PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Relationship between body composition and bone mass in normal-weight and overweight adolescents
items: The impact of aging and physical training on angiogenesis in the musculoskeletal system
items: Differences in leaf and root litter decomposition in tropical montane rainforests are mediated by soil microorganisms not by decomposer microarthropods
items: Diagnostic performance of circulating tumor DNA as a minimally invasive biomarker for hepatocellular carcinoma: a systematic review and meta-analysis
items: Comparison of epiphytic and intestinal bacterial communities in freshwater snails (Bellamya aeruginosa) living on submerged plants
items: Publication delays and associated factors in ophthalmology journals
items: Gender differences in general health and happiness: a study on Iranian engineering students
items: Nitrogen fertilizer amount has minimal effect on rhizosphere bacterial diversity during different growth stages of peanut
items: Molecular phylogeny of Columbellidae (Gastropoda: Neogastropoda)
items: Cranial osteology, taxonomic reassessment, and phylogenetic relationships of the Early Cretaceous (Aptian-Albian) turtle Trinitichelys hiatti (Paracryptodira)

Relationship between body composition and bone mass in normal-weight and overweight adolescents
type: item
type: AcademicArticle
description: Adolescence is a period characterized by large accumulation of bone mass. Body composition is an important determinant of bone mass. This study aimed to assess the relationship of bone mass with lean mass (LM) and fat mass (FM) in normal-weight and overweight adolescents with consideration of sex, sexual maturation and physical activity covariates. A total of 118 adolescents (60 girls and 58 boys) aged between 10 and 14 years participated in the study. Individuals were classified as normal weight or overweight according to body mass index. Bone mineral density (BMD), bone mineral content (BMC), LM, and FM were measured by dual-energy X-ray absorptiometry. In normal-weight adolescents, LM (β = 0.725, p < 0.001) and FM (β = 0.185, p = 0.019) were associated with lumbar spine BMC, whereas in overweight adolescents only LM (β = 0.736, p < 0.001) was associated with lumbar spine BMC. Furthermore, in the normal-weight group, FM and LM were associated with total body less head BMD (LM, β = 0.792, p < 0.001; FM, β = 0.257, p = 0.007) and lumbar spine BMD (LM, β = 0.553, p < 0.001; FM, β = 0.199, p < 0.035). In the overweight group, only LM was associated with total body less head BMD (β = 0.682, p < 0.001) and lumbar spine BMD (β = 0.528, p < 0.001). LM was the main predictor of bone mass in normal-weight and overweight adolescents. FM was associated with bone mass in normal-weight adolescents only. LM may be considered an important and useful marker in adolescents, when investigating bone health in this population. Activities that promote LM gain to reduce the risk of bone fractures and diseases in adulthood are recommended.
format: application/pdf
format: text/html
creator: Mateus Augusto Bim
creator: André de Araujo Pinto
creator: Hector Cris Colares de Angelo
creator: Isadora Gonzaga
creator: Adriana Coutinho de Azevedo Guimarães
creator: Érico Pereira Gomes Felden
creator: Wellington Roberto Gomes de Carvalho
creator: Karen Hind
creator: Andreia Pelegrini
subject: Epidemiology
subject: Orthopedics
subject: Pediatrics
subject: Public Health
subject: Obesity
description: doi:10.7717/peerj.14108
publisher: PeerJ Inc.
rights: © 2022 Bim et al.
abstract: Adolescence is a period characterized by large accumulation of bone mass. Body composition is an important determinant of bone mass. This study aimed to assess the relationship of bone mass with lean mass (LM) and fat mass (FM) in normal-weight and overweight adolescents with consideration of sex, sexual maturation and physical activity covariates. A total of 118 adolescents (60 girls and 58 boys) aged between 10 and 14 years participated in the study. Individuals were classified as normal weight or overweight according to body mass index. Bone mineral density (BMD), bone mineral content (BMC), LM, and FM were measured by dual-energy X-ray absorptiometry. In normal-weight adolescents, LM (β = 0.725, p < 0.001) and FM (β = 0.185, p = 0.019) were associated with lumbar spine BMC, whereas in overweight adolescents only LM (β = 0.736, p < 0.001) was associated with lumbar spine BMC. Furthermore, in the normal-weight group, FM and LM were associated with total body less head BMD (LM, β = 0.792, p < 0.001; FM, β = 0.257, p = 0.007) and lumbar spine BMD (LM, β = 0.553, p < 0.001; FM, β = 0.199, p < 0.035). In the overweight group, only LM was associated with total body less head BMD (β = 0.682, p < 0.001) and lumbar spine BMD (β = 0.528, p < 0.001). LM was the main predictor of bone mass in normal-weight and overweight adolescents. FM was associated with bone mass in normal-weight adolescents only. LM may be considered an important and useful marker in adolescents, when investigating bone health in this population. Activities that promote LM gain to reduce the risk of bone fractures and diseases in adulthood are recommended.
bibliographic citation: Bim et al. (2022) Relationship between body composition and bone mass in normal-weight and overweight adolescents. PeerJ 10:e14108 https://doi.org/10.7717/peerj.14108
date submitted: 2022-06-02
date accepted: 2022-09-02
issued: 2022-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bim
  given name: Mateus Augusto
author list: Agent
  family name: Pinto
  given name: André de Araujo
author list: Agent
  family name: Angelo
  given name: Hector Cris Colares de
author list: Agent
  family name: Gonzaga
  given name: Isadora
author list: Agent
  family name: Guimarães
  given name: Adriana Coutinho de Azevedo
author list: Agent
  family name: Felden
  given name: Érico Pereira Gomes
author list: Agent
  family name: Carvalho
  given name: Wellington Roberto Gomes de
author list: Agent
  family name: Hind
  given name: Karen
author list: Agent
  family name: Pelegrini
  given name: Andreia
doi: 10.7717/peerj.14108
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-03
copyright: ©2022 Bim et al.
attribution name: Bim et al.

The impact of aging and physical training on angiogenesis in the musculoskeletal system
type: item
type: AcademicArticle
description: Angiogenesis is the physiological process of capillary growth. It is strictly regulated by the balanced activity of agents that promote the formation of capillaries (pro-angiogenic factors) on the one hand and inhibit their growth on the other hand (anti-angiogenic factors). Capillary rarefaction and insufficient angiogenesis are some of the main causes that limit blood flow during aging, whereas physical training is a potent non-pharmacological method to intensify capillary growth in the musculoskeletal system. The main purpose of this study is to present the current state of knowledge concerning the key signalling molecules implicated in the regulation of skeletal muscle and bone angiogenesis during aging and physical training.
format: application/pdf
format: text/html
creator: Magdalena Zmudzka
creator: Jerzy A. Zoladz
creator: Joanna Majerczak
subject: Cardiology
subject: Geriatrics
subject: Kinesiology
subject: Public Health
subject: Population Biology
description: doi:10.7717/peerj.14228
publisher: PeerJ Inc.
rights: © 2022 Zmudzka et al.
abstract: Angiogenesis is the physiological process of capillary growth. It is strictly regulated by the balanced activity of agents that promote the formation of capillaries (pro-angiogenic factors) on the one hand and inhibit their growth on the other hand (anti-angiogenic factors). Capillary rarefaction and insufficient angiogenesis are some of the main causes that limit blood flow during aging, whereas physical training is a potent non-pharmacological method to intensify capillary growth in the musculoskeletal system. The main purpose of this study is to present the current state of knowledge concerning the key signalling molecules implicated in the regulation of skeletal muscle and bone angiogenesis during aging and physical training.
bibliographic citation: Zmudzka et al. (2022) The impact of aging and physical training on angiogenesis in the musculoskeletal system. PeerJ 10:e14228 https://doi.org/10.7717/peerj.14228
date submitted: 2022-05-16
date accepted: 2022-09-22
issued: 2022-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zmudzka
  given name: Magdalena
author list: Agent
  family name: Zoladz
  given name: Jerzy A.
author list: Agent
  family name: Majerczak
  given name: Joanna
doi: 10.7717/peerj.14228
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-03
copyright: ©2022 Zmudzka et al.
attribution name: Zmudzka et al.

Differences in leaf and root litter decomposition in tropical montane rainforests are mediated by soil microorganisms not by decomposer microarthropods
type: item
type: AcademicArticle
description: Background Plant litter decomposition is a key process in carbon and nutrient cycling. Among the factors determining litter decomposition rates, the role of soil biota in the decomposition of different plant litter types and its modification by variations in climatic conditions is not well understood. Methods In this study, we used litterbags with different mesh sizes (45 µm, 1 mm and 4 mm) to investigate the effect of microorganisms and decomposer microarthropods on leaf and root litter decomposition along an altitudinal gradient of tropical montane rainforests in Ecuador. We examined decomposition rates, litter C and N concentrations, microbial biomass and activity, as well as decomposer microarthropod abundance over one year of exposure at three different altitudes (1,000, 2,000 and 3,000 m). Results Leaf litter mass loss did not differ between the 1,000 and 2,000 m sites, while root litter mass loss decreased with increasing altitude. Changes in microbial biomass and activity paralleled the changes in litter decomposition rates. Access of microarthropods to litterbags only increased root litter mass loss significantly at 3,000 m. The results suggest that the impacts of climatic conditions differentially affect the decomposition of leaf and root litter, and these modifications are modulated by the quality of the local litter material. The findings also highlight litter quality as the dominant force structuring detritivore communities. Overall, the results support the view that microorganisms mostly drive decomposition processes in tropical montane rainforests with soil microarthropods playing a more important role in decomposing low-quality litter material.
format: application/pdf
format: text/html
creator: Laura M. Sánchez-Galindo
creator: Dorothee Sandmann
creator: Franca Marian
creator: Tobias Lauermann
creator: Mark Maraun
creator: Stefan Scheu
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Soil Science
subject: Zoology
description: doi:10.7717/peerj.14264
publisher: PeerJ Inc.
rights: © 2022 Sánchez-Galindo et al.
abstract: Background Plant litter decomposition is a key process in carbon and nutrient cycling. Among the factors determining litter decomposition rates, the role of soil biota in the decomposition of different plant litter types and its modification by variations in climatic conditions is not well understood. Methods In this study, we used litterbags with different mesh sizes (45 µm, 1 mm and 4 mm) to investigate the effect of microorganisms and decomposer microarthropods on leaf and root litter decomposition along an altitudinal gradient of tropical montane rainforests in Ecuador. We examined decomposition rates, litter C and N concentrations, microbial biomass and activity, as well as decomposer microarthropod abundance over one year of exposure at three different altitudes (1,000, 2,000 and 3,000 m). Results Leaf litter mass loss did not differ between the 1,000 and 2,000 m sites, while root litter mass loss decreased with increasing altitude. Changes in microbial biomass and activity paralleled the changes in litter decomposition rates. Access of microarthropods to litterbags only increased root litter mass loss significantly at 3,000 m. The results suggest that the impacts of climatic conditions differentially affect the decomposition of leaf and root litter, and these modifications are modulated by the quality of the local litter material. The findings also highlight litter quality as the dominant force structuring detritivore communities. Overall, the results support the view that microorganisms mostly drive decomposition processes in tropical montane rainforests with soil microarthropods playing a more important role in decomposing low-quality litter material.
bibliographic citation: Sánchez-Galindo et al. (2022) Differences in leaf and root litter decomposition in tropical montane rainforests are mediated by soil microorganisms not by decomposer microarthropods. PeerJ 10:e14264 https://doi.org/10.7717/peerj.14264
date submitted: 2022-04-01
date accepted: 2022-09-27
issued: 2022-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sánchez-Galindo
  given name: Laura M.
author list: Agent
  family name: Sandmann
  given name: Dorothee
author list: Agent
  family name: Marian
  given name: Franca
author list: Agent
  family name: Lauermann
  given name: Tobias
author list: Agent
  family name: Maraun
  given name: Mark
author list: Agent
  family name: Scheu
  given name: Stefan
doi: 10.7717/peerj.14264
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-03
copyright: ©2022 Sánchez-Galindo et al.
attribution name: Sánchez-Galindo et al.

Diagnostic performance of circulating tumor DNA as a minimally invasive biomarker for hepatocellular carcinoma: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Purpose This study aimed to assess the diagnostic performance of circulating tumor DNA (ctDNA) in hepatocellular carcinoma (HCC). Materials and Methods We enrolled all relevant studies published up to 5 January 2022. Three primary subgroups were investigated: qualitative or quantitative ctDNA analyses, combined alpha-fetoprotein (AFP), and ctDNA assay. In addition to the three primary subgroups, we also evaluated the diagnostic value of methylated SEPTIN9 (mSEPT9), which has been studied extensively in the diagnosis of hepatocellular carcinoma. After a search based on four primary databases, we used a bivariate linear mixed model to analyze the pooled sensitivity (SEN), specificity (SPE), positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR). We also plotted hierarchical summary receiver operating characteristics (HSROC) and utilized lambda as well as the area under the curve (AUC) to create summary receiver operating characteristic (SROC) curves to estimate the diagnostic value of ctDNA. Results A total of 59 qualified articles with 9,766 subjects were incorporated into our meta-analysis. The integrated SEN, SPE, and DOR in the qualitative studies were 0.50 (95% CI [0.43–0.56]), 0.90 (95% CI [0.86–0.93]), and 8.72 (95% CI [6.18–12.32]), respectively, yielding an AUC of 0.78 and lambda of 1.93 (95% CI [1.56–2.33]). For quantitative studies, the corresponding values were 0.69 (95% CI [0.63–0.74]), 0.84 (95% CI [0.77–0.89]), 11.88 (95% CI [7.78–18.12]), 0.81, and 2.32 (95% CI [1.96–2.69]), respectively. Six studies were included to evaluate the SETP9 methylation, which yielded an AUC of 0.86, a SEN of 0.80 (95% CI [0.71–0.87]), and a SPE of 0.77 (95% CI [0.68–0.85]). Likewise, ctDNA concentration yielded an AUC of 0.73, with a SEN of 0.63 (95% CI [0.56–0.70]) and a SPE of 0.86 (95% CI [0.74–0.93]). AFP combined with ctDNA assay resulted in an AUC of 0.89, with a SEN of 0.82 (95% CI [0.77–0.86]) and a SPE of 0.84 (95% CI [0.7…
format: application/pdf
format: text/html
creator: Jia Jie Li
creator: Yanqing Lv
creator: Huifan Ji
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.14303
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Purpose This study aimed to assess the diagnostic performance of circulating tumor DNA (ctDNA) in hepatocellular carcinoma (HCC). Materials and Methods We enrolled all relevant studies published up to 5 January 2022. Three primary subgroups were investigated: qualitative or quantitative ctDNA analyses, combined alpha-fetoprotein (AFP), and ctDNA assay. In addition to the three primary subgroups, we also evaluated the diagnostic value of methylated SEPTIN9 (mSEPT9), which has been studied extensively in the diagnosis of hepatocellular carcinoma. After a search based on four primary databases, we used a bivariate linear mixed model to analyze the pooled sensitivity (SEN), specificity (SPE), positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR). We also plotted hierarchical summary receiver operating characteristics (HSROC) and utilized lambda as well as the area under the curve (AUC) to create summary receiver operating characteristic (SROC) curves to estimate the diagnostic value of ctDNA. Results A total of 59 qualified articles with 9,766 subjects were incorporated into our meta-analysis. The integrated SEN, SPE, and DOR in the qualitative studies were 0.50 (95% CI [0.43–0.56]), 0.90 (95% CI [0.86–0.93]), and 8.72 (95% CI [6.18–12.32]), respectively, yielding an AUC of 0.78 and lambda of 1.93 (95% CI [1.56–2.33]). For quantitative studies, the corresponding values were 0.69 (95% CI [0.63–0.74]), 0.84 (95% CI [0.77–0.89]), 11.88 (95% CI [7.78–18.12]), 0.81, and 2.32 (95% CI [1.96–2.69]), respectively. Six studies were included to evaluate the SETP9 methylation, which yielded an AUC of 0.86, a SEN of 0.80 (95% CI [0.71–0.87]), and a SPE of 0.77 (95% CI [0.68–0.85]). Likewise, ctDNA concentration yielded an AUC of 0.73, with a SEN of 0.63 (95% CI [0.56–0.70]) and a SPE of 0.86 (95% CI [0.74–0.93]). AFP combined with ctDNA assay resulted in an AUC of 0.89, with a SEN of 0.82 (95% CI [0.77–0.86]) and a SPE of 0.84 (95% CI [0.7…
bibliographic citation: Li et al. (2022) Diagnostic performance of circulating tumor DNA as a minimally invasive biomarker for hepatocellular carcinoma: a systematic review and meta-analysis. PeerJ 10:e14303 https://doi.org/10.7717/peerj.14303
date submitted: 2022-05-05
date accepted: 2022-10-05
issued: 2022-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jia Jie
author list: Agent
  family name: Lv
  given name: Yanqing
author list: Agent
  family name: Ji
  given name: Huifan
doi: 10.7717/peerj.14303
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-03
copyright: ©2022 Li et al.
attribution name: Li et al.

Comparison of epiphytic and intestinal bacterial communities in freshwater snails (Bellamya aeruginosa) living on submerged plants
type: item
type: AcademicArticle
description: The combination of submerged plants and snails can combat eutrophication of freshwater systems by suppressing algal growth and assimilating nutrients. By consuming epiphytes, snails can benefit the growth of submerged plants. However, the efficiency of this phytoremediation strategy may depend on the microbes associated with the plants and snails. In this study, we compared the epiphytic bacterial communities on submerged plants (Vallisneria natans and Cabomba caroliniana) and intestinal bacterial communities of a snail, Bellamya aeruginosa, found on these plants using 16S rRNA gene sequencing. Epiphytic bacterial communities were similar between the two plant species and snails shared a high proportion of snail intestinal bacterial OTUs (75%) and genera (85%) with plants they grazed on. However, significant variations of Bray-Curtis distances differentiated epiphytic and intestinal bacterial communities. In addition, between the top 50 genera shared by intestinal and epiphytic bacterial communities, more Spearman correlations were detected within bacterial communities associated with snails than between communities associated with plants (190 vs. 143), and the correlations in epiphytic bacterial networks were more concentrated on certain genera, indicating they possessed distinct bacterial networks. This suggests the bacterial communities associated with snails do not depend strongly on the plant they graze on, which may be important for better understanding the role of snails in aquatic eco-restoration.
format: application/pdf
format: text/html
creator: Fucai Liu
creator: Kejun Li
subject: Microbiology
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.14318
publisher: PeerJ Inc.
rights: © 2022 Liu and Li
abstract: The combination of submerged plants and snails can combat eutrophication of freshwater systems by suppressing algal growth and assimilating nutrients. By consuming epiphytes, snails can benefit the growth of submerged plants. However, the efficiency of this phytoremediation strategy may depend on the microbes associated with the plants and snails. In this study, we compared the epiphytic bacterial communities on submerged plants (Vallisneria natans and Cabomba caroliniana) and intestinal bacterial communities of a snail, Bellamya aeruginosa, found on these plants using 16S rRNA gene sequencing. Epiphytic bacterial communities were similar between the two plant species and snails shared a high proportion of snail intestinal bacterial OTUs (75%) and genera (85%) with plants they grazed on. However, significant variations of Bray-Curtis distances differentiated epiphytic and intestinal bacterial communities. In addition, between the top 50 genera shared by intestinal and epiphytic bacterial communities, more Spearman correlations were detected within bacterial communities associated with snails than between communities associated with plants (190 vs. 143), and the correlations in epiphytic bacterial networks were more concentrated on certain genera, indicating they possessed distinct bacterial networks. This suggests the bacterial communities associated with snails do not depend strongly on the plant they graze on, which may be important for better understanding the role of snails in aquatic eco-restoration.
bibliographic citation: Liu et al. (2022) Comparison of epiphytic and intestinal bacterial communities in freshwater snails (Bellamya aeruginosa) living on submerged plants. PeerJ 10:e14318 https://doi.org/10.7717/peerj.14318
date submitted: 2022-07-07
date accepted: 2022-10-09
issued: 2022-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Fucai
author list: Agent
  family name: Li
  given name: Kejun
doi: 10.7717/peerj.14318
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-03
copyright: ©2022 Liu and Li
attribution name: Liu and Li

Publication delays and associated factors in ophthalmology journals
type: item
type: AcademicArticle
description: Introduction This study aimed to evaluate the publication delays and correlative factors of peer-reviewed ophthalmology journals. Methods The ophthalmology journals listed in the Journal Citation Report 2020 were retrieved from the Web of Science database. The first original research article of each journal issue from January to December 2020 was extracted, and its submission, final revision, acceptance, and publication dates were obtained. Information on impact factors, advance online publication (AOP) status, open access (OA) rate and acceptance rate in 2020 was also collected. The correlations between publication delays and potential associated factors were analyzed. Results A total of 58 ophthalmology journals were included and information on 685 articles was collected. The median times from submission to acceptance, from acceptance to publication, and from submission to publication were 118.0 (IQR, 74.0–185.0) days, 31.0 (IQR, 15.0–64.0) days, and 161.0 (IQR, 111.0–232.0) days, respectively. A higher impact factor was correlated with shorter delays of acceptance and publication (P < 0.05). There was a positive correlation between acceptance rates and publication delays (r = 0.726, P = 0.007). Forty-seven (81.03%) journals provided AOP. There was no statistically significant difference for impact factors and publication delays between journal with and without AOP (all P > 0.05). No correlation between OA rate and publication delays or impact factors was detected (all P > 0.05). Conclusions Journals with higher impact factors and lower acceptance rates tend to have quicker publication processes. No significant associations were detected between publication delays and AOP or OA rate.
format: application/pdf
format: text/html
creator: Yinglin Yu
creator: Wei Li
creator: Chaoqun Xu
creator: Yuan Tan
creator: Weining Zhu
creator: Bowen Zhang
creator: Yingshi Zou
creator: Leyi Hu
creator: Guangming Jin
creator: Zhenzhen Liu
subject: Ophthalmology
subject: Science and Medical Education
description: doi:10.7717/peerj.14331
publisher: PeerJ Inc.
rights: © 2022 Yu et al.
abstract: Introduction This study aimed to evaluate the publication delays and correlative factors of peer-reviewed ophthalmology journals. Methods The ophthalmology journals listed in the Journal Citation Report 2020 were retrieved from the Web of Science database. The first original research article of each journal issue from January to December 2020 was extracted, and its submission, final revision, acceptance, and publication dates were obtained. Information on impact factors, advance online publication (AOP) status, open access (OA) rate and acceptance rate in 2020 was also collected. The correlations between publication delays and potential associated factors were analyzed. Results A total of 58 ophthalmology journals were included and information on 685 articles was collected. The median times from submission to acceptance, from acceptance to publication, and from submission to publication were 118.0 (IQR, 74.0–185.0) days, 31.0 (IQR, 15.0–64.0) days, and 161.0 (IQR, 111.0–232.0) days, respectively. A higher impact factor was correlated with shorter delays of acceptance and publication (P < 0.05). There was a positive correlation between acceptance rates and publication delays (r = 0.726, P = 0.007). Forty-seven (81.03%) journals provided AOP. There was no statistically significant difference for impact factors and publication delays between journal with and without AOP (all P > 0.05). No correlation between OA rate and publication delays or impact factors was detected (all P > 0.05). Conclusions Journals with higher impact factors and lower acceptance rates tend to have quicker publication processes. No significant associations were detected between publication delays and AOP or OA rate.
bibliographic citation: Yu et al. (2022) Publication delays and associated factors in ophthalmology journals. PeerJ 10:e14331 https://doi.org/10.7717/peerj.14331
date submitted: 2022-06-21
date accepted: 2022-10-11
issued: 2022-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Yinglin
author list: Agent
  family name: Li
  given name: Wei
author list: Agent
  family name: Xu
  given name: Chaoqun
author list: Agent
  family name: Tan
  given name: Yuan
author list: Agent
  family name: Zhu
  given name: Weining
author list: Agent
  family name: Zhang
  given name: Bowen
author list: Agent
  family name: Zou
  given name: Yingshi
author list: Agent
  family name: Hu
  given name: Leyi
author list: Agent
  family name: Jin
  given name: Guangming
author list: Agent
  family name: Liu
  given name: Zhenzhen
doi: 10.7717/peerj.14331
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-03
copyright: © 2022 Yu et al.
attribution name: Yu et al.

Gender differences in general health and happiness: a study on Iranian engineering students
type: item
type: AcademicArticle
description: This article aims to determine the relationship between general health and happiness in male and female engineering students in Iran. The analysis relies on a unique dataset collected through two questionnaires (Oxford Happiness and GHQ28) from a representative sample (n = 2,000). Although similar data have been collected quite independently by different communities of researchers, and empirical evidence points to very similar underlying mechanisms, but they did not consider non-normal distribution samples. In this study, data were analyzed by Kruskal–Wallis and Wilcoxon’s signed rank tests. The mean happiness and general health were 42.89 ± 14.84 and 23.76 ± 13.28, respectively. There was a positive and significant relationship between these two variables (P ≤ 0.05, r = 0.59). Happiness showed significant differences in males and females, but general health did not. In general, female students enjoyed more health and happiness. This study argues that clarifying the relationship between happiness and health in different genders can help academic authorities and youth planners to pay special attention to this issue and provide particular programs.
format: application/pdf
format: text/html
creator: Asieh Namazi
subject: Psychiatry and Psychology
subject: Public Health
subject: Science and Medical Education
subject: Mental Health
description: doi:10.7717/peerj.14339
publisher: PeerJ Inc.
rights: © 2022 Namazi
abstract: This article aims to determine the relationship between general health and happiness in male and female engineering students in Iran. The analysis relies on a unique dataset collected through two questionnaires (Oxford Happiness and GHQ28) from a representative sample (n = 2,000). Although similar data have been collected quite independently by different communities of researchers, and empirical evidence points to very similar underlying mechanisms, but they did not consider non-normal distribution samples. In this study, data were analyzed by Kruskal–Wallis and Wilcoxon’s signed rank tests. The mean happiness and general health were 42.89 ± 14.84 and 23.76 ± 13.28, respectively. There was a positive and significant relationship between these two variables (P ≤ 0.05, r = 0.59). Happiness showed significant differences in males and females, but general health did not. In general, female students enjoyed more health and happiness. This study argues that clarifying the relationship between happiness and health in different genders can help academic authorities and youth planners to pay special attention to this issue and provide particular programs.
bibliographic citation: Namazi (2022) Gender differences in general health and happiness: a study on Iranian engineering students. PeerJ 10:e14339 https://doi.org/10.7717/peerj.14339
date submitted: 2022-09-16
date accepted: 2022-10-13
issued: 2022-11-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Namazi
  given name: Asieh
doi: 10.7717/peerj.14339
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-03
copyright: © 2022 Namazi
attribution name: Namazi

Nitrogen fertilizer amount has minimal effect on rhizosphere bacterial diversity during different growth stages of peanut
type: item
type: AcademicArticle
description: The impact of short-term nitrogen fertilizer input on the structure and diversity of peanut rhizosphere microbiota (RM) at different growth stages (GSs) was explored in the southern paddy soil planting environment. Three levels of nitrogen were applied in the field: control (LN, 0 kg/hm2), medium nitrogen (MN, 55.68 kg/hm2), and high nitrogen (HN, 111.36 kg/hm2). The rhizosphere soil was collected during four GSs for high-throughput sequencing and chemical properties analysis. The effect of nitrogen fertilizer application on peanut RM was minimal and was obvious only at the seedling stage. In the four peanut GSs, a significant increase in relative abundance was observed for only one operational taxonomic unit (OTU) of Nitrospira under HN conditions at the seedling stage and mature stage, while there was no consistent change in other OTUs. The difference in RM among different peanut GSs was greater than that caused by the amount of nitrogen fertilizer. This may be due to the substantial differences in soil chemical properties (especially alkali-hydrolyzable nitrogen, pH, and available potassium or total potassium) among peanut GSs, as these significantly affected the RM structure. These results are of great value to facilitate deeper understanding of the effect of nitrogen fertilizer on peanut RM structure.
format: application/pdf
format: text/html
creator: Zheng Yang
creator: Lin Li
creator: Wenjuan Zhu
creator: Siyuan Xiao
creator: Siyu Chen
creator: Jing Liu
creator: Qian Xu
creator: Feng Guo
creator: Shile Lan
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13962
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: The impact of short-term nitrogen fertilizer input on the structure and diversity of peanut rhizosphere microbiota (RM) at different growth stages (GSs) was explored in the southern paddy soil planting environment. Three levels of nitrogen were applied in the field: control (LN, 0 kg/hm2), medium nitrogen (MN, 55.68 kg/hm2), and high nitrogen (HN, 111.36 kg/hm2). The rhizosphere soil was collected during four GSs for high-throughput sequencing and chemical properties analysis. The effect of nitrogen fertilizer application on peanut RM was minimal and was obvious only at the seedling stage. In the four peanut GSs, a significant increase in relative abundance was observed for only one operational taxonomic unit (OTU) of Nitrospira under HN conditions at the seedling stage and mature stage, while there was no consistent change in other OTUs. The difference in RM among different peanut GSs was greater than that caused by the amount of nitrogen fertilizer. This may be due to the substantial differences in soil chemical properties (especially alkali-hydrolyzable nitrogen, pH, and available potassium or total potassium) among peanut GSs, as these significantly affected the RM structure. These results are of great value to facilitate deeper understanding of the effect of nitrogen fertilizer on peanut RM structure.
bibliographic citation: Yang et al. (2022) Nitrogen fertilizer amount has minimal effect on rhizosphere bacterial diversity during different growth stages of peanut. PeerJ 10:e13962 https://doi.org/10.7717/peerj.13962
date submitted: 2022-04-08
date accepted: 2022-08-08
issued: 2022-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Zheng
author list: Agent
  family name: Li
  given name: Lin
author list: Agent
  family name: Zhu
  given name: Wenjuan
author list: Agent
  family name: Xiao
  given name: Siyuan
author list: Agent
  family name: Chen
  given name: Siyu
author list: Agent
  family name: Liu
  given name: Jing
author list: Agent
  family name: Xu
  given name: Qian
author list: Agent
  family name: Guo
  given name: Feng
author list: Agent
  family name: Lan
  given name: Shile
doi: 10.7717/peerj.13962
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-02
copyright: © 2022 Yang et al.
attribution name: Yang et al.

Molecular phylogeny of Columbellidae (Gastropoda: Neogastropoda)
type: item
type: AcademicArticle
description: The neogastropod family Columbellidae is a highly successful group of small, primarily epibenthic marine snails distributed worldwide and most abundant in the tropics. The great diversity of the group makes them attractive for studying evolutionary shifts in gastropod anatomy, morphology, ecology and diversity. The existing classification of the family has been based to a large degree on the morphology of the shell and radula. Indeed, membership in the family is traditionally confirmed using the unique morphology of the radula. To reconstruct columbellid phylogeny and assess monophyly of the group, we assembled a multilocus dataset including five mitochondrial and nuclear genes, for 70 species in 31 genera. Phylogenetic analyses using Bayesian inference and maximum likelihood are not well enough resolved to support a subfamilial classification, but do support the monophyly of the family and of several well-defined genera and supra-generic groupings. Two of the most diverse nominal genera, Mitrella and Anachis, are supported as highly polyphyletic. Overall, the resulting topologies indicate that the generic and subfamilial classification is in need of extensive revision but that phylogenomic data are needed to resolve columbellid relationships.
format: application/pdf
format: text/html
creator: Marta deMaintenon
creator: Ellen E. Strong
subject: Biodiversity
subject: Evolutionary Studies
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.13996
publisher: PeerJ Inc.
rights: © 2022 deMaintenon and Strong
abstract: The neogastropod family Columbellidae is a highly successful group of small, primarily epibenthic marine snails distributed worldwide and most abundant in the tropics. The great diversity of the group makes them attractive for studying evolutionary shifts in gastropod anatomy, morphology, ecology and diversity. The existing classification of the family has been based to a large degree on the morphology of the shell and radula. Indeed, membership in the family is traditionally confirmed using the unique morphology of the radula. To reconstruct columbellid phylogeny and assess monophyly of the group, we assembled a multilocus dataset including five mitochondrial and nuclear genes, for 70 species in 31 genera. Phylogenetic analyses using Bayesian inference and maximum likelihood are not well enough resolved to support a subfamilial classification, but do support the monophyly of the family and of several well-defined genera and supra-generic groupings. Two of the most diverse nominal genera, Mitrella and Anachis, are supported as highly polyphyletic. Overall, the resulting topologies indicate that the generic and subfamilial classification is in need of extensive revision but that phylogenomic data are needed to resolve columbellid relationships.
bibliographic citation: deMaintenon et al. (2022) Molecular phylogeny of Columbellidae (Gastropoda: Neogastropoda). PeerJ 10:e13996 https://doi.org/10.7717/peerj.13996
date submitted: 2022-03-02
date accepted: 2022-08-12
issued: 2022-11-02
is part of: PeerJ
license: open-government-licence
author list: Agent
  family name: deMaintenon
  given name: Marta
author list: Agent
  family name: Strong
  given name: Ellen E.
doi: 10.7717/peerj.13996
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-02
copyright: ©2022 deMaintenon and Strong
attribution name: deMaintenon and Strong

Cranial osteology, taxonomic reassessment, and phylogenetic relationships of the Early Cretaceous (Aptian-Albian) turtle Trinitichelys hiatti (Paracryptodira)
type: item
type: AcademicArticle
description: We describe the skull of the Early Cretaceous (Aptian-Albian) baenid turtle Trinitichelys hiatti using micro-computed tomography to provide new insights into the cranial anatomy of basal baenids and into the evolution of paracryptodires. We show that the validity of Trinitichelys hiatti vs Arundelemys dardeni still holds true, that the most basal known baenids for which skull material is known share an intriguing combination of features that are typical of either Pleurosternidae or Baenidae, and that the carotid system of Trinitichelys hiatti is intermediate to that of pleurosternids and more advanced baenids. Our expanded phylogenetic analysis confirms the traditional placement of Arundelemys dardeni, Lakotemys australodakotensis, and Trinitichelys hiatti as basal baenids, retrieves Helochelydridae along the stem of Baenoidea, but recovers Dinochelys whitei, Glyptops ornatus, Dorsetochelys typocardium, and Uluops uluops as basal branching Paracryptodira.
format: application/pdf
format: text/html
creator: Yann Rollot
creator: Serjoscha W. Evers
creator: Stephanie E. Pierce
creator: Walter G. Joyce
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.14138
publisher: PeerJ Inc.
rights: © 2022 Rollot et al.
abstract: We describe the skull of the Early Cretaceous (Aptian-Albian) baenid turtle Trinitichelys hiatti using micro-computed tomography to provide new insights into the cranial anatomy of basal baenids and into the evolution of paracryptodires. We show that the validity of Trinitichelys hiatti vs Arundelemys dardeni still holds true, that the most basal known baenids for which skull material is known share an intriguing combination of features that are typical of either Pleurosternidae or Baenidae, and that the carotid system of Trinitichelys hiatti is intermediate to that of pleurosternids and more advanced baenids. Our expanded phylogenetic analysis confirms the traditional placement of Arundelemys dardeni, Lakotemys australodakotensis, and Trinitichelys hiatti as basal baenids, retrieves Helochelydridae along the stem of Baenoidea, but recovers Dinochelys whitei, Glyptops ornatus, Dorsetochelys typocardium, and Uluops uluops as basal branching Paracryptodira.
bibliographic citation: Rollot et al. (2022) Cranial osteology, taxonomic reassessment, and phylogenetic relationships of the Early Cretaceous (Aptian-Albian) turtle Trinitichelys hiatti (Paracryptodira). PeerJ 10:e14138 https://doi.org/10.7717/peerj.14138
date submitted: 2022-03-21
date accepted: 2022-09-06
issued: 2022-11-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rollot
  given name: Yann
author list: Agent
  family name: Evers
  given name: Serjoscha W.
author list: Agent
  family name: Pierce
  given name: Stephanie E.
author list: Agent
  family name: Joyce
  given name: Walter G.
doi: 10.7717/peerj.14138
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-02
copyright: © 2022 Rollot et al.
attribution name: Rollot et al.

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