percutaneous coronary intervention
items: Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin

Molecular identification of critically endangered European eels (Anguilla anguilla) in US retail outlets
type: item
type: AcademicArticle
description: The European eel (Anguilla anguilla) has declined by over 90% since the early 1980s and has been listed as critically endangered. Yet, despite strict export bans from the European Union, the European eel is still sold illegally in many countries. Efforts to monitor the trade of European eels have been primarily concentrated in Asian markets where concerningly high rates of European eel have been reported. Comparably fewer studies have assessed the identities of eel samples from the United States (US), despite the obvious implications for eel conservation. To address this knowledge gap, we purchased 137 eel products (134 freshwater eels and three saltwater eels) from grocers, sushi bars, and restaurants in nine states across the US from 2019 to 2021. Seven samples (5.2%) labeled as freshwater eels (or “unagi”) were identified as European eels using a combination of mitochondrial (cytochrome b) and nuclear (18S rRNA) restriction digestion assays, a fast and inexpensive molecular tool for seafood identification that can identify hybrids between European eels (A. anguilla) and American eels (A. rostrata). No hybrids between European and American eels were found and all seven samples identified with restriction digestion as European eels were confirmed by sequencing of cytochrome b and 18S rRNA. Frequency of European eels in US markets did not significantly correlate with state or retail type. Although illegal eel exports are likely reaching US consumers, the frequency of European eel samples in this study of the US market is much lower than found in other non-European countries.
format: application/pdf
format: text/html
creator: Taylor Ely
creator: Nathaniel Patten
creator: Lewis C. Naisbett-Jones
creator: Erin T. Spencer
creator: Demian A. Willette
creator: Peter B. Marko
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.14531
publisher: PeerJ Inc.
rights: © 2023 Ely et al.
abstract: The European eel (Anguilla anguilla) has declined by over 90% since the early 1980s and has been listed as critically endangered. Yet, despite strict export bans from the European Union, the European eel is still sold illegally in many countries. Efforts to monitor the trade of European eels have been primarily concentrated in Asian markets where concerningly high rates of European eel have been reported. Comparably fewer studies have assessed the identities of eel samples from the United States (US), despite the obvious implications for eel conservation. To address this knowledge gap, we purchased 137 eel products (134 freshwater eels and three saltwater eels) from grocers, sushi bars, and restaurants in nine states across the US from 2019 to 2021. Seven samples (5.2%) labeled as freshwater eels (or “unagi”) were identified as European eels using a combination of mitochondrial (cytochrome b) and nuclear (18S rRNA) restriction digestion assays, a fast and inexpensive molecular tool for seafood identification that can identify hybrids between European eels (A. anguilla) and American eels (A. rostrata). No hybrids between European and American eels were found and all seven samples identified with restriction digestion as European eels were confirmed by sequencing of cytochrome b and 18S rRNA. Frequency of European eels in US markets did not significantly correlate with state or retail type. Although illegal eel exports are likely reaching US consumers, the frequency of European eel samples in this study of the US market is much lower than found in other non-European countries.
bibliographic citation: Ely et al. (2023) Molecular identification of critically endangered European eels (Anguilla anguilla) in US retail outlets. PeerJ 11:e14531 https://doi.org/10.7717/peerj.14531
date submitted: 2022-06-27
date accepted: 2022-11-16
issued: 2023-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ely
  given name: Taylor
author list: Agent
  family name: Patten
  given name: Nathaniel
author list: Agent
  family name: Naisbett-Jones
  given name: Lewis C.
author list: Agent
  family name: Spencer
  given name: Erin T.
author list: Agent
  family name: Willette
  given name: Demian A.
author list: Agent
  family name: Marko
  given name: Peter B.
doi: 10.7717/peerj.14531
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-06
copyright: ©2023 Ely et al.
attribution name: Ely et al.

Remote sensing technology for rapid extraction of burned areas and ecosystem environmental assessment
type: item
type: AcademicArticle
description: Forest fires are one of the significant disturbances in forest ecosystems. It is essential to extract burned areas rapidly and accurately to formulate forest restoration strategies and plan restoration plans. In this work, we constructed decision trees and used a combination of differential normalized burn ratio (dNBR) index and OTSU threshold method to extract the heavily and mildly burned areas. The applicability of this method was evaluated with three fires in Muli County, Sichuan, China, and we concluded that the extraction accuracy of this method could reach 97.69% and 96.37% for small area forest fires, while the extraction accuracy was lower for large area fires, only 89.32%. In addition, the remote sensing environment index (RSEI) was used to evaluate the ecological environment changes. It analyzed the change of the RSEI level through the transition matrix, and all three fires showed that the changes in RSEI were stronger for heavily burned areas than for mildly burned areas, after the forest fire the ecological environment (RSEI) was reduced from good to moderate. These results realized the quantitative evaluation and dynamic evaluation of the ecological environment condition, providing an essential basis for the restoration, decision making and management of the affected forests.
format: application/pdf
format: text/html
creator: Shiqi Zhang
creator: Maoyang Bai
creator: Xiao Wang
creator: Xuefeng Peng
creator: Ailin Chen
creator: Peihao Peng
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.14557
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Forest fires are one of the significant disturbances in forest ecosystems. It is essential to extract burned areas rapidly and accurately to formulate forest restoration strategies and plan restoration plans. In this work, we constructed decision trees and used a combination of differential normalized burn ratio (dNBR) index and OTSU threshold method to extract the heavily and mildly burned areas. The applicability of this method was evaluated with three fires in Muli County, Sichuan, China, and we concluded that the extraction accuracy of this method could reach 97.69% and 96.37% for small area forest fires, while the extraction accuracy was lower for large area fires, only 89.32%. In addition, the remote sensing environment index (RSEI) was used to evaluate the ecological environment changes. It analyzed the change of the RSEI level through the transition matrix, and all three fires showed that the changes in RSEI were stronger for heavily burned areas than for mildly burned areas, after the forest fire the ecological environment (RSEI) was reduced from good to moderate. These results realized the quantitative evaluation and dynamic evaluation of the ecological environment condition, providing an essential basis for the restoration, decision making and management of the affected forests.
bibliographic citation: Zhang et al. (2023) Remote sensing technology for rapid extraction of burned areas and ecosystem environmental assessment. PeerJ 11:e14557 https://doi.org/10.7717/peerj.14557
date submitted: 2022-08-15
date accepted: 2022-11-21
issued: 2023-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Shiqi
author list: Agent
  family name: Bai
  given name: Maoyang
author list: Agent
  family name: Wang
  given name: Xiao
author list: Agent
  family name: Peng
  given name: Xuefeng
author list: Agent
  family name: Chen
  given name: Ailin
author list: Agent
  family name: Peng
  given name: Peihao
doi: 10.7717/peerj.14557
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-06
copyright: © 2023 Zhang et al.
attribution name: Zhang et al.

Putative source and niche shift pattern of a new alien ant species (Odontomachus troglodytes) in Taiwan
type: item
type: AcademicArticle
description: Alien species may pose substantial impacts on biodiversity around the globe through international trade and travel. A niche shift hypothesis was proposed to explain the adaptive change of alien or invasive species in new habitats. However, whether niche shifts occur in alien species likely depends on both characteristics inherent to the species itself and its original distribution. Here we identified a newly exotic trap-jaw ant (Odontomachus troglodytes) in Taiwan by morphological and phylogenetic analyses. The possible distribution range and the niche shift pattern were evaluated using ecological niche modelling. The results indicated that exotic O. troglodytes in the newly distributed area displayed a significant niche shift with low niche overlap and high niche expansion. This study reveals a long-distance invasive event from central Africa to Southeast Asia (more than 10,000 km) and predicts the potential distribution range of this new alien species in Taiwan.
format: application/pdf
format: text/html
creator: Tzong-Han Lin
creator: Kai-Wei Chan
creator: Feng-Chuan Hsu
creator: Chung-Chi Lin
creator: Hui-Yun Tseng
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.14718
publisher: PeerJ Inc.
rights: © 2023 Lin et al.
abstract: Alien species may pose substantial impacts on biodiversity around the globe through international trade and travel. A niche shift hypothesis was proposed to explain the adaptive change of alien or invasive species in new habitats. However, whether niche shifts occur in alien species likely depends on both characteristics inherent to the species itself and its original distribution. Here we identified a newly exotic trap-jaw ant (Odontomachus troglodytes) in Taiwan by morphological and phylogenetic analyses. The possible distribution range and the niche shift pattern were evaluated using ecological niche modelling. The results indicated that exotic O. troglodytes in the newly distributed area displayed a significant niche shift with low niche overlap and high niche expansion. This study reveals a long-distance invasive event from central Africa to Southeast Asia (more than 10,000 km) and predicts the potential distribution range of this new alien species in Taiwan.
bibliographic citation: Lin et al. (2023) Putative source and niche shift pattern of a new alien ant species (Odontomachus troglodytes) in Taiwan. PeerJ 11:e14718 https://doi.org/10.7717/peerj.14718
date submitted: 2022-10-03
date accepted: 2022-12-19
issued: 2023-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Tzong-Han
author list: Agent
  family name: Chan
  given name: Kai-Wei
author list: Agent
  family name: Hsu
  given name: Feng-Chuan
author list: Agent
  family name: Lin
  given name: Chung-Chi
author list: Agent
  family name: Tseng
  given name: Hui-Yun
doi: 10.7717/peerj.14718
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-06
copyright: ©2023 Lin et al.
attribution name: Lin et al.

Cross-sectional associations between body mass index, waist circumference, and multimorbidity: Pró-Saúde study
type: item
type: AcademicArticle
description: Background This study aimed (1) To investigate the association between the Body Mass Index (BMI) and waist circumference (WC) with multimorbidity (MM), and (2) To identify patterns of MM and investigate the relationship between BMI and WC with specific combinations of MM (patterns of MM). Methods A cross-sectional study was conducted with 2,698 participants of the fourth phase of the Brazilian Longitudinal Study of Adult Health (Pró-Saúde Study). MM was defined by the presence of two or more morbidities. MM patterns were identified by exploratory factor analysis based on tetrachoric correlations. Logistic regression models were used to assess associations (odds ratios (OR) with the respective confidence intervals (CI)). Results Of the total number of participants, 39.5% were overweight and 30.0% were obese; 89.0% (n = 1,468) of women and 77.0% (n = 952) of men were abdominally obese. Indeed, 60.7% (n = 1,635) was identified with MM. For the category four or more morbidities, OR values of 5.98 (95% CI 4.84–7.13) and 7.48 (95% CI 6.14–8.18) were found for each point of increase in BMI, and 6.74 (95% CI 5.48–7.99) and 8.48 (95% CI 7.64–9.29) for each additional centimeter in the WC, for female and male, respectively. Five patterns of MM were identified: respiratory, osteoarticular, cardiometabolic, gastric, and thyroid diseases (56.4% of the total variance). Positive associations were found between BMI and patterns of cardiometabolic, osteoarticular, thyroid and gastric diseases (higher OR of 1.09 [95% CI 1.04–1.14]) and less pronounced between WC and patterns of cardiometabolic and osteoarticular (higher OR of 1.04 [95% CI 1.03–1.04]). Conclusions The results showed that an increase of both BMI and WC was associated with a higher number of morbidities and with patterns of cardiometabolic and osteoarticular diseases.
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creator: Fernanda Muniz de Macedo Stumpf
creator: Alessandra Silva Dias de Oliveira
creator: Eduardo Faerstein
creator: Cintia Chaves Curioni
subject: Epidemiology
subject: Nutrition
subject: Public Health
subject: Obesity
description: doi:10.7717/peerj.14744
publisher: PeerJ Inc.
rights: © 2023 Stumpf et al.
abstract: Background This study aimed (1) To investigate the association between the Body Mass Index (BMI) and waist circumference (WC) with multimorbidity (MM), and (2) To identify patterns of MM and investigate the relationship between BMI and WC with specific combinations of MM (patterns of MM). Methods A cross-sectional study was conducted with 2,698 participants of the fourth phase of the Brazilian Longitudinal Study of Adult Health (Pró-Saúde Study). MM was defined by the presence of two or more morbidities. MM patterns were identified by exploratory factor analysis based on tetrachoric correlations. Logistic regression models were used to assess associations (odds ratios (OR) with the respective confidence intervals (CI)). Results Of the total number of participants, 39.5% were overweight and 30.0% were obese; 89.0% (n = 1,468) of women and 77.0% (n = 952) of men were abdominally obese. Indeed, 60.7% (n = 1,635) was identified with MM. For the category four or more morbidities, OR values of 5.98 (95% CI 4.84–7.13) and 7.48 (95% CI 6.14–8.18) were found for each point of increase in BMI, and 6.74 (95% CI 5.48–7.99) and 8.48 (95% CI 7.64–9.29) for each additional centimeter in the WC, for female and male, respectively. Five patterns of MM were identified: respiratory, osteoarticular, cardiometabolic, gastric, and thyroid diseases (56.4% of the total variance). Positive associations were found between BMI and patterns of cardiometabolic, osteoarticular, thyroid and gastric diseases (higher OR of 1.09 [95% CI 1.04–1.14]) and less pronounced between WC and patterns of cardiometabolic and osteoarticular (higher OR of 1.04 [95% CI 1.03–1.04]). Conclusions The results showed that an increase of both BMI and WC was associated with a higher number of morbidities and with patterns of cardiometabolic and osteoarticular diseases.
bibliographic citation: Stumpf et al. (2023) Cross-sectional associations between body mass index, waist circumference, and multimorbidity: Pró-Saúde study. PeerJ 11:e14744 https://doi.org/10.7717/peerj.14744
date submitted: 2022-09-23
date accepted: 2022-12-23
issued: 2023-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stumpf
  given name: Fernanda Muniz de Macedo
author list: Agent
  family name: de Oliveira
  given name: Alessandra Silva Dias
author list: Agent
  family name: Faerstein
  given name: Eduardo
author list: Agent
  family name: Curioni
  given name: Cintia Chaves
doi: 10.7717/peerj.14744
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-06
copyright: ©2023 Stumpf et al.
attribution name: Stumpf et al.

Efficacy of Saccharothrix algeriensis NRRL B-24137 to suppress Fusarium oxysporum f.sp. vasinfectum induced wilt disease in cotton
type: item
type: AcademicArticle
description: Fusarium cotton wilt is a devastating disease of the cotton crop throughout the world, caused by Fusarium oxysporum f.sp. vasinfectum (FOV). Chemical control has many side effects, so, biological controls have been widely used for the management of Fusarium wilt. This study aimed to investigate the possible use of an actinomycetes Saccharothrix algeriensis (SA) NRRL B-24137 to control FOV. To access in-vitro anti-Fusarium ability of SA NRRL B-24137, dual culture assay, spore germination and seed germination tests were carried out. Following in-vitro investigations, several pot tests in a greenhouse environment were used to evaluate the biological control potential of SA NRRL B-24137 against FOV. Dual culture assay and spore germination revealed that SA NRRL B-24137 showed significant anti-Fusarium activity.During spore germination 87.77% inhibition of spore germination were observed. In pot experiments, SA NRRL B-24137 primed cotton seeds resulted in a 74.0% reduction in disease incidence. In soil there was a significant reduction in FOV spores in the presence of SA NRRL B-24137. Positive correlation was also observed on different concentrations of SA NRRL B-24137 towards FOV reduction. The results of this study showed that SA NRRL B-24137 has the potential to be employed as a biocontrol agent against Fusarium cotton wilt, improving cotton growth characteristics and yield.
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creator: Rizwan Asif
creator: Muhammad Hussnain Siddique
creator: Sumreen Hayat
creator: Ijaz Rasul
creator: Habibullah Nadeem
creator: Muhammad Faisal
creator: Muhammad Waseem
creator: Shahbaz Ahmad Zakki
creator: Abdelghani Zitouni
creator: Saima Muzammil
subject: Microbiology
subject: Mycology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.14754
publisher: PeerJ Inc.
rights: © 2023 Asif et al.
abstract: Fusarium cotton wilt is a devastating disease of the cotton crop throughout the world, caused by Fusarium oxysporum f.sp. vasinfectum (FOV). Chemical control has many side effects, so, biological controls have been widely used for the management of Fusarium wilt. This study aimed to investigate the possible use of an actinomycetes Saccharothrix algeriensis (SA) NRRL B-24137 to control FOV. To access in-vitro anti-Fusarium ability of SA NRRL B-24137, dual culture assay, spore germination and seed germination tests were carried out. Following in-vitro investigations, several pot tests in a greenhouse environment were used to evaluate the biological control potential of SA NRRL B-24137 against FOV. Dual culture assay and spore germination revealed that SA NRRL B-24137 showed significant anti-Fusarium activity.During spore germination 87.77% inhibition of spore germination were observed. In pot experiments, SA NRRL B-24137 primed cotton seeds resulted in a 74.0% reduction in disease incidence. In soil there was a significant reduction in FOV spores in the presence of SA NRRL B-24137. Positive correlation was also observed on different concentrations of SA NRRL B-24137 towards FOV reduction. The results of this study showed that SA NRRL B-24137 has the potential to be employed as a biocontrol agent against Fusarium cotton wilt, improving cotton growth characteristics and yield.
bibliographic citation: Asif et al. (2023) Efficacy of Saccharothrix algeriensis NRRL B-24137 to suppress Fusarium oxysporum f.sp. vasinfectum induced wilt disease in cotton. PeerJ 11:e14754 https://doi.org/10.7717/peerj.14754
date submitted: 2022-08-24
date accepted: 2022-12-27
issued: 2023-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Asif
  given name: Rizwan
author list: Agent
  family name: Siddique
  given name: Muhammad Hussnain
author list: Agent
  family name: Hayat
  given name: Sumreen
author list: Agent
  family name: Rasul
  given name: Ijaz
author list: Agent
  family name: Nadeem
  given name: Habibullah
author list: Agent
  family name: Faisal
  given name: Muhammad
author list: Agent
  family name: Waseem
  given name: Muhammad
author list: Agent
  family name: Zakki
  given name: Shahbaz Ahmad
author list: Agent
  family name: Zitouni
  given name: Abdelghani
author list: Agent
  family name: Muzammil
  given name: Saima
doi: 10.7717/peerj.14754
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-06
copyright: ©2023 Asif et al.
attribution name: Asif et al.

Prohexadione calcium enhances rice growth and tillering under NaCl stress
type: item
type: AcademicArticle
description: Salt stress affects crop quality and reduces crop yields, and growth regulators enhance salt tolerance of crop plants. In this report, we examined the effects of prohexadione-calcium (Pro-Ca) on improving rice (Oryza sativa L.) growth and tillering under salt stress. We found that NaCl stress inhibited the growth of two rice varieties and increased malondialdehyde (MDA) levels, electrolyte leakage, and the activities of the antioxidant enzymes. Foliar application of Pro-Ca reduced seedling height and increased stem base width and lodging resistance of rice. Further analyses showed that Pro-Ca application reduced MDA content, electrolyte leakage, and membrane damage in rice leaves under NaCl stress. Pro-Ca enhanced the net photosynthetic rate (Pn), stomatal conductance (Gs), and intercellular CO2 concentration (Ci) of rice seedlings, while increasing the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbic acid peroxidase (APX) at the tillering stage under salt stress. Overall, Pro-Ca improves salt tolerance of rice seedlings at the tillering stage by enhancing lodging resistance, reducing membrane damages, and enhancing photosynthesis and antioxidant capacities of rice seedlings.
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format: text/html
creator: Rongjun Zhang
creator: Dianfeng Zheng
creator: Naijie Feng
creator: Quan-Sheng Qiu
creator: Hang Zhou
creator: Meiling Liu
creator: Yao Li
creator: Fengyan Meng
creator: XiXin Huang
creator: Anqi Huang
creator: Yixiang Li
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Soil Science
subject: Ecotoxicology
description: doi:10.7717/peerj.14804
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Salt stress affects crop quality and reduces crop yields, and growth regulators enhance salt tolerance of crop plants. In this report, we examined the effects of prohexadione-calcium (Pro-Ca) on improving rice (Oryza sativa L.) growth and tillering under salt stress. We found that NaCl stress inhibited the growth of two rice varieties and increased malondialdehyde (MDA) levels, electrolyte leakage, and the activities of the antioxidant enzymes. Foliar application of Pro-Ca reduced seedling height and increased stem base width and lodging resistance of rice. Further analyses showed that Pro-Ca application reduced MDA content, electrolyte leakage, and membrane damage in rice leaves under NaCl stress. Pro-Ca enhanced the net photosynthetic rate (Pn), stomatal conductance (Gs), and intercellular CO2 concentration (Ci) of rice seedlings, while increasing the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbic acid peroxidase (APX) at the tillering stage under salt stress. Overall, Pro-Ca improves salt tolerance of rice seedlings at the tillering stage by enhancing lodging resistance, reducing membrane damages, and enhancing photosynthesis and antioxidant capacities of rice seedlings.
bibliographic citation: Zhang et al. (2023) Prohexadione calcium enhances rice growth and tillering under NaCl stress. PeerJ 11:e14804 https://doi.org/10.7717/peerj.14804
date submitted: 2022-09-15
date accepted: 2023-01-05
issued: 2023-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Rongjun
author list: Agent
  family name: Zheng
  given name: Dianfeng
author list: Agent
  family name: Feng
  given name: Naijie
author list: Agent
  family name: Qiu
  given name: Quan-Sheng
author list: Agent
  family name: Zhou
  given name: Hang
author list: Agent
  family name: Liu
  given name: Meiling
author list: Agent
  family name: Li
  given name: Yao
author list: Agent
  family name: Meng
  given name: Fengyan
author list: Agent
  family name: Huang
  given name: XiXin
author list: Agent
  family name: Huang
  given name: Anqi
author list: Agent
  family name: Li
  given name: Yixiang
doi: 10.7717/peerj.14804
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-06
copyright: ©2023 Zhang et al.
attribution name: Zhang et al.

Influence of resin modified glass ionomer cement incorporating protein-repellent and antimicrobial agents on supragingival microbiome around brackets: an in-vivo split-mouth 3-month study
type: item
type: AcademicArticle
description: Objective To explore the influence of resin modified glass ionomer cement (RMGIC) adhesives containing protein-repellent and quaternary ammonium salt agents on supragingival microbiome, enamel and gingival health around brackets. Materials and Methods Ten patients (21.4 ± 3.5 years) about to receive fixed orthodontics were enrolled in this study. Unilateral upper teeth bonded with RMGIC incorporating 2-Methacryloyloxyethyl phosphorylcholine (MPC) and Dimethylaminohexadecyl methacrylate (DMAHDM) were regarded as experimental group (RMD), while contralateral upper teeth bonded with RMGIC were control group (RMGIC), using a split-mouth design. Supragingival plaque was collected from both groups before treatment (T0), and at 1 month (T1) and 3 months (T2) of treatment. High-throughput sequencing was performed targeting v3–v4 of 16S rRNA gene. Streptococcus mutans and Fusobacterium nucleatum quantification was done by qPCR analysis. Bracket failures, enamel decalcification index (EDI), DIAGNODent scores (Dd), plaque index (PI) and gingival index (GI) were monitored at indicated time points. Results Within 3 months, alpha and beta diversity of supragingival plaque had no difference between RMGIC and RMD groups. From T0 to T2, the relative abundance of Streptococcus depleted in RMD but remained steady in RMGIC group. Streptococcus, Prevotella, and Fusobacterium became depleted in RMD, Haemophilus and Capnocytophaga became depleted in RMGIC group but Prevotella enriched. Quantification of Fusbacterium nucleatum and Streptococcus mutans showed significant difference between RMGIC and RMD groups at T2. Teeth bonded with RMD had significant lower plaque index (PI) and DIAGNODent (Dd) score at T2, compared with teeth bonded with RMGIC (p < 0.05). No difference in bracket failure rate was examined between both groups (p > 0.05). Conclusion By incorporating MPC and DMAHDM into RMGIC, the material could affect the supragingival microbial composition, inhibit the progress of plaque…
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creator: Yansong Ma
creator: Chengjun Su
creator: Hao Yang
creator: Hockin H.K. Xu
creator: Yuxing Bai
creator: Yan Xu
creator: Xiaoxia Che
creator: Ning Zhang
subject: Microbiology
subject: Dentistry
description: doi:10.7717/peerj.14820
publisher: PeerJ Inc.
rights: © 2023 Ma et al.
abstract: Objective To explore the influence of resin modified glass ionomer cement (RMGIC) adhesives containing protein-repellent and quaternary ammonium salt agents on supragingival microbiome, enamel and gingival health around brackets. Materials and Methods Ten patients (21.4 ± 3.5 years) about to receive fixed orthodontics were enrolled in this study. Unilateral upper teeth bonded with RMGIC incorporating 2-Methacryloyloxyethyl phosphorylcholine (MPC) and Dimethylaminohexadecyl methacrylate (DMAHDM) were regarded as experimental group (RMD), while contralateral upper teeth bonded with RMGIC were control group (RMGIC), using a split-mouth design. Supragingival plaque was collected from both groups before treatment (T0), and at 1 month (T1) and 3 months (T2) of treatment. High-throughput sequencing was performed targeting v3–v4 of 16S rRNA gene. Streptococcus mutans and Fusobacterium nucleatum quantification was done by qPCR analysis. Bracket failures, enamel decalcification index (EDI), DIAGNODent scores (Dd), plaque index (PI) and gingival index (GI) were monitored at indicated time points. Results Within 3 months, alpha and beta diversity of supragingival plaque had no difference between RMGIC and RMD groups. From T0 to T2, the relative abundance of Streptococcus depleted in RMD but remained steady in RMGIC group. Streptococcus, Prevotella, and Fusobacterium became depleted in RMD, Haemophilus and Capnocytophaga became depleted in RMGIC group but Prevotella enriched. Quantification of Fusbacterium nucleatum and Streptococcus mutans showed significant difference between RMGIC and RMD groups at T2. Teeth bonded with RMD had significant lower plaque index (PI) and DIAGNODent (Dd) score at T2, compared with teeth bonded with RMGIC (p < 0.05). No difference in bracket failure rate was examined between both groups (p > 0.05). Conclusion By incorporating MPC and DMAHDM into RMGIC, the material could affect the supragingival microbial composition, inhibit the progress of plaque…
bibliographic citation: Ma et al. (2023) Influence of resin modified glass ionomer cement incorporating protein-repellent and antimicrobial agents on supragingival microbiome around brackets: an in-vivo split-mouth 3-month study. PeerJ 11:e14820 https://doi.org/10.7717/peerj.14820
date submitted: 2022-10-31
date accepted: 2023-01-06
issued: 2023-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Yansong
author list: Agent
  family name: Su
  given name: Chengjun
author list: Agent
  family name: Yang
  given name: Hao
author list: Agent
  family name: Xu
  given name: Hockin H.K.
author list: Agent
  family name: Bai
  given name: Yuxing
author list: Agent
  family name: Xu
  given name: Yan
author list: Agent
  family name: Che
  given name: Xiaoxia
author list: Agent
  family name: Zhang
  given name: Ning
doi: 10.7717/peerj.14820
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-06
copyright: ©2023 Ma et al.
attribution name: Ma et al.

Construction and validation of a fatty acid metabolism-related gene signature for predicting prognosis and therapeutic response in patients with prostate cancer
type: item
type: AcademicArticle
description: Background Reprogramming of fatty acid metabolism is a newly-identified hallmark of malignancy. However, no studies have systematically investigated the fatty acid metabolism related-gene set in prostate cancer (PCa). Methods A cohort of 381 patients with gene expression and clinical data from The Cancer Genome Atlas was used as the training set, while another cohort of 90 patients with PCa from GEO (GSE70769) was used as the validation set. Differentially expressed fatty acid metabolism-related genes were subjected to least absolute shrinkage and selection operator (LASSO)-Cox regression to establish a fatty acid metabolism-related risk score. Associations between the risk score and clinical characteristics, immune cell infiltration, tumor mutation burden (TMB), tumor immune dysfunction and exclusion (TIDE) score, and response to chemotherapy were analyzed. Finally, the expression level of genes included in the model was validated using real-time PCR. Results A prognostic risk model based on five fatty acid metabolism related genes (ALDH1A1, CPT1B, CA2, CROT, and NUDT19) were constructed. Tumors with higher risk score were associated with larger tumor size, lymph node involvement, higher Gleason score, and poorer biochemical recurrence (BCR)-free survival. Furthermore, the high- and low-risk tumors exhibited distinct immune cell infiltration features and immune-related pathway activation. High-risk tumors were associated with favorable response to immunotherapy as indicated by high TMB and low TIDE score, but poor response to bicalutamide and docetaxel chemotherapy. Conclusion This study established a fatty acid metabolism-related gene signature which was predictive of BCR and response to chemotherapy and immunotherapy, providing a novel therapeutic biomarker for PCa.
format: application/pdf
format: text/html
creator: Hongjun Zhao
creator: Tong Wu
creator: Zehao Luo
creator: Qinyao Huang
creator: Sihua Zhu
creator: Chunling Li
creator: Zubing Zhang
creator: Jiahao Zhang
creator: Jianwen Zeng
creator: Yuying Zhang
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.14854
publisher: PeerJ Inc.
rights: © 2023 Zhao et al.
abstract: Background Reprogramming of fatty acid metabolism is a newly-identified hallmark of malignancy. However, no studies have systematically investigated the fatty acid metabolism related-gene set in prostate cancer (PCa). Methods A cohort of 381 patients with gene expression and clinical data from The Cancer Genome Atlas was used as the training set, while another cohort of 90 patients with PCa from GEO (GSE70769) was used as the validation set. Differentially expressed fatty acid metabolism-related genes were subjected to least absolute shrinkage and selection operator (LASSO)-Cox regression to establish a fatty acid metabolism-related risk score. Associations between the risk score and clinical characteristics, immune cell infiltration, tumor mutation burden (TMB), tumor immune dysfunction and exclusion (TIDE) score, and response to chemotherapy were analyzed. Finally, the expression level of genes included in the model was validated using real-time PCR. Results A prognostic risk model based on five fatty acid metabolism related genes (ALDH1A1, CPT1B, CA2, CROT, and NUDT19) were constructed. Tumors with higher risk score were associated with larger tumor size, lymph node involvement, higher Gleason score, and poorer biochemical recurrence (BCR)-free survival. Furthermore, the high- and low-risk tumors exhibited distinct immune cell infiltration features and immune-related pathway activation. High-risk tumors were associated with favorable response to immunotherapy as indicated by high TMB and low TIDE score, but poor response to bicalutamide and docetaxel chemotherapy. Conclusion This study established a fatty acid metabolism-related gene signature which was predictive of BCR and response to chemotherapy and immunotherapy, providing a novel therapeutic biomarker for PCa.
bibliographic citation: Zhao et al. (2023) Construction and validation of a fatty acid metabolism-related gene signature for predicting prognosis and therapeutic response in patients with prostate cancer. PeerJ 11:e14854 https://doi.org/10.7717/peerj.14854
date submitted: 2022-11-17
date accepted: 2023-01-13
issued: 2023-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Hongjun
author list: Agent
  family name: Wu
  given name: Tong
author list: Agent
  family name: Luo
  given name: Zehao
author list: Agent
  family name: Huang
  given name: Qinyao
author list: Agent
  family name: Zhu
  given name: Sihua
author list: Agent
  family name: Li
  given name: Chunling
author list: Agent
  family name: Zhang
  given name: Zubing
author list: Agent
  family name: Zhang
  given name: Jiahao
author list: Agent
  family name: Zeng
  given name: Jianwen
author list: Agent
  family name: Zhang
  given name: Yuying
doi: 10.7717/peerj.14854
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-06
copyright: © 2023 Zhao et al.
attribution name: Zhao et al.

Elevated serum FGF21 levels predict heart failure during hospitalization of STEMI patients after emergency percutaneous coronary intervention
type: item
type: AcademicArticle
description: Background Fibroblast growth factor 21 (FGF21) has multiple cardioprotective effects including modulation of glucolipid metabolism, anti-inflammation, and anti-oxidative stress, but its association with the heart failure during hospitalization in patients with ST-segment elevation myocardial infarction (STEMI) undergoing emergency percutaneous coronary intervention (PCI) has not been reported. Methods A total of 348 STEMI patients treated with emergency PCI were included from January 2016 to December 2018. Relevant biochemical indicators were measured by central laboratory. Serum FGF21 levels were measured by ELISA. The occurrence of heart failure during hospitalization was recorded. Patients’ cardiac function was assessed by echocardiography. Results Serum FGF21 levels were significantly higher in the STEMI group with heart failure than in the group without heart failure (249.95 ± 25.52 vs. 209.98 ± 36.35, P < 0.001). Serum FGF21 levels showed a strong positive correlation with N-terminal precursor B-type natriuretic peptide (NT-proBNP) in STEMI patients (r = 0.749, P < 0.001). FGF21 was found to be an independent risk factor for the development of heart failure during hospitalization in STEMI patients by binary logistic regression analysis. The area under curve (AUC) for FGF21 to predict the development of heart failure during hospitalization in STEMI patients was 0.816 (95% CI [0.770–0.863]) according to the receiver operating characteristic (ROC) curve analysis. Conclusion Elevated serum FGF21 levels have been shown to be a strong predictor of heart failure during hospitalization in patients with STEMI after emergency PCI.
format: application/pdf
format: text/html
creator: Lingyun Gu
creator: Wenxi Jiang
creator: Wenlong Jiang
creator: Zhuowen Xu
creator: Weizhang Li
creator: Hua Zhang
subject: Hematology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.14855
publisher: PeerJ Inc.
rights: © 2023 Gu et al.
abstract: Background Fibroblast growth factor 21 (FGF21) has multiple cardioprotective effects including modulation of glucolipid metabolism, anti-inflammation, and anti-oxidative stress, but its association with the heart failure during hospitalization in patients with ST-segment elevation myocardial infarction (STEMI) undergoing emergency percutaneous coronary intervention (PCI) has not been reported. Methods A total of 348 STEMI patients treated with emergency PCI were included from January 2016 to December 2018. Relevant biochemical indicators were measured by central laboratory. Serum FGF21 levels were measured by ELISA. The occurrence of heart failure during hospitalization was recorded. Patients’ cardiac function was assessed by echocardiography. Results Serum FGF21 levels were significantly higher in the STEMI group with heart failure than in the group without heart failure (249.95 ± 25.52 vs. 209.98 ± 36.35, P < 0.001). Serum FGF21 levels showed a strong positive correlation with N-terminal precursor B-type natriuretic peptide (NT-proBNP) in STEMI patients (r = 0.749, P < 0.001). FGF21 was found to be an independent risk factor for the development of heart failure during hospitalization in STEMI patients by binary logistic regression analysis. The area under curve (AUC) for FGF21 to predict the development of heart failure during hospitalization in STEMI patients was 0.816 (95% CI [0.770–0.863]) according to the receiver operating characteristic (ROC) curve analysis. Conclusion Elevated serum FGF21 levels have been shown to be a strong predictor of heart failure during hospitalization in patients with STEMI after emergency PCI.
bibliographic citation: Gu et al. (2023) Elevated serum FGF21 levels predict heart failure during hospitalization of STEMI patients after emergency percutaneous coronary intervention. PeerJ 11:e14855 https://doi.org/10.7717/peerj.14855
date submitted: 2022-10-03
date accepted: 2023-01-14
issued: 2023-02-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gu
  given name: Lingyun
author list: Agent
  family name: Jiang
  given name: Wenxi
author list: Agent
  family name: Jiang
  given name: Wenlong
author list: Agent
  family name: Xu
  given name: Zhuowen
author list: Agent
  family name: Li
  given name: Weizhang
author list: Agent
  family name: Zhang
  given name: Hua
doi: 10.7717/peerj.14855
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-06
copyright: © 2023 Gu et al.
attribution name: Gu et al.

Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin
type: item
type: AcademicArticle
description: The genus Phoebe (Lauraceae) includes about 90 evergreen tree species that are an ideal source of timber. Habitat destruction and deforestation have resulted in most of them being endemic to China. The accurate identification of endangered Phoebe species in China is necessary for their conservation. Chloroplast genome sequences can play an important role in species identification. In this study, comparative chloroplast genome analyses were conducted on diverse Phoebe species that are primarily distributed in China. Despite the conserved nature of chloroplast genomes, we detected some highly divergent intergenic regions (petA–psbE, ndhF–rpl32, and psbM–trnD-GUC) as well as three highly divergent genes (rbcL, ycf1, and ycf2) that have potential applications in phylogenetics and evolutionary analysis. The phylogenetic analysis indicated that various Phoebe species in China were divided into three clades. The complete chloroplast genome was better suited for phylogenetic analysis of Phoebe species. In addition, based on the phylogeographical analysis of Phoebe species in China, we inferred that the Phoebe species in China first originated in Yunnan and then spread to other southern areas of the Yangtze River. The results of this research will add to existing case studies on the phylogenetic analysis of Phoebe species and have the potential to contribute to the conservation of Phoebe species that are in danger of extinction.
format: application/pdf
format: text/html
creator: Wenbo Shi
creator: Weicai Song
creator: Zimeng Chen
creator: Haohong Cai
creator: Qin Gong
creator: Jin Liu
creator: Chao Shi
creator: Shuo Wang
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.14573
publisher: PeerJ Inc.
rights: © 2023 Shi et al.
abstract: The genus Phoebe (Lauraceae) includes about 90 evergreen tree species that are an ideal source of timber. Habitat destruction and deforestation have resulted in most of them being endemic to China. The accurate identification of endangered Phoebe species in China is necessary for their conservation. Chloroplast genome sequences can play an important role in species identification. In this study, comparative chloroplast genome analyses were conducted on diverse Phoebe species that are primarily distributed in China. Despite the conserved nature of chloroplast genomes, we detected some highly divergent intergenic regions (petA–psbE, ndhF–rpl32, and psbM–trnD-GUC) as well as three highly divergent genes (rbcL, ycf1, and ycf2) that have potential applications in phylogenetics and evolutionary analysis. The phylogenetic analysis indicated that various Phoebe species in China were divided into three clades. The complete chloroplast genome was better suited for phylogenetic analysis of Phoebe species. In addition, based on the phylogeographical analysis of Phoebe species in China, we inferred that the Phoebe species in China first originated in Yunnan and then spread to other southern areas of the Yangtze River. The results of this research will add to existing case studies on the phylogenetic analysis of Phoebe species and have the potential to contribute to the conservation of Phoebe species that are in danger of extinction.
bibliographic citation: Shi et al. (2023) Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin. PeerJ 11:e14573 https://doi.org/10.7717/peerj.14573
date submitted: 2022-08-26
date accepted: 2022-11-28
issued: 2023-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Wenbo
author list: Agent
  family name: Song
  given name: Weicai
author list: Agent
  family name: Chen
  given name: Zimeng
author list: Agent
  family name: Cai
  given name: Haohong
author list: Agent
  family name: Gong
  given name: Qin
author list: Agent
  family name: Liu
  given name: Jin
author list: Agent
  family name: Shi
  given name: Chao
author list: Agent
  family name: Wang
  given name: Shuo
doi: 10.7717/peerj.14573
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-03
copyright: ©2023 Shi et al.
attribution name: Shi et al.

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