PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Automated mapping of Portulacaria afra canopies for restoration monitoring with convolutional neural networks and heterogeneous unmanned aerial vehicle imagery
items: Coral reef fish assemblages exhibit signs of depletion in two protected areas from the eastern of Los Canarreos archipelago (Cuba, Caribbean Sea)
items: Postpartum depression and health-related quality of life: a Saudi Arabian perspective
items: Ribovirus classification by a polymerase barcode sequence
items: Planting Cyperus esculentus augments soil microbial biomass and diversity, but not enzymatic activities
items: Revision of the Late Triassic metoposaurid “Metoposaurus” bakeri (Amphibia: Temnospondyli) from Texas, USA and a phylogenetic analysis of the Metoposauridae
items: Prevalence and associated risk factors of avian influenza A virus subtypes H5N1 and H9N2 in LBMs of East Java province, Indonesia: a cross-sectional study
items: Telomerase activity, relative telomere length, and longevity in alfalfa (Medicago sativa L.)
items: Glycyrrhizic acid Poly(D,L-lactide-co-glycolide) nanoparticles: anti-aging cosmeceutical formulation for topical applications
items: Body distribution of impetigo and association with host and pathogen factors

Automated mapping of Portulacaria afra canopies for restoration monitoring with convolutional neural networks and heterogeneous unmanned aerial vehicle imagery
type: item
type: AcademicArticle
description: Ecosystem restoration and reforestation often operate at large scales, whereas monitoring practices are usually limited to spatially restricted field measurements that are (i) time- and labour-intensive, and (ii) unable to accurately quantify restoration success over hundreds to thousands of hectares. Recent advances in remote sensing technologies paired with deep learning algorithms provide an unprecedented opportunity for monitoring changes in vegetation cover at spatial and temporal scales. Such data can feed directly into adaptive management practices and provide insights into restoration and regeneration dynamics. Here, we demonstrate that convolutional neural network (CNN) segmentation algorithms can accurately classify the canopy cover of Portulacaria afra Jacq. in imagery acquired using different models of unoccupied aerial vehicles (UAVs) and under variable light intensities. Portulacaria afra is the target species for the restoration of Albany Subtropical Thicket vegetation, endemic to South Africa, where canopy cover is challenging to measure due to the dense, tangled structure of this vegetation. The automated classification strategy presented here is widely transferable to restoration monitoring as its application does not require any knowledge of the CNN model or specialist training, and can be applied to imagery generated by a range of UAV models. This will reduce the sampling effort required to track restoration trajectories in space and time, contributing to more effective management of restoration sites, and promoting collaboration between scientists, practitioners and landowners.
format: application/pdf
format: text/html
creator: Nicholas C. Galuszynski
creator: Robbert Duker
creator: Alastair J. Potts
creator: Teja Kattenborn
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Natural Resource Management
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.14219
publisher: PeerJ Inc.
rights: © 2022 Galuszynski et al.
abstract: Ecosystem restoration and reforestation often operate at large scales, whereas monitoring practices are usually limited to spatially restricted field measurements that are (i) time- and labour-intensive, and (ii) unable to accurately quantify restoration success over hundreds to thousands of hectares. Recent advances in remote sensing technologies paired with deep learning algorithms provide an unprecedented opportunity for monitoring changes in vegetation cover at spatial and temporal scales. Such data can feed directly into adaptive management practices and provide insights into restoration and regeneration dynamics. Here, we demonstrate that convolutional neural network (CNN) segmentation algorithms can accurately classify the canopy cover of Portulacaria afra Jacq. in imagery acquired using different models of unoccupied aerial vehicles (UAVs) and under variable light intensities. Portulacaria afra is the target species for the restoration of Albany Subtropical Thicket vegetation, endemic to South Africa, where canopy cover is challenging to measure due to the dense, tangled structure of this vegetation. The automated classification strategy presented here is widely transferable to restoration monitoring as its application does not require any knowledge of the CNN model or specialist training, and can be applied to imagery generated by a range of UAV models. This will reduce the sampling effort required to track restoration trajectories in space and time, contributing to more effective management of restoration sites, and promoting collaboration between scientists, practitioners and landowners.
bibliographic citation: Galuszynski et al. (2022) Automated mapping of Portulacaria afra canopies for restoration monitoring with convolutional neural networks and heterogeneous unmanned aerial vehicle imagery. PeerJ 10:e14219 https://doi.org/10.7717/peerj.14219
date submitted: 2022-06-03
date accepted: 2022-09-20
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Galuszynski
  given name: Nicholas C.
author list: Agent
  family name: Duker
  given name: Robbert
author list: Agent
  family name: Potts
  given name: Alastair J.
author list: Agent
  family name: Kattenborn
  given name: Teja
doi: 10.7717/peerj.14219
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: © 2022 Galuszynski et al.
attribution name: Galuszynski et al.

Coral reef fish assemblages exhibit signs of depletion in two protected areas from the eastern of Los Canarreos archipelago (Cuba, Caribbean Sea)
type: item
type: AcademicArticle
description: Understanding the impact of marine protected areas on the distribution and composition of fishes is key to the protection and management of coral reef ecosystems, and especially for fish-based activities such as SCUBA diving and recreational fishing. The aim of this research is to compare the ichthyofauna structure in three areas in the eastern part of Los Canarreos archipelago in Cuba with different management schemes: Cayo Campos-Cayo Rosario Fauna Refuge (CCCR), Cayo Largo Ecological Reserve (CL) and non-protected area (nMPA), and considering habitat differences and depth variation. A total of 131 video transects were conducted using diver operated stereo-video (stereo-DOV) in November, 2015 in backreef and forereef along the CCCR, CL and the adjacent nMPA. We recorded 84 species and 27 functional groups suggesting high complementarity of functions. Several multispecies schools were observed along surveys, which explain the biomass peaks in some sites, mainly for Lutjanidae, Haemulidae and Carangidae. A concerning issue was the bare representation of critical functional groups and threatened species. The effect of sites nested within habitats was significant and the most important driver structuring fish assemblages, while MPA condition was not evident. Favorable habitat features (habitat heterogeneity and surrounding coastal ecosystems) are likely enhancing fish assemblages and counteracting the effects of pouching derived from insufficient management. We recommend immediate actions within a strategy of precautionary management including, but not limited to, the appointment of staff for the administration of CL, frequent monitoring and effective enforcement.
format: application/pdf
format: text/html
creator: Zenaida María Navarro-Martínez
creator: Maickel Armenteros
creator: Leonardo Espinosa
creator: Patricia González-Díaz
creator: Amy Apprill
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.14229
publisher: PeerJ Inc.
rights: © 2022 Navarro-Martínez et al.
abstract: Understanding the impact of marine protected areas on the distribution and composition of fishes is key to the protection and management of coral reef ecosystems, and especially for fish-based activities such as SCUBA diving and recreational fishing. The aim of this research is to compare the ichthyofauna structure in three areas in the eastern part of Los Canarreos archipelago in Cuba with different management schemes: Cayo Campos-Cayo Rosario Fauna Refuge (CCCR), Cayo Largo Ecological Reserve (CL) and non-protected area (nMPA), and considering habitat differences and depth variation. A total of 131 video transects were conducted using diver operated stereo-video (stereo-DOV) in November, 2015 in backreef and forereef along the CCCR, CL and the adjacent nMPA. We recorded 84 species and 27 functional groups suggesting high complementarity of functions. Several multispecies schools were observed along surveys, which explain the biomass peaks in some sites, mainly for Lutjanidae, Haemulidae and Carangidae. A concerning issue was the bare representation of critical functional groups and threatened species. The effect of sites nested within habitats was significant and the most important driver structuring fish assemblages, while MPA condition was not evident. Favorable habitat features (habitat heterogeneity and surrounding coastal ecosystems) are likely enhancing fish assemblages and counteracting the effects of pouching derived from insufficient management. We recommend immediate actions within a strategy of precautionary management including, but not limited to, the appointment of staff for the administration of CL, frequent monitoring and effective enforcement.
bibliographic citation: Navarro-Martínez et al. (2022) Coral reef fish assemblages exhibit signs of depletion in two protected areas from the eastern of Los Canarreos archipelago (Cuba, Caribbean Sea). PeerJ 10:e14229 https://doi.org/10.7717/peerj.14229
date submitted: 2022-07-14
date accepted: 2022-09-22
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Navarro-Martínez
  given name: Zenaida María
author list: Agent
  family name: Armenteros
  given name: Maickel
author list: Agent
  family name: Espinosa
  given name: Leonardo
author list: Agent
  family name: González-Díaz
  given name: Patricia
author list: Agent
  family name: Apprill
  given name: Amy
doi: 10.7717/peerj.14229
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: © 2022 Navarro-Martínez et al.
attribution name: Navarro-Martínez et al.

Postpartum depression and health-related quality of life: a Saudi Arabian perspective
type: item
type: AcademicArticle
description: Background and Objectives The mental and physical functioning of an individual is partly determined by their health-related quality of life (HRQOL), which is a multifaceted component. Women who have recently given birth must have a good quality of life to provide proper care and development for their infant. The purpose of this study was to assess the relationship between postpartum depression (PPD) and HRQOL in Saudi Arabian women and to identify potential risk factors that could influence them. Methods This study comprised 253 mothers aged 1–24 weeks postpartum from several health centers in Saudi Arabia, recruited by random purposive sampling. The study’s questionnaire featured three sections: the first section had demographic information; the second and third sections contained the Edinburgh Postnatal Depression Scale (EPDS) scale and the HRQOL scale (SF-12), respectively. Data were analyzed using descriptive statistics, chi square analyses, independent samples t-tests and binary logistic regression analysis using IBM SPSS 25. Results Results of current study indicate that 59.68% of the patients exhibited probable post-partum depression symptoms. Participants who were depressed had significantly lower mental component (MCS) and physical component scores than participants who were in good health. When compared to non-smokers, smokers have a 21-fold higher risk of developing depression. Similar to this, mothers who worked had a 3.98 times higher risk of depression, and patients with a history of depression had a 3.6 times higher chance of getting PPD. The probability of developing PPD was also significantly higher in those who lived outside the Riyadh region, had given birth more than twice before this time, and had experienced undesired pregnancies. Conclusion Our study demonstrated an inverse correlation between postpartum depression and health-related quality of life scores. Treatment for depression, particularly among mothers, is crucial for improving their qu…
format: application/pdf
format: text/html
creator: Mansour Almuqbil
creator: Nora Kraidiye
creator: Hatoun Alshmaimri
creator: Amerah Ali kaabi
creator: Atheer Almutiri
creator: Abeer Alanazi
creator: Ayat Hjeij
creator: Abdulhakeem S. Alamri
creator: Wala F. Alsanie
creator: Majid Alhomrani
creator: Syed Mohammed Basheeruddin Asdaq
subject: Health Policy
subject: Psychiatry and Psychology
subject: Women’s Health
subject: Mental Health
description: doi:10.7717/peerj.14240
publisher: PeerJ Inc.
rights: © 2022 Almuqbil et al.
abstract: Background and Objectives The mental and physical functioning of an individual is partly determined by their health-related quality of life (HRQOL), which is a multifaceted component. Women who have recently given birth must have a good quality of life to provide proper care and development for their infant. The purpose of this study was to assess the relationship between postpartum depression (PPD) and HRQOL in Saudi Arabian women and to identify potential risk factors that could influence them. Methods This study comprised 253 mothers aged 1–24 weeks postpartum from several health centers in Saudi Arabia, recruited by random purposive sampling. The study’s questionnaire featured three sections: the first section had demographic information; the second and third sections contained the Edinburgh Postnatal Depression Scale (EPDS) scale and the HRQOL scale (SF-12), respectively. Data were analyzed using descriptive statistics, chi square analyses, independent samples t-tests and binary logistic regression analysis using IBM SPSS 25. Results Results of current study indicate that 59.68% of the patients exhibited probable post-partum depression symptoms. Participants who were depressed had significantly lower mental component (MCS) and physical component scores than participants who were in good health. When compared to non-smokers, smokers have a 21-fold higher risk of developing depression. Similar to this, mothers who worked had a 3.98 times higher risk of depression, and patients with a history of depression had a 3.6 times higher chance of getting PPD. The probability of developing PPD was also significantly higher in those who lived outside the Riyadh region, had given birth more than twice before this time, and had experienced undesired pregnancies. Conclusion Our study demonstrated an inverse correlation between postpartum depression and health-related quality of life scores. Treatment for depression, particularly among mothers, is crucial for improving their qu…
bibliographic citation: Almuqbil et al. (2022) Postpartum depression and health-related quality of life: a Saudi Arabian perspective. PeerJ 10:e14240 https://doi.org/10.7717/peerj.14240
date submitted: 2022-02-14
date accepted: 2022-09-23
issued: 2022-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Almuqbil
  given name: Mansour
author list: Agent
  family name: Kraidiye
  given name: Nora
author list: Agent
  family name: Alshmaimri
  given name: Hatoun
author list: Agent
  family name: Ali kaabi
  given name: Amerah
author list: Agent
  family name: Almutiri
  given name: Atheer
author list: Agent
  family name: Alanazi
  given name: Abeer
author list: Agent
  family name: Hjeij
  given name: Ayat
author list: Agent
  family name: Alamri
  given name: Abdulhakeem S.
author list: Agent
  family name: Alsanie
  given name: Wala F.
author list: Agent
  family name: Alhomrani
  given name: Majid
author list: Agent
  family name: Asdaq
  given name: Syed Mohammed Basheeruddin
doi: 10.7717/peerj.14240
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-14
copyright: © 2022 Almuqbil et al.
attribution name: Almuqbil et al.

Ribovirus classification by a polymerase barcode sequence
type: item
type: AcademicArticle
description: RNA viruses encoding a polymerase gene (riboviruses) dominate the known eukaryotic virome. High-throughput sequencing is revealing a wealth of new riboviruses known only from sequence, precluding classification by traditional taxonomic methods. Sequence classification is often based on polymerase sequences, but standardised methods to support this approach are currently lacking. To address this need, we describe the polymerase palmprint, a segment of the palm sub-domain robustly delineated by well-conserved catalytic motifs. We present an algorithm, Palmscan, which identifies palmprints in nucleotide and amino acid sequences; PALMdb, a collection of palmprints derived from public sequence databases; and palmID, a public website implementing palmprint identification, search, and annotation. Together, these methods demonstrate a proof-of-concept workflow for high-throughput characterisation of RNA viruses, paving the path for the continued rapid growth in RNA virus discovery anticipated in the coming decade.
format: application/pdf
format: text/html
creator: Artem Babaian
creator: Robert Edgar
subject: Bioinformatics
subject: Taxonomy
subject: Virology
description: doi:10.7717/peerj.14055
publisher: PeerJ Inc.
rights: © 2022 Babaian and Edgar
abstract: RNA viruses encoding a polymerase gene (riboviruses) dominate the known eukaryotic virome. High-throughput sequencing is revealing a wealth of new riboviruses known only from sequence, precluding classification by traditional taxonomic methods. Sequence classification is often based on polymerase sequences, but standardised methods to support this approach are currently lacking. To address this need, we describe the polymerase palmprint, a segment of the palm sub-domain robustly delineated by well-conserved catalytic motifs. We present an algorithm, Palmscan, which identifies palmprints in nucleotide and amino acid sequences; PALMdb, a collection of palmprints derived from public sequence databases; and palmID, a public website implementing palmprint identification, search, and annotation. Together, these methods demonstrate a proof-of-concept workflow for high-throughput characterisation of RNA viruses, paving the path for the continued rapid growth in RNA virus discovery anticipated in the coming decade.
bibliographic citation: Babaian et al. (2022) Ribovirus classification by a polymerase barcode sequence. PeerJ 10:e14055 https://doi.org/10.7717/peerj.14055
date submitted: 2022-04-26
date accepted: 2022-08-24
issued: 2022-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Babaian
  given name: Artem
author list: Agent
  family name: Edgar
  given name: Robert
doi: 10.7717/peerj.14055
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-13
copyright: © 2022 Babaian and Edgar
attribution name: Babaian and Edgar

Planting Cyperus esculentus augments soil microbial biomass and diversity, but not enzymatic activities
type: item
type: AcademicArticle
description: The planting of Cyperus esculentus, a member of the grass family Cyperaceae which includes nut sedge weeds, is being increasingly promoted in northern China’s semi-arid and arid regions. Yet the effects of planting C. esculentus upon soil quality and soil microbial characteristics of sandy land remain unclear. This study examined the short-term (1 year) impact of this grass species on soil microbial biomass indices, enzymatic activities, and microbiome characteristics in the Horqin Sandy Land area of China. The results show that planting C. esculentus could increase microbial biomass in the form of carbon (MBC), nitrogen (MBN), and phosphorus (MBP), but it negligibly influenced the enzymatic activities of soil β-1,4-glucosidase (BG), cellobiohydrolase (CBH), leucine aminopeptidase (LAP), and β-1,4-N-acetaminoglycosidase (NAG). Over 1 year, we found that planting C. esculentus significantly increased the soil bacterial richness and diversity of sandy land, yet also altered community composition of soil bacteria and eukaryotes in way that could promote their homogenization. In this respect, the relative abundances of Acidobacteria and Proteobacteria significantly decreased and increased, respectively; hence, they may be considered for use as important indicators of soil nutrient-rich conditions. Overall, the results could be explained by greater soil organic carbon (SOC) and total nitrogen (TN), mainly derived from cumulative plant litter input to soils, which then increased the sandy soil’s C:N ratio. Future research should focus on exploring the long-term effects of planting C. esculentus on soil quality and soil microbial characteristics of sandy lands in China and abroad.
format: application/pdf
format: text/html
creator: Yulong Duan
creator: Wei Ren
creator: Jianhua Zhao
creator: Chun Luo
creator: Yang Liu
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14199
publisher: PeerJ Inc.
rights: © 2022 Duan et al.
abstract: The planting of Cyperus esculentus, a member of the grass family Cyperaceae which includes nut sedge weeds, is being increasingly promoted in northern China’s semi-arid and arid regions. Yet the effects of planting C. esculentus upon soil quality and soil microbial characteristics of sandy land remain unclear. This study examined the short-term (1 year) impact of this grass species on soil microbial biomass indices, enzymatic activities, and microbiome characteristics in the Horqin Sandy Land area of China. The results show that planting C. esculentus could increase microbial biomass in the form of carbon (MBC), nitrogen (MBN), and phosphorus (MBP), but it negligibly influenced the enzymatic activities of soil β-1,4-glucosidase (BG), cellobiohydrolase (CBH), leucine aminopeptidase (LAP), and β-1,4-N-acetaminoglycosidase (NAG). Over 1 year, we found that planting C. esculentus significantly increased the soil bacterial richness and diversity of sandy land, yet also altered community composition of soil bacteria and eukaryotes in way that could promote their homogenization. In this respect, the relative abundances of Acidobacteria and Proteobacteria significantly decreased and increased, respectively; hence, they may be considered for use as important indicators of soil nutrient-rich conditions. Overall, the results could be explained by greater soil organic carbon (SOC) and total nitrogen (TN), mainly derived from cumulative plant litter input to soils, which then increased the sandy soil’s C:N ratio. Future research should focus on exploring the long-term effects of planting C. esculentus on soil quality and soil microbial characteristics of sandy lands in China and abroad.
bibliographic citation: Duan et al. (2022) Planting Cyperus esculentus augments soil microbial biomass and diversity, but not enzymatic activities. PeerJ 10:e14199 https://doi.org/10.7717/peerj.14199
date submitted: 2022-05-24
date accepted: 2022-09-16
issued: 2022-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Duan
  given name: Yulong
author list: Agent
  family name: Ren
  given name: Wei
author list: Agent
  family name: Zhao
  given name: Jianhua
author list: Agent
  family name: Luo
  given name: Chun
author list: Agent
  family name: Liu
  given name: Yang
doi: 10.7717/peerj.14199
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-13
copyright: ©2022 Duan et al.
attribution name: Duan et al.

Revision of the Late Triassic metoposaurid “Metoposaurus” bakeri (Amphibia: Temnospondyli) from Texas, USA and a phylogenetic analysis of the Metoposauridae
type: item
type: AcademicArticle
description: Metoposaurids are a clade of large-bodied temnospondyls commonly found in non-marine Late Triassic deposits across northern Pangea. Three taxa are known from North America: Anaschisma browni, Apachesaurus gregorii, and “Metoposaurus” bakeri. While the osteology of most metoposaurids has been recently revised, that of a few taxa, including “Metoposaurus” bakeri remains poorly characterized. This taxon was formally described in 1931 as “Buettneria bakeri,” and its taxonomy has remained in flux ever since then. “Metoposaurus” bakeri is the earliest appearing metoposaurid in North America (Carnian of Texas), and Metoposaurus has frequently been utilized as an index taxon of the Otischalkian estimated holochron (‘land vertebrate faunachron’) and for biostratigraphic correlations with other geographic regions. The taxonomy of this species is therefore relevant for both taxonomic experts and biostratigraphers. Here we redescribe all material from the type locality of “M.” bakeri, the Elkins Place bone bed, and perform a phylogenetic analysis using a revised matrix assembled from several previous studies. Anatomical comparisons and phylogenetic analyses do not support placement in either Metoposaurus, a taxon otherwise only found in Europe, or Anaschisma, the only other large-bodied taxon from North America. Therefore, we erect a new genus, Buettnererpeton gen. nov., to accommodate this species. Metoposaurus is consequently absent from North America, and this genus cannot be used in global biostratigraphy. Phylogenetic analyses provide evidence that the phylogeny of the Metoposauridae remains extremely labile, with drastic differences in topological resolution and structure being linked to just a handful of characters and scores. Metoposaurids’ morphological conservatism and the increased recognition of intraspecific variation thus continue to be major confounds to elucidating the evolutionary history of this clade.
format: application/pdf
format: text/html
creator: Bryan M. Gee
creator: Aaron M. Kufner
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.14065
publisher: PeerJ Inc.
rights: © 2022 Gee and Kufner
abstract: Metoposaurids are a clade of large-bodied temnospondyls commonly found in non-marine Late Triassic deposits across northern Pangea. Three taxa are known from North America: Anaschisma browni, Apachesaurus gregorii, and “Metoposaurus” bakeri. While the osteology of most metoposaurids has been recently revised, that of a few taxa, including “Metoposaurus” bakeri remains poorly characterized. This taxon was formally described in 1931 as “Buettneria bakeri,” and its taxonomy has remained in flux ever since then. “Metoposaurus” bakeri is the earliest appearing metoposaurid in North America (Carnian of Texas), and Metoposaurus has frequently been utilized as an index taxon of the Otischalkian estimated holochron (‘land vertebrate faunachron’) and for biostratigraphic correlations with other geographic regions. The taxonomy of this species is therefore relevant for both taxonomic experts and biostratigraphers. Here we redescribe all material from the type locality of “M.” bakeri, the Elkins Place bone bed, and perform a phylogenetic analysis using a revised matrix assembled from several previous studies. Anatomical comparisons and phylogenetic analyses do not support placement in either Metoposaurus, a taxon otherwise only found in Europe, or Anaschisma, the only other large-bodied taxon from North America. Therefore, we erect a new genus, Buettnererpeton gen. nov., to accommodate this species. Metoposaurus is consequently absent from North America, and this genus cannot be used in global biostratigraphy. Phylogenetic analyses provide evidence that the phylogeny of the Metoposauridae remains extremely labile, with drastic differences in topological resolution and structure being linked to just a handful of characters and scores. Metoposaurids’ morphological conservatism and the increased recognition of intraspecific variation thus continue to be major confounds to elucidating the evolutionary history of this clade.
bibliographic citation: Gee et al. (2022) Revision of the Late Triassic metoposaurid “Metoposaurus” bakeri (Amphibia: Temnospondyli) from Texas, USA and a phylogenetic analysis of the Metoposauridae. PeerJ 10:e14065 https://doi.org/10.7717/peerj.14065
date submitted: 2022-02-10
date accepted: 2022-08-26
issued: 2022-10-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gee
  given name: Bryan M.
author list: Agent
  family name: Kufner
  given name: Aaron M.
doi: 10.7717/peerj.14065
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-12
copyright: © 2022 Gee and Kufner
attribution name: Gee and Kufner

Prevalence and associated risk factors of avian influenza A virus subtypes H5N1 and H9N2 in LBMs of East Java province, Indonesia: a cross-sectional study
type: item
type: AcademicArticle
description: Background Avian influenza A virus subtypes H5N1 and H9N2 are contagious zoonotic diseases that are circulating in Indonesia and have raised increasing concern about their potential impacts on poultry and public health. A cross-sectional study was carried out to investigate the prevalence and associated risk factors of avian influenza A virus subtypes H5N1 and H9N2 among poultry in the live bird markets of four cities in East Java province, Indonesia. Methods A total of 600 tracheal and cloacal swabs (267 from backyards, 179 from broilers, and 154 from layers) from healthy birds were collected. The samples were inoculated into specific pathogenic-free embryonated eggs at 9-day-old via the allantoic cavity. qRT-PCR was used for further identification of avian influenza. Results The overall prevalence of circulating influenza A virus subtypes H5N1 and H9N2 was 3.8% (23/600, 95%CI [0.0229–0.0537]). Prevalence was higher in backyards at 5.99% (16/267) followed by broilers (2.23% (4/179)) and layers (1.68% (3/154)). The final multivariable model revealed five risk factors for H9N2 infections: presence of ducks (p = 0.003, OR = 38.2), turkeys (p = 0.017 OR = 0.032), and pheasants in the stall (p = 0.04, OR = 18.422), dry (p = 0.006) and rainy season (p < 0.001), and household birds (p = 0.002) and seven factors for H5N1 infections including: observing rodents (p = 0.036, OR = 0.005), stray dogs access (p = 0.004 OR ≤ 0.001), presence of turkeys (p = 0.03 OR = 0.007), chukars/partridges (p = 0.024 OR = 2500), and peafowls in the stalls (p = 0.0043 OR ≤ 0.001), rainy season (p = 0.001) and birds from the household sources (p = 0.002) in the live bird markets. Conclusions The findings of the current study illustrate the recurring infection and presence of both avian influenza viruses and associated risk factors in the surveyed marketplaces. Effective protective measures and mitigation strategies for risks outlined in this study could help to reduce the burden of H5N1 and H9N…
format: application/pdf
format: text/html
creator: Saifur Rehman
creator: Mustofa Helmi Effendi
creator: Aamir Shehzad
creator: Attaur Rahman
creator: Jola Rahmahani
creator: Adiana Mutamsari Witaningrum
creator: Muhammad Bilal
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Virology
subject: Zoology
description: doi:10.7717/peerj.14095
publisher: PeerJ Inc.
rights: © 2022 Rehman et al.
abstract: Background Avian influenza A virus subtypes H5N1 and H9N2 are contagious zoonotic diseases that are circulating in Indonesia and have raised increasing concern about their potential impacts on poultry and public health. A cross-sectional study was carried out to investigate the prevalence and associated risk factors of avian influenza A virus subtypes H5N1 and H9N2 among poultry in the live bird markets of four cities in East Java province, Indonesia. Methods A total of 600 tracheal and cloacal swabs (267 from backyards, 179 from broilers, and 154 from layers) from healthy birds were collected. The samples were inoculated into specific pathogenic-free embryonated eggs at 9-day-old via the allantoic cavity. qRT-PCR was used for further identification of avian influenza. Results The overall prevalence of circulating influenza A virus subtypes H5N1 and H9N2 was 3.8% (23/600, 95%CI [0.0229–0.0537]). Prevalence was higher in backyards at 5.99% (16/267) followed by broilers (2.23% (4/179)) and layers (1.68% (3/154)). The final multivariable model revealed five risk factors for H9N2 infections: presence of ducks (p = 0.003, OR = 38.2), turkeys (p = 0.017 OR = 0.032), and pheasants in the stall (p = 0.04, OR = 18.422), dry (p = 0.006) and rainy season (p < 0.001), and household birds (p = 0.002) and seven factors for H5N1 infections including: observing rodents (p = 0.036, OR = 0.005), stray dogs access (p = 0.004 OR ≤ 0.001), presence of turkeys (p = 0.03 OR = 0.007), chukars/partridges (p = 0.024 OR = 2500), and peafowls in the stalls (p = 0.0043 OR ≤ 0.001), rainy season (p = 0.001) and birds from the household sources (p = 0.002) in the live bird markets. Conclusions The findings of the current study illustrate the recurring infection and presence of both avian influenza viruses and associated risk factors in the surveyed marketplaces. Effective protective measures and mitigation strategies for risks outlined in this study could help to reduce the burden of H5N1 and H9N…
bibliographic citation: Rehman et al. (2022) Prevalence and associated risk factors of avian influenza A virus subtypes H5N1 and H9N2 in LBMs of East Java province, Indonesia: a cross-sectional study. PeerJ 10:e14095 https://doi.org/10.7717/peerj.14095
date submitted: 2022-06-10
date accepted: 2022-08-30
issued: 2022-10-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rehman
  given name: Saifur
author list: Agent
  family name: Effendi
  given name: Mustofa Helmi
author list: Agent
  family name: Shehzad
  given name: Aamir
author list: Agent
  family name: Rahman
  given name: Attaur
author list: Agent
  family name: Rahmahani
  given name: Jola
author list: Agent
  family name: Witaningrum
  given name: Adiana Mutamsari
author list: Agent
  family name: Bilal
  given name: Muhammad
doi: 10.7717/peerj.14095
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-12
copyright: ©2022 Rehman et al.
attribution name: Rehman et al.

Telomerase activity, relative telomere length, and longevity in alfalfa (Medicago sativa L.)
type: item
type: AcademicArticle
description: Background Medicago sativa L. ‘Qingshui’ is a valuable rhizomatous forage germplasm resource. We previously crossed Qingshui with the high-yielding Medicago sativa L. ‘WL168’ and obtained novel rhizomatous hybrid strains (RSA-01, RSA-02, and RSA-03). Telomere dynamics are more accurate predictors of survival and mortality than chronological age. Based on telomere analyses, we aimed to identify alfalfa varieties with increased stamina and longevity for the establishment of artificial grazing grasslands. Methods In this study, we performed longitudinal analysis of telomerase activity and relative telomere length in five alfalfa varieties (Qingshui, WL168, RSA-01, RSA-02, and RSA-03) at the age of 1 year and 5 years to examine the relationship among telomerase activity, rate of change in relative telomere length, and longevity. We further aimed to evaluate the longevity of the examined varieties. Telomerase activity and relative telomere length were measured using enzyme-linked immunosorbent assay and real-time polymerase chain reaction, respectively. Results We observed significant differences in telomerase activity between plants aged 1 year and those aged 5 years in all varieties except WL168, and the rate of change in telomerase activity does not differ reliably with age. As telomerase activity and relative telomere length are complex phenomena, further studies examining the molecular mechanisms of telomere-related proteins are needed. Relative telomere lengths of Qingshui, WL168, RSA-01, RSA-02, and RSA-03 in plants aged 5 years were higher than those aged 1 year by 11.41, 11.24, 9.21, 10.23, and 11.41, respectively. Relative telomere length of alfalfa tended to increase with age. Accordingly, alfalfa varieties can be classified according to rate of change in relative telomere length as long-lived (Qingshui, WL168, and RSA-03), medium-lived (RSA-02) and short-lived (RSA-01). The differences in relative telomere length distances of Qingshui, WL168, RSA-01, RSA-02, …
format: application/pdf
format: text/html
creator: Yun A
creator: Shangli Shi
creator: Shoujiang Sun
creator: Yuanyuan Jing
creator: Zili Li
creator: Xiaoyan Zhang
creator: Xiaolong Li
creator: Fang Wu
subject: Agricultural Science
subject: Developmental Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14102
publisher: PeerJ Inc.
rights: © 2022 A et al.
abstract: Background Medicago sativa L. ‘Qingshui’ is a valuable rhizomatous forage germplasm resource. We previously crossed Qingshui with the high-yielding Medicago sativa L. ‘WL168’ and obtained novel rhizomatous hybrid strains (RSA-01, RSA-02, and RSA-03). Telomere dynamics are more accurate predictors of survival and mortality than chronological age. Based on telomere analyses, we aimed to identify alfalfa varieties with increased stamina and longevity for the establishment of artificial grazing grasslands. Methods In this study, we performed longitudinal analysis of telomerase activity and relative telomere length in five alfalfa varieties (Qingshui, WL168, RSA-01, RSA-02, and RSA-03) at the age of 1 year and 5 years to examine the relationship among telomerase activity, rate of change in relative telomere length, and longevity. We further aimed to evaluate the longevity of the examined varieties. Telomerase activity and relative telomere length were measured using enzyme-linked immunosorbent assay and real-time polymerase chain reaction, respectively. Results We observed significant differences in telomerase activity between plants aged 1 year and those aged 5 years in all varieties except WL168, and the rate of change in telomerase activity does not differ reliably with age. As telomerase activity and relative telomere length are complex phenomena, further studies examining the molecular mechanisms of telomere-related proteins are needed. Relative telomere lengths of Qingshui, WL168, RSA-01, RSA-02, and RSA-03 in plants aged 5 years were higher than those aged 1 year by 11.41, 11.24, 9.21, 10.23, and 11.41, respectively. Relative telomere length of alfalfa tended to increase with age. Accordingly, alfalfa varieties can be classified according to rate of change in relative telomere length as long-lived (Qingshui, WL168, and RSA-03), medium-lived (RSA-02) and short-lived (RSA-01). The differences in relative telomere length distances of Qingshui, WL168, RSA-01, RSA-02, …
bibliographic citation: A et al. (2022) Telomerase activity, relative telomere length, and longevity in alfalfa (Medicago sativa L.). PeerJ 10:e14102 https://doi.org/10.7717/peerj.14102
date submitted: 2022-06-06
date accepted: 2022-09-01
issued: 2022-10-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: A
  given name: Yun
author list: Agent
  family name: Shi
  given name: Shangli
author list: Agent
  family name: Sun
  given name: Shoujiang
author list: Agent
  family name: Jing
  given name: Yuanyuan
author list: Agent
  family name: Li
  given name: Zili
author list: Agent
  family name: Zhang
  given name: Xiaoyan
author list: Agent
  family name: Li
  given name: Xiaolong
author list: Agent
  family name: Wu
  given name: Fang
doi: 10.7717/peerj.14102
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-12
copyright: ©2022 A et al.
attribution name: A et al.

Glycyrrhizic acid Poly(D,L-lactide-co-glycolide) nanoparticles: anti-aging cosmeceutical formulation for topical applications
type: item
type: AcademicArticle
description: Glycyrrhizic acid (GA) is one of the components of licorice roots (Glycyrrhiza glabra L.). GA is a triterpenoid saponin can be used as a medicinal plant with its antiallergic, antiviral, anti-inflammatory, anti-ulcer, hepatoprotective, anticancer, anti-oxidation activities and several other therapeutic properties. The aim of this study is to develop an anti-aging formulation for topical application containing GA. In this context, GA-loaded Poly (D,L-lactide-co-glycolide) (PLGA) nanoparticles (NPs) were prepared using the double emulsion method, and were characterized by various spectroscopic methods. The efficacy of GA-PLGA NPs was evaluated with in vitro and in silico methods. The encapsulation efficiency and loading capacity were calculated. The in vitro release study was conducted, and the GA release profile was determined. The genotoxic activity of GA and GA-PLGA NPs was evaluated by the Ames test using TA98 and TA100 mutant strains of Salmonella typhimurium. The cytotoxic potential of GA-PLGA NPs was evaluated on the HaCaT cell line using the MTT assay. According to the genotoxicity and cytotoxicity results, it was found that the GA-PLGA NP formulation did not exhibit genotoxic and cytotoxic effects. Moreover, the efficacy of GA in preventing UVB-induced photo-aging in HaCaT cells and the clarification of the molecular mechanism of GA binding to MMPs were revealed by molecular docking analysis. In addition, through molecular dynamics (MD) analysis, the binding interaction of GA with MMPs in a dynamic system, and protein-ligand stability were predicted as a result of 50 ns MD simulation studies considering various analysis parameters. Finally, it was evaluated that GA-PLGA nanoformulation might be used as an alternative anti-aging skin care product candidate via topical application.
format: application/pdf
format: text/html
creator: Cigdem Cetin Aluc
creator: Bahar Gok
creator: Serda Kecel-Gunduz
creator: Yasemin Budama-Kilinc
subject: Bioengineering
subject: Computational Biology
subject: Toxicology
subject: Dermatology
subject: Drugs and Devices
description: doi:10.7717/peerj.14139
publisher: PeerJ Inc.
rights: © 2022 Cetin Aluc et al.
abstract: Glycyrrhizic acid (GA) is one of the components of licorice roots (Glycyrrhiza glabra L.). GA is a triterpenoid saponin can be used as a medicinal plant with its antiallergic, antiviral, anti-inflammatory, anti-ulcer, hepatoprotective, anticancer, anti-oxidation activities and several other therapeutic properties. The aim of this study is to develop an anti-aging formulation for topical application containing GA. In this context, GA-loaded Poly (D,L-lactide-co-glycolide) (PLGA) nanoparticles (NPs) were prepared using the double emulsion method, and were characterized by various spectroscopic methods. The efficacy of GA-PLGA NPs was evaluated with in vitro and in silico methods. The encapsulation efficiency and loading capacity were calculated. The in vitro release study was conducted, and the GA release profile was determined. The genotoxic activity of GA and GA-PLGA NPs was evaluated by the Ames test using TA98 and TA100 mutant strains of Salmonella typhimurium. The cytotoxic potential of GA-PLGA NPs was evaluated on the HaCaT cell line using the MTT assay. According to the genotoxicity and cytotoxicity results, it was found that the GA-PLGA NP formulation did not exhibit genotoxic and cytotoxic effects. Moreover, the efficacy of GA in preventing UVB-induced photo-aging in HaCaT cells and the clarification of the molecular mechanism of GA binding to MMPs were revealed by molecular docking analysis. In addition, through molecular dynamics (MD) analysis, the binding interaction of GA with MMPs in a dynamic system, and protein-ligand stability were predicted as a result of 50 ns MD simulation studies considering various analysis parameters. Finally, it was evaluated that GA-PLGA nanoformulation might be used as an alternative anti-aging skin care product candidate via topical application.
bibliographic citation: Cetin Aluc et al. (2022) Glycyrrhizic acid Poly(D,L-lactide-co-glycolide) nanoparticles: anti-aging cosmeceutical formulation for topical applications. PeerJ 10:e14139 https://doi.org/10.7717/peerj.14139
date submitted: 2022-06-20
date accepted: 2022-09-06
issued: 2022-10-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cetin Aluc
  given name: Cigdem
author list: Agent
  family name: Gok
  given name: Bahar
author list: Agent
  family name: Kecel-Gunduz
  given name: Serda
author list: Agent
  family name: Budama-Kilinc
  given name: Yasemin
doi: 10.7717/peerj.14139
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-12
copyright: © 2022 Cetin Aluc et al.
attribution name: Cetin Aluc et al.

Body distribution of impetigo and association with host and pathogen factors
type: item
type: AcademicArticle
description: Background Impetigo or skin sores are estimated to affect >162 million people worldwide. Detailed descriptions of the anatomical location of skin sores are lacking. Methods We used prospectively collected data from a randomised control trial of treatments for impetigo in Aboriginal children in Australia. We generated heat-map distributions of skin sores on the human body from 56 predefined anatomical locations and stratified skin sore distribution by sex, age, causative pathogen and co-infection with scabies, tinea and head lice. We compared the distribution of sores between males and females, between sores with only Streptococcus pyogenes and sores with only Staphylococcus aureus; and across age groups with a Fisher’s exact test. Results There were 663 episodes of impetigo infections among 508 children enrolled in the trial. For all 663 episodes, the lower limbs were the most affected body sites followed by the distal upper limbs, face and scalp. On the anterior surface of the body, the pre-tibial region was the most affected while on the posterior surface, the dorsum of the hands and calves predominated. There was no observable difference between males and females in distribution of sores. Children up to 3 years of age were more likely to have sores on the upper posterior lower limbs and scalp than older age groups, with the distribution of sores differing across age groups (p = 3 × 10−5). Sores from which only Staphylococcus aureus was cultured differed in distribution to those with only Streptococcus pyogenes cultured (p = 3 × 10−4) and were more commonly found on the upper posterior lower limbs. Conclusions Skin sores were predominantly found on exposed regions of the lower leg and distal upper limbs. The distribution of sores varied by age group and pathogen. These results highlight key areas of the body for clinicians to pay attention to when examining children for skin sores.
format: application/pdf
format: text/html
creator: Arvind Yerramilli
creator: Asha C. Bowen
creator: Adrian J. Marcato
creator: Jodie McVernon
creator: Jonathan R. Carapetis
creator: Patricia T. Campbell
creator: Steven YC Tong
subject: Dermatology
subject: Epidemiology
subject: Global Health
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.14154
publisher: PeerJ Inc.
rights: © 2022 Yerramilli et al.
abstract: Background Impetigo or skin sores are estimated to affect >162 million people worldwide. Detailed descriptions of the anatomical location of skin sores are lacking. Methods We used prospectively collected data from a randomised control trial of treatments for impetigo in Aboriginal children in Australia. We generated heat-map distributions of skin sores on the human body from 56 predefined anatomical locations and stratified skin sore distribution by sex, age, causative pathogen and co-infection with scabies, tinea and head lice. We compared the distribution of sores between males and females, between sores with only Streptococcus pyogenes and sores with only Staphylococcus aureus; and across age groups with a Fisher’s exact test. Results There were 663 episodes of impetigo infections among 508 children enrolled in the trial. For all 663 episodes, the lower limbs were the most affected body sites followed by the distal upper limbs, face and scalp. On the anterior surface of the body, the pre-tibial region was the most affected while on the posterior surface, the dorsum of the hands and calves predominated. There was no observable difference between males and females in distribution of sores. Children up to 3 years of age were more likely to have sores on the upper posterior lower limbs and scalp than older age groups, with the distribution of sores differing across age groups (p = 3 × 10−5). Sores from which only Staphylococcus aureus was cultured differed in distribution to those with only Streptococcus pyogenes cultured (p = 3 × 10−4) and were more commonly found on the upper posterior lower limbs. Conclusions Skin sores were predominantly found on exposed regions of the lower leg and distal upper limbs. The distribution of sores varied by age group and pathogen. These results highlight key areas of the body for clinicians to pay attention to when examining children for skin sores.
bibliographic citation: Yerramilli et al. (2022) Body distribution of impetigo and association with host and pathogen factors. PeerJ 10:e14154 https://doi.org/10.7717/peerj.14154
date submitted: 2022-04-05
date accepted: 2022-09-07
issued: 2022-10-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yerramilli
  given name: Arvind
author list: Agent
  family name: Bowen
  given name: Asha C.
author list: Agent
  family name: Marcato
  given name: Adrian J.
author list: Agent
  family name: McVernon
  given name: Jodie
author list: Agent
  family name: Carapetis
  given name: Jonathan R.
author list: Agent
  family name: Campbell
  given name: Patricia T.
author list: Agent
  family name: Tong
  given name: Steven YC
doi: 10.7717/peerj.14154
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-12
copyright: © 2022 Yerramilli et al.
attribution name: Yerramilli et al.

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