PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: In silico analysis of serum miRNA profiles in seronegative and seropositive rheumatoid arthritis patients by small RNA sequencing
items: The complete mitochondrial genome and description of a new cryptic Brazilian species of Metopiellus Raffray (Coleoptera: Staphylinidae: Pselaphinae)
items: Metabolic cost of walking with electromechanical ankle exoskeletons under proportional myoelectric control on a treadmill and outdoors
items: Protective effect of fustin against adjuvant-induced arthritis through the restoration of proinflammatory response and oxidative stress
items: Effects of high-risk human papillomavirus infection on P53, pRb, and survivin in lung adenocarcinoma—a retrospective study
items: Recombination of endophytic bacteria in asexual plant Ligusticum chuanxiong Hort. caused by transplanting
items: Dapagliflozin-affected endothelial dysfunction and altered gut microbiota in mice with heart failure
items: Utilization of hepatitis B surface antigen-positive donors in liver transplantation for recipients with hepatocellular carcinoma: a retrospective and propensity score matching analysis
items: Unique antimicrobial activity in honey from the Australian honeypot ant (Camponotus inflatus)
items: Effect of finger rest positions on upper limb muscle activity during pre-clinical procedures

In silico analysis of serum miRNA profiles in seronegative and seropositive rheumatoid arthritis patients by small RNA sequencing
type: item
type: AcademicArticle
description: Rheumatoid arthritis (RA) is a refractory autoimmune disease, affecting about 1% of the world’s population. RA is divided into seronegative RA and seropositive RA. However, biomarkers for discriminating between seronegative and seropositive RA have not been reported. In this study, we profiled serum miRNAs in seronegative RA patients (N-RA), seropositive RA patients (P-RA) and healthy controls (HC) by small RNA sequencing. Results indicated that compared with HC group, there were one up-regulated and four downregulated miRNAs in N-RA group (fold change ≥ 2 and P value < 0.05); compared with P-RA group, there were two up-regulated and four downregulated miRNAs in N-RA group; compared with HC group, there were three up-regulated and four downregulated miRNAs in P-RA group. Among them, the level of hsa-miR-362-5p in N-RA group was up-regulated compared with that in HC group and P-RA group, and the level of hsa-miR-6855-5p and hsa-miR-187-3p in P-RA group was upregulated compared with that in N-RA group and HC group. Validation by qPCR confirmed that serum hsa-miR-362-5p level was elevated in N-RA group. Subsequently, by analyzing the target genes using RNAhybrid, PITA, Miranda and TargetScan and functions of differential miRNAs utilizing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), we found that the target genes and molecular pathways regulated by miRNAs in seronegative RA and seropositive RA were roughly the same, and miRNAs in these two diseases may participate in the occurrence and development of diseases by regulating the immune system. In conclusion, this study revealed the profiles of serum miRNAs in seronegative and seropositive RA patients for the first time, providing potential biomarkers and targets for the diagnosis and treatment of seronegative and seropositive RA.
format: application/pdf
format: text/html
creator: Xiao-Hong He
creator: Yun-Ting Xiao
creator: Wen-Ying Chen
creator: Mao-Jie Wang
creator: Xiao-Dong Wu
creator: Li-Yan Mei
creator: Kai-Xin Gao
creator: Qing-Chun Huang
creator: Run-Yue Huang
creator: Xiu-Min Chen
subject: Cell Biology
subject: Immunology
subject: Rheumatology
description: doi:10.7717/peerj.15690
publisher: PeerJ Inc.
rights: © 2023 He et al.
abstract: Rheumatoid arthritis (RA) is a refractory autoimmune disease, affecting about 1% of the world’s population. RA is divided into seronegative RA and seropositive RA. However, biomarkers for discriminating between seronegative and seropositive RA have not been reported. In this study, we profiled serum miRNAs in seronegative RA patients (N-RA), seropositive RA patients (P-RA) and healthy controls (HC) by small RNA sequencing. Results indicated that compared with HC group, there were one up-regulated and four downregulated miRNAs in N-RA group (fold change ≥ 2 and P value < 0.05); compared with P-RA group, there were two up-regulated and four downregulated miRNAs in N-RA group; compared with HC group, there were three up-regulated and four downregulated miRNAs in P-RA group. Among them, the level of hsa-miR-362-5p in N-RA group was up-regulated compared with that in HC group and P-RA group, and the level of hsa-miR-6855-5p and hsa-miR-187-3p in P-RA group was upregulated compared with that in N-RA group and HC group. Validation by qPCR confirmed that serum hsa-miR-362-5p level was elevated in N-RA group. Subsequently, by analyzing the target genes using RNAhybrid, PITA, Miranda and TargetScan and functions of differential miRNAs utilizing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), we found that the target genes and molecular pathways regulated by miRNAs in seronegative RA and seropositive RA were roughly the same, and miRNAs in these two diseases may participate in the occurrence and development of diseases by regulating the immune system. In conclusion, this study revealed the profiles of serum miRNAs in seronegative and seropositive RA patients for the first time, providing potential biomarkers and targets for the diagnosis and treatment of seronegative and seropositive RA.
bibliographic citation: He et al. (2023) In silico analysis of serum miRNA profiles in seronegative and seropositive rheumatoid arthritis patients by small RNA sequencing. PeerJ 11:e15690 https://doi.org/10.7717/peerj.15690
date submitted: 2023-01-30
date accepted: 2023-06-14
issued: 2023-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Xiao-Hong
author list: Agent
  family name: Xiao
  given name: Yun-Ting
author list: Agent
  family name: Chen
  given name: Wen-Ying
author list: Agent
  family name: Wang
  given name: Mao-Jie
author list: Agent
  family name: Wu
  given name: Xiao-Dong
author list: Agent
  family name: Mei
  given name: Li-Yan
author list: Agent
  family name: Gao
  given name: Kai-Xin
author list: Agent
  family name: Huang
  given name: Qing-Chun
author list: Agent
  family name: Huang
  given name: Run-Yue
author list: Agent
  family name: Chen
  given name: Xiu-Min
doi: 10.7717/peerj.15690
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-27
copyright: © 2023 He et al.
attribution name: He et al.

The complete mitochondrial genome and description of a new cryptic Brazilian species of Metopiellus Raffray (Coleoptera: Staphylinidae: Pselaphinae)
type: item
type: AcademicArticle
description: Metopiellus Raffray, 1908 is a genus of South American rove beetles typically found in tropical humid forests. Here we describe a new cryptic species from Eastern Amazon, in northern Brazil, Metopiellus crypticus Asenjo sp. nov., and its major morphologic diagnostic features, which were photographed and illustrated. In addition, we bring the complete mitochondrial genome sequence of M. crypticus sp. nov., and its position within the phylogenetic context of the family, including previously available mitogenomes of Staphylinidae species.
format: application/pdf
format: text/html
creator: Angélico Asenjo
creator: Marcus Paulo Alves de Oliveira
creator: Renato R.M. Oliveira
creator: Eder Soares Pires
creator: Marcely Valois
creator: Guilherme Oliveira
creator: Santelmo Vasconcelos
subject: Entomology
subject: Genomics
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15697
publisher: PeerJ Inc.
rights: © 2023 Asenjo et al.
abstract: Metopiellus Raffray, 1908 is a genus of South American rove beetles typically found in tropical humid forests. Here we describe a new cryptic species from Eastern Amazon, in northern Brazil, Metopiellus crypticus Asenjo sp. nov., and its major morphologic diagnostic features, which were photographed and illustrated. In addition, we bring the complete mitochondrial genome sequence of M. crypticus sp. nov., and its position within the phylogenetic context of the family, including previously available mitogenomes of Staphylinidae species.
bibliographic citation: Asenjo et al. (2023) The complete mitochondrial genome and description of a new cryptic Brazilian species of Metopiellus Raffray (Coleoptera: Staphylinidae: Pselaphinae). PeerJ 11:e15697 https://doi.org/10.7717/peerj.15697
date submitted: 2023-03-23
date accepted: 2023-06-14
issued: 2023-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Asenjo
  given name: Angélico
author list: Agent
  family name: de Oliveira
  given name: Marcus Paulo Alves
author list: Agent
  family name: Oliveira
  given name: Renato R.M.
author list: Agent
  family name: Pires
  given name: Eder Soares
author list: Agent
  family name: Valois
  given name: Marcely
author list: Agent
  family name: Oliveira
  given name: Guilherme
author list: Agent
  family name: Vasconcelos
  given name: Santelmo
doi: 10.7717/peerj.15697
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-27
copyright: ©2023 Asenjo et al.
attribution name: Asenjo et al.

Metabolic cost of walking with electromechanical ankle exoskeletons under proportional myoelectric control on a treadmill and outdoors
type: item
type: AcademicArticle
description: Lower limb robotic exoskeletons are often studied in the context of steady state treadmill walking in a laboratory environment. However, the end goal for exoskeletons is to be used in real world, complex environments. To reach the point that exoskeletons are openly adopted into our everyday lives, we need to understand how the human and robot interact outside of a laboratory. Metabolic cost is often viewed as a gold standard metric for measuring exoskeleton performance but is rarely used to evaluate performance at non steady state walking outside of a laboratory. In this study, we tested the effects of robotic ankle exoskeletons under proportional myoelectric control on the cost of transport of walking both inside on a treadmill and outside overground. We hypothesized that walking with the exoskeletons would lead to a lower cost of transport compared to walking without them both on a treadmill and outside. We saw no significant increases or decreases in cost of transport or exoskeleton mechanics when walking with the exoskeletons compared to walking without them both on a treadmill and outside. We saw a strong negative correlation between walking speed and cost of transport when walking with and without the exoskeletons. In the future, research should consider how performing more difficult tasks, such as incline and loaded walking, affects the cost of transport while walking with and without robotic ankle exoskeletons. The value of this study to the literature is that it emphasizes the importance of both hardware dynamics and controller design towards reducing metabolic cost of transport with robotic ankle exoskeletons. When comparing our results to other studies using the same hardware with different controllers or very similar controllers with different hardware, there are a wide range of outcomes as to metabolic benefit.
format: application/pdf
format: text/html
creator: Rachel Hybart
creator: K. Siena Villancio-Wolter
creator: Daniel Perry Ferris
subject: Human-Computer Interaction
subject: Biomechanics
description: doi:10.7717/peerj.15775
publisher: PeerJ Inc.
rights: © 2023 Hybart et al.
abstract: Lower limb robotic exoskeletons are often studied in the context of steady state treadmill walking in a laboratory environment. However, the end goal for exoskeletons is to be used in real world, complex environments. To reach the point that exoskeletons are openly adopted into our everyday lives, we need to understand how the human and robot interact outside of a laboratory. Metabolic cost is often viewed as a gold standard metric for measuring exoskeleton performance but is rarely used to evaluate performance at non steady state walking outside of a laboratory. In this study, we tested the effects of robotic ankle exoskeletons under proportional myoelectric control on the cost of transport of walking both inside on a treadmill and outside overground. We hypothesized that walking with the exoskeletons would lead to a lower cost of transport compared to walking without them both on a treadmill and outside. We saw no significant increases or decreases in cost of transport or exoskeleton mechanics when walking with the exoskeletons compared to walking without them both on a treadmill and outside. We saw a strong negative correlation between walking speed and cost of transport when walking with and without the exoskeletons. In the future, research should consider how performing more difficult tasks, such as incline and loaded walking, affects the cost of transport while walking with and without robotic ankle exoskeletons. The value of this study to the literature is that it emphasizes the importance of both hardware dynamics and controller design towards reducing metabolic cost of transport with robotic ankle exoskeletons. When comparing our results to other studies using the same hardware with different controllers or very similar controllers with different hardware, there are a wide range of outcomes as to metabolic benefit.
bibliographic citation: Hybart et al. (2023) Metabolic cost of walking with electromechanical ankle exoskeletons under proportional myoelectric control on a treadmill and outdoors. PeerJ 11:e15775 https://doi.org/10.7717/peerj.15775
date submitted: 2023-04-13
date accepted: 2023-06-29
issued: 2023-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hybart
  given name: Rachel
author list: Agent
  family name: Villancio-Wolter
  given name: K. Siena
author list: Agent
  family name: Ferris
  given name: Daniel Perry
doi: 10.7717/peerj.15775
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-27
copyright: ©2023 Hybart et al.
attribution name: Hybart et al.

Protective effect of fustin against adjuvant-induced arthritis through the restoration of proinflammatory response and oxidative stress
type: item
type: AcademicArticle
description: Rheumatoid arthritis causes irreparable damage to joints. The present research sought to check fustin’s anti-arthritic efficacy against the complete Freund’s adjuvant-induced arthritis paradigm in animals by altering the inflammatory response. In the rats, complete Freund’s adjuvant was used to trigger arthritis and they received fustin at 50 and 100 mg/kg for 21 days. At regular intervals, the hind paw volume and arthritic score were assessed. After the trial period, hematological, antioxidant, pro-inflammatory cytokines, and other biochemical parameters were estimated. Fustin-treated rats showed the down-regulation of hind paw volume, arthritic score, and altered hematological parameters (TLC, DLC (neutrophil, lymphocyte, monocyte, eosinophil, basophil)). Furthermore, fustin significantly mitigates proinflammatory cytokine (reduced interleukin, tumor necrosis factor-a (TNF-α), IL-6, IL-1β), oxidative stress (attenuated malondialdehyde (MDA), catalase (CAT), glutathione (GSH), superoxide dismutase (SOD)), attenuated production of prostaglandin E2 and myeloperoxidase (MPO) and improved nuclear factor erythroid 2-related factor (Nrf2) action. Fustin led to the benefit in arthritis-prone animals elicited by complete Freund’s adjuvant via pro-inflammatory cytokine.
format: application/pdf
format: text/html
creator: Sultan Alshehri
creator: Shareefa A. AlGhamdi
creator: Amira M. Alghamdi
creator: Syed Sarim Imam
creator: Wael A. Mahdi
creator: Mohammad A. Almaniea
creator: Baraa Mohammed Hajjar
creator: Fahad A. Al-Abbasi
creator: Nadeem Sayyed
creator: Imran Kazmi
subject: Biochemistry
subject: Immunology
subject: Rheumatology
description: doi:10.7717/peerj.15532
publisher: PeerJ Inc.
rights: © 2023 Alshehri et al.
abstract: Rheumatoid arthritis causes irreparable damage to joints. The present research sought to check fustin’s anti-arthritic efficacy against the complete Freund’s adjuvant-induced arthritis paradigm in animals by altering the inflammatory response. In the rats, complete Freund’s adjuvant was used to trigger arthritis and they received fustin at 50 and 100 mg/kg for 21 days. At regular intervals, the hind paw volume and arthritic score were assessed. After the trial period, hematological, antioxidant, pro-inflammatory cytokines, and other biochemical parameters were estimated. Fustin-treated rats showed the down-regulation of hind paw volume, arthritic score, and altered hematological parameters (TLC, DLC (neutrophil, lymphocyte, monocyte, eosinophil, basophil)). Furthermore, fustin significantly mitigates proinflammatory cytokine (reduced interleukin, tumor necrosis factor-a (TNF-α), IL-6, IL-1β), oxidative stress (attenuated malondialdehyde (MDA), catalase (CAT), glutathione (GSH), superoxide dismutase (SOD)), attenuated production of prostaglandin E2 and myeloperoxidase (MPO) and improved nuclear factor erythroid 2-related factor (Nrf2) action. Fustin led to the benefit in arthritis-prone animals elicited by complete Freund’s adjuvant via pro-inflammatory cytokine.
bibliographic citation: Alshehri et al. (2023) Protective effect of fustin against adjuvant-induced arthritis through the restoration of proinflammatory response and oxidative stress. PeerJ 11:e15532 https://doi.org/10.7717/peerj.15532
date submitted: 2023-01-18
date accepted: 2023-05-19
issued: 2023-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alshehri
  given name: Sultan
author list: Agent
  family name: AlGhamdi
  given name: Shareefa A.
author list: Agent
  family name: Alghamdi
  given name: Amira M.
author list: Agent
  family name: Imam
  given name: Syed Sarim
author list: Agent
  family name: Mahdi
  given name: Wael A.
author list: Agent
  family name: Almaniea
  given name: Mohammad A.
author list: Agent
  family name: Hajjar
  given name: Baraa Mohammed
author list: Agent
  family name: Al-Abbasi
  given name: Fahad A.
author list: Agent
  family name: Sayyed
  given name: Nadeem
author list: Agent
  family name: Kazmi
  given name: Imran
doi: 10.7717/peerj.15532
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-26
copyright: ©2023 Alshehri et al.
attribution name: Alshehri et al.

Effects of high-risk human papillomavirus infection on P53, pRb, and survivin in lung adenocarcinoma—a retrospective study
type: item
type: AcademicArticle
description: Objective To observe the effects of high-risk human papillomavirus (HR-HPV) infection on P53, pRb, and survivin in lung adenocarcinoma (LUAD). Methods The cancerous and cancer-adjacent tissues of 102 patients with LUAD from January 2020 to April 2022 were selected for the study. HR-HPV infection was detected by flow fluorescence method, and P53, pRb, and survivin protein expression was detected by immunohistochemical staining method. Statistical analysis was performed to determine the differences in the HR-HPV infection and the expression of P53, pRb, and survivin proteins between LUAD tissues and cancer-adjacent tissues; the correlation between HR-HPV infection and P53, pRb, and survivin protein expression in cancer tissues; and the correlation between HR-HPV infection and clinicopathological features of LUAD. Results The infection rate of HR-HPV was higher in the LUAD tissues (28.43%) than in cancer-adjacent tissues (7.84%), and the difference was statistically significant (P < 0.05). The positive rates of P53 and survivin protein were higher in the LUAD group (33.33% and 67.16%, respectively) than in the cancer-adjacent group (3.92% and 11.73%, respectively), and the difference was statistically significant (P < 0.05). The positive rate of pRb protein was lower in the LUAD group (58.82%) than in the cancer-adjacent group (92.14%), and the difference was statistically significant (P < 0.05). The positive rates of P53 and survivin proteins were significantly higher in the HR-HPV LUAD group (58.62% and 86.21%, respectively) than in the non-HR-HPV LUAD group (41.38% and 67.12%, respectively), and the difference was statistically significant (P < 0.05). The expression rate of pRb protein was significantly lower in the HR-HPV LUAD group (37.93%) than in the non-HR-HPV LUAD group (67.12%), and the difference was statistically significant (P < 0.05). The expression of p53 and survivin protein was positively correlated with HR-HPV infection (r = 0.338 and 0.444, P < 0.05)…
format: application/pdf
format: text/html
creator: Wenwen Sun
creator: Hui Yang
creator: Lu Cao
creator: Ruochen Wu
creator: Baoqi Ding
creator: Xiaocui Liu
creator: Xinli Wang
creator: Qiang Zhang
subject: Biochemistry
subject: Molecular Biology
subject: Immunology
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.15570
publisher: PeerJ Inc.
rights: © 2023 Sun et al.
abstract: Objective To observe the effects of high-risk human papillomavirus (HR-HPV) infection on P53, pRb, and survivin in lung adenocarcinoma (LUAD). Methods The cancerous and cancer-adjacent tissues of 102 patients with LUAD from January 2020 to April 2022 were selected for the study. HR-HPV infection was detected by flow fluorescence method, and P53, pRb, and survivin protein expression was detected by immunohistochemical staining method. Statistical analysis was performed to determine the differences in the HR-HPV infection and the expression of P53, pRb, and survivin proteins between LUAD tissues and cancer-adjacent tissues; the correlation between HR-HPV infection and P53, pRb, and survivin protein expression in cancer tissues; and the correlation between HR-HPV infection and clinicopathological features of LUAD. Results The infection rate of HR-HPV was higher in the LUAD tissues (28.43%) than in cancer-adjacent tissues (7.84%), and the difference was statistically significant (P < 0.05). The positive rates of P53 and survivin protein were higher in the LUAD group (33.33% and 67.16%, respectively) than in the cancer-adjacent group (3.92% and 11.73%, respectively), and the difference was statistically significant (P < 0.05). The positive rate of pRb protein was lower in the LUAD group (58.82%) than in the cancer-adjacent group (92.14%), and the difference was statistically significant (P < 0.05). The positive rates of P53 and survivin proteins were significantly higher in the HR-HPV LUAD group (58.62% and 86.21%, respectively) than in the non-HR-HPV LUAD group (41.38% and 67.12%, respectively), and the difference was statistically significant (P < 0.05). The expression rate of pRb protein was significantly lower in the HR-HPV LUAD group (37.93%) than in the non-HR-HPV LUAD group (67.12%), and the difference was statistically significant (P < 0.05). The expression of p53 and survivin protein was positively correlated with HR-HPV infection (r = 0.338 and 0.444, P < 0.05)…
bibliographic citation: Sun et al. (2023) Effects of high-risk human papillomavirus infection on P53, pRb, and survivin in lung adenocarcinoma—a retrospective study. PeerJ 11:e15570 https://doi.org/10.7717/peerj.15570
date submitted: 2023-04-13
date accepted: 2023-05-25
issued: 2023-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Wenwen
author list: Agent
  family name: Yang
  given name: Hui
author list: Agent
  family name: Cao
  given name: Lu
author list: Agent
  family name: Wu
  given name: Ruochen
author list: Agent
  family name: Ding
  given name: Baoqi
author list: Agent
  family name: Liu
  given name: Xiaocui
author list: Agent
  family name: Wang
  given name: Xinli
author list: Agent
  family name: Zhang
  given name: Qiang
doi: 10.7717/peerj.15570
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-26
copyright: ©2023 Sun et al.
attribution name: Sun et al.

Recombination of endophytic bacteria in asexual plant Ligusticum chuanxiong Hort. caused by transplanting
type: item
type: AcademicArticle
description: Background Long-term asexual reproduction can easily lead to the degradation of plant germplasm, serious diseases and insect pests, reduction of production and even catastrophic crop failure. “Mountain Breeding and Dam Cultivation” is the main cultivation mode of Ligusticum chuanxiong Hort., which successfully avoided the germplasm degradation caused by long-term asexual reproduction. The recombination of endophytic fungi of L. chuanxiong caused by off-site transplantation was considered to be an important reason for its germplasm rejuvenation. However, whether bacteria have the same regularity is not yet known. Methods In this study, we carried out the experiment of cultivating propagation materials of L. chuanxiong in different regions and transplanting them to the same region. High-throughput sequencing was performed to analyze the bacterial communities in L. chuanxiong and its soil. Results The results showed that after transplanting, the plant height, tiller number, fresh weight, etc. of L. chuanxiong in mountainous areas were significantly higher than those in dam areas. At the same time, significant changes had taken place in the endophytic bacteria in reproductive material stem nodes (Lingzi, abbreviated as LZ). The diversity and abundance of bacteria in dam area LZ (YL) are significantly higher than those in mountainous area LZ (ML). The relative abundance of bacteria such as Xanthobacteraceae, Micromonosporaceae, Beijerinkiaceae, Rhodanobacteria, in ML is significantly higher than YL, mainly classified in Proteobateria and Actinobacteriota. In addition, the abundance advantage of Actinobacteriota still exists in MY (underground mature rhizomes obtained by ML). Meanwhile, the bacterial community was different in different area of transplanting. The diversity of bacterial communities in dam soil (YLS) is significantly higher than that in mountain soil (MLS). MLS had more Acidobacteriota than YLS. Comparative analysis showed that 74.38% of bacteria in ML are …
format: application/pdf
format: text/html
creator: Wanting Xiao
creator: Zhanling Zhang
creator: Hai Wang
creator: Guiqi Han
creator: Zhu-Yun Yan
creator: Dongmei He
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.15579
publisher: PeerJ Inc.
rights: © 2023 Xiao et al.
abstract: Background Long-term asexual reproduction can easily lead to the degradation of plant germplasm, serious diseases and insect pests, reduction of production and even catastrophic crop failure. “Mountain Breeding and Dam Cultivation” is the main cultivation mode of Ligusticum chuanxiong Hort., which successfully avoided the germplasm degradation caused by long-term asexual reproduction. The recombination of endophytic fungi of L. chuanxiong caused by off-site transplantation was considered to be an important reason for its germplasm rejuvenation. However, whether bacteria have the same regularity is not yet known. Methods In this study, we carried out the experiment of cultivating propagation materials of L. chuanxiong in different regions and transplanting them to the same region. High-throughput sequencing was performed to analyze the bacterial communities in L. chuanxiong and its soil. Results The results showed that after transplanting, the plant height, tiller number, fresh weight, etc. of L. chuanxiong in mountainous areas were significantly higher than those in dam areas. At the same time, significant changes had taken place in the endophytic bacteria in reproductive material stem nodes (Lingzi, abbreviated as LZ). The diversity and abundance of bacteria in dam area LZ (YL) are significantly higher than those in mountainous area LZ (ML). The relative abundance of bacteria such as Xanthobacteraceae, Micromonosporaceae, Beijerinkiaceae, Rhodanobacteria, in ML is significantly higher than YL, mainly classified in Proteobateria and Actinobacteriota. In addition, the abundance advantage of Actinobacteriota still exists in MY (underground mature rhizomes obtained by ML). Meanwhile, the bacterial community was different in different area of transplanting. The diversity of bacterial communities in dam soil (YLS) is significantly higher than that in mountain soil (MLS). MLS had more Acidobacteriota than YLS. Comparative analysis showed that 74.38% of bacteria in ML are …
bibliographic citation: Xiao et al. (2023) Recombination of endophytic bacteria in asexual plant Ligusticum chuanxiong Hort. caused by transplanting. PeerJ 11:e15579 https://doi.org/10.7717/peerj.15579
date submitted: 2023-02-24
date accepted: 2023-05-25
issued: 2023-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Wanting
author list: Agent
  family name: Zhang
  given name: Zhanling
author list: Agent
  family name: Wang
  given name: Hai
author list: Agent
  family name: Han
  given name: Guiqi
author list: Agent
  family name: Yan
  given name: Zhu-Yun
author list: Agent
  family name: He
  given name: Dongmei
doi: 10.7717/peerj.15579
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-26
copyright: ©2023 Xiao et al.
attribution name: Xiao et al.

Dapagliflozin-affected endothelial dysfunction and altered gut microbiota in mice with heart failure
type: item
type: AcademicArticle
description: Aim To investigate the potential microbiome profile of a mouse model with heart failure (HF) during dapagliflozin treatment. Method An HF model was constructed in 8-week-old male mice, and cardiac tissues were analyzed using histological staining. Hemodynamic indexes were measured, and fecal samples were collected for 16S rDNA sequencing. Chao1, Shannon, and Simpson were used for α-diversity analysis. b-Diversity analysis was conducted using principal coordinate analysis (PCoA) and non-metric multidimensional scaling (NMDS) based on the Bray–Curtis distance. Linear discriminant analysis coupled with effect size measurements (LEfSe) was used to identify signature gut microbiota, and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was used to predict the function of altered gut microbiota. Result Dapagliflozin treatment reduced inflammation, infarction area, and cardiac fibrosis in HF mice. It also increased endothelial-dependent dilation and inflammation in mice with HF. Dapagliflozin decreased the ratio of Firmicutes/Bacteroidetes, which was increased in HF mice. There was no significant statistical difference in α-diversity among the control, HF, and HF+dapagliflozin groups. Desulfovibrio, AF12, and Paraprevotella were enriched in HF+dapagliflozin, while Rikenella and Mucispirillum were enriched in HF based on LEfSe. KEGG analysis revealed that altered gut microbiota was associated with fermentation, amino acid biosynthesis, nucleoside and nucleotide biosynthesis/degradation, fatty acid and lipid biosynthesis, carbohydrate biosynthesis/degradation, and cofactor/prosthetic group/electron carrier/vitamin biosynthesis. Conclusion Understanding the microbiome profile helps elucidate the mechanism of dapagliflozin for HF. The signature genera identified in this study could be used as a convenient method to distinguish between HF patients and healthy individuals.
format: application/pdf
format: text/html
creator: Nandi Bao
creator: Xiaoli Liu
creator: Xiaoling Zhong
creator: Shuangshuang Jia
creator: Ning Hua
creator: Li Zhang
creator: Guoxin Mo
subject: Molecular Biology
subject: Cardiology
description: doi:10.7717/peerj.15589
publisher: PeerJ Inc.
rights: © 2023 Bao et al.
abstract: Aim To investigate the potential microbiome profile of a mouse model with heart failure (HF) during dapagliflozin treatment. Method An HF model was constructed in 8-week-old male mice, and cardiac tissues were analyzed using histological staining. Hemodynamic indexes were measured, and fecal samples were collected for 16S rDNA sequencing. Chao1, Shannon, and Simpson were used for α-diversity analysis. b-Diversity analysis was conducted using principal coordinate analysis (PCoA) and non-metric multidimensional scaling (NMDS) based on the Bray–Curtis distance. Linear discriminant analysis coupled with effect size measurements (LEfSe) was used to identify signature gut microbiota, and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was used to predict the function of altered gut microbiota. Result Dapagliflozin treatment reduced inflammation, infarction area, and cardiac fibrosis in HF mice. It also increased endothelial-dependent dilation and inflammation in mice with HF. Dapagliflozin decreased the ratio of Firmicutes/Bacteroidetes, which was increased in HF mice. There was no significant statistical difference in α-diversity among the control, HF, and HF+dapagliflozin groups. Desulfovibrio, AF12, and Paraprevotella were enriched in HF+dapagliflozin, while Rikenella and Mucispirillum were enriched in HF based on LEfSe. KEGG analysis revealed that altered gut microbiota was associated with fermentation, amino acid biosynthesis, nucleoside and nucleotide biosynthesis/degradation, fatty acid and lipid biosynthesis, carbohydrate biosynthesis/degradation, and cofactor/prosthetic group/electron carrier/vitamin biosynthesis. Conclusion Understanding the microbiome profile helps elucidate the mechanism of dapagliflozin for HF. The signature genera identified in this study could be used as a convenient method to distinguish between HF patients and healthy individuals.
bibliographic citation: Bao et al. (2023) Dapagliflozin-affected endothelial dysfunction and altered gut microbiota in mice with heart failure. PeerJ 11:e15589 https://doi.org/10.7717/peerj.15589
date submitted: 2023-02-20
date accepted: 2023-05-26
issued: 2023-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bao
  given name: Nandi
author list: Agent
  family name: Liu
  given name: Xiaoli
author list: Agent
  family name: Zhong
  given name: Xiaoling
author list: Agent
  family name: Jia
  given name: Shuangshuang
author list: Agent
  family name: Hua
  given name: Ning
author list: Agent
  family name: Zhang
  given name: Li
author list: Agent
  family name: Mo
  given name: Guoxin
doi: 10.7717/peerj.15589
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-26
copyright: © 2023 Bao et al.
attribution name: Bao et al.

Utilization of hepatitis B surface antigen-positive donors in liver transplantation for recipients with hepatocellular carcinoma: a retrospective and propensity score matching analysis
type: item
type: AcademicArticle
description: Introduction The use of extended criteria donor (ECD) grafts such as donor with infection of hepatitis B virus (HBV) is a potential solution for organ shortage. In this study, we aimed to evaluate the safety and long-term survival of utilization of hepatitis B surface antigen-positive (HBsAg+) donor livers in HCC patients using propensity score matching (PSM) analysis. Methods Forty-eight donors with HBsAg-positive and 279 donors with HBsAg-negative were transplanted and enrolled in this study. PSM analysis were used to eliminate selection bias. Perioperative data and survival were collected and analyzed. Results PSM generated 44 patient pairs. When comparing intra- and post-operative data, no significant difference was found between groups (P > 0.05). Patients with a HBsAg-positive donor had significantly worse progression-free survival (1-year: 65.9% vs. 90.9%; 3-year: 18.1% vs. 70.4%, P = 0.0060) and overall survival (1-year: 84.1% and 95.4%; 3-year: 27.2% vs. 79.5%, P = 0.0039). In multivariate analysis, donor HBsAg-positivity was an independent risk factor for survival and occurrence (P = 0.005 and 0.025, respectively). Conclusion In conclusion, with adequate antiviral prophylaxis and treatment, utilization of HBsAg positive liver grafts did not increase the incidence of early-stage complications. However, patient with an HBsAg-positive graft had poorer progression-free survival and overall survival.
format: application/pdf
format: text/html
creator: Zhitao Chen
creator: Yihao Ma
creator: Yuqi Dong
creator: Chuanbao Chen
creator: Hanyu Wang
creator: Tielong Wang
creator: Jia Yu
creator: Xitao Hong
creator: Maogen Chen
creator: Xiaoshun He
creator: Weiqiang Ju
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.15620
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Introduction The use of extended criteria donor (ECD) grafts such as donor with infection of hepatitis B virus (HBV) is a potential solution for organ shortage. In this study, we aimed to evaluate the safety and long-term survival of utilization of hepatitis B surface antigen-positive (HBsAg+) donor livers in HCC patients using propensity score matching (PSM) analysis. Methods Forty-eight donors with HBsAg-positive and 279 donors with HBsAg-negative were transplanted and enrolled in this study. PSM analysis were used to eliminate selection bias. Perioperative data and survival were collected and analyzed. Results PSM generated 44 patient pairs. When comparing intra- and post-operative data, no significant difference was found between groups (P > 0.05). Patients with a HBsAg-positive donor had significantly worse progression-free survival (1-year: 65.9% vs. 90.9%; 3-year: 18.1% vs. 70.4%, P = 0.0060) and overall survival (1-year: 84.1% and 95.4%; 3-year: 27.2% vs. 79.5%, P = 0.0039). In multivariate analysis, donor HBsAg-positivity was an independent risk factor for survival and occurrence (P = 0.005 and 0.025, respectively). Conclusion In conclusion, with adequate antiviral prophylaxis and treatment, utilization of HBsAg positive liver grafts did not increase the incidence of early-stage complications. However, patient with an HBsAg-positive graft had poorer progression-free survival and overall survival.
bibliographic citation: Chen et al. (2023) Utilization of hepatitis B surface antigen-positive donors in liver transplantation for recipients with hepatocellular carcinoma: a retrospective and propensity score matching analysis. PeerJ 11:e15620 https://doi.org/10.7717/peerj.15620
date submitted: 2022-11-29
date accepted: 2023-06-01
issued: 2023-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Zhitao
author list: Agent
  family name: Ma
  given name: Yihao
author list: Agent
  family name: Dong
  given name: Yuqi
author list: Agent
  family name: Chen
  given name: Chuanbao
author list: Agent
  family name: Wang
  given name: Hanyu
author list: Agent
  family name: Wang
  given name: Tielong
author list: Agent
  family name: Yu
  given name: Jia
author list: Agent
  family name: Hong
  given name: Xitao
author list: Agent
  family name: Chen
  given name: Maogen
author list: Agent
  family name: He
  given name: Xiaoshun
author list: Agent
  family name: Ju
  given name: Weiqiang
doi: 10.7717/peerj.15620
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-26
copyright: ©2023 Chen et al.
attribution name: Chen et al.

Unique antimicrobial activity in honey from the Australian honeypot ant (Camponotus inflatus)
type: item
type: AcademicArticle
description: Honey produced by the Australian honeypot ant (Camponotus inflatus) is valued nutritionally and medicinally by Indigenous peoples, but its antimicrobial activity has never been formally studied. Here, we determine the activity of honeypot ant honey (HPAH) against a panel of bacterial and fungal pathogens, investigate its chemical properties, and profile the bacterial and fungal microbiome of the honeypot ant for the first time. We found HPAH to have strong total activity against Staphylococcus aureus but not against other bacteria, and strong non-peroxide activity against Cryptococcus and Aspergillus sp. When compared with therapeutic-grade jarrah and manuka honey produced by honey bees, we found HPAH to have a markedly different antimicrobial activity and chemical properties, suggesting HPAH has a unique mode of antimicrobial action. We found the bacterial microbiome of honeypot ants to be dominated by the known endosymbiont genus Candidatus Blochmannia (99.75%), and the fungal microbiome to be dominated by the plant-associated genus Neocelosporium (92.77%). This study demonstrates that HPAH has unique antimicrobial characteristics that validate its therapeutic use by Indigenous peoples and may provide a lead for the discovery of novel antimicrobial compounds.
format: application/pdf
format: text/html
creator: Andrew Z. Dong
creator: Nural Cokcetin
creator: Dee A. Carter
creator: Kenya E. Fernandes
subject: Entomology
subject: Food Science and Technology
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.15645
publisher: PeerJ Inc.
rights: © 2023 Dong et al.
abstract: Honey produced by the Australian honeypot ant (Camponotus inflatus) is valued nutritionally and medicinally by Indigenous peoples, but its antimicrobial activity has never been formally studied. Here, we determine the activity of honeypot ant honey (HPAH) against a panel of bacterial and fungal pathogens, investigate its chemical properties, and profile the bacterial and fungal microbiome of the honeypot ant for the first time. We found HPAH to have strong total activity against Staphylococcus aureus but not against other bacteria, and strong non-peroxide activity against Cryptococcus and Aspergillus sp. When compared with therapeutic-grade jarrah and manuka honey produced by honey bees, we found HPAH to have a markedly different antimicrobial activity and chemical properties, suggesting HPAH has a unique mode of antimicrobial action. We found the bacterial microbiome of honeypot ants to be dominated by the known endosymbiont genus Candidatus Blochmannia (99.75%), and the fungal microbiome to be dominated by the plant-associated genus Neocelosporium (92.77%). This study demonstrates that HPAH has unique antimicrobial characteristics that validate its therapeutic use by Indigenous peoples and may provide a lead for the discovery of novel antimicrobial compounds.
bibliographic citation: Dong et al. (2023) Unique antimicrobial activity in honey from the Australian honeypot ant (Camponotus inflatus). PeerJ 11:e15645 https://doi.org/10.7717/peerj.15645
date submitted: 2023-04-26
date accepted: 2023-06-05
issued: 2023-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Andrew Z.
author list: Agent
  family name: Cokcetin
  given name: Nural
author list: Agent
  family name: Carter
  given name: Dee A.
author list: Agent
  family name: Fernandes
  given name: Kenya E.
doi: 10.7717/peerj.15645
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-26
copyright: © 2023 Dong et al.
attribution name: Dong et al.

Effect of finger rest positions on upper limb muscle activity during pre-clinical procedures
type: item
type: AcademicArticle
description: Objectives This study aimed to observe the effect of different finger rest positions on the muscular activity of the hand, forearm, arm, shoulder, thorax, and neck, as well as on the angular deviation from the neutral position of the neck, trunk, upper arm, and forearm on the working side during pre-clinical procedures. Methods An experimental laboratory study was performed. Response variables were muscle activation of the abductor pollicis, brachioradialis, biceps brachii, deltoid, pectoralis major, and right sternocleidomastoid muscles and angular deviation from the neutral position of the neck, trunk, arm, and forearm during simulated clinical procedures. Independent variable was finger-rest position during cavity preparation (no finger rest, usual rest, and ergonomic rest). Class I cavity preparations (N = 120) were performed on artificial first molars (16, 26, 36, and 46) (N = 120). Muscular activation was assessed by surface electromyography and angular deviations using Software for Postural Assessment (SAPO) version 0.69. One-way analysis of variance and Tukey’s or Games-Howell’s post-hoc tests were performed (α = 0.05). Results For the sternocleidomastoid muscle, there was no statistically significant difference between the different rest positions. For the deltoid muscle, work with no finger rest resulted in greater muscle activation (p < 0.001) during work on tooth 36. Regarding the pectoralis major and right brachioradialis muscles, we observed that for both teeth 16 and 26, working with ergonomic rest showed less muscle activation. Muscle activation of the right biceps brachii was higher for work with no rest in both the upper and lower arches, differing significantly only from the usual rest in tooth 16 (p < 0.001), usual rest and ergonomic rest in teeth 26 and 46 (p < 0.001), and only ergonomic rest in tooth 36 (p = 0.044). In the right abductor pollicis muscle, work with ergonomic rest resulted in less muscle activation for cavity preparation in teeth…
format: application/pdf
format: text/html
creator: Júlia Margato Pazos
creator: Mariana Segnini Tiberti
creator: Simone Cecilio Hallak Regalo
creator: Lívia Nordi Dovigo
creator: Patricia Petromilli Nordi Sasso Garcia
subject: Dentistry
subject: Science and Medical Education
subject: Environmental Health
description: doi:10.7717/peerj.15663
publisher: PeerJ Inc.
rights: © 2023 Margato Pazos et al.
abstract: Objectives This study aimed to observe the effect of different finger rest positions on the muscular activity of the hand, forearm, arm, shoulder, thorax, and neck, as well as on the angular deviation from the neutral position of the neck, trunk, upper arm, and forearm on the working side during pre-clinical procedures. Methods An experimental laboratory study was performed. Response variables were muscle activation of the abductor pollicis, brachioradialis, biceps brachii, deltoid, pectoralis major, and right sternocleidomastoid muscles and angular deviation from the neutral position of the neck, trunk, arm, and forearm during simulated clinical procedures. Independent variable was finger-rest position during cavity preparation (no finger rest, usual rest, and ergonomic rest). Class I cavity preparations (N = 120) were performed on artificial first molars (16, 26, 36, and 46) (N = 120). Muscular activation was assessed by surface electromyography and angular deviations using Software for Postural Assessment (SAPO) version 0.69. One-way analysis of variance and Tukey’s or Games-Howell’s post-hoc tests were performed (α = 0.05). Results For the sternocleidomastoid muscle, there was no statistically significant difference between the different rest positions. For the deltoid muscle, work with no finger rest resulted in greater muscle activation (p < 0.001) during work on tooth 36. Regarding the pectoralis major and right brachioradialis muscles, we observed that for both teeth 16 and 26, working with ergonomic rest showed less muscle activation. Muscle activation of the right biceps brachii was higher for work with no rest in both the upper and lower arches, differing significantly only from the usual rest in tooth 16 (p < 0.001), usual rest and ergonomic rest in teeth 26 and 46 (p < 0.001), and only ergonomic rest in tooth 36 (p = 0.044). In the right abductor pollicis muscle, work with ergonomic rest resulted in less muscle activation for cavity preparation in teeth…
bibliographic citation: Margato Pazos et al. (2023) Effect of finger rest positions on upper limb muscle activity during pre-clinical procedures. PeerJ 11:e15663 https://doi.org/10.7717/peerj.15663
date submitted: 2022-12-21
date accepted: 2023-06-07
issued: 2023-07-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Margato Pazos
  given name: Júlia
author list: Agent
  family name: Segnini Tiberti
  given name: Mariana
author list: Agent
  family name: Cecilio Hallak Regalo
  given name: Simone
author list: Agent
  family name: Nordi Dovigo
  given name: Lívia
author list: Agent
  family name: Garcia
  given name: Patricia Petromilli Nordi Sasso
doi: 10.7717/peerj.15663
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-26
copyright: © 2023 Margato Pazos et al.
attribution name: Margato Pazos et al.

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