PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Biogeography of the Southern Ocean: environmental factors driving mesoplankton distribution South of Africa
items: Nostolepis scale remains (stem Chondrichthyes) from the Lower Devonian of Qujing, Yunnan, China
items: Type of organic fertilizer rather than organic amendment per se increases abundance of soil biota
items: The regulation of immune checkpoints by the hypoxic tumor microenvironment
items: DNA methylome and transcriptome analysis established a model of four differentially methylated positions (DMPs) as a diagnostic marker in esophageal adenocarcinoma early detection
items: Transgenerational effects on development following microplastic exposure in Drosophila melanogaster
items: The impact of COVID-19 pandemic on nitrogen dioxide levels in Nigeria
items: Effects of education methods on self-efficacy of smoking cessation counseling among medical students
items: Competing endogenous RNA network identifies mRNA biomarkers for overall survival of lung adenocarcinoma: two novel on-line precision medicine predictive tools
items: https://peerj.com/articles/11179

Biogeography of the Southern Ocean: environmental factors driving mesoplankton distribution South of Africa
type: item
type: AcademicArticle
description: Spatial distribution of zooplankton communities depends on numerous factors, especially temperature and salinity conditions (hydrological factor), sampled depth, chlorophyll concentration, and diel cycle. We analyzed and compared the impact of these factors on mesoplankton abundance, biodiversity, quantitative structure based on proportion of taxa and qualitative structure based on presence/absence of taxa in the Southern Ocean. Samples (43 stations, three vertical strata sampled at each station, 163 taxa identified) were collected with a Juday net along the SR02 transect in December 2009. Mesoplankton abundance in discrete vertical layers ranged from 0.2 to 13,743.6 ind. m−3, i.e., five orders of magnitude, maximal and minimal values were recorded in the upper mixed and in the deepest layer, respectively. Within the combined 300-m layer, abundances ranged from 16.0 to 1,455.0 ind. m−3, i.e., two orders of magnitude suggesting that integral samples provide little information about actual variations of mesoplankton abundances. A set of analyses showed that depth was the major driver of mesoplankton distribution (abundance, biodiversity, quantitative structure), hydrological factors influenced two of them (quantitative and qualitative structure), chlorophyll concentration strongly affected only quantitative structure, and diel cycle had an insignificant effect on mesoplankton distribution. Using our current knowledge of the fine structure of the Antarctic Circumpolar Current, we compared effects of four hydrological fronts, i.e., boundaries between different water-masses with distinct environmental characteristics, and eight dynamic jets (narrow yet very intense currents) on mesoplankton distribution. Subtropical, Polar, and Subantarctic Fronts drove quantitative and qualitative structure of mesoplankton assemblages (decreasing in order of influence), while the Southern Boundary affected only qualitative structure. Effects of dynamic jets were insignificant. We sugges…
format: application/pdf
format: text/html
creator: Alexander Vereshchaka
creator: Eteri Musaeva
creator: Anastasiia Lunina
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Biological Oceanography
description: doi:10.7717/peerj.11411
publisher: PeerJ Inc.
rights: © 2021 Vereshchaka et al.
abstract: Spatial distribution of zooplankton communities depends on numerous factors, especially temperature and salinity conditions (hydrological factor), sampled depth, chlorophyll concentration, and diel cycle. We analyzed and compared the impact of these factors on mesoplankton abundance, biodiversity, quantitative structure based on proportion of taxa and qualitative structure based on presence/absence of taxa in the Southern Ocean. Samples (43 stations, three vertical strata sampled at each station, 163 taxa identified) were collected with a Juday net along the SR02 transect in December 2009. Mesoplankton abundance in discrete vertical layers ranged from 0.2 to 13,743.6 ind. m−3, i.e., five orders of magnitude, maximal and minimal values were recorded in the upper mixed and in the deepest layer, respectively. Within the combined 300-m layer, abundances ranged from 16.0 to 1,455.0 ind. m−3, i.e., two orders of magnitude suggesting that integral samples provide little information about actual variations of mesoplankton abundances. A set of analyses showed that depth was the major driver of mesoplankton distribution (abundance, biodiversity, quantitative structure), hydrological factors influenced two of them (quantitative and qualitative structure), chlorophyll concentration strongly affected only quantitative structure, and diel cycle had an insignificant effect on mesoplankton distribution. Using our current knowledge of the fine structure of the Antarctic Circumpolar Current, we compared effects of four hydrological fronts, i.e., boundaries between different water-masses with distinct environmental characteristics, and eight dynamic jets (narrow yet very intense currents) on mesoplankton distribution. Subtropical, Polar, and Subantarctic Fronts drove quantitative and qualitative structure of mesoplankton assemblages (decreasing in order of influence), while the Southern Boundary affected only qualitative structure. Effects of dynamic jets were insignificant. We sugges…
bibliographic citation: Vereshchaka et al. (2021) Biogeography of the Southern Ocean: environmental factors driving mesoplankton distribution South of Africa. PeerJ 9:e11411 https://doi.org/10.7717/peerj.11411
date submitted: 2020-10-19
date accepted: 2021-04-14
issued: 2021-05-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vereshchaka
  given name: Alexander
author list: Agent
  family name: Musaeva
  given name: Eteri
author list: Agent
  family name: Lunina
  given name: Anastasiia
doi: 10.7717/peerj.11411
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-10
copyright: © 2021 Vereshchaka et al.
attribution name: Vereshchaka et al.

Nostolepis scale remains (stem Chondrichthyes) from the Lower Devonian of Qujing, Yunnan, China
type: item
type: AcademicArticle
description: Based initially on microfossils, Nostolepis is one of the first known ‘acanthodians’, which constitute a paraphyletic assemblage of plesiomorphic members of the total group Chondrichthyes. Its wide distribution has potential implications for stratigraphic comparisons worldwide. Six species of Nostolepis have been reported in China, including one species from the Xitun Formation (Lochkovian, Lower Devonian) of Qujing, eastern Yunnan. Acid preparation of rock samples from the Xitun Formation has yielded abundant acanthodian remains. Based on both morphological and histological examinations, here we identify five species of Nostolepis, including two new species. N. qujingensis sp. nov. is characterized by thin scales devoid of the neck anteriorly and the dentine tubules rarely present in the anterior part of the crown. N. digitus sp. nov. is characterized by parallel ridges on anterior and lateral margins of the crown, and the neck constricted and ornamented with pore openings. We extend the duration of N. striata in China from the Pridoli of Silurian (Yulungssu Formation) to the Lower Devonian in Qujing and report the first occurrences of N. amplifica and N. consueta in this region. This study increases the diversity of the Lower Devonian Xitun Fauna and provides a better understanding of the paleogeographic distribution of Nostolepis.
format: application/pdf
format: text/html
creator: Qiang Li
creator: Xindong Cui
creator: Plamen Stanislavov Andreev
creator: Wenjin Zhao
creator: Jianhua Wang
creator: Lijian Peng
creator: Min Zhu
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11093
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Based initially on microfossils, Nostolepis is one of the first known ‘acanthodians’, which constitute a paraphyletic assemblage of plesiomorphic members of the total group Chondrichthyes. Its wide distribution has potential implications for stratigraphic comparisons worldwide. Six species of Nostolepis have been reported in China, including one species from the Xitun Formation (Lochkovian, Lower Devonian) of Qujing, eastern Yunnan. Acid preparation of rock samples from the Xitun Formation has yielded abundant acanthodian remains. Based on both morphological and histological examinations, here we identify five species of Nostolepis, including two new species. N. qujingensis sp. nov. is characterized by thin scales devoid of the neck anteriorly and the dentine tubules rarely present in the anterior part of the crown. N. digitus sp. nov. is characterized by parallel ridges on anterior and lateral margins of the crown, and the neck constricted and ornamented with pore openings. We extend the duration of N. striata in China from the Pridoli of Silurian (Yulungssu Formation) to the Lower Devonian in Qujing and report the first occurrences of N. amplifica and N. consueta in this region. This study increases the diversity of the Lower Devonian Xitun Fauna and provides a better understanding of the paleogeographic distribution of Nostolepis.
bibliographic citation: Li et al. (2021) Nostolepis scale remains (stem Chondrichthyes) from the Lower Devonian of Qujing, Yunnan, China. PeerJ 9:e11093 https://doi.org/10.7717/peerj.11093
date submitted: 2021-01-07
date accepted: 2021-02-21
issued: 2021-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Qiang
author list: Agent
  family name: Cui
  given name: Xindong
author list: Agent
  family name: Andreev
  given name: Plamen Stanislavov
author list: Agent
  family name: Zhao
  given name: Wenjin
author list: Agent
  family name: Wang
  given name: Jianhua
author list: Agent
  family name: Peng
  given name: Lijian
author list: Agent
  family name: Zhu
  given name: Min
doi: 10.7717/peerj.11093
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-07
copyright: ©2021 Li et al.
attribution name: Li et al.

Type of organic fertilizer rather than organic amendment per se increases abundance of soil biota
type: item
type: AcademicArticle
description: Addition of organic amendments is a commonly used practice to offset potential loss of soil organic matter from agricultural soils. The aim of the present study was to examine how long-term addition of organic matter affects the abundance of different soil biota across trophic levels and the role that the quality of the organic amendments plays. Here we used a 17-year-old fertilization experiment to investigate soil biota responses to four different organic fertilizers, compared with two mineral nitrogen fertilizers and no fertilization, where the organic fertilizers had similar carbon content but varied in their carbon to nitrogen ratios. We collected soil samples and measured a wide range of organisms belonging to different functional groups and trophic levels of the soil food web. Long-term addition of organic and mineral fertilizers had beneficial effects on the abundances of most soil organisms compared with unfertilized soil, but the responses differed between soil biota. The organic fertilizers generally enhanced bacteria and earthworms. Fungi and nematodes responded positively to certain mineral and organic fertilizers, indicating that multiple factors influenced by the fertilization may affect these heterogeneous groups. Springtails and mites were less affected by fertilization than the other groups, as they were present at relatively high abundances even in the unfertilized treatment. However, soil pH had a great influence on springtail abundance. In summary, the specific fertilizer was more important in determining the numerical and compositional responses of soil biota than whether it was mineral or organic. Overall, biennial organic amendments emerge as insufficient, by themselves, to promote soil organisms in the long run, and would need to be added annually or combined with other practices affecting soil quality, such as no or reduced tillage and other crop rotations, to have a beneficial effect.
format: application/pdf
format: text/html
creator: Maria Viketoft
creator: Laura G.A. Riggi
creator: Riccardo Bommarco
creator: Sara Hallin
creator: Astrid R. Taylor
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.11204
publisher: PeerJ Inc.
rights: © 2021 Viketoft et al.
abstract: Addition of organic amendments is a commonly used practice to offset potential loss of soil organic matter from agricultural soils. The aim of the present study was to examine how long-term addition of organic matter affects the abundance of different soil biota across trophic levels and the role that the quality of the organic amendments plays. Here we used a 17-year-old fertilization experiment to investigate soil biota responses to four different organic fertilizers, compared with two mineral nitrogen fertilizers and no fertilization, where the organic fertilizers had similar carbon content but varied in their carbon to nitrogen ratios. We collected soil samples and measured a wide range of organisms belonging to different functional groups and trophic levels of the soil food web. Long-term addition of organic and mineral fertilizers had beneficial effects on the abundances of most soil organisms compared with unfertilized soil, but the responses differed between soil biota. The organic fertilizers generally enhanced bacteria and earthworms. Fungi and nematodes responded positively to certain mineral and organic fertilizers, indicating that multiple factors influenced by the fertilization may affect these heterogeneous groups. Springtails and mites were less affected by fertilization than the other groups, as they were present at relatively high abundances even in the unfertilized treatment. However, soil pH had a great influence on springtail abundance. In summary, the specific fertilizer was more important in determining the numerical and compositional responses of soil biota than whether it was mineral or organic. Overall, biennial organic amendments emerge as insufficient, by themselves, to promote soil organisms in the long run, and would need to be added annually or combined with other practices affecting soil quality, such as no or reduced tillage and other crop rotations, to have a beneficial effect.
bibliographic citation: Viketoft et al. (2021) Type of organic fertilizer rather than organic amendment per se increases abundance of soil biota. PeerJ 9:e11204 https://doi.org/10.7717/peerj.11204
date submitted: 2020-10-14
date accepted: 2021-03-11
issued: 2021-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Viketoft
  given name: Maria
author list: Agent
  family name: Riggi
  given name: Laura G.A.
author list: Agent
  family name: Bommarco
  given name: Riccardo
author list: Agent
  family name: Hallin
  given name: Sara
author list: Agent
  family name: Taylor
  given name: Astrid R.
doi: 10.7717/peerj.11204
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-07
copyright: ©2021 Viketoft et al.
attribution name: Viketoft et al.

The regulation of immune checkpoints by the hypoxic tumor microenvironment
type: item
type: AcademicArticle
description: The tumor microenvironment (TME) influences the occurrence and progression of tumors, and hypoxia is an important characteristic of the TME. The expression of programmed death 1 (PD1)/programmed death-ligand 1 (PDL1), cytotoxic T-lymphocyte-associated antigen 4 (CTLA4), and other immune checkpoints in hypoxic malignant tumors is often significantly increased, and is associated with poor prognosis. The application of immune checkpoint inhibitors (ICIs) for treating lung cancer, urothelial carcinoma, and gynecological tumors has achieved encouraging efficacy; however, the rate of efficacy of ICI single-drug treatment is only about 20%. In the present review, we discuss the possible mechanisms by which the hypoxic TME regulates immune checkpoints. By activating hypoxia-inducible factor-1α (HIF-1α), regulating the adenosine (Ado)-A2aR pathway, regulating the glycolytic pathway, and driving epithelial-mesenchymal transition (EMT) and other biological pathways, hypoxia regulates the expression levels of CTLA4, PD1, PDL1, CD47, lymphocyte activation gene 3 (LAG3), T-cell immunoglobulin and mucin domain 3 (TIM3), and other immune checkpoints, which interfere with the immune effector cell anti-tumor response and provide convenient conditions for tumors to escape immune surveillance. The combination of HIF-1α inhibitors, Ado-inhibiting tumor immune microenvironment regulatory drugs, and other drugs with ICIs has good efficacy in both preclinical studies and phase I-II clinical studies. Exploring the effects of TME hypoxia on the expression of immune checkpoints and the function of infiltrating immune cells has greatly clarified the relationship between the hypoxic TME and immune escape, which is of great significance for the development of new drugs and the search for predictive markers of the efficacy of immunotherapy for treating malignant tumors. In the future, combination therapy with hypoxia pathway inhibitors and ICIs may be an effective anti-tumor treatment strategy.
format: application/pdf
format: text/html
creator: Min Hu
creator: Yongfu Li
creator: Yuting Lu
creator: Miao Wang
creator: Yingrui Li
creator: Chaoying Wang
creator: Qin Li
creator: Hong Zhao
subject: Biochemistry
subject: Genetics
subject: Molecular Biology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.11306
publisher: PeerJ Inc.
rights: © 2021 Hu et al.
abstract: The tumor microenvironment (TME) influences the occurrence and progression of tumors, and hypoxia is an important characteristic of the TME. The expression of programmed death 1 (PD1)/programmed death-ligand 1 (PDL1), cytotoxic T-lymphocyte-associated antigen 4 (CTLA4), and other immune checkpoints in hypoxic malignant tumors is often significantly increased, and is associated with poor prognosis. The application of immune checkpoint inhibitors (ICIs) for treating lung cancer, urothelial carcinoma, and gynecological tumors has achieved encouraging efficacy; however, the rate of efficacy of ICI single-drug treatment is only about 20%. In the present review, we discuss the possible mechanisms by which the hypoxic TME regulates immune checkpoints. By activating hypoxia-inducible factor-1α (HIF-1α), regulating the adenosine (Ado)-A2aR pathway, regulating the glycolytic pathway, and driving epithelial-mesenchymal transition (EMT) and other biological pathways, hypoxia regulates the expression levels of CTLA4, PD1, PDL1, CD47, lymphocyte activation gene 3 (LAG3), T-cell immunoglobulin and mucin domain 3 (TIM3), and other immune checkpoints, which interfere with the immune effector cell anti-tumor response and provide convenient conditions for tumors to escape immune surveillance. The combination of HIF-1α inhibitors, Ado-inhibiting tumor immune microenvironment regulatory drugs, and other drugs with ICIs has good efficacy in both preclinical studies and phase I-II clinical studies. Exploring the effects of TME hypoxia on the expression of immune checkpoints and the function of infiltrating immune cells has greatly clarified the relationship between the hypoxic TME and immune escape, which is of great significance for the development of new drugs and the search for predictive markers of the efficacy of immunotherapy for treating malignant tumors. In the future, combination therapy with hypoxia pathway inhibitors and ICIs may be an effective anti-tumor treatment strategy.
bibliographic citation: Hu et al. (2021) The regulation of immune checkpoints by the hypoxic tumor microenvironment. PeerJ 9:e11306 https://doi.org/10.7717/peerj.11306
date submitted: 2020-12-07
date accepted: 2021-03-29
issued: 2021-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Min
author list: Agent
  family name: Li
  given name: Yongfu
author list: Agent
  family name: Lu
  given name: Yuting
author list: Agent
  family name: Wang
  given name: Miao
author list: Agent
  family name: Li
  given name: Yingrui
author list: Agent
  family name: Wang
  given name: Chaoying
author list: Agent
  family name: Li
  given name: Qin
author list: Agent
  family name: Zhao
  given name: Hong
doi: 10.7717/peerj.11306
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-07
copyright: ©2021 Hu et al.
attribution name: Hu et al.

DNA methylome and transcriptome analysis established a model of four differentially methylated positions (DMPs) as a diagnostic marker in esophageal adenocarcinoma early detection
type: item
type: AcademicArticle
description: Background Esophageal carcinogenesis involves in alterations of DNA methylation and gene transcription. This study profiled genomic DNA methylome vs. gene expression using transcriptome data on esophageal adenocarcinoma (EAC) tissues from the online databases in order to identify methylation biomarkers in EAC early diagnosis. Materials and Methods The DNA methylome and transcriptome data were downloaded from the UCSC Xena, Gene Expression Omnibus (GEO), and The Cancer Genome Atlas (TCGA) databases and then bioinformatically analyzed for the differentially methylated positions (DMPs) vs. gene expression between EAC and normal tissues. The highly methylated DMPs vs. reduced gene expression in EAC were selected and then stratified with those of the corresponding normal blood samples and other common human cancers to construct an EAC-specific diagnostic model. The usefulness of this model was further verified in other three GEO datasets of EAC tissues. Result A total of 841 DMPs were associated with expression of 320 genes, some of which were aberrantly methylated in EAC tissues. Further analysis showed that four (cg07589773, cg10474350, cg13011388 and cg15208375 mapped to gene IKZF1, HOXA7, EFS and TSHZ3, respectively) of these 841 DMPs could form and establish a diagnostic model after stratified them with the corresponding normal blood samples and other common human cancers. The data were further validated in other three GEO datasets on EAC tissues in early EAC diagnosis. Conclusion This study revealed a diagnostic model of four genes methylation to diagnose EAC early. Further study will confirm the usefulness of this model in a prospective EAC cases.
format: application/pdf
format: text/html
creator: Weilin Peng
creator: Guangxu Tu
creator: Zhenyu Zhao
creator: Boxue He
creator: Qidong Cai
creator: Pengfei Zhang
creator: Xiong Peng
creator: Shuai Shi
creator: Xiang Wang
subject: Bioinformatics
subject: Oncology
subject: Otorhinolaryngology
subject: Medical Genetics
description: doi:10.7717/peerj.11355
publisher: PeerJ Inc.
rights: © 2021 Peng et al.
abstract: Background Esophageal carcinogenesis involves in alterations of DNA methylation and gene transcription. This study profiled genomic DNA methylome vs. gene expression using transcriptome data on esophageal adenocarcinoma (EAC) tissues from the online databases in order to identify methylation biomarkers in EAC early diagnosis. Materials and Methods The DNA methylome and transcriptome data were downloaded from the UCSC Xena, Gene Expression Omnibus (GEO), and The Cancer Genome Atlas (TCGA) databases and then bioinformatically analyzed for the differentially methylated positions (DMPs) vs. gene expression between EAC and normal tissues. The highly methylated DMPs vs. reduced gene expression in EAC were selected and then stratified with those of the corresponding normal blood samples and other common human cancers to construct an EAC-specific diagnostic model. The usefulness of this model was further verified in other three GEO datasets of EAC tissues. Result A total of 841 DMPs were associated with expression of 320 genes, some of which were aberrantly methylated in EAC tissues. Further analysis showed that four (cg07589773, cg10474350, cg13011388 and cg15208375 mapped to gene IKZF1, HOXA7, EFS and TSHZ3, respectively) of these 841 DMPs could form and establish a diagnostic model after stratified them with the corresponding normal blood samples and other common human cancers. The data were further validated in other three GEO datasets on EAC tissues in early EAC diagnosis. Conclusion This study revealed a diagnostic model of four genes methylation to diagnose EAC early. Further study will confirm the usefulness of this model in a prospective EAC cases.
bibliographic citation: Peng et al. (2021) DNA methylome and transcriptome analysis established a model of four differentially methylated positions (DMPs) as a diagnostic marker in esophageal adenocarcinoma early detection. PeerJ 9:e11355 https://doi.org/10.7717/peerj.11355
date submitted: 2020-12-23
date accepted: 2021-04-05
issued: 2021-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peng
  given name: Weilin
author list: Agent
  family name: Tu
  given name: Guangxu
author list: Agent
  family name: Zhao
  given name: Zhenyu
author list: Agent
  family name: He
  given name: Boxue
author list: Agent
  family name: Cai
  given name: Qidong
author list: Agent
  family name: Zhang
  given name: Pengfei
author list: Agent
  family name: Peng
  given name: Xiong
author list: Agent
  family name: Shi
  given name: Shuai
author list: Agent
  family name: Wang
  given name: Xiang
doi: 10.7717/peerj.11355
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-07
copyright: © 2021 Peng et al.
attribution name: Peng et al.

Transgenerational effects on development following microplastic exposure in Drosophila melanogaster
type: item
type: AcademicArticle
description: Background Plastic pollution affects all ecosystems, and detrimental effects to animals have been reported in a growing number of studies. However, there is a paucity of evidence for effects on terrestrial animals in comparison to those in the marine realm. Methods We used the fly Drosophila melanogaster to study the effects that exposure to plastics may have on life history traits and immune response. We reared flies in four conditions: In media containing 1% virgin polyethylene, with no chemical additives; in media supplemented with 1% or 4% polyvinyl chloride, known to have a high content of added chemicals; and control flies in non-supplemented media. Plastic particle size ranged from 23–500 µm. We studied fly survival to viral infection, the length of the larval and pupal stage, sex ratios, fertility and the size of the resultant adult flies. We then performed crossings of F1 flies in non-supplemented media and looked at the life history traits of the F2. Results Flies treated with plastics in the food media showed changes in fertility and sex ratio, but showed no differences in developmental times, adult size or the capacity to fight infections in comparison with controls. However, the offspring of treated flies reared in non-supplemented food had shorter life cycles, and those coming from both polyvinyl chloride treatments were smaller than those offspring of controls.
format: application/pdf
format: text/html
creator: Eva Jimenez-Guri
creator: Katherine E. Roberts
creator: Francisca C. García
creator: Maximiliano Tourmente
creator: Ben Longdon
creator: Brendan J. Godley
subject: Developmental Biology
subject: Entomology
subject: Zoology
subject: Ecotoxicology
description: doi:10.7717/peerj.11369
publisher: PeerJ Inc.
rights: © 2021 Jimenez-Guri et al.
abstract: Background Plastic pollution affects all ecosystems, and detrimental effects to animals have been reported in a growing number of studies. However, there is a paucity of evidence for effects on terrestrial animals in comparison to those in the marine realm. Methods We used the fly Drosophila melanogaster to study the effects that exposure to plastics may have on life history traits and immune response. We reared flies in four conditions: In media containing 1% virgin polyethylene, with no chemical additives; in media supplemented with 1% or 4% polyvinyl chloride, known to have a high content of added chemicals; and control flies in non-supplemented media. Plastic particle size ranged from 23–500 µm. We studied fly survival to viral infection, the length of the larval and pupal stage, sex ratios, fertility and the size of the resultant adult flies. We then performed crossings of F1 flies in non-supplemented media and looked at the life history traits of the F2. Results Flies treated with plastics in the food media showed changes in fertility and sex ratio, but showed no differences in developmental times, adult size or the capacity to fight infections in comparison with controls. However, the offspring of treated flies reared in non-supplemented food had shorter life cycles, and those coming from both polyvinyl chloride treatments were smaller than those offspring of controls.
bibliographic citation: Jimenez-Guri et al. (2021) Transgenerational effects on development following microplastic exposure in Drosophila melanogaster. PeerJ 9:e11369 https://doi.org/10.7717/peerj.11369
date submitted: 2021-01-26
date accepted: 2021-04-07
issued: 2021-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jimenez-Guri
  given name: Eva
author list: Agent
  family name: Roberts
  given name: Katherine E.
author list: Agent
  family name: García
  given name: Francisca C.
author list: Agent
  family name: Tourmente
  given name: Maximiliano
author list: Agent
  family name: Longdon
  given name: Ben
author list: Agent
  family name: Godley
  given name: Brendan J.
doi: 10.7717/peerj.11369
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-07
copyright: ©2021 Jimenez-Guri et al.
attribution name: Jimenez-Guri et al.

The impact of COVID-19 pandemic on nitrogen dioxide levels in Nigeria
type: item
type: AcademicArticle
description: The Coronavirus disease (COVID-19) has been transmitted worldwide over a very short time after it originated in China in December 2019. In an attempt to control its spread and reduce its health impacts, several countries including those in the African continent imposed restrictive measures that was termed “lockdown”. The outcomes of this lockdown have been reported to be beneficial to air quality worldwide. The main objective of this study is to assess the impact of lockdown due to COVID-19 on nitrogen dioxide (NO2) levels over six major cities in Nigeria. Maps extracted from satellite (Sentinel-5P) were used to indicate the significant reduction in the level of NO2 in the selected cities in Nigeria during two time-intervals, pre-lockdown (December, 2019) and during lockdown (April, 2020). The results show a significant reduction in NO2 levels during the lockdown period compared with its levels during the pre-lockdown period in 2019. The reduction in NO2 concentration levels during lockdown is likely due to less traffic, social distancing and restrictions on business and human activities. There could be an element of uncertainty in the results due to seasonality, as the comparison is done with a different season. However, the magnitude of change due to lockdown is probably much higher than the seasonal variability. Although COVID-19 has negatively impacted the health and economic status of all regions worldwide, it has benefited some aspects of air quality in most countries including Nigeria. This indicates that anthropogenic activities may be managed to reduce air pollution and positively impact the health of human beings.
format: application/pdf
format: text/html
creator: Johnson Adedeji Olusola
creator: Adebola Adekunle Shote
creator: Abdellah Ouigmane
creator: Rima J. Isaifan
subject: Global Health
subject: Public Health
subject: Environmental Impacts
description: doi:10.7717/peerj.11387
publisher: PeerJ Inc.
rights: © 2021 Olusola et al.
abstract: The Coronavirus disease (COVID-19) has been transmitted worldwide over a very short time after it originated in China in December 2019. In an attempt to control its spread and reduce its health impacts, several countries including those in the African continent imposed restrictive measures that was termed “lockdown”. The outcomes of this lockdown have been reported to be beneficial to air quality worldwide. The main objective of this study is to assess the impact of lockdown due to COVID-19 on nitrogen dioxide (NO2) levels over six major cities in Nigeria. Maps extracted from satellite (Sentinel-5P) were used to indicate the significant reduction in the level of NO2 in the selected cities in Nigeria during two time-intervals, pre-lockdown (December, 2019) and during lockdown (April, 2020). The results show a significant reduction in NO2 levels during the lockdown period compared with its levels during the pre-lockdown period in 2019. The reduction in NO2 concentration levels during lockdown is likely due to less traffic, social distancing and restrictions on business and human activities. There could be an element of uncertainty in the results due to seasonality, as the comparison is done with a different season. However, the magnitude of change due to lockdown is probably much higher than the seasonal variability. Although COVID-19 has negatively impacted the health and economic status of all regions worldwide, it has benefited some aspects of air quality in most countries including Nigeria. This indicates that anthropogenic activities may be managed to reduce air pollution and positively impact the health of human beings.
bibliographic citation: Olusola et al. (2021) The impact of COVID-19 pandemic on nitrogen dioxide levels in Nigeria. PeerJ 9:e11387 https://doi.org/10.7717/peerj.11387
date submitted: 2020-09-13
date accepted: 2021-04-10
issued: 2021-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olusola
  given name: Johnson Adedeji
author list: Agent
  family name: Shote
  given name: Adebola Adekunle
author list: Agent
  family name: Ouigmane
  given name: Abdellah
author list: Agent
  family name: Isaifan
  given name: Rima J.
doi: 10.7717/peerj.11387
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-07
copyright: © 2021 Olusola et al.
attribution name: Olusola et al.

Effects of education methods on self-efficacy of smoking cessation counseling among medical students
type: item
type: AcademicArticle
description: Background Medical students need to receive training in providing smoking cessation counseling to provide effective smoking cessation interventions to smokers when they become doctors. This study examined the smoking cessation education curricula and factors affecting counseling self-efficacy (CSE) in smoking cessation treatment among medical students. Methods In a multicenter cross-sectional study, we obtained demographic information, personal history of tobacco use and intention to quit smoking, exposure to secondhand smoke in the school premises during the past week, the experience of learning about tobacco in each medical school, tobacco-related medical knowledge, and self-efficacy in smoking cessation counseling on medical students of four Korean medical schools. Results Among 1,416 medical students eligible, 313 (22.1%) students completed a self-administered questionnaire. Only 20.3% of the students reported positive CSE on smoking cessation. The factors affecting positive CSE were scores of ≥ 60 on tobacco-related medical knowledge, smoking experience, and blended learning (p = 0.014, 0.005, and 0.015, respectively). Conclusion This study shows that high scores in tobacco-related medical knowledge and blended learning are correlated with positive CSE for smoking cessation counseling.
format: application/pdf
format: text/html
creator: Ara Cho
creator: Jeonggyu Lee
creator: YunJin Kim
creator: Byung Mann Cho
creator: Sang Yeoup Lee
creator: Eunhee Kong
creator: Minjeong Kim
creator: Jinseung Kim
creator: Dong Sik Jung
creator: Seongho Han
subject: Public Health
subject: Respiratory Medicine
subject: Science and Medical Education
description: doi:10.7717/peerj.11408
publisher: PeerJ Inc.
rights: © 2021 Cho et al.
abstract: Background Medical students need to receive training in providing smoking cessation counseling to provide effective smoking cessation interventions to smokers when they become doctors. This study examined the smoking cessation education curricula and factors affecting counseling self-efficacy (CSE) in smoking cessation treatment among medical students. Methods In a multicenter cross-sectional study, we obtained demographic information, personal history of tobacco use and intention to quit smoking, exposure to secondhand smoke in the school premises during the past week, the experience of learning about tobacco in each medical school, tobacco-related medical knowledge, and self-efficacy in smoking cessation counseling on medical students of four Korean medical schools. Results Among 1,416 medical students eligible, 313 (22.1%) students completed a self-administered questionnaire. Only 20.3% of the students reported positive CSE on smoking cessation. The factors affecting positive CSE were scores of ≥ 60 on tobacco-related medical knowledge, smoking experience, and blended learning (p = 0.014, 0.005, and 0.015, respectively). Conclusion This study shows that high scores in tobacco-related medical knowledge and blended learning are correlated with positive CSE for smoking cessation counseling.
bibliographic citation: Cho et al. (2021) Effects of education methods on self-efficacy of smoking cessation counseling among medical students. PeerJ 9:e11408 https://doi.org/10.7717/peerj.11408
date submitted: 2021-01-28
date accepted: 2021-04-14
issued: 2021-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cho
  given name: Ara
author list: Agent
  family name: Lee
  given name: Jeonggyu
author list: Agent
  family name: Kim
  given name: YunJin
author list: Agent
  family name: Cho
  given name: Byung Mann
author list: Agent
  family name: Lee
  given name: Sang Yeoup
author list: Agent
  family name: Kong
  given name: Eunhee
author list: Agent
  family name: Kim
  given name: Minjeong
author list: Agent
  family name: Kim
  given name: Jinseung
author list: Agent
  family name: Jung
  given name: Dong Sik
author list: Agent
  family name: Han
  given name: Seongho
doi: 10.7717/peerj.11408
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-07
copyright: ©2021 Cho et al.
attribution name: Cho et al.

Competing endogenous RNA network identifies mRNA biomarkers for overall survival of lung adenocarcinoma: two novel on-line precision medicine predictive tools
type: item
type: AcademicArticle
description: Background Individual mortality risk predicted curve at the individual level can provide valuable information for directing individual treatment decision. The present study attempted to explore potential post-transcriptional biological regulatory mechanism related with overall survival of lung adenocarcinoma (LUAD) patients through competitive endogenous RNA (ceRNA) network and develop two precision medicine predictive tools for predicting the individual mortality risk curves for overall survival of LUAD patients. Methods Multivariable Cox regression analyses were performed to explore the potential prognostic indicators, which were used to construct a prognostic model for overall survival of LUAD patients. Time-dependent receiver operating characteristic (ROC) curves were used to assess the predictive performance of prognostic model. Results There were 494 LUAD patients in model cohort and 233 LUAD patients in validation cohort. Differentially expressed mRNAs, miRNAs, and lncRNAs were identified between LUAD tissues and normal tissues. A ceRNA regulatory network was constructed on previous differentially expressed mRNAs, miRNAs, and lncRNAs. Fourteen mRNA biomarkers were identified as independent risk factors by multivariate Cox regression and used to develop a prognostic model for overall survival of LUAD patients. The C-indexes of prognostic model in model group were 0.786 (95% CI [0.744–0.828]), 0.736 (95% CI [0.694–0.778]) and 0.766 (95% CI [0.724–0.808]) for one year, two year and three year overall survival respectively. Two precision medicine predicted tools were developed for predicting individual mortality risk curves for LUAD patients. Conclusion The current study explored potential post-transcriptional biological regulatory mechanism and prognostic biomarkers for overall survival of LUAD patients. Two on-line precision medicine predictive tools were helpful to predict the individual mortality risk predicted curves for overall survival of LUAD patients. Sm…
format: application/pdf
format: text/html
creator: Jinsong Lin
creator: Shubiao Lu
creator: Zhijian Jiang
creator: Chongjing Hu
creator: Zhiqiao Zhang
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.11412
publisher: PeerJ Inc.
rights: © 2021 Lin et al.
abstract: Background Individual mortality risk predicted curve at the individual level can provide valuable information for directing individual treatment decision. The present study attempted to explore potential post-transcriptional biological regulatory mechanism related with overall survival of lung adenocarcinoma (LUAD) patients through competitive endogenous RNA (ceRNA) network and develop two precision medicine predictive tools for predicting the individual mortality risk curves for overall survival of LUAD patients. Methods Multivariable Cox regression analyses were performed to explore the potential prognostic indicators, which were used to construct a prognostic model for overall survival of LUAD patients. Time-dependent receiver operating characteristic (ROC) curves were used to assess the predictive performance of prognostic model. Results There were 494 LUAD patients in model cohort and 233 LUAD patients in validation cohort. Differentially expressed mRNAs, miRNAs, and lncRNAs were identified between LUAD tissues and normal tissues. A ceRNA regulatory network was constructed on previous differentially expressed mRNAs, miRNAs, and lncRNAs. Fourteen mRNA biomarkers were identified as independent risk factors by multivariate Cox regression and used to develop a prognostic model for overall survival of LUAD patients. The C-indexes of prognostic model in model group were 0.786 (95% CI [0.744–0.828]), 0.736 (95% CI [0.694–0.778]) and 0.766 (95% CI [0.724–0.808]) for one year, two year and three year overall survival respectively. Two precision medicine predicted tools were developed for predicting individual mortality risk curves for LUAD patients. Conclusion The current study explored potential post-transcriptional biological regulatory mechanism and prognostic biomarkers for overall survival of LUAD patients. Two on-line precision medicine predictive tools were helpful to predict the individual mortality risk predicted curves for overall survival of LUAD patients. Sm…
bibliographic citation: Lin et al. (2021) Competing endogenous RNA network identifies mRNA biomarkers for overall survival of lung adenocarcinoma: two novel on-line precision medicine predictive tools. PeerJ 9:e11412 https://doi.org/10.7717/peerj.11412
date submitted: 2020-09-08
date accepted: 2021-04-15
issued: 2021-05-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Lin
  given name: Jinsong
author list: Agent
  family name: Lu
  given name: Shubiao
author list: Agent
  family name: Jiang
  given name: Zhijian
author list: Agent
  family name: Hu
  given name: Chongjing
author list: Agent
  family name: Zhang
  given name: Zhiqiao
doi: 10.7717/peerj.11412
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-07
copyright: ©2021 Lin et al.
attribution name: Lin et al.

https://peerj.com/articles/11179
type: item
type: AcademicArticle
title: Cranial anatomy of Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 (Reptilia: Ichthyosauria) from the Middle Triassic Besano Formation of Monte San Giorgio, Italy/Switzerland: taxonomic and palaeobiological implications
description: Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 was described on the basis of a single fossil excavated near Besano (Italy) nearly three decades ago. Here, we re-examine its cranial osteology and assign five additional specimens to B. leptorhynchus, four of which were so far undescribed. All of the referred specimens were collected from the Middle Triassic outcrops of the Monte San Giorgio area (Italy/Switzerland) and are housed in various museum collections in Europe. The revised diagnosis of the taxon includes the following combination of cranial characters: extreme longirostry; an elongate frontal not participating in the supratemporal fenestra; a prominent ‘triangular process’ of the quadrate; a caudoventral exposure of the postorbital on the skull roof; a prominent coronoid (preglenoid) process of the surangular; tiny conical teeth with coarsely-striated crown surfaces and deeply-grooved roots; mesial maxillary teeth set in sockets; distal maxillary teeth set in a short groove. All these characters are shared with the holotype of Mikadocephalus gracilirostris Maisch & Matzke, 1997, which we consider as a junior synonym of B. leptorhynchus. An updated phylogenetic analysis, which includes revised scores for B. leptorhynchus and several other shastasaurids, recovers B. leptorhynchus as a basal merriamosaurian, but it is unclear if Shastasauridae form a clade, or represent a paraphyletic group. The inferred body length of the examined specimens ranges from 1 m to about 8 m. The extreme longirostry suggests that B. leptorhynchus primarily fed on small and elusive prey, feeding lower in the food web than an apex predator: a novel ecological specialisation never reported before the Anisian in a large diapsid. This specialization might have triggered an increase of body size and helped to maintain low competition among the diverse ichthyosaur fauna of the Besano Formation.
format: application/pdf
format: text/html
creator: Gabriele Bindellini
creator: Andrzej S. Wolniewicz
creator: Feiko Miedema
creator: Torsten M. Scheyer
creator: Cristiano Dal Sasso
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.11179
publisher: PeerJ Inc.
rights: © 2021 Bindellini et al.
abstract: Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 was described on the basis of a single fossil excavated near Besano (Italy) nearly three decades ago. Here, we re-examine its cranial osteology and assign five additional specimens to B. leptorhynchus, four of which were so far undescribed. All of the referred specimens were collected from the Middle Triassic outcrops of the Monte San Giorgio area (Italy/Switzerland) and are housed in various museum collections in Europe. The revised diagnosis of the taxon includes the following combination of cranial characters: extreme longirostry; an elongate frontal not participating in the supratemporal fenestra; a prominent ‘triangular process’ of the quadrate; a caudoventral exposure of the postorbital on the skull roof; a prominent coronoid (preglenoid) process of the surangular; tiny conical teeth with coarsely-striated crown surfaces and deeply-grooved roots; mesial maxillary teeth set in sockets; distal maxillary teeth set in a short groove. All these characters are shared with the holotype of Mikadocephalus gracilirostris Maisch & Matzke, 1997, which we consider as a junior synonym of B. leptorhynchus. An updated phylogenetic analysis, which includes revised scores for B. leptorhynchus and several other shastasaurids, recovers B. leptorhynchus as a basal merriamosaurian, but it is unclear if Shastasauridae form a clade, or represent a paraphyletic group. The inferred body length of the examined specimens ranges from 1 m to about 8 m. The extreme longirostry suggests that B. leptorhynchus primarily fed on small and elusive prey, feeding lower in the food web than an apex predator: a novel ecological specialisation never reported before the Anisian in a large diapsid. This specialization might have triggered an increase of body size and helped to maintain low competition among the diverse ichthyosaur fauna of the Besano Formation.
bibliographic citation: Bindellini et al. (2021) Cranial anatomy of Besanosaurus leptorhynchus Dal Sasso & Pinna, 1996 (Reptilia: Ichthyosauria) from the Middle Triassic Besano Formation of Monte San Giorgio, Italy/Switzerland: taxonomic and palaeobiological implications. PeerJ 9:e11179 https://doi.org/10.7717/peerj.11179
date submitted: 2020-11-04
date accepted: 2021-03-08
issued: 2021-05-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bindellini
  given name: Gabriele
author list: Agent
  family name: Wolniewicz
  given name: Andrzej S.
author list: Agent
  family name: Miedema
  given name: Feiko
author list: Agent
  family name: Scheyer
  given name: Torsten M.
author list: Agent
  family name: Dal Sasso
  given name: Cristiano
doi: 10.7717/peerj.11179
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-06
copyright: © 2021 Bindellini et al.
attribution name: Bindellini et al.

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