PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Five decades of change in somatic growth of Pacific hake from Puget Sound and Strait of Georgia
items: Assessing availability of European plant protection product data: an example evaluating basic area treated
items: Seeds harvested during mowing from semi-natural grasslands as an ad hoc but effective solution for grassland restoration
items: Genetic population structure and reproductive system of two invasive Asian earthworms, Amynthas tokioensis and Amynthas agrestis
items: Changes in the core species of the ant-plant network of oak forest converted to grassland: replacement of its ant functional groups
items: Oxygen uptake efficiency slope in healthy normal weight young males: an applicable framework for calculation and interpretation
items: Are aerosol control devices effective in preventing the spread of dental aerosol?
items: Insights into mobile genetic elements and the role of conjugative plasmid in transferring aminoglycoside resistance in extensively drug-resistant Acinetobacter baumannii AB329
items: JMJD3 suppresses tumor progression in oral tongue squamous cell carcinoma patients receiving surgical resection
items: Short physical performance battery as a predictor of mortality in community-dwelling older adults: a longitudinal study in the Brazilian Amazon region

Five decades of change in somatic growth of Pacific hake from Puget Sound and Strait of Georgia
type: item
type: AcademicArticle
description: Declines in fish body size have been reported in many populations and these changes likely have important ramifications for the sustainability of harvested species and ecosystem function. Pacific hake, Merluccius productus, have shown declines in size over the last several decades for populations located in Puget Sound (PS), Washington, USA, and Strait of Georgia (SoG), British Columbia, Canada. To examine this decrease in size, we used archived otoliths from both populations to assess when the decrease in somatic growth occurred and explored what factors and processes might explain the decline, including otolith microchemistry to infer the environment experienced by fish at different ages. Results indicated that substantial changes in juvenile somatic growth have occurred across decades. The divergence in body size occurred in the second summer, whereby SoG fish grew, on average, 18% more than PS fish. Within the PS population, somatic growth differed significantly among fish that hatched in the 1980s, 1990s, and 2010s, such that the more recently hatched fish grew 26% more in their first summer and 71% less in their second summer relative to those that hatched in the 1980s. In comparison, growth of SoG fish did not differ between those that hatched in 1970s and 1990s. For both populations growth in the first and third summer was positively and negatively related, respectively, to the abundance of harbor seals, while growth in the first and second summer was negatively related to salinity. Overall, this study highlights the complicated nature of Pacific hake population recovery under dynamic, and typically uncontrollable, variation in biotic and abiotic conditions.
format: application/pdf
format: text/html
creator: Paul Chittaro
creator: Chris Grandin
creator: Robert Pacunski
creator: Rich Zabel
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.13577
publisher: PeerJ Inc.
rights: © 2022 Chittaro et al.
abstract: Declines in fish body size have been reported in many populations and these changes likely have important ramifications for the sustainability of harvested species and ecosystem function. Pacific hake, Merluccius productus, have shown declines in size over the last several decades for populations located in Puget Sound (PS), Washington, USA, and Strait of Georgia (SoG), British Columbia, Canada. To examine this decrease in size, we used archived otoliths from both populations to assess when the decrease in somatic growth occurred and explored what factors and processes might explain the decline, including otolith microchemistry to infer the environment experienced by fish at different ages. Results indicated that substantial changes in juvenile somatic growth have occurred across decades. The divergence in body size occurred in the second summer, whereby SoG fish grew, on average, 18% more than PS fish. Within the PS population, somatic growth differed significantly among fish that hatched in the 1980s, 1990s, and 2010s, such that the more recently hatched fish grew 26% more in their first summer and 71% less in their second summer relative to those that hatched in the 1980s. In comparison, growth of SoG fish did not differ between those that hatched in 1970s and 1990s. For both populations growth in the first and third summer was positively and negatively related, respectively, to the abundance of harbor seals, while growth in the first and second summer was negatively related to salinity. Overall, this study highlights the complicated nature of Pacific hake population recovery under dynamic, and typically uncontrollable, variation in biotic and abiotic conditions.
bibliographic citation: Chittaro et al. (2022) Five decades of change in somatic growth of Pacific hake from Puget Sound and Strait of Georgia. PeerJ 10:e13577 https://doi.org/10.7717/peerj.13577
date submitted: 2021-12-22
date accepted: 2022-05-22
issued: 2022-07-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chittaro
  given name: Paul
author list: Agent
  family name: Grandin
  given name: Chris
author list: Agent
  family name: Pacunski
  given name: Robert
author list: Agent
  family name: Zabel
  given name: Rich
doi: 10.7717/peerj.13577
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-13
copyright: ©2022 Chittaro et al.
attribution name: Chittaro et al.

Assessing availability of European plant protection product data: an example evaluating basic area treated
type: item
type: AcademicArticle
description: Besides the benefits of plant protection products (PPPs) for agricultural production, there is an increasing acknowledgement of the associated potential environmental risks. Here, we examine the feasibility of summarizing the extent of PPP usage at the country level, using Ireland as a case study, as well as at the European level. We used the area over which PPPs are applied (basic area) as an example variable that is relevant to initially assess the geographic extent of environmental risk. In Irish agricultural systems, which are primarily grass-based, herbicides fluroxypyr and glyphosate are the most widely applied active substances (ASs) in terms of basic area, followed by the fungicides chlorothalonil and prothioconazole that are closely associated with arable crops. Although all EU countries are subject to Regulation (EC) No 1185/2009, which sets the obligation of PPP usage data reporting at the national level, we only found usable data that met our criteria for Estonia, Germany, Finland, and Spain (4 of 30 countries reviewed). Overall, the most widely applied fungicide and herbicide in terms of basic area were prothioconazole (20%, 7% and 5% of national cultivated areas of Germany, Estonia and Ireland) and glyphosate (11%, 8% and 5% of national cultivated areas of Spain, Estonia and Ireland) respectively, although evaluations using application frequency may result in the observation of different trends. Several recommendations are proposed to tackle current data gaps and deficiencies in accessibility and usability of pesticide usage data across the EU in order to better inform environmental risk assessment and promote evidence-based policymaking.
format: application/pdf
format: text/html
creator: Ana López-Ballesteros
creator: Aoife Delaney
creator: James Quirke
creator: Jane C. Stout
creator: Matthew Saunders
creator: James C. Carolan
creator: Blánaid White
creator: Dara A. Stanley
subject: Biodiversity
subject: Science Policy
subject: Natural Resource Management
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.13586
publisher: PeerJ Inc.
rights: © 2022 López-Ballesteros et al.
abstract: Besides the benefits of plant protection products (PPPs) for agricultural production, there is an increasing acknowledgement of the associated potential environmental risks. Here, we examine the feasibility of summarizing the extent of PPP usage at the country level, using Ireland as a case study, as well as at the European level. We used the area over which PPPs are applied (basic area) as an example variable that is relevant to initially assess the geographic extent of environmental risk. In Irish agricultural systems, which are primarily grass-based, herbicides fluroxypyr and glyphosate are the most widely applied active substances (ASs) in terms of basic area, followed by the fungicides chlorothalonil and prothioconazole that are closely associated with arable crops. Although all EU countries are subject to Regulation (EC) No 1185/2009, which sets the obligation of PPP usage data reporting at the national level, we only found usable data that met our criteria for Estonia, Germany, Finland, and Spain (4 of 30 countries reviewed). Overall, the most widely applied fungicide and herbicide in terms of basic area were prothioconazole (20%, 7% and 5% of national cultivated areas of Germany, Estonia and Ireland) and glyphosate (11%, 8% and 5% of national cultivated areas of Spain, Estonia and Ireland) respectively, although evaluations using application frequency may result in the observation of different trends. Several recommendations are proposed to tackle current data gaps and deficiencies in accessibility and usability of pesticide usage data across the EU in order to better inform environmental risk assessment and promote evidence-based policymaking.
bibliographic citation: López-Ballesteros et al. (2022) Assessing availability of European plant protection product data: an example evaluating basic area treated. PeerJ 10:e13586 https://doi.org/10.7717/peerj.13586
date submitted: 2022-01-21
date accepted: 2022-05-23
issued: 2022-07-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: López-Ballesteros
  given name: Ana
author list: Agent
  family name: Delaney
  given name: Aoife
author list: Agent
  family name: Quirke
  given name: James
author list: Agent
  family name: Stout
  given name: Jane C.
author list: Agent
  family name: Saunders
  given name: Matthew
author list: Agent
  family name: Carolan
  given name: James C.
author list: Agent
  family name: White
  given name: Blánaid
author list: Agent
  family name: Stanley
  given name: Dara A.
doi: 10.7717/peerj.13586
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-13
copyright: ©2022 López-Ballesteros et al.
attribution name: López-Ballesteros et al.

Seeds harvested during mowing from semi-natural grasslands as an ad hoc but effective solution for grassland restoration
type: item
type: AcademicArticle
description: Species-rich grasslands formed by local ecotypes of native species provide numerous ecosystem services both in rural areas as well as urban grasslands. Nonetheless, their area is still too small, making grasslands one of the most frequently restored habitats. Successful restoration requires high-quality seed material, which is expensive and often not easy to acquire. In this study, we tested the potential of seeds accidentally collected during the mowing of a semi-natural grassland for grassland restoration. We tested seed purity, species composition, and germination capability in both laboratory and field conditions. Ninety percent of the collected material consisted of pure seeds of numerous species. Their germination capability was relatively low but still sufficient for successful grassland restoration under a typical seed density/mass per unit area seeding ratio. The germination capacity was the highest in the first two weeks after sowing and increased with overwintering seed storage. The results suggested that the seeds could be successfully used for species-rich grassland restoration. In terms of advantages, the seed mixture had a low cost and contained native species seeds representing local ecotypes. In terms of disadvantages, there was a relatively low amount of seed material and an inability to plan the time of seed harvesting. Thus, the use of the accidentally collected seeds can be considered an effective but rather ad hoc solution.
format: application/pdf
format: text/html
creator: Peliyagodage Chathura Dineth Perera
creator: Zofia Nocoń
creator: Hassanali Mollashahi
creator: Malwina Wierzbicka
creator: Tomasz H. Szymura
creator: Magdalena Szymura
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
description: doi:10.7717/peerj.13621
publisher: PeerJ Inc.
rights: © 2022 Perera et al.
abstract: Species-rich grasslands formed by local ecotypes of native species provide numerous ecosystem services both in rural areas as well as urban grasslands. Nonetheless, their area is still too small, making grasslands one of the most frequently restored habitats. Successful restoration requires high-quality seed material, which is expensive and often not easy to acquire. In this study, we tested the potential of seeds accidentally collected during the mowing of a semi-natural grassland for grassland restoration. We tested seed purity, species composition, and germination capability in both laboratory and field conditions. Ninety percent of the collected material consisted of pure seeds of numerous species. Their germination capability was relatively low but still sufficient for successful grassland restoration under a typical seed density/mass per unit area seeding ratio. The germination capacity was the highest in the first two weeks after sowing and increased with overwintering seed storage. The results suggested that the seeds could be successfully used for species-rich grassland restoration. In terms of advantages, the seed mixture had a low cost and contained native species seeds representing local ecotypes. In terms of disadvantages, there was a relatively low amount of seed material and an inability to plan the time of seed harvesting. Thus, the use of the accidentally collected seeds can be considered an effective but rather ad hoc solution.
bibliographic citation: Perera et al. (2022) Seeds harvested during mowing from semi-natural grasslands as an ad hoc but effective solution for grassland restoration. PeerJ 10:e13621 https://doi.org/10.7717/peerj.13621
date submitted: 2022-03-29
date accepted: 2022-06-02
issued: 2022-07-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Perera
  given name: Peliyagodage Chathura Dineth
author list: Agent
  family name: Nocoń
  given name: Zofia
author list: Agent
  family name: Mollashahi
  given name: Hassanali
author list: Agent
  family name: Wierzbicka
  given name: Malwina
author list: Agent
  family name: Szymura
  given name: Tomasz H.
author list: Agent
  family name: Szymura
  given name: Magdalena
doi: 10.7717/peerj.13621
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-13
copyright: ©2022 Perera et al.
attribution name: Perera et al.

Genetic population structure and reproductive system of two invasive Asian earthworms, Amynthas tokioensis and Amynthas agrestis
type: item
type: AcademicArticle
description: The invasive Asian earthworms, Amynthas tokioensis and A. agrestis, have been successful in entering North American forests in recent decades, with significant damage to both soils and above-ground environments. This success could be driven in part by a polyploid genetic system and parthenogenetic reproduction, often suggested as benefits for invasive species. Therefore, we assessed the genetic population structure, genetic diversity, and reproductive system of both species using morphological traits and panels of microsatellite markers. A total of 216 A. tokioensis and 196 A. agrestis from six sites in Vermont USA were analyzed. Although all worms were morphologically hermaphroditic, all the A. agrestis lacked the male pore (the structure allowing pass of sperm between individuals), and only 19% of the A. tokioensis possessed the male pore. All A. tokioensis earthworms were triploid (scored for three alleles for at least 1 locus, and usually several), and A. agrestis was a mix of triploid and diploid individuals. Notable was the high proportion (80%) of A. agrestis earthworms that were diploid at one site. There was clearly clonal reproduction, with identical seven- locus genotypes observed for earthworms from each site, with as many as 45 individuals with the identical genotype at one site. However, the earthworms were also genetically diverse, with 14 genotypes observed for A. tokioensis and 54 for A. agrestis, and with many singleton genotypes (a single individual). Most genotypes (71% for A. tokioensis and 92% for A. agrestis) were found at a single site. The greatest number of genotypes was found at a commercial nursery where fully 23/26 A. agrestis earthworms were singleton genotypes. As expected for the pattern of private clone alleles at sites, several measures of geographic genetic differentiation were positive, and as expected for triploid systems, an AMOVA analysis showed high within-individual genetic diversity. The paradox of clear clonal reproduction,…
format: application/pdf
format: text/html
creator: Maryam Nouri-Aiin
creator: Samantha Connolly
creator: Cheryl Keough
creator: Annie Jean Smigelsky
creator: Yiyi Wen
creator: Jeremy Howland
creator: Jos. J. Schall
creator: Josef H. Görres
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Soil Science
subject: Zoology
description: doi:10.7717/peerj.13622
publisher: PeerJ Inc.
rights: © 2022 Nouri-Aiin et al.
abstract: The invasive Asian earthworms, Amynthas tokioensis and A. agrestis, have been successful in entering North American forests in recent decades, with significant damage to both soils and above-ground environments. This success could be driven in part by a polyploid genetic system and parthenogenetic reproduction, often suggested as benefits for invasive species. Therefore, we assessed the genetic population structure, genetic diversity, and reproductive system of both species using morphological traits and panels of microsatellite markers. A total of 216 A. tokioensis and 196 A. agrestis from six sites in Vermont USA were analyzed. Although all worms were morphologically hermaphroditic, all the A. agrestis lacked the male pore (the structure allowing pass of sperm between individuals), and only 19% of the A. tokioensis possessed the male pore. All A. tokioensis earthworms were triploid (scored for three alleles for at least 1 locus, and usually several), and A. agrestis was a mix of triploid and diploid individuals. Notable was the high proportion (80%) of A. agrestis earthworms that were diploid at one site. There was clearly clonal reproduction, with identical seven- locus genotypes observed for earthworms from each site, with as many as 45 individuals with the identical genotype at one site. However, the earthworms were also genetically diverse, with 14 genotypes observed for A. tokioensis and 54 for A. agrestis, and with many singleton genotypes (a single individual). Most genotypes (71% for A. tokioensis and 92% for A. agrestis) were found at a single site. The greatest number of genotypes was found at a commercial nursery where fully 23/26 A. agrestis earthworms were singleton genotypes. As expected for the pattern of private clone alleles at sites, several measures of geographic genetic differentiation were positive, and as expected for triploid systems, an AMOVA analysis showed high within-individual genetic diversity. The paradox of clear clonal reproduction,…
bibliographic citation: Nouri-Aiin et al. (2022) Genetic population structure and reproductive system of two invasive Asian earthworms, Amynthas tokioensis and Amynthas agrestis. PeerJ 10:e13622 https://doi.org/10.7717/peerj.13622
date submitted: 2022-03-14
date accepted: 2022-06-02
issued: 2022-07-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nouri-Aiin
  given name: Maryam
author list: Agent
  family name: Connolly
  given name: Samantha
author list: Agent
  family name: Keough
  given name: Cheryl
author list: Agent
  family name: Smigelsky
  given name: Annie Jean
author list: Agent
  family name: Wen
  given name: Yiyi
author list: Agent
  family name: Howland
  given name: Jeremy
author list: Agent
  family name: Schall
  given name: Jos. J.
author list: Agent
  family name: Görres
  given name: Josef H.
doi: 10.7717/peerj.13622
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-13
copyright: ©2022 Nouri-Aiin et al.
attribution name: Nouri-Aiin et al.

Changes in the core species of the ant-plant network of oak forest converted to grassland: replacement of its ant functional groups
type: item
type: AcademicArticle
description: Land-use change in terrestrial environments is one of the main threats to biodiversity. The study of ant-plant networks has increased our knowledge of the diversity of interactions and structure of these communities; however, little is known about how land-use change affects ant-plant networks. Here we determine whether the change in land use, from native oak forest to induced grassland, affected the network properties of ant-plant networks in a temperate forest in Mexico. We hypothesize that the disturbed vegetation will be more nested and generalized due to the addition of generalist species to the network. The oak forest network comprises 47 plant species and 11 ant species, while the induced grassland network has 35 and 13, respectively. Floral nectar was the resource used most intensely by the ants in both vegetation types. The ant-plant network of the induced grassland was significantly more nested and generalist than that of the oak forest; however, none of the networks were nested when considering the frequency of interaction. In both vegetation types, the ants were more specialized than the plants, and niche overlap was low. This could be related to the dominant species present in each type of vegetation: Prenolepis imparis in the oak forest and Camponotus rubrithorax in the grassland. The central core of cold climate ant species in the oak forest was replaced by a central core of subordinate Camponotini and tropical specialists in the induced grassland. These results suggest that the increase in nestedness and generalization in the grassland may be related to the loss of the cold climate specialists from the core of the oak forest network. Our findings provide evidence that land-use change increases the level of generalization in the ant-plant interaction networks of temperate forests.
format: application/pdf
format: text/html
creator: Mariana Cuautle
creator: Cecilia Díaz-Castelazo
creator: Citlalli Castillo-Guevara
creator: Carolina Guadalupe Torres Lagunes
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.13679
publisher: PeerJ Inc.
rights: © 2022 Cuautle et al.
abstract: Land-use change in terrestrial environments is one of the main threats to biodiversity. The study of ant-plant networks has increased our knowledge of the diversity of interactions and structure of these communities; however, little is known about how land-use change affects ant-plant networks. Here we determine whether the change in land use, from native oak forest to induced grassland, affected the network properties of ant-plant networks in a temperate forest in Mexico. We hypothesize that the disturbed vegetation will be more nested and generalized due to the addition of generalist species to the network. The oak forest network comprises 47 plant species and 11 ant species, while the induced grassland network has 35 and 13, respectively. Floral nectar was the resource used most intensely by the ants in both vegetation types. The ant-plant network of the induced grassland was significantly more nested and generalist than that of the oak forest; however, none of the networks were nested when considering the frequency of interaction. In both vegetation types, the ants were more specialized than the plants, and niche overlap was low. This could be related to the dominant species present in each type of vegetation: Prenolepis imparis in the oak forest and Camponotus rubrithorax in the grassland. The central core of cold climate ant species in the oak forest was replaced by a central core of subordinate Camponotini and tropical specialists in the induced grassland. These results suggest that the increase in nestedness and generalization in the grassland may be related to the loss of the cold climate specialists from the core of the oak forest network. Our findings provide evidence that land-use change increases the level of generalization in the ant-plant interaction networks of temperate forests.
bibliographic citation: Cuautle et al. (2022) Changes in the core species of the ant-plant network of oak forest converted to grassland: replacement of its ant functional groups. PeerJ 10:e13679 https://doi.org/10.7717/peerj.13679
date submitted: 2022-01-11
date accepted: 2022-06-13
issued: 2022-07-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cuautle
  given name: Mariana
author list: Agent
  family name: Díaz-Castelazo
  given name: Cecilia
author list: Agent
  family name: Castillo-Guevara
  given name: Citlalli
author list: Agent
  family name: Torres Lagunes
  given name: Carolina Guadalupe
doi: 10.7717/peerj.13679
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-13
copyright: ©2022 Cuautle et al.
attribution name: Cuautle et al.

Oxygen uptake efficiency slope in healthy normal weight young males: an applicable framework for calculation and interpretation
type: item
type: AcademicArticle
description: Background The oxygen uptake efficiency slope (OUES) is considered a reliable indicator of cardiorespiratory fitness in young and clinical populations who cannot achieve maximal effort during a graded exercise test. However, OUES accuracy depends on the data points used for its calculation and it is still not clear if the submaximal OUES can accurately assess CRF in healthy young males. Objective We investigated the association between peak oxygen uptake and peak and submaximal OUES, and the agreement between submaximal OUES and peak OUES in male adolescents and young adults. Methods In this cross-sectional, observational study, fifty normal weight healthy participants (age 14–22 years, peak oxygen uptake 43.8 ± 7.3 mL·min−1·kg−1) performed a graded exercise test on a cycle ergometer and pulmonary gas exchange was assessed using breath-by-breath analysis. Peak oxygen uptake, and oxygen consumption at the aerobic and at the anaerobic threshold were determined as the 30-s average of the oxygen consumption values. Peak OUES (up to peak) and submaximal OUES (up to the aerobic and anaerobic thresholds) were calculated from the logarithmic relation between oxygen consumption and pulmonary ventilation. Results Very strong correlations were observed between peak oxygen uptake and peak OUES (r = 0.80–0.88) while fair-to-very strong correlations were observed between the peak oxygen uptake and the two submaximal OUES (r = 0.32–0.81). The level of agreement between peak OUES and OUES up to the anaerobic threshold (r = 0.89–0.93; Typical percentage error 6%; Intraclass correlation coefficient = 0.89–0.93) was greater than the one between the peak oxygen uptake with OUES up to the aerobic threshold (r = 0.39–0.56; Typical percentage error 15%; Intraclass correlation coefficient = 0.38–0.56). Conclusions . The peak OUES is a better indicator of aerobic fitness than the OUES up to the anaerobic threshold in healthy, young males. The OUES up to the anaerobic threshold is a valid al…
format: application/pdf
format: text/html
creator: Lavinia Falcioni
creator: Laura Guidetti
creator: Carlo Baldari
creator: Maria Chiara Gallotta
creator: Marco Meucci
subject: Anatomy and Physiology
subject: Pediatrics
subject: Respiratory Medicine
description: doi:10.7717/peerj.13709
publisher: PeerJ Inc.
rights: © 2022 Falcioni et al.
abstract: Background The oxygen uptake efficiency slope (OUES) is considered a reliable indicator of cardiorespiratory fitness in young and clinical populations who cannot achieve maximal effort during a graded exercise test. However, OUES accuracy depends on the data points used for its calculation and it is still not clear if the submaximal OUES can accurately assess CRF in healthy young males. Objective We investigated the association between peak oxygen uptake and peak and submaximal OUES, and the agreement between submaximal OUES and peak OUES in male adolescents and young adults. Methods In this cross-sectional, observational study, fifty normal weight healthy participants (age 14–22 years, peak oxygen uptake 43.8 ± 7.3 mL·min−1·kg−1) performed a graded exercise test on a cycle ergometer and pulmonary gas exchange was assessed using breath-by-breath analysis. Peak oxygen uptake, and oxygen consumption at the aerobic and at the anaerobic threshold were determined as the 30-s average of the oxygen consumption values. Peak OUES (up to peak) and submaximal OUES (up to the aerobic and anaerobic thresholds) were calculated from the logarithmic relation between oxygen consumption and pulmonary ventilation. Results Very strong correlations were observed between peak oxygen uptake and peak OUES (r = 0.80–0.88) while fair-to-very strong correlations were observed between the peak oxygen uptake and the two submaximal OUES (r = 0.32–0.81). The level of agreement between peak OUES and OUES up to the anaerobic threshold (r = 0.89–0.93; Typical percentage error 6%; Intraclass correlation coefficient = 0.89–0.93) was greater than the one between the peak oxygen uptake with OUES up to the aerobic threshold (r = 0.39–0.56; Typical percentage error 15%; Intraclass correlation coefficient = 0.38–0.56). Conclusions . The peak OUES is a better indicator of aerobic fitness than the OUES up to the anaerobic threshold in healthy, young males. The OUES up to the anaerobic threshold is a valid al…
bibliographic citation: Falcioni et al. (2022) Oxygen uptake efficiency slope in healthy normal weight young males: an applicable framework for calculation and interpretation. PeerJ 10:e13709 https://doi.org/10.7717/peerj.13709
date submitted: 2022-03-16
date accepted: 2022-06-19
issued: 2022-07-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Falcioni
  given name: Lavinia
author list: Agent
  family name: Guidetti
  given name: Laura
author list: Agent
  family name: Baldari
  given name: Carlo
author list: Agent
  family name: Gallotta
  given name: Maria Chiara
author list: Agent
  family name: Meucci
  given name: Marco
doi: 10.7717/peerj.13709
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-13
copyright: © 2022 Falcioni et al.
attribution name: Falcioni et al.

Are aerosol control devices effective in preventing the spread of dental aerosol?
type: item
type: AcademicArticle
description: Background In dental clinics, aerosols produced from dental instruments have become a matter of concern following breakout of coronavirus disease 19 (COVID-19) evolving into a pandemic. This study compared aerosol reduction systems and in terms of their ability to reduce Enterococcus faecalis (E. faecalis) contaminated aerosol in a simulated dental office set-up. Methods Closed clinic model with manikin and mandibular molar typodont was simulated. For 10 min, the air and water dispersed by the rotating bur mounted on an aerator was contaminated by pouring the suspension containing 1–3 × 108 CFU/mL E. faecalis directly on the bur. During and after the procedures, the air within the cabin was also sampled. CFU count was recorded and scored. The mean CFU scores obtained from agar plate count and air sampling device was compared using Kruskal–Wallis H test among groups with 5% significance threshold. Results The use of WS Aerosol Defender device led to greater CFU scores on the agars levelled to patient’s chest compared to other directions (p = 0.001). Combined use of VacStation and WS Aerosol Defender resulted in significantly decreased CFU score in the air samples compared to experimental and positive control groups (p = 0 < 0.05). Conclusions Although the devices prevented the spread of aerosol around the patient to some extent, they could not completely eliminate the contaminated aerosol load in the cabin environment.
format: application/pdf
format: text/html
creator: Elif Seher Böke
creator: Ali Keleş
creator: Cangül Keskin
creator: Yeliz Tanrıverdi Çaycı
creator: Tugba Turk
subject: Dentistry
subject: COVID-19
description: doi:10.7717/peerj.13714
publisher: PeerJ Inc.
rights: © 2022 Böke et al.
abstract: Background In dental clinics, aerosols produced from dental instruments have become a matter of concern following breakout of coronavirus disease 19 (COVID-19) evolving into a pandemic. This study compared aerosol reduction systems and in terms of their ability to reduce Enterococcus faecalis (E. faecalis) contaminated aerosol in a simulated dental office set-up. Methods Closed clinic model with manikin and mandibular molar typodont was simulated. For 10 min, the air and water dispersed by the rotating bur mounted on an aerator was contaminated by pouring the suspension containing 1–3 × 108 CFU/mL E. faecalis directly on the bur. During and after the procedures, the air within the cabin was also sampled. CFU count was recorded and scored. The mean CFU scores obtained from agar plate count and air sampling device was compared using Kruskal–Wallis H test among groups with 5% significance threshold. Results The use of WS Aerosol Defender device led to greater CFU scores on the agars levelled to patient’s chest compared to other directions (p = 0.001). Combined use of VacStation and WS Aerosol Defender resulted in significantly decreased CFU score in the air samples compared to experimental and positive control groups (p = 0 < 0.05). Conclusions Although the devices prevented the spread of aerosol around the patient to some extent, they could not completely eliminate the contaminated aerosol load in the cabin environment.
bibliographic citation: Böke et al. (2022) Are aerosol control devices effective in preventing the spread of dental aerosol?. PeerJ 10:e13714 https://doi.org/10.7717/peerj.13714
date submitted: 2022-03-23
date accepted: 2022-06-21
issued: 2022-07-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Böke
  given name: Elif Seher
author list: Agent
  family name: Keleş
  given name: Ali
author list: Agent
  family name: Keskin
  given name: Cangül
author list: Agent
  family name: Tanrıverdi Çaycı
  given name: Yeliz
author list: Agent
  family name: Turk
  given name: Tugba
doi: 10.7717/peerj.13714
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-13
copyright: ©2022 Böke et al.
attribution name: Böke et al.

Insights into mobile genetic elements and the role of conjugative plasmid in transferring aminoglycoside resistance in extensively drug-resistant Acinetobacter baumannii AB329
type: item
type: AcademicArticle
description: Acinetobacter baumannii is a major cause of nosocomial infection, and the incidence of extensively drug-resistant A. baumannii (XDRAB) infections has dramatically increased worldwide. In this study, we aimed to explore the complete genome sequence of XDRAB 329, ST1166/98 (Oxford/Pasteur), which is an outbreak clone from a hospital in Thailand. Whole-genome sequencing (WGS) was performed using short-read Illumina and long-read PacBio sequencing, and a conjugation assay of its plasmid was performed. The complete genome sequence of A. baumannii AB329 revealed a circular chromosome 3,948,038 bp in length with 39% GC content. Antibiotic resistance genes (ARGs), including beta-lactam resistance (blaOXA-51, blaADC-25, blaOXA-23, blaTEM-1D), aminoglycoside resistance (aph(3′)-Ia, aph(3″)-Ib, aph(6)-Id, armA), tetracycline resistance (tet(B), tet (R)), macrolide resistance (mph(E), msr(E)), and efflux pumps, were found. Mobile genetic elements (MGEs) analysis of A. baumannii AB329 revealed two plasmids (pAB329a and pAB329b), three prophages, 19 genomic islands (GIs), and 33 insertion sequences (ISs). pAB329a is a small circular plasmid of 8,731 bp, and pAB329b is a megaplasmid of 82,120 bp. aph(3′)-VIa was detected in pAB329b, and a major facilitator superfamily (MFS) transporter was detected in the prophage. Acinetobacter baumannii resistance island 4 (AbaR4) harboring tetracycline and aminoglycoside resistance was detected in the genome of A. baumannii AB329. pAB329b, which belongs to Rep-type GR6 (plasmid lineage LN_1), is a conjugative plasmid with the ability to transfer an aminoglycoside resistance gene to sodium azide-resistant A. baumannii. This study provides insights into the features of the MGEs of XDRAB, which are the main reservoir and source of dissemination of ARGs.
format: application/pdf
format: text/html
creator: Supat Khongfak
creator: Rapee Thummeepak
creator: Udomluk Leungtongkam
creator: Kannipa Tasanapak
creator: Aunchalee Thanwisai
creator: Sutthirat Sitthisak
subject: Genetics
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.13718
publisher: PeerJ Inc.
rights: © 2022 Khongfak et al.
abstract: Acinetobacter baumannii is a major cause of nosocomial infection, and the incidence of extensively drug-resistant A. baumannii (XDRAB) infections has dramatically increased worldwide. In this study, we aimed to explore the complete genome sequence of XDRAB 329, ST1166/98 (Oxford/Pasteur), which is an outbreak clone from a hospital in Thailand. Whole-genome sequencing (WGS) was performed using short-read Illumina and long-read PacBio sequencing, and a conjugation assay of its plasmid was performed. The complete genome sequence of A. baumannii AB329 revealed a circular chromosome 3,948,038 bp in length with 39% GC content. Antibiotic resistance genes (ARGs), including beta-lactam resistance (blaOXA-51, blaADC-25, blaOXA-23, blaTEM-1D), aminoglycoside resistance (aph(3′)-Ia, aph(3″)-Ib, aph(6)-Id, armA), tetracycline resistance (tet(B), tet (R)), macrolide resistance (mph(E), msr(E)), and efflux pumps, were found. Mobile genetic elements (MGEs) analysis of A. baumannii AB329 revealed two plasmids (pAB329a and pAB329b), three prophages, 19 genomic islands (GIs), and 33 insertion sequences (ISs). pAB329a is a small circular plasmid of 8,731 bp, and pAB329b is a megaplasmid of 82,120 bp. aph(3′)-VIa was detected in pAB329b, and a major facilitator superfamily (MFS) transporter was detected in the prophage. Acinetobacter baumannii resistance island 4 (AbaR4) harboring tetracycline and aminoglycoside resistance was detected in the genome of A. baumannii AB329. pAB329b, which belongs to Rep-type GR6 (plasmid lineage LN_1), is a conjugative plasmid with the ability to transfer an aminoglycoside resistance gene to sodium azide-resistant A. baumannii. This study provides insights into the features of the MGEs of XDRAB, which are the main reservoir and source of dissemination of ARGs.
bibliographic citation: Khongfak et al. (2022) Insights into mobile genetic elements and the role of conjugative plasmid in transferring aminoglycoside resistance in extensively drug-resistant Acinetobacter baumannii AB329. PeerJ 10:e13718 https://doi.org/10.7717/peerj.13718
date submitted: 2022-05-05
date accepted: 2022-06-21
issued: 2022-07-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khongfak
  given name: Supat
author list: Agent
  family name: Thummeepak
  given name: Rapee
author list: Agent
  family name: Leungtongkam
  given name: Udomluk
author list: Agent
  family name: Tasanapak
  given name: Kannipa
author list: Agent
  family name: Thanwisai
  given name: Aunchalee
author list: Agent
  family name: Sitthisak
  given name: Sutthirat
doi: 10.7717/peerj.13718
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-13
copyright: ©2022 Khongfak et al.
attribution name: Khongfak et al.

JMJD3 suppresses tumor progression in oral tongue squamous cell carcinoma patients receiving surgical resection
type: item
type: AcademicArticle
description: Background Jumonji domain-containing-3 (JMJD3) is reported to be a histone H3 lysine 27 (H3K27) demethylase and a tumor suppressor gene. The present study designed to investigate the crucial role of JMJD3 in oral tongue squamous cell carcinoma (OTSCC) patients who received surgical resection. Methods We enrolled a total of 156 OTSCC patients receiving surgical resection, including 73 patients (47%) with high expression of JMJD3 and 83 patients (53%) harboring low expression of JMJD3. Two OTSCC cell lines, SAS and Cal 27, were used to explore the modulation of cancer. GSK-J4, a potent inhibitor of JMJD3, was used to treat the two OTSCC cell lines. The Chi-square test was performed to examine between-group differences in categorical variables; the Kaplan–Meier method was used to investigate survival outcome in univariate analysis, and the Cox regression model was used for multivariate analysis. Results The median follow-up period was 59.2 months and he five-year disease-free survival (DFS) and overall survival (OS) rates were 46.2% and 50.0%, respectively. Better five-year DFS (59% versus 35%) and five-year OS (63% versus 39%) were mentioned in patients with high expression of JMJD3 compared to those with low expression of JMJD3. High expression of JMJD3 was significantly associated with superior DFS and OS in the univariate and multivariate analyses. Following successful inhibition of JMJD3 by GSK-J4, western blotting analysis showed the decreased expression of Rb and p21. Conclusion Our study showed that high expression of JMJD3 is a good prognostic factor in OTSCC patients who underwent surgical resection.
format: application/pdf
format: text/html
creator: Yen-Hao Chen
creator: Chang-Han Chen
creator: Chih-Yen Chien
creator: Yan-Ye Su
creator: Sheng-Dean Luo
creator: Shau-Hsuan Li
subject: Oncology
subject: Otorhinolaryngology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.13759
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: Background Jumonji domain-containing-3 (JMJD3) is reported to be a histone H3 lysine 27 (H3K27) demethylase and a tumor suppressor gene. The present study designed to investigate the crucial role of JMJD3 in oral tongue squamous cell carcinoma (OTSCC) patients who received surgical resection. Methods We enrolled a total of 156 OTSCC patients receiving surgical resection, including 73 patients (47%) with high expression of JMJD3 and 83 patients (53%) harboring low expression of JMJD3. Two OTSCC cell lines, SAS and Cal 27, were used to explore the modulation of cancer. GSK-J4, a potent inhibitor of JMJD3, was used to treat the two OTSCC cell lines. The Chi-square test was performed to examine between-group differences in categorical variables; the Kaplan–Meier method was used to investigate survival outcome in univariate analysis, and the Cox regression model was used for multivariate analysis. Results The median follow-up period was 59.2 months and he five-year disease-free survival (DFS) and overall survival (OS) rates were 46.2% and 50.0%, respectively. Better five-year DFS (59% versus 35%) and five-year OS (63% versus 39%) were mentioned in patients with high expression of JMJD3 compared to those with low expression of JMJD3. High expression of JMJD3 was significantly associated with superior DFS and OS in the univariate and multivariate analyses. Following successful inhibition of JMJD3 by GSK-J4, western blotting analysis showed the decreased expression of Rb and p21. Conclusion Our study showed that high expression of JMJD3 is a good prognostic factor in OTSCC patients who underwent surgical resection.
bibliographic citation: Chen et al. (2022) JMJD3 suppresses tumor progression in oral tongue squamous cell carcinoma patients receiving surgical resection. PeerJ 10:e13759 https://doi.org/10.7717/peerj.13759
date submitted: 2021-08-18
date accepted: 2022-06-29
issued: 2022-07-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yen-Hao
author list: Agent
  family name: Chen
  given name: Chang-Han
author list: Agent
  family name: Chien
  given name: Chih-Yen
author list: Agent
  family name: Su
  given name: Yan-Ye
author list: Agent
  family name: Luo
  given name: Sheng-Dean
author list: Agent
  family name: Li
  given name: Shau-Hsuan
doi: 10.7717/peerj.13759
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-13
copyright: ©2022 Chen et al.
attribution name: Chen et al.

Short physical performance battery as a predictor of mortality in community-dwelling older adults: a longitudinal study in the Brazilian Amazon region
type: item
type: AcademicArticle
description: Background The Short Physical Performance Battery (SPPB) is an instrument for assessing physical performance widely used in research among the elderly in multiple settings. We did not find Brazilian longitudinal studies that aimed to analyze the predictive capacity and accuracy of the SPPB among community-dwelling older adults and no systematic reviews were found on the accuracy of the SPPB in predicting mortality in community- dwelling older adults. This study aimed to analyze the capacity and accuracy of the SPPB for predicting mortality in community-dwelling older adults, as well as to determine cut-off points for men and women. Method Longitudinal observational study conducted with 411 (70.1 ± 7.25 years) community-dwelling older adults, between 2017 and 2020 (37.7 ± 6.24 months). Physical performance was evaluated using the SPPB and information on the all-cause mortality rate was also recorded. Multivariate Cox regression analyses and curves were performed using the Kaplan–Meier method. Receiver Operating Characteristic (ROC) curves were constructed, with the parameters of area under the ROC curve (AUC) to determine cutoff points for discriminating mortality, considering a significance level of 5% (p < 0.05) and 95% confidence interval (CI) 95%. Results Older adults with very low and low physical performance in the SPPB, showed higher risks of mortality (HR = 9.67; 95% CI [1.20–77.65]; HR = 4.06; 95% CI [1.09–15.01]), respectively. In the subtest’s analysis, older adults with low performance in the balance (HR = 0.54; 95% CI [0.36–0.81]) and gait speed tests (HR = 0.50; 95% CI [0.33–0.76]) showed greater risks of dying. The same was reproduced for categories in each test (participants that scored 2 points in the balance test had an HR = 5.86; 95% CI [1.84–18.61] and 2 points in the gait speed test, HR = 5.07; 95% CI [1.76–14.58]. The cutoff point ≤ 9 in the SPPB set the discriminator criterion for mortality in older people of both sexes. Conclusions The SPPB, a…
format: application/pdf
format: text/html
creator: Caroline de Fátima Ribeiro Silva
creator: Daniela Gonçalves Ohara
creator: Areolino Pena Matos
creator: Ana Carolina Pereira Nunes Pinto
creator: Maycon Sousa Pegorari
subject: Epidemiology
subject: Geriatrics
subject: Kinesiology
description: doi:10.7717/peerj.13630
publisher: PeerJ Inc.
rights: © 2022 Silva et al.
abstract: Background The Short Physical Performance Battery (SPPB) is an instrument for assessing physical performance widely used in research among the elderly in multiple settings. We did not find Brazilian longitudinal studies that aimed to analyze the predictive capacity and accuracy of the SPPB among community-dwelling older adults and no systematic reviews were found on the accuracy of the SPPB in predicting mortality in community- dwelling older adults. This study aimed to analyze the capacity and accuracy of the SPPB for predicting mortality in community-dwelling older adults, as well as to determine cut-off points for men and women. Method Longitudinal observational study conducted with 411 (70.1 ± 7.25 years) community-dwelling older adults, between 2017 and 2020 (37.7 ± 6.24 months). Physical performance was evaluated using the SPPB and information on the all-cause mortality rate was also recorded. Multivariate Cox regression analyses and curves were performed using the Kaplan–Meier method. Receiver Operating Characteristic (ROC) curves were constructed, with the parameters of area under the ROC curve (AUC) to determine cutoff points for discriminating mortality, considering a significance level of 5% (p < 0.05) and 95% confidence interval (CI) 95%. Results Older adults with very low and low physical performance in the SPPB, showed higher risks of mortality (HR = 9.67; 95% CI [1.20–77.65]; HR = 4.06; 95% CI [1.09–15.01]), respectively. In the subtest’s analysis, older adults with low performance in the balance (HR = 0.54; 95% CI [0.36–0.81]) and gait speed tests (HR = 0.50; 95% CI [0.33–0.76]) showed greater risks of dying. The same was reproduced for categories in each test (participants that scored 2 points in the balance test had an HR = 5.86; 95% CI [1.84–18.61] and 2 points in the gait speed test, HR = 5.07; 95% CI [1.76–14.58]. The cutoff point ≤ 9 in the SPPB set the discriminator criterion for mortality in older people of both sexes. Conclusions The SPPB, a…
bibliographic citation: Silva et al. (2022) Short physical performance battery as a predictor of mortality in community-dwelling older adults: a longitudinal study in the Brazilian Amazon region. PeerJ 10:e13630 https://doi.org/10.7717/peerj.13630
date submitted: 2022-03-10
date accepted: 2022-06-02
issued: 2022-07-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Caroline de Fátima Ribeiro
author list: Agent
  family name: Gonçalves Ohara
  given name: Daniela
author list: Agent
  family name: Pena Matos
  given name: Areolino
author list: Agent
  family name: Nunes Pinto
  given name: Ana Carolina Pereira
author list: Agent
  family name: Sousa Pegorari
  given name: Maycon
doi: 10.7717/peerj.13630
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-12
copyright: ©2022 Silva et al.
attribution name: Silva et al.

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