PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea
items: Fuel trait effects on flammability of native and invasive alien shrubs in coastal fynbos and thicket (Cape Floristic Region)
items: Autotoxicity effect of water extracts from rhizosphere soil of Elymus sibiricus in different planting years on seed germination, physiological characteristics and phytohormones of seedlings
items: Maize-peanut rotational strip intercropping improves peanut growth and soil properties by optimizing microbial community diversity
items: Quality of care and prescription patterns among patients with diabetic kidney disease—a large-scale cohort study from Taiwanese clinics
items: Spatial variation in diatom abundance and composition in Biwase Bay and Hamanaka Bay (Eastern Hokkaido, Japan), with reference to environmental features
items: Postoperative pain intensity and incidence following single visit root canal treatment with different obturation techniques: a randomized clinical trial
items: Effects of bone morphogenetic protein 4 on TGF-β1-induced cell proliferation, apoptosis, activation and differentiation in mouse lung fibroblasts via ERK/p38 MAPK signaling pathway
items: Effects of six weeks outdoor versus treadmill running on physical fitness and body composition in recreationally active young males: a pilot study
items: Weight change-related factors during the COVID-19 pandemic: a population-based cross-sectional study using social cognitive theory

Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea
type: item
type: AcademicArticle
description: Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-SerAGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-SerAGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.
format: application/pdf
format: text/html
creator: Shao’e Sun
creator: Ning Xiao
creator: Zhongli Sha
subject: Evolutionary Studies
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.13730
publisher: PeerJ Inc.
rights: © 2022 Sun et al.
abstract: Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-SerAGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-SerAGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.
bibliographic citation: Sun et al. (2022) Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea. PeerJ 10:e13730 https://doi.org/10.7717/peerj.13730
date submitted: 2022-04-22
date accepted: 2022-06-23
issued: 2022-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Shao’e
author list: Agent
  family name: Xiao
  given name: Ning
author list: Agent
  family name: Sha
  given name: Zhongli
doi: 10.7717/peerj.13730
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-28
copyright: ©2022 Sun et al.
attribution name: Sun et al.

Fuel trait effects on flammability of native and invasive alien shrubs in coastal fynbos and thicket (Cape Floristic Region)
type: item
type: AcademicArticle
description: In June 2017, extreme fires along the southern Cape coast of South Africa burnt native fynbos and thicket vegetation and caused extensive damage to plantations and residential properties. Invasive alien plants (IAPs) occur commonly in the area and were thought to have changed the behaviour of these fires through their modification of fuel properties relative to that of native vegetation. This study experimentally compared various measures of flammability across groups of native and alien invasive shrub species in relation to their fuel traits. Live plant shoots of 30 species (10 species each of native fynbos, native thicket, and IAPs) were sampled to measure live fuel moisture, dry biomass, fuel bed porosity and the proportions of fine-, coarse- and dead fuels. These shoots were burnt experimentally, and flammability measured in terms of maximum temperature (combustibility), completeness of burn (consumability), and time-to-ignition (ignitability). Multiple regression models were used to assess the relationships between flammability responses and fuel traits, while the Kruskal-Wallis H test was used to establish if differences existed in flammability measures and fuel traits among the vegetation groups. Dry biomass significantly enhanced, while live fuel moisture significantly reduced, maximum temperature, whereas the proportion of fine fuels significantly increased completeness of burn. Unlike other similar studies, the proportion of dead fuels and fuel bed porosity were not retained by any of the models to account for variation in flammability. Species of fynbos and IAPs generally exhibited greater flammability in the form of higher completeness of burn and more rapid ignition than species of thicket. Little distinction in flammability and fuel traits could be made between species of fynbos and IAPs, except that fynbos species had a greater proportion of fine fuels. Thicket species had higher proportions of coarse fuels and greater dry biomass (~fuel loading) than…
format: application/pdf
format: text/html
creator: Tineke Kraaij
creator: Samukelisiwe T. Msweli
creator: Alastair J. Potts
subject: Ecology
subject: Plant Science
subject: Biosphere Interactions
subject: Natural Resource Management
description: doi:10.7717/peerj.13765
publisher: PeerJ Inc.
rights: © 2022 Kraaij et al.
abstract: In June 2017, extreme fires along the southern Cape coast of South Africa burnt native fynbos and thicket vegetation and caused extensive damage to plantations and residential properties. Invasive alien plants (IAPs) occur commonly in the area and were thought to have changed the behaviour of these fires through their modification of fuel properties relative to that of native vegetation. This study experimentally compared various measures of flammability across groups of native and alien invasive shrub species in relation to their fuel traits. Live plant shoots of 30 species (10 species each of native fynbos, native thicket, and IAPs) were sampled to measure live fuel moisture, dry biomass, fuel bed porosity and the proportions of fine-, coarse- and dead fuels. These shoots were burnt experimentally, and flammability measured in terms of maximum temperature (combustibility), completeness of burn (consumability), and time-to-ignition (ignitability). Multiple regression models were used to assess the relationships between flammability responses and fuel traits, while the Kruskal-Wallis H test was used to establish if differences existed in flammability measures and fuel traits among the vegetation groups. Dry biomass significantly enhanced, while live fuel moisture significantly reduced, maximum temperature, whereas the proportion of fine fuels significantly increased completeness of burn. Unlike other similar studies, the proportion of dead fuels and fuel bed porosity were not retained by any of the models to account for variation in flammability. Species of fynbos and IAPs generally exhibited greater flammability in the form of higher completeness of burn and more rapid ignition than species of thicket. Little distinction in flammability and fuel traits could be made between species of fynbos and IAPs, except that fynbos species had a greater proportion of fine fuels. Thicket species had higher proportions of coarse fuels and greater dry biomass (~fuel loading) than…
bibliographic citation: Kraaij et al. (2022) Fuel trait effects on flammability of native and invasive alien shrubs in coastal fynbos and thicket (Cape Floristic Region). PeerJ 10:e13765 https://doi.org/10.7717/peerj.13765
date submitted: 2022-03-16
date accepted: 2022-06-30
issued: 2022-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kraaij
  given name: Tineke
author list: Agent
  family name: Msweli
  given name: Samukelisiwe T.
author list: Agent
  family name: Potts
  given name: Alastair J.
doi: 10.7717/peerj.13765
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-28
copyright: © 2022 Kraaij et al.
attribution name: Kraaij et al.

Autotoxicity effect of water extracts from rhizosphere soil of Elymus sibiricus in different planting years on seed germination, physiological characteristics and phytohormones of seedlings
type: item
type: AcademicArticle
description: Elymus sibiricus is a highly valuable perennial forage that is widely planted in the Qinghai-Tibet Plateau (QTP) region. However, E. sibiricus artificial grasslands have a short utilization lifespan, and reach the highest yield in the 2nd and 3rd year of plantation, then rapidly drop its productivity. We hypothesized that autotoxicity is one of the mechanisms for the reduction of the productivity. To test this hypothesis, we prepared the water extract from rhizosphere soils of E. sibiricus planted for 3, 4, 5, and 8 years and examined the effects of the extract concentrations at 0.05, 0.1, 0.2, and 0.5 g/mL on seed germination, seedling growth, physiological characteristics and phytohormones in the aboveground and roots of E. sibiricus. The results showed that the soil extract concentration, planting years, and their interaction had significant influences on the most of these indices. The soil extract inhibited the seed germination and growth of seedlings, and the inhibitory effects appeared to be stronger at the 0.5 g/mL rhizosphere soil extract for 5 and 8 years. The superoxide dismultase and peroxide activities, the free proline concentration, soluble sugar concentration were altered. The malondialdehyde concentration was, in general, increased, especially in 8 years soil extract. The indole acetic acid and gibberellic acids concentrations were lowered, while the abscisic acid concentration varied. These changes were depending on the extract concentration and the years of planting, without clear patterns in some of them in response to the extract concentration and planting years. In summary, autotoxicity can be a contributor to the retardation of the growth and development of artificial E. sibiricus grasslands. The inhibitory effects could be attribute to impaired antioxidant capacity and disturbance of osmortic-regulatory substances and plant hormones, and are more profound on the root than on the aboveground part of the seedlings.
format: application/pdf
format: text/html
creator: Hang Yang
creator: Jinglong Su
creator: Juan Qi
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.13768
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Elymus sibiricus is a highly valuable perennial forage that is widely planted in the Qinghai-Tibet Plateau (QTP) region. However, E. sibiricus artificial grasslands have a short utilization lifespan, and reach the highest yield in the 2nd and 3rd year of plantation, then rapidly drop its productivity. We hypothesized that autotoxicity is one of the mechanisms for the reduction of the productivity. To test this hypothesis, we prepared the water extract from rhizosphere soils of E. sibiricus planted for 3, 4, 5, and 8 years and examined the effects of the extract concentrations at 0.05, 0.1, 0.2, and 0.5 g/mL on seed germination, seedling growth, physiological characteristics and phytohormones in the aboveground and roots of E. sibiricus. The results showed that the soil extract concentration, planting years, and their interaction had significant influences on the most of these indices. The soil extract inhibited the seed germination and growth of seedlings, and the inhibitory effects appeared to be stronger at the 0.5 g/mL rhizosphere soil extract for 5 and 8 years. The superoxide dismultase and peroxide activities, the free proline concentration, soluble sugar concentration were altered. The malondialdehyde concentration was, in general, increased, especially in 8 years soil extract. The indole acetic acid and gibberellic acids concentrations were lowered, while the abscisic acid concentration varied. These changes were depending on the extract concentration and the years of planting, without clear patterns in some of them in response to the extract concentration and planting years. In summary, autotoxicity can be a contributor to the retardation of the growth and development of artificial E. sibiricus grasslands. The inhibitory effects could be attribute to impaired antioxidant capacity and disturbance of osmortic-regulatory substances and plant hormones, and are more profound on the root than on the aboveground part of the seedlings.
bibliographic citation: Yang et al. (2022) Autotoxicity effect of water extracts from rhizosphere soil of Elymus sibiricus in different planting years on seed germination, physiological characteristics and phytohormones of seedlings. PeerJ 10:e13768 https://doi.org/10.7717/peerj.13768
date submitted: 2022-04-12
date accepted: 2022-07-01
issued: 2022-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Hang
author list: Agent
  family name: Su
  given name: Jinglong
author list: Agent
  family name: Qi
  given name: Juan
doi: 10.7717/peerj.13768
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-28
copyright: ©2022 Yang et al.
attribution name: Yang et al.

Maize-peanut rotational strip intercropping improves peanut growth and soil properties by optimizing microbial community diversity
type: item
type: AcademicArticle
description: Rotational strip intercropping (RSI) of cereals and legumes has been developed and widely carried out to alleviate continuous cropping obstacles, to control erosion and to improve field use efficiency. In this study, a four-year fixed-field experiment was carried out in northeast China with three treatments: continuous cropping of maize, continuous cropping of peanuts and rotational strip intercropping of maize and peanut. The results show that crop rotation improved the main-stem height, branch number, lateral branch length, and yield and quality of peanuts; the yield was the highest in 2018, when it was increased by 39.5%. RSI improved the contents of total N, available N, total P, available P, total K and available K; the content of available N was the highest in 2018, with an increase of 70%. Rhizosphere soil urease and catalase activities were significantly increased and were the highest in 2017, reaching 183.13% and 91.21%, respectively. According to a high-throughput sequencing analysis, the rhizosphere soil bacterial richness and specific OTUs decreased in peanut rhizosphere soil, while the fungal increased. There were differences in the bacterial and fungal community structures; specifically, the abundance of Acidobacteria and Planctomycetes increased among bacteria and the abundance of beneficial microorganisms such as Ascomycota increased among fungi. In conclusion, rotational strip intercropping of maize and peanut increased the yield and quality of peanuts and conducive to alleviating the obstacles facing the continuous cropping of peanuts. Among then, soil physicochemical properties, enzyme activity and microbial diversity were significantly affected the yield of peanut.
format: application/pdf
format: text/html
creator: Yi Han
creator: Qiqi Dong
creator: Kezhao Zhang
creator: Dejian Sha
creator: Chunji Jiang
creator: Xu Yang
creator: Xibo Liu
creator: He Zhang
creator: Xiaoguang Wang
creator: Feng Guo
creator: Zheng Zhang
creator: Shubo Wan
creator: Xinhua Zhao
creator: Haiqiu Yu
subject: Ecology
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.13777
publisher: PeerJ Inc.
rights: © 2022 Han et al.
abstract: Rotational strip intercropping (RSI) of cereals and legumes has been developed and widely carried out to alleviate continuous cropping obstacles, to control erosion and to improve field use efficiency. In this study, a four-year fixed-field experiment was carried out in northeast China with three treatments: continuous cropping of maize, continuous cropping of peanuts and rotational strip intercropping of maize and peanut. The results show that crop rotation improved the main-stem height, branch number, lateral branch length, and yield and quality of peanuts; the yield was the highest in 2018, when it was increased by 39.5%. RSI improved the contents of total N, available N, total P, available P, total K and available K; the content of available N was the highest in 2018, with an increase of 70%. Rhizosphere soil urease and catalase activities were significantly increased and were the highest in 2017, reaching 183.13% and 91.21%, respectively. According to a high-throughput sequencing analysis, the rhizosphere soil bacterial richness and specific OTUs decreased in peanut rhizosphere soil, while the fungal increased. There were differences in the bacterial and fungal community structures; specifically, the abundance of Acidobacteria and Planctomycetes increased among bacteria and the abundance of beneficial microorganisms such as Ascomycota increased among fungi. In conclusion, rotational strip intercropping of maize and peanut increased the yield and quality of peanuts and conducive to alleviating the obstacles facing the continuous cropping of peanuts. Among then, soil physicochemical properties, enzyme activity and microbial diversity were significantly affected the yield of peanut.
bibliographic citation: Han et al. (2022) Maize-peanut rotational strip intercropping improves peanut growth and soil properties by optimizing microbial community diversity. PeerJ 10:e13777 https://doi.org/10.7717/peerj.13777
date submitted: 2022-04-05
date accepted: 2022-07-01
issued: 2022-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Yi
author list: Agent
  family name: Dong
  given name: Qiqi
author list: Agent
  family name: Zhang
  given name: Kezhao
author list: Agent
  family name: Sha
  given name: Dejian
author list: Agent
  family name: Jiang
  given name: Chunji
author list: Agent
  family name: Yang
  given name: Xu
author list: Agent
  family name: Liu
  given name: Xibo
author list: Agent
  family name: Zhang
  given name: He
author list: Agent
  family name: Wang
  given name: Xiaoguang
author list: Agent
  family name: Guo
  given name: Feng
author list: Agent
  family name: Zhang
  given name: Zheng
author list: Agent
  family name: Wan
  given name: Shubo
author list: Agent
  family name: Zhao
  given name: Xinhua
author list: Agent
  family name: Yu
  given name: Haiqiu
doi: 10.7717/peerj.13777
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-28
copyright: ©2022 Han et al.
attribution name: Han et al.

Quality of care and prescription patterns among patients with diabetic kidney disease—a large-scale cohort study from Taiwanese clinics
type: item
type: AcademicArticle
description: Aims To investigate the quality of care and prescription patterns of patients with diabetic kidney disease (DKD) receiving primary care at local clinics in Taiwan. Methods A retrospective chart review was conducted in 43 primary care clinics in Taiwan. The patients’ baseline characteristics, laboratory tests, presence of complications and antidiabetic agents prescribed were analyzed. Results 7,200 patients with type 2 diabetes mellitus were enrolled. Percentage of HbA1c, blood pressure (BP), and low density lipoprotein cholesterol (LDL-C) goals reached were 52.5% in HbA1c < 7%, 40.9% in BP < 130/80 mmHg and 79.7% in LDL-C < 2.59 mmol/L. 18.3% achieved all three ABC goals. However, patients with DKD had a lower rate of ABC goal attainment and higher rate of complications. Among DKD patients with eGFR ≥ 30 ml/min/1.73 m2 and on monotherapy, metformin was most frequently prescribed. As for dual therapy, the most common combinations were metformin with sulfonylurea and metformin with DPP-4 inhibitors. Conclusions Diabetes patients in Taiwan receiving primary diabetes care at local clinics had generally satisfactory management performance. However, more aggressive HbA1c, BP, and LDL-C management among DKD patients should be emphasized. Contrary to current recommendations, SGLT-2 inhibitors and GLP-1 receptor agonists as frontline therapy were under-prescribed.
format: application/pdf
format: text/html
creator: Kun-Yuan Tsai
creator: Samuel Chen
creator: Chien-Wen Chou
creator: Thing-Fong Tzeng
creator: Yau-Jiunn Lee
creator: Min-ling Chen
subject: Diabetes and Endocrinology
subject: Internal Medicine
subject: Nephrology
subject: Public Health
description: doi:10.7717/peerj.13636
publisher: PeerJ Inc.
rights: © 2022 Tsai et al.
abstract: Aims To investigate the quality of care and prescription patterns of patients with diabetic kidney disease (DKD) receiving primary care at local clinics in Taiwan. Methods A retrospective chart review was conducted in 43 primary care clinics in Taiwan. The patients’ baseline characteristics, laboratory tests, presence of complications and antidiabetic agents prescribed were analyzed. Results 7,200 patients with type 2 diabetes mellitus were enrolled. Percentage of HbA1c, blood pressure (BP), and low density lipoprotein cholesterol (LDL-C) goals reached were 52.5% in HbA1c < 7%, 40.9% in BP < 130/80 mmHg and 79.7% in LDL-C < 2.59 mmol/L. 18.3% achieved all three ABC goals. However, patients with DKD had a lower rate of ABC goal attainment and higher rate of complications. Among DKD patients with eGFR ≥ 30 ml/min/1.73 m2 and on monotherapy, metformin was most frequently prescribed. As for dual therapy, the most common combinations were metformin with sulfonylurea and metformin with DPP-4 inhibitors. Conclusions Diabetes patients in Taiwan receiving primary diabetes care at local clinics had generally satisfactory management performance. However, more aggressive HbA1c, BP, and LDL-C management among DKD patients should be emphasized. Contrary to current recommendations, SGLT-2 inhibitors and GLP-1 receptor agonists as frontline therapy were under-prescribed.
bibliographic citation: Tsai et al. (2022) Quality of care and prescription patterns among patients with diabetic kidney disease—a large-scale cohort study from Taiwanese clinics. PeerJ 10:e13636 https://doi.org/10.7717/peerj.13636
date submitted: 2022-01-27
date accepted: 2022-06-06
issued: 2022-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Tsai
  given name: Kun-Yuan
author list: Agent
  family name: Chen
  given name: Samuel
author list: Agent
  family name: Chou
  given name: Chien-Wen
author list: Agent
  family name: Tzeng
  given name: Thing-Fong
author list: Agent
  family name: Lee
  given name: Yau-Jiunn
author list: Agent
  family name: Chen
  given name: Min-ling
doi: 10.7717/peerj.13636
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-27
copyright: ©2022 Tsai et al.
attribution name: Tsai et al.

Spatial variation in diatom abundance and composition in Biwase Bay and Hamanaka Bay (Eastern Hokkaido, Japan), with reference to environmental features
type: item
type: AcademicArticle
description: This study aims to examine the spatial variation of diatom abundance and composition along the nearshore areas of Biwase Bay and Hamanaka Bay, eastern Hokkaido. Terrestrial input via Kiritappu Wetland is expected to affect variation and composition differently depending on the position of the two bays. We conducted an oceanographic survey in June 2014 to measure seawater temperature, salinity, colored dissolved organic matter (CDOM) absorption, nutrient concentrations, and total and size-fractionated chlorophyll (Chl) a concentration at 11 stations of the shallowest (<5 m) parts of the bays. These were grouped into four areas (Areas 1 and 2 in Biwase Bay, and Areas 3 and 4 in Hamanaka Bay) based on the distance of the location from the wetland outlet (nearest in Area 1 to the farthest in Area 4). Diatoms are the major primary producers in the water column. Therefore, we also determined genus level cell abundance and diversity of diatoms to compare similarity among areas. Sea surface temperature was the lowest at Area 4, whereas sea surface salinity was the lowest at Area 1. The contribution of CDOM absorption, an indicator of wetland-influenced river discharge, and silica concentration was highest at Area 1. Total amount of nitrite and nitrate concentrations was the highest at Area 4. Total amount of Chl a concentration was also lowest in Area 1. Our size-fractionated Chl a results revealed that while the size composition of phytoplankton varied among areas, micro-sized (>10 µm) phytoplankton were predominant in Area 4. Finally, diatom composition at the genus level differed greatly among areas. Pennate diatoms were predominant in Areas 1 and 2, but centric diatoms dominated in Areas 3 and 4. Our results suggested great spatial variability in oceanographic conditions among areas, with less influence of wetland and more influence of Coastal Oyashio Water based on distance from the wetland outlet. Diatom composition showed geographical division between Biwase and Hama…
format: application/pdf
format: text/html
creator: Hyojin Ahn
creator: Miho Ito
creator: Naoko Kouchi
creator: Kentaro Watanabe
creator: Hiroya Abe
creator: Tomonori Isada
creator: Masahiro Nakaoka
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Marine Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.13705
publisher: PeerJ Inc.
rights: © 2022 Ahn et al.
abstract: This study aims to examine the spatial variation of diatom abundance and composition along the nearshore areas of Biwase Bay and Hamanaka Bay, eastern Hokkaido. Terrestrial input via Kiritappu Wetland is expected to affect variation and composition differently depending on the position of the two bays. We conducted an oceanographic survey in June 2014 to measure seawater temperature, salinity, colored dissolved organic matter (CDOM) absorption, nutrient concentrations, and total and size-fractionated chlorophyll (Chl) a concentration at 11 stations of the shallowest (<5 m) parts of the bays. These were grouped into four areas (Areas 1 and 2 in Biwase Bay, and Areas 3 and 4 in Hamanaka Bay) based on the distance of the location from the wetland outlet (nearest in Area 1 to the farthest in Area 4). Diatoms are the major primary producers in the water column. Therefore, we also determined genus level cell abundance and diversity of diatoms to compare similarity among areas. Sea surface temperature was the lowest at Area 4, whereas sea surface salinity was the lowest at Area 1. The contribution of CDOM absorption, an indicator of wetland-influenced river discharge, and silica concentration was highest at Area 1. Total amount of nitrite and nitrate concentrations was the highest at Area 4. Total amount of Chl a concentration was also lowest in Area 1. Our size-fractionated Chl a results revealed that while the size composition of phytoplankton varied among areas, micro-sized (>10 µm) phytoplankton were predominant in Area 4. Finally, diatom composition at the genus level differed greatly among areas. Pennate diatoms were predominant in Areas 1 and 2, but centric diatoms dominated in Areas 3 and 4. Our results suggested great spatial variability in oceanographic conditions among areas, with less influence of wetland and more influence of Coastal Oyashio Water based on distance from the wetland outlet. Diatom composition showed geographical division between Biwase and Hama…
bibliographic citation: Ahn et al. (2022) Spatial variation in diatom abundance and composition in Biwase Bay and Hamanaka Bay (Eastern Hokkaido, Japan), with reference to environmental features. PeerJ 10:e13705 https://doi.org/10.7717/peerj.13705
date submitted: 2022-04-13
date accepted: 2022-06-19
issued: 2022-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahn
  given name: Hyojin
author list: Agent
  family name: Ito
  given name: Miho
author list: Agent
  family name: Kouchi
  given name: Naoko
author list: Agent
  family name: Watanabe
  given name: Kentaro
author list: Agent
  family name: Abe
  given name: Hiroya
author list: Agent
  family name: Isada
  given name: Tomonori
author list: Agent
  family name: Nakaoka
  given name: Masahiro
doi: 10.7717/peerj.13705
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-27
copyright: © 2022 Ahn et al.
attribution name: Ahn et al.

Postoperative pain intensity and incidence following single visit root canal treatment with different obturation techniques: a randomized clinical trial
type: item
type: AcademicArticle
description: Background There are few studies in the literature about the effect of obturation techniques on postoperative pain. Besides, GuttaFlow2 was used for the first time in this study regarding postoperative pain. This study aimed to compare the postoperative pain levels and incidence following single-visit root canal treatment with different canal filling techniques; cold lateral compaction (CLC), thermoplasticised solid-core carrier (GuttaCore) based filling and cold free-flow compaction (GuttaFlow2) technique. Methods The patients (n = 93) having single-rooted teeth with a single canal diagnosed with asymptomatic irreversible pulpitis or single-rooted vital teeth with a single canal requiring endodontic treatment because of prosthetic reasons were enrolled in this study. Patients were randomized into three groups (n = 31) according to the obturation technique. A single operator performed all the treatments in a single visit. Data on obturation levels, postoperative pain and analgesic intake frequency were recorded at postoperative 6, 12 and 24 h and daily afterward until the 7th day. Postoperative pain was measured by visual analogue scale (VAS). The date were statistically analyzed with chi-squared tests (for the analyses of the categorical data), the nonparametric Kruskal-Wallis test (for the comparisons of VAS score) and with the Friedman test (for the assessments of the changes in VAS scores over time). Results The GuttaCore group recorded the higher pain levels, except first 12 h, on the other hand, the GuttaFlow2 group recorded the lower pain levels at all time periods. Significant differences occurred among the groups during the first 4 days (p < 0.05), except at 12 h (p = 0.054). The patients in the CLC and GuttaFlow2 groups did not need to use the prescribed analgesic; however, one patient in the GuttaCore group used it once. Conclusions Postoperative pain levels following root canal therapy were affected by the obturation technique especially first 4 days fol…
format: application/pdf
format: text/html
creator: Aliye Koçer
creator: Hicran Dönmez Özkan
creator: Tugba Turk
subject: Anesthesiology and Pain Management
subject: Clinical Trials
subject: Dentistry
description: doi:10.7717/peerj.13756
publisher: PeerJ Inc.
rights: © 2022 Koçer et al.
abstract: Background There are few studies in the literature about the effect of obturation techniques on postoperative pain. Besides, GuttaFlow2 was used for the first time in this study regarding postoperative pain. This study aimed to compare the postoperative pain levels and incidence following single-visit root canal treatment with different canal filling techniques; cold lateral compaction (CLC), thermoplasticised solid-core carrier (GuttaCore) based filling and cold free-flow compaction (GuttaFlow2) technique. Methods The patients (n = 93) having single-rooted teeth with a single canal diagnosed with asymptomatic irreversible pulpitis or single-rooted vital teeth with a single canal requiring endodontic treatment because of prosthetic reasons were enrolled in this study. Patients were randomized into three groups (n = 31) according to the obturation technique. A single operator performed all the treatments in a single visit. Data on obturation levels, postoperative pain and analgesic intake frequency were recorded at postoperative 6, 12 and 24 h and daily afterward until the 7th day. Postoperative pain was measured by visual analogue scale (VAS). The date were statistically analyzed with chi-squared tests (for the analyses of the categorical data), the nonparametric Kruskal-Wallis test (for the comparisons of VAS score) and with the Friedman test (for the assessments of the changes in VAS scores over time). Results The GuttaCore group recorded the higher pain levels, except first 12 h, on the other hand, the GuttaFlow2 group recorded the lower pain levels at all time periods. Significant differences occurred among the groups during the first 4 days (p < 0.05), except at 12 h (p = 0.054). The patients in the CLC and GuttaFlow2 groups did not need to use the prescribed analgesic; however, one patient in the GuttaCore group used it once. Conclusions Postoperative pain levels following root canal therapy were affected by the obturation technique especially first 4 days fol…
bibliographic citation: Koçer et al. (2022) Postoperative pain intensity and incidence following single visit root canal treatment with different obturation techniques: a randomized clinical trial. PeerJ 10:e13756 https://doi.org/10.7717/peerj.13756
date submitted: 2022-02-16
date accepted: 2022-06-28
issued: 2022-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Koçer
  given name: Aliye
author list: Agent
  family name: Dönmez Özkan
  given name: Hicran
author list: Agent
  family name: Turk
  given name: Tugba
doi: 10.7717/peerj.13756
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-27
copyright: © 2022 Koçer et al.
attribution name: Koçer et al.

Effects of bone morphogenetic protein 4 on TGF-β1-induced cell proliferation, apoptosis, activation and differentiation in mouse lung fibroblasts via ERK/p38 MAPK signaling pathway
type: item
type: AcademicArticle
description: Fibroblasts, in particular myofibroblasts, are the critical effector cells in idiopathic pulmonary fibrosis (IPF), a deadly lung disease characterized by abnormal lung remodeling and the formation of “fibroblastic foci”. Aberrant activation of TGF-β1 is frequently encountered and promotes fibroblast proliferation, activation, and differentiation in pulmonary fibrosis. Hence, the inhibition of TGF-β1-induced lung fibroblast activation holds promise as a therapeutic strategy for IPF. The present study aimed to investigate the potential effect and underlying mechanisms of bone morphogenetic protein 4 (BMP4) on TGF-β1-induced proliferation, apoptosis, activation and myofibroblast differentiation of adult lung fibroblasts. Here, we demonstrated that BMP4 expression was significantly decreased in TGF-β1-stimulated mouse primary lung fibroblasts (PLFs). BMP4 inhibited proliferation and apoptosis resistance of TGF-β1-stimulated mouse PLFs. BMP4 suppressed TGF-β1-induced fibroblast activation and differentiation in mouse PLFs. We also found that BMP4 inhibited TGF-β1-induced ERK and p38 MAPK phosphorylation. Our findings indicate that BMP4 exerts its anti-fibrotic effects by regulating fibroblast proliferation, apoptosis, activation and differentiation via the inhibition of the ERK/p38 MAPK signaling pathway, and thus has a potential for the treatment of pulmonary fibrosis.
format: application/pdf
format: text/html
creator: Zhou Cai
creator: Hua Guo
creator: Jing Qian
creator: Wei Liu
creator: Yuanyuan Li
creator: Liang Yuan
creator: You Zhou
creator: Ran Lin
creator: Xiaohui Xie
creator: Qiong Yang
creator: Guoying Wu
creator: Qiongqiong Li
creator: Li Zhao
creator: Fei Liu
creator: Jian Wang
creator: Wenju Lu
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.13775
publisher: PeerJ Inc.
rights: © 2022 Cai et al.
abstract: Fibroblasts, in particular myofibroblasts, are the critical effector cells in idiopathic pulmonary fibrosis (IPF), a deadly lung disease characterized by abnormal lung remodeling and the formation of “fibroblastic foci”. Aberrant activation of TGF-β1 is frequently encountered and promotes fibroblast proliferation, activation, and differentiation in pulmonary fibrosis. Hence, the inhibition of TGF-β1-induced lung fibroblast activation holds promise as a therapeutic strategy for IPF. The present study aimed to investigate the potential effect and underlying mechanisms of bone morphogenetic protein 4 (BMP4) on TGF-β1-induced proliferation, apoptosis, activation and myofibroblast differentiation of adult lung fibroblasts. Here, we demonstrated that BMP4 expression was significantly decreased in TGF-β1-stimulated mouse primary lung fibroblasts (PLFs). BMP4 inhibited proliferation and apoptosis resistance of TGF-β1-stimulated mouse PLFs. BMP4 suppressed TGF-β1-induced fibroblast activation and differentiation in mouse PLFs. We also found that BMP4 inhibited TGF-β1-induced ERK and p38 MAPK phosphorylation. Our findings indicate that BMP4 exerts its anti-fibrotic effects by regulating fibroblast proliferation, apoptosis, activation and differentiation via the inhibition of the ERK/p38 MAPK signaling pathway, and thus has a potential for the treatment of pulmonary fibrosis.
bibliographic citation: Cai et al. (2022) Effects of bone morphogenetic protein 4 on TGF-β1-induced cell proliferation, apoptosis, activation and differentiation in mouse lung fibroblasts via ERK/p38 MAPK signaling pathway. PeerJ 10:e13775 https://doi.org/10.7717/peerj.13775
date submitted: 2022-04-14
date accepted: 2022-07-01
issued: 2022-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Zhou
author list: Agent
  family name: Guo
  given name: Hua
author list: Agent
  family name: Qian
  given name: Jing
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Li
  given name: Yuanyuan
author list: Agent
  family name: Yuan
  given name: Liang
author list: Agent
  family name: Zhou
  given name: You
author list: Agent
  family name: Lin
  given name: Ran
author list: Agent
  family name: Xie
  given name: Xiaohui
author list: Agent
  family name: Yang
  given name: Qiong
author list: Agent
  family name: Wu
  given name: Guoying
author list: Agent
  family name: Li
  given name: Qiongqiong
author list: Agent
  family name: Zhao
  given name: Li
author list: Agent
  family name: Liu
  given name: Fei
author list: Agent
  family name: Wang
  given name: Jian
author list: Agent
  family name: Lu
  given name: Wenju
doi: 10.7717/peerj.13775
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-27
copyright: ©2022 Cai et al.
attribution name: Cai et al.

Effects of six weeks outdoor versus treadmill running on physical fitness and body composition in recreationally active young males: a pilot study
type: item
type: AcademicArticle
description: Background Running as exercise may be performed either on an outdoor surface or treadmill surface. However, previous research has indicated that the nature of both the surfaces differ significantly and therefore the training outcomes from running in these surfaces may also vary. Aim Therefore, the aim of this pilot study was to compare the effects of 6-weeks of supervised outdoor running (OT) vs treadmill running (TT) on physical fitness and body composition in recreationally active young males. Methods Participants (age: 19.82 ± 1.28 years, height: 172.6 ± 4.9 cm, body mass: 64.3 ± 8.7 kg) were randomly assigned to OT (n = 14) or TT (n = 14), and assessed for physical fitness, i.e., 50 m sprint, cardiorespiratory endurance (i.e., 1,600 m run time-trial), standing long jump (SLJ), flexibility (i.e., sit-and-reach test), and upper-body muscle endurance (i.e., push-ups repetitions), alongside body composition, i.e., body mass, body mass index (BMI), fat percentage, fat free mass, and leg skeletal muscle mass (SMM). A two (pre-post intervention) by two (OT, TT) mixed ANOVA analysed exercise-specific effects. For significant group-by-time interactions, Bonferroni adjusted paired (within-group) and independent (between-group comparisons at post) t-tests were used for post-hoc analyses. Results Significant time-effect was found in all physical fitness variables (all p < 0.001, ηp2 = 0.67–0.91), body mass (p = 0.23, ηp2 = 0.18), BMI (p = 0.009, ηp2 = 0.24), body fat percentage (p = 0.001, ηp2 = 0.38), and leg SMM (p = 0.002–0.007, ηp2 = 0.25–0.33). Significant group-by-time interaction was found for 50 m sprint (p = < 0.001, ηp2 = 0.74), 1,600 m run (p = 0.001, ηp2 = 0.35), and SLJ (p < 0.001, ηp2 = 0.43), favouring OT. Group-specific post-hoc tests showed improvements in all physical fitness variables after OT (p = < 0.001–0.001, g = 0.69–2.32, %Δ = 3.0–12.4) and TT (p = < 0.001–0.017, g = 0.15–0.65, %Δ = 0.9–11.7), and fat percentage after OT and TT (p = 0.002–0.041, g =…
format: application/pdf
format: text/html
creator: Gaurav Singh
creator: Gaurav Kushwah
creator: Tanvi Singh
creator: Rodrigo Ramírez-Campillo
creator: Rohit K. Thapa
subject: Kinesiology
subject: Public Health
subject: Obesity
subject: Sports Medicine
description: doi:10.7717/peerj.13791
publisher: PeerJ Inc.
rights: © 2022 Singh et al.
abstract: Background Running as exercise may be performed either on an outdoor surface or treadmill surface. However, previous research has indicated that the nature of both the surfaces differ significantly and therefore the training outcomes from running in these surfaces may also vary. Aim Therefore, the aim of this pilot study was to compare the effects of 6-weeks of supervised outdoor running (OT) vs treadmill running (TT) on physical fitness and body composition in recreationally active young males. Methods Participants (age: 19.82 ± 1.28 years, height: 172.6 ± 4.9 cm, body mass: 64.3 ± 8.7 kg) were randomly assigned to OT (n = 14) or TT (n = 14), and assessed for physical fitness, i.e., 50 m sprint, cardiorespiratory endurance (i.e., 1,600 m run time-trial), standing long jump (SLJ), flexibility (i.e., sit-and-reach test), and upper-body muscle endurance (i.e., push-ups repetitions), alongside body composition, i.e., body mass, body mass index (BMI), fat percentage, fat free mass, and leg skeletal muscle mass (SMM). A two (pre-post intervention) by two (OT, TT) mixed ANOVA analysed exercise-specific effects. For significant group-by-time interactions, Bonferroni adjusted paired (within-group) and independent (between-group comparisons at post) t-tests were used for post-hoc analyses. Results Significant time-effect was found in all physical fitness variables (all p < 0.001, ηp2 = 0.67–0.91), body mass (p = 0.23, ηp2 = 0.18), BMI (p = 0.009, ηp2 = 0.24), body fat percentage (p = 0.001, ηp2 = 0.38), and leg SMM (p = 0.002–0.007, ηp2 = 0.25–0.33). Significant group-by-time interaction was found for 50 m sprint (p = < 0.001, ηp2 = 0.74), 1,600 m run (p = 0.001, ηp2 = 0.35), and SLJ (p < 0.001, ηp2 = 0.43), favouring OT. Group-specific post-hoc tests showed improvements in all physical fitness variables after OT (p = < 0.001–0.001, g = 0.69–2.32, %Δ = 3.0–12.4) and TT (p = < 0.001–0.017, g = 0.15–0.65, %Δ = 0.9–11.7), and fat percentage after OT and TT (p = 0.002–0.041, g =…
bibliographic citation: Singh et al. (2022) Effects of six weeks outdoor versus treadmill running on physical fitness and body composition in recreationally active young males: a pilot study. PeerJ 10:e13791 https://doi.org/10.7717/peerj.13791
date submitted: 2022-04-07
date accepted: 2022-07-05
issued: 2022-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Singh
  given name: Gaurav
author list: Agent
  family name: Kushwah
  given name: Gaurav
author list: Agent
  family name: Singh
  given name: Tanvi
author list: Agent
  family name: Ramírez-Campillo
  given name: Rodrigo
author list: Agent
  family name: Thapa
  given name: Rohit K.
doi: 10.7717/peerj.13791
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-27
copyright: © 2022 Singh et al.
attribution name: Singh et al.

Weight change-related factors during the COVID-19 pandemic: a population-based cross-sectional study using social cognitive theory
type: item
type: AcademicArticle
description: Background Published studies during the Coronavirus-19 (COVID-19) pandemic have focused on eating and exercise behaviors and failed to portray a comprehensive understanding of the factors associated with weight change in a setting of a behavioral change framework. This study explores factors associated with weight change during the COVID-19 pandemic among Lebanese residents using the Social Cognitive Theory (SCT) framework, integrating behavioral, environmental, and cognitive factors. Materials & Methods This study uses a cross-sectional design using an anonymous online survey. Participants were recruited from a tertiary hospital patient portal and social media posts. The survey included four domains: demographics, cognitive, behavioral, psychological, and environmental factors. Multiple validated self-reported instruments were included Generalized Anxiety Disorder-2 items (GAD-2), Patient Health Questionnaire-2 (PHQ-2), General Self Efficacy Scale (GSES), Alcohol Use Disorders Identification Test-Concise (AUDIT-C), and the dietary pattern evaluation tool. Results A sample of 335 complete responses was obtained. Mean age was 39.0 ± 13.4 years old. Participants were mostly females (n = 224, 66.9%), employed (n = 191, 57.4%), nonsmokers (n = 227, 70.5%), reporting depression (n = 224, 80.3%) and anxiety (n = 242, 84.3%). Mean weight change was −7.0 ± 6.0 kg in the decrease weight group and 6.4 ± 5.0 kg in the increase group. When compared to stable weight, the multinomial logistic model factors that were found to correlate significantly to weight gain were: overeating/binge eating (p-value = 0.001) and unbalanced food pattern (p-value = 0.012). Baseline BMI (p-value = 0.003), anxiety (p-value = 0.020) and smoking (p-value = 0.004) were significant factors of weight loss as compared to stable weight. Conclusions COVID-19-related weight change is multifactorial and is associated with specific behavior and individual characteristics. Hence, addressing people’s behaviors …
format: application/pdf
format: text/html
creator: Roxane Assaf
creator: Jumana Antoun
subject: Nutrition
subject: Public Health
subject: Obesity
subject: COVID-19
description: doi:10.7717/peerj.13829
publisher: PeerJ Inc.
rights: © 2022 Assaf and Antoun
abstract: Background Published studies during the Coronavirus-19 (COVID-19) pandemic have focused on eating and exercise behaviors and failed to portray a comprehensive understanding of the factors associated with weight change in a setting of a behavioral change framework. This study explores factors associated with weight change during the COVID-19 pandemic among Lebanese residents using the Social Cognitive Theory (SCT) framework, integrating behavioral, environmental, and cognitive factors. Materials & Methods This study uses a cross-sectional design using an anonymous online survey. Participants were recruited from a tertiary hospital patient portal and social media posts. The survey included four domains: demographics, cognitive, behavioral, psychological, and environmental factors. Multiple validated self-reported instruments were included Generalized Anxiety Disorder-2 items (GAD-2), Patient Health Questionnaire-2 (PHQ-2), General Self Efficacy Scale (GSES), Alcohol Use Disorders Identification Test-Concise (AUDIT-C), and the dietary pattern evaluation tool. Results A sample of 335 complete responses was obtained. Mean age was 39.0 ± 13.4 years old. Participants were mostly females (n = 224, 66.9%), employed (n = 191, 57.4%), nonsmokers (n = 227, 70.5%), reporting depression (n = 224, 80.3%) and anxiety (n = 242, 84.3%). Mean weight change was −7.0 ± 6.0 kg in the decrease weight group and 6.4 ± 5.0 kg in the increase group. When compared to stable weight, the multinomial logistic model factors that were found to correlate significantly to weight gain were: overeating/binge eating (p-value = 0.001) and unbalanced food pattern (p-value = 0.012). Baseline BMI (p-value = 0.003), anxiety (p-value = 0.020) and smoking (p-value = 0.004) were significant factors of weight loss as compared to stable weight. Conclusions COVID-19-related weight change is multifactorial and is associated with specific behavior and individual characteristics. Hence, addressing people’s behaviors …
bibliographic citation: Assaf et al. (2022) Weight change-related factors during the COVID-19 pandemic: a population-based cross-sectional study using social cognitive theory. PeerJ 10:e13829 https://doi.org/10.7717/peerj.13829
date submitted: 2022-06-14
date accepted: 2022-07-11
issued: 2022-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Assaf
  given name: Roxane
author list: Agent
  family name: Antoun
  given name: Jumana
doi: 10.7717/peerj.13829
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-27
copyright: © 2022 Assaf and Antoun
attribution name: Assaf and Antoun

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