PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Climate change favours connectivity between virus-bearing pest and rice cultivations in sub-Saharan Africa, depressing local economies
items: Commercial utilities and future perspective of nanomedicines
items: Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia
items: Analysis of core genes for colorectal cancer prognosis based on immune and stromal scores
items: Both landscape heterogeneity and configuration determine Woodlarks (Lullula arborea) breeding territories
items: Toxicity of clothianidin to common Eastern North American fireflies
items: Real-world experience of switching from tenofovir disoproxil fumarate to tenofovir alafenamide in patients with chronic hepatitis B: a retrospective study
items: UBE2E3 regulates cellular senescence and osteogenic differentiation of BMSCs during aging
items: Misinformation effects in an online sample: results of an experimental study with a five day retention interval
items: De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins

Climate change favours connectivity between virus-bearing pest and rice cultivations in sub-Saharan Africa, depressing local economies
type: item
type: AcademicArticle
description: Aims Rice is a staple food for many countries, being fundamental for a large part of the worlds’ population. In sub-Saharan Africa, its importance is currently high and is likely to become even more relevant, considering that the number of people and the per-capita consumption are both predicted to increase. The flea beetles belonging to the Chaetocnema pulla species group (pulla group), a harmful rice pest, are an important vector of the Rice Yellow Mottle Virus, a disease which leads even to 80–100% yield losses in rice production. We present a continental-scale study aiming at: (1) locating current and future suitable territories for both pulla group and rice; (2) identifying areas where rice cultivations may occur without suffering the presence of pulla group using an Ecological Niche Modelling (ENM) approach; (3) estimating current and future connectivity among pulla group populations and areas predicted to host rice cultivations, based on the most recent land-use estimates for future agricultural trends; (4) proposing a new connectivity index called “Pest Aggression Index” (PAI) to measure the agricultural susceptibility to the potential future invasions of pests and disease; (5) quantifying losses in terms of production when rice cultivations co‐occur with the pulla group and identifying the SSA countries which, in the future inferred scenarios, will potentially suffer the greatest losses. Location Sub-Saharan Africa. Methods Since the ongoing climate and land-use changes affect species’ distributions, we first assess the impact of these changes through a spatially-jackknifed Maxent-based Ecological Niche Modelling in GIS environment, for both the pulla group and rice, in two climatic/socioeconomic future scenarios (SSP_2.45 and 3.70). We then assess the connectivity potential of the pulla group populations towards rice cultivations, for both current and future predictions, through a circuit theory-based approach (Circuitscape implemented in Julia language). …
format: application/pdf
format: text/html
creator: Mattia Iannella
creator: Walter De Simone
creator: Paola D’Alessandro
creator: Maurizio Biondi
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Climate Change Biology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.12387
publisher: PeerJ Inc.
rights: © 2021 Iannella et al.
abstract: Aims Rice is a staple food for many countries, being fundamental for a large part of the worlds’ population. In sub-Saharan Africa, its importance is currently high and is likely to become even more relevant, considering that the number of people and the per-capita consumption are both predicted to increase. The flea beetles belonging to the Chaetocnema pulla species group (pulla group), a harmful rice pest, are an important vector of the Rice Yellow Mottle Virus, a disease which leads even to 80–100% yield losses in rice production. We present a continental-scale study aiming at: (1) locating current and future suitable territories for both pulla group and rice; (2) identifying areas where rice cultivations may occur without suffering the presence of pulla group using an Ecological Niche Modelling (ENM) approach; (3) estimating current and future connectivity among pulla group populations and areas predicted to host rice cultivations, based on the most recent land-use estimates for future agricultural trends; (4) proposing a new connectivity index called “Pest Aggression Index” (PAI) to measure the agricultural susceptibility to the potential future invasions of pests and disease; (5) quantifying losses in terms of production when rice cultivations co‐occur with the pulla group and identifying the SSA countries which, in the future inferred scenarios, will potentially suffer the greatest losses. Location Sub-Saharan Africa. Methods Since the ongoing climate and land-use changes affect species’ distributions, we first assess the impact of these changes through a spatially-jackknifed Maxent-based Ecological Niche Modelling in GIS environment, for both the pulla group and rice, in two climatic/socioeconomic future scenarios (SSP_2.45 and 3.70). We then assess the connectivity potential of the pulla group populations towards rice cultivations, for both current and future predictions, through a circuit theory-based approach (Circuitscape implemented in Julia language). …
bibliographic citation: Iannella et al. (2021) Climate change favours connectivity between virus-bearing pest and rice cultivations in sub-Saharan Africa, depressing local economies. PeerJ 9:e12387 https://doi.org/10.7717/peerj.12387
date submitted: 2021-07-22
date accepted: 2021-10-04
issued: 2021-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Iannella
  given name: Mattia
author list: Agent
  family name: De Simone
  given name: Walter
author list: Agent
  family name: D’Alessandro
  given name: Paola
author list: Agent
  family name: Biondi
  given name: Maurizio
doi: 10.7717/peerj.12387
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-19
copyright: © 2021 Iannella et al.
attribution name: Iannella et al.

Commercial utilities and future perspective of nanomedicines
type: item
type: AcademicArticle
description: The present review aims to describe the commercial utilities and future perspectives of nanomedicines. Nanomedicines are intended to increase precision medicine and decrease the adverse effects on the patient. Nanomedicines are produced, engineered, and industrialized at the cellular, chemical, and macromolecular levels. This study describes the various aspects of nanomedicine such as governing outlooks over high use of nanomedicine, regulatory advancements for nanomedicines, standards, and guidelines for nanomedicines as per Therapeutic Goods Administration (TGA). This review also focuses on the patents and clinical trials based on nanoformulation, along with nanomedicines utilization as drug therapy and their market value. The present study concludes that nanomedicines are of high importance in biomedical and pharmaceutical production and offer better therapeutic effects especially in the case of drugs that possess low aqueous solubility. The factual data presented in this study will assist the researchers and health care professionals in understanding the applications of nanomedicine for better diagnosis and effective treatment of a disease.
format: application/pdf
format: text/html
creator: Rishabha Malviya
creator: Shivkanya Fuloria
creator: Swati Verma
creator: Vetriselvan Subramaniyan
creator: Kathiresan V. Sathasivam
creator: Vinoth Kumarasamy
creator: Darnal Hari Kumar
creator: Shalini Vellasamy
creator: Dhanalekshmi Unnikrishnan Meenakshi
creator: Shikha Yadav
creator: Akanksha Sharma
creator: Neeraj Kumar Fuloria
subject: Biotechnology
subject: Drugs and Devices
subject: Pharmacology
description: doi:10.7717/peerj.12392
publisher: PeerJ Inc.
rights: © 2021 Malviya et al.
abstract: The present review aims to describe the commercial utilities and future perspectives of nanomedicines. Nanomedicines are intended to increase precision medicine and decrease the adverse effects on the patient. Nanomedicines are produced, engineered, and industrialized at the cellular, chemical, and macromolecular levels. This study describes the various aspects of nanomedicine such as governing outlooks over high use of nanomedicine, regulatory advancements for nanomedicines, standards, and guidelines for nanomedicines as per Therapeutic Goods Administration (TGA). This review also focuses on the patents and clinical trials based on nanoformulation, along with nanomedicines utilization as drug therapy and their market value. The present study concludes that nanomedicines are of high importance in biomedical and pharmaceutical production and offer better therapeutic effects especially in the case of drugs that possess low aqueous solubility. The factual data presented in this study will assist the researchers and health care professionals in understanding the applications of nanomedicine for better diagnosis and effective treatment of a disease.
bibliographic citation: Malviya et al. (2021) Commercial utilities and future perspective of nanomedicines. PeerJ 9:e12392 https://doi.org/10.7717/peerj.12392
date submitted: 2021-06-07
date accepted: 2021-10-05
issued: 2021-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malviya
  given name: Rishabha
author list: Agent
  family name: Fuloria
  given name: Shivkanya
author list: Agent
  family name: Verma
  given name: Swati
author list: Agent
  family name: Subramaniyan
  given name: Vetriselvan
author list: Agent
  family name: Sathasivam
  given name: Kathiresan V.
author list: Agent
  family name: Kumarasamy
  given name: Vinoth
author list: Agent
  family name: Hari Kumar
  given name: Darnal
author list: Agent
  family name: Vellasamy
  given name: Shalini
author list: Agent
  family name: Meenakshi
  given name: Dhanalekshmi Unnikrishnan
author list: Agent
  family name: Yadav
  given name: Shikha
author list: Agent
  family name: Sharma
  given name: Akanksha
author list: Agent
  family name: Fuloria
  given name: Neeraj Kumar
doi: 10.7717/peerj.12392
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-19
copyright: © 2021 Malviya et al.
attribution name: Malviya et al.

Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia
type: item
type: AcademicArticle
description: Background Walnut is an important economic tree species with prominent economic value and ecological functions. However, in recent years, walnuts have become susceptible to drought stress, resulting in a decline in comprehensive benefits. Therefore, it is necessary to identify the regulatory molecular mechanism associated with walnut response to drought. In many plants, ethylene responsive factor (ERF) gene family plays important roles in response to biotic and abiotic stress, especial drought. Therefore, the identification and characterisation of walnut ERF genes will benefit walnut with regard to the clarification of drought response mechanism as well as the management, production, and quality of plantations. Methods ‘ERF’ was compared against the walnut transcriptome, and the JrERFs with a complete open reading frame (ORF) were identified by ORF Finder. The molecular weights, amino acid residues, and theoretical isoelectric point (pI) were predicted by ExPASy. The distribution of JrERFs in chromosome locations was determined based on walnut genome data from NCBI. The intron-exon structures and conserved domains were analysed using Gene Structure Display Server 2.0 and CD-Search, accordingly. Multi-sequence alignment and a phylogenetic tree were constructed by ClustalX2.1 and MEGA7, respectively. The conserved motifs were acquired using MEME. Total RNA was isolated using the cetyltrimethylammonium ammonium bromide (CTAB) method (Yang et al., 2018). Gene expression was determined by using real-time quantitative polymerase chain reaction (qRT-PCR) analysis and calculated according to the 2−ΔΔCT method (Livak & Schmittgen, 2001). Results A total of 44 JrERFs were identified from the walnut transcriptome, whose ORFs were 450–1,239 bp in length. The molecular weights of the JrERF proteins (consisting 149–412 amino acids) were 16.81–43.71 kDa, with pI ranging from 4.8 (JrERF11) to 9.89 (JrERF03). The JrERFs can be divided into six groups (B1–B6), and among the groups, B…
format: application/pdf
format: text/html
creator: Tianyu Wang
creator: Xiangqian Gao
creator: Sisi Chen
creator: Dapei Li
creator: Shuwen Chen
creator: Muhong Xie
creator: Zhenggang Xu
creator: Guiyan Yang
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12429
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Background Walnut is an important economic tree species with prominent economic value and ecological functions. However, in recent years, walnuts have become susceptible to drought stress, resulting in a decline in comprehensive benefits. Therefore, it is necessary to identify the regulatory molecular mechanism associated with walnut response to drought. In many plants, ethylene responsive factor (ERF) gene family plays important roles in response to biotic and abiotic stress, especial drought. Therefore, the identification and characterisation of walnut ERF genes will benefit walnut with regard to the clarification of drought response mechanism as well as the management, production, and quality of plantations. Methods ‘ERF’ was compared against the walnut transcriptome, and the JrERFs with a complete open reading frame (ORF) were identified by ORF Finder. The molecular weights, amino acid residues, and theoretical isoelectric point (pI) were predicted by ExPASy. The distribution of JrERFs in chromosome locations was determined based on walnut genome data from NCBI. The intron-exon structures and conserved domains were analysed using Gene Structure Display Server 2.0 and CD-Search, accordingly. Multi-sequence alignment and a phylogenetic tree were constructed by ClustalX2.1 and MEGA7, respectively. The conserved motifs were acquired using MEME. Total RNA was isolated using the cetyltrimethylammonium ammonium bromide (CTAB) method (Yang et al., 2018). Gene expression was determined by using real-time quantitative polymerase chain reaction (qRT-PCR) analysis and calculated according to the 2−ΔΔCT method (Livak & Schmittgen, 2001). Results A total of 44 JrERFs were identified from the walnut transcriptome, whose ORFs were 450–1,239 bp in length. The molecular weights of the JrERF proteins (consisting 149–412 amino acids) were 16.81–43.71 kDa, with pI ranging from 4.8 (JrERF11) to 9.89 (JrERF03). The JrERFs can be divided into six groups (B1–B6), and among the groups, B…
bibliographic citation: Wang et al. (2021) Genome-wide identification and expression analysis of ethylene responsive factor family transcription factors in Juglans regia. PeerJ 9:e12429 https://doi.org/10.7717/peerj.12429
date submitted: 2021-04-19
date accepted: 2021-10-12
issued: 2021-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Tianyu
author list: Agent
  family name: Gao
  given name: Xiangqian
author list: Agent
  family name: Chen
  given name: Sisi
author list: Agent
  family name: Li
  given name: Dapei
author list: Agent
  family name: Chen
  given name: Shuwen
author list: Agent
  family name: Xie
  given name: Muhong
author list: Agent
  family name: Xu
  given name: Zhenggang
author list: Agent
  family name: Yang
  given name: Guiyan
doi: 10.7717/peerj.12429
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-19
copyright: © 2021 Wang et al.
attribution name: Wang et al.

Analysis of core genes for colorectal cancer prognosis based on immune and stromal scores
type: item
type: AcademicArticle
description: Background Colorectal cancer (CRC) is one of the most common malignancies.An early diagnosis and an accurate prognosis are major focuses of CRC research. Tumor microenvironment cells and the extent of infiltrating immune and stromal cells contribute significantly to the tumor prognosis. Methods Immune and stromal scores were calculated based on the ESTIMATE algorithm using the sample expression profile of the The Cancer Genome Atlas (TCGA) database. GSE102479 was used as the validation database. Differentially expressed genes whose expression was significantly associated with the prognosis of CRC patients were identified based on the immune matrix score. Survival analysis was conducted on the union of the differentially expressed genes. A protein–protein interaction (PPI) network was constructed using the STRING database to identify the closely connected modules. To conduct functional enrichment analysis of the relevant genes, GO and KEGG pathway analyses were performed with Cluster Profiler. Pivot analysis of the ncRNAs and TFs was performed by using the RAID2.0 database and TRRUST v2 database. TF-mRNA regulatory relationships were analyzed in the TRRUST V2 database. Hubgene targeting relationships were screened in the TargetScan, miRTarBase and miRDB databases. The SNV data of the hub genes were analyzed by using the R maftools package. A ROC curve was drawn based on the TCGA database. The proportion of immune cells was estimated using CIBERSORT and the LM22 feature matrix. Results The results showed that the matrix score was significantly correlated with colorectal cancer stage T. A total of 789 differentially expressed genes and 121 survival-related prognostic genes were identified. The PPI network showed that 22 core genes were related to the CRC prognosis. Furthermore, four ncRNAs that regulated the core prognosis genes, 11 TFs with regulatory effects on the core prognosis genes, and two drugs, quercetin and pseudoephedrine, that have regulatory effects on col…
format: application/pdf
format: text/html
creator: Yi Zhu
creator: Yuan Zhou
creator: HongGang Jiang
creator: ZhiHeng Chen
creator: BoHao Lu
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.12452
publisher: PeerJ Inc.
rights: © 2021 Zhu et al.
abstract: Background Colorectal cancer (CRC) is one of the most common malignancies.An early diagnosis and an accurate prognosis are major focuses of CRC research. Tumor microenvironment cells and the extent of infiltrating immune and stromal cells contribute significantly to the tumor prognosis. Methods Immune and stromal scores were calculated based on the ESTIMATE algorithm using the sample expression profile of the The Cancer Genome Atlas (TCGA) database. GSE102479 was used as the validation database. Differentially expressed genes whose expression was significantly associated with the prognosis of CRC patients were identified based on the immune matrix score. Survival analysis was conducted on the union of the differentially expressed genes. A protein–protein interaction (PPI) network was constructed using the STRING database to identify the closely connected modules. To conduct functional enrichment analysis of the relevant genes, GO and KEGG pathway analyses were performed with Cluster Profiler. Pivot analysis of the ncRNAs and TFs was performed by using the RAID2.0 database and TRRUST v2 database. TF-mRNA regulatory relationships were analyzed in the TRRUST V2 database. Hubgene targeting relationships were screened in the TargetScan, miRTarBase and miRDB databases. The SNV data of the hub genes were analyzed by using the R maftools package. A ROC curve was drawn based on the TCGA database. The proportion of immune cells was estimated using CIBERSORT and the LM22 feature matrix. Results The results showed that the matrix score was significantly correlated with colorectal cancer stage T. A total of 789 differentially expressed genes and 121 survival-related prognostic genes were identified. The PPI network showed that 22 core genes were related to the CRC prognosis. Furthermore, four ncRNAs that regulated the core prognosis genes, 11 TFs with regulatory effects on the core prognosis genes, and two drugs, quercetin and pseudoephedrine, that have regulatory effects on col…
bibliographic citation: Zhu et al. (2021) Analysis of core genes for colorectal cancer prognosis based on immune and stromal scores. PeerJ 9:e12452 https://doi.org/10.7717/peerj.12452
date submitted: 2021-03-08
date accepted: 2021-10-18
issued: 2021-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Yi
author list: Agent
  family name: Zhou
  given name: Yuan
author list: Agent
  family name: Jiang
  given name: HongGang
author list: Agent
  family name: Chen
  given name: ZhiHeng
author list: Agent
  family name: Lu
  given name: BoHao
doi: 10.7717/peerj.12452
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-19
copyright: ©2021 Zhu et al.
attribution name: Zhu et al.

Both landscape heterogeneity and configuration determine Woodlarks (Lullula arborea) breeding territories
type: item
type: AcademicArticle
description: Farmland birds have declined in the last decades mostly due to agriculture intensification. The Woodlark Lullula arborea, a farmland species of conservation concern and protected by the European Bird Directive, occurs in a variety of habitats across its geographic range. Although habitat heterogeneity has been recognized as a key feature, the preference or avoidance of particular habitat attributes might differ across its range because different localities may have distinct conditions. Such variation would challenge conservation efforts at the local level. Our aim was to assess habitat associations of Woodlarks and determine whether the habitat attributes identified as important in other locations across its range could be generalised and applied to Austrian populations. In addition, habitat associations can be influenced by land-use change. We examined changes in land use from 2007 to 2016 in 15 municipalities surrounding areas occupied by Woodlarks. We quantified the composition and configuration of the local landscape surrounding 18 singing males’ territories and 16 non-territory sites. We found that the probability of Woodlarks territories increased with landscape heterogeneity between 50% and 70%, increased with dispersed bare soil patches, decreased with overall patch density and were away from dirt roads. Contrary to our expectation, there was no indication of land-use change. In contrast to previous studies, vegetation height, the presence and proximity to woodland were not identified as important habitat characteristics. Thus, some conservation recommendations can be derived from other localities, for example, maintaining or enhancing landscape heterogeneity. However, others should be adapted to local conditions. In Austria, conservation efforts should focus on including dispersed patches of bare soil and limiting the development of dirt roads nearby Woodlark territories, in addition to promoting a heterogeneous landscape.
format: application/pdf
format: text/html
creator: Marlies Resch
creator: Marcela Suarez-Rubio
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.12476
publisher: PeerJ Inc.
rights: © 2021 Resch and Suarez-Rubio
abstract: Farmland birds have declined in the last decades mostly due to agriculture intensification. The Woodlark Lullula arborea, a farmland species of conservation concern and protected by the European Bird Directive, occurs in a variety of habitats across its geographic range. Although habitat heterogeneity has been recognized as a key feature, the preference or avoidance of particular habitat attributes might differ across its range because different localities may have distinct conditions. Such variation would challenge conservation efforts at the local level. Our aim was to assess habitat associations of Woodlarks and determine whether the habitat attributes identified as important in other locations across its range could be generalised and applied to Austrian populations. In addition, habitat associations can be influenced by land-use change. We examined changes in land use from 2007 to 2016 in 15 municipalities surrounding areas occupied by Woodlarks. We quantified the composition and configuration of the local landscape surrounding 18 singing males’ territories and 16 non-territory sites. We found that the probability of Woodlarks territories increased with landscape heterogeneity between 50% and 70%, increased with dispersed bare soil patches, decreased with overall patch density and were away from dirt roads. Contrary to our expectation, there was no indication of land-use change. In contrast to previous studies, vegetation height, the presence and proximity to woodland were not identified as important habitat characteristics. Thus, some conservation recommendations can be derived from other localities, for example, maintaining or enhancing landscape heterogeneity. However, others should be adapted to local conditions. In Austria, conservation efforts should focus on including dispersed patches of bare soil and limiting the development of dirt roads nearby Woodlark territories, in addition to promoting a heterogeneous landscape.
bibliographic citation: Resch et al. (2021) Both landscape heterogeneity and configuration determine Woodlarks (Lullula arborea) breeding territories. PeerJ 9:e12476 https://doi.org/10.7717/peerj.12476
date submitted: 2021-06-16
date accepted: 2021-10-20
issued: 2021-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Resch
  given name: Marlies
author list: Agent
  family name: Suarez-Rubio
  given name: Marcela
doi: 10.7717/peerj.12476
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-19
copyright: © 2021 Resch and Suarez-Rubio
attribution name: Resch and Suarez-Rubio

Toxicity of clothianidin to common Eastern North American fireflies
type: item
type: AcademicArticle
description: Background Previous research suggests that fireflies (Coleoptera: Lampyridae) are susceptible to commonly used insecticides. In the United States, there has been a rapid and widespread adoption of neonicotinoid insecticides, predominantly used as seed coatings on large-acreage crops like corn, soy, and cotton. Neonicotinoid insecticides are persistent in soil yet mobile in water, so they have potential to contaminate firefly habitats both in and adjacent to application sites. As a result, fireflies may be at high risk of exposure to neonicotinoids, possibly jeopardizing this already at-risk group of charismatic insects. Methods To assess the sensitivity of fireflies to neonicotinoids, we exposed larvae of Photuris versicolor complex and Photinus pyralis to multiple levels of clothianidin-treated soil and monitored feeding behavior, protective soil chamber formation, intoxication, and mortality. Results Pt. versicolor and Pn. pyralis larvae exhibited long-term intoxication and mortality at concentrations above 1,000 ng g−1 soil (1 ppm). Under sub-lethal clothianidin exposure, firefly larvae fed less and spent less time in protective soil chambers, two behavioral changes that could decrease larval survival in the wild. Discussion Both firefly species demonstrated sub-lethal responses in the lab to clothianidin exposure at field-realistic concentrations, although Pt. versicolor and Pn. pyralis appeared to tolerate higher clothianidin exposure relative to other soil invertebrates and beetle species. While these two firefly species, which are relatively widespread in North America, appear somewhat tolerant of neonicotinoid exposure in a laboratory setting, further work is needed to extend this conclusion to wild populations, especially in rare or declining taxa.
format: application/pdf
format: text/html
creator: Kirsten Ann Pearsons
creator: Sarah E. Lower
creator: John F. Tooker
subject: Entomology
subject: Toxicology
subject: Ecotoxicology
description: doi:10.7717/peerj.12495
publisher: PeerJ Inc.
rights: © 2021 Pearsons et al.
abstract: Background Previous research suggests that fireflies (Coleoptera: Lampyridae) are susceptible to commonly used insecticides. In the United States, there has been a rapid and widespread adoption of neonicotinoid insecticides, predominantly used as seed coatings on large-acreage crops like corn, soy, and cotton. Neonicotinoid insecticides are persistent in soil yet mobile in water, so they have potential to contaminate firefly habitats both in and adjacent to application sites. As a result, fireflies may be at high risk of exposure to neonicotinoids, possibly jeopardizing this already at-risk group of charismatic insects. Methods To assess the sensitivity of fireflies to neonicotinoids, we exposed larvae of Photuris versicolor complex and Photinus pyralis to multiple levels of clothianidin-treated soil and monitored feeding behavior, protective soil chamber formation, intoxication, and mortality. Results Pt. versicolor and Pn. pyralis larvae exhibited long-term intoxication and mortality at concentrations above 1,000 ng g−1 soil (1 ppm). Under sub-lethal clothianidin exposure, firefly larvae fed less and spent less time in protective soil chambers, two behavioral changes that could decrease larval survival in the wild. Discussion Both firefly species demonstrated sub-lethal responses in the lab to clothianidin exposure at field-realistic concentrations, although Pt. versicolor and Pn. pyralis appeared to tolerate higher clothianidin exposure relative to other soil invertebrates and beetle species. While these two firefly species, which are relatively widespread in North America, appear somewhat tolerant of neonicotinoid exposure in a laboratory setting, further work is needed to extend this conclusion to wild populations, especially in rare or declining taxa.
bibliographic citation: Pearsons et al. (2021) Toxicity of clothianidin to common Eastern North American fireflies. PeerJ 9:e12495 https://doi.org/10.7717/peerj.12495
date submitted: 2021-09-16
date accepted: 2021-10-25
issued: 2021-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pearsons
  given name: Kirsten Ann
author list: Agent
  family name: Lower
  given name: Sarah E.
author list: Agent
  family name: Tooker
  given name: John F.
doi: 10.7717/peerj.12495
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-19
copyright: ©2021 Pearsons et al.
attribution name: Pearsons et al.

Real-world experience of switching from tenofovir disoproxil fumarate to tenofovir alafenamide in patients with chronic hepatitis B: a retrospective study
type: item
type: AcademicArticle
description: Background Tenofovir alafenamide (TAF) has good viral suppression efficacy and less adverse effect than tenofovir disoproxil fumarate (TDF). Real-world studies on the antiviral efficacy and safety of switching from TDF to TAF in patients with chronic hepatitis B (CHB) are limited. Methods This retrospective study included 167 nucleos(t)ide analogue (NA)-naive patients with CHB. All the patients received TDF at least 12 months before switching and TAF at least 12 months after switching at a single medical center. The Friedman test with Dunn–Bonferroni post hoc tests and repeated-measures analysis of variance was used to analyze the effect of complete viral suppression, alanine aminotransferase (ALT) level normalization, renal function changes, body weight, and body mass index in the periods before and after switching. Results The mean age and TDF treatment duration were 52 ± 11 years and 2.8 years (interquartile range, 1.51–5.15 years), respectively. The complete viral suppression rate was similar between the time of switching and 48 weeks after switching to TAF (77.8% vs 76%, P = 1.000). The percentage of alanine aminotransferase (ALT) normalization increased from 26.3% at TDF start to 81.4% (P < 0.001) at time of switching and 89.2% at 48 weeks after switching to TAF (P = 0.428). The median estimated glomerular filtration rate decreased from 100.09 mL/min/1.73 m² at TDF start to 91.97 mL/min/1.73 m² (P < 0.001) at the time of switching and stabilized at 48 weeks after switching to TAF (93.47 mL/min/1.73m², P = 1.000). The body weight decreased from 69.2 ± 12.2 kg at TDF start to 67.4 ± 12.1 kg (P < 0.001) at the time of switching to TAF and returned to 68.7 ± 12.7 kg (P < 0.001) 48 weeks thereafter. The body mass index (BMI) decreased from 25 ± 3.3 kg/m² at TDF start to 24.5 ± 3.3 kg/m² (P = 0.002) at the time of switching to TAF and returned to 25.1 ± 3.6 kg/m² (P < 0.001) 48 weeks thereafter. Conclusions Our study showed that switching to TAF from TDF had good an…
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format: text/html
creator: Pei-Yuan Su
creator: Wei-Wen Su
creator: Yu-Chun Hsu
creator: Siou-Ping Huang
creator: Hsu-Heng Yen
subject: Drugs and Devices
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
description: doi:10.7717/peerj.12527
publisher: PeerJ Inc.
rights: © 2021 Su et al.
abstract: Background Tenofovir alafenamide (TAF) has good viral suppression efficacy and less adverse effect than tenofovir disoproxil fumarate (TDF). Real-world studies on the antiviral efficacy and safety of switching from TDF to TAF in patients with chronic hepatitis B (CHB) are limited. Methods This retrospective study included 167 nucleos(t)ide analogue (NA)-naive patients with CHB. All the patients received TDF at least 12 months before switching and TAF at least 12 months after switching at a single medical center. The Friedman test with Dunn–Bonferroni post hoc tests and repeated-measures analysis of variance was used to analyze the effect of complete viral suppression, alanine aminotransferase (ALT) level normalization, renal function changes, body weight, and body mass index in the periods before and after switching. Results The mean age and TDF treatment duration were 52 ± 11 years and 2.8 years (interquartile range, 1.51–5.15 years), respectively. The complete viral suppression rate was similar between the time of switching and 48 weeks after switching to TAF (77.8% vs 76%, P = 1.000). The percentage of alanine aminotransferase (ALT) normalization increased from 26.3% at TDF start to 81.4% (P < 0.001) at time of switching and 89.2% at 48 weeks after switching to TAF (P = 0.428). The median estimated glomerular filtration rate decreased from 100.09 mL/min/1.73 m² at TDF start to 91.97 mL/min/1.73 m² (P < 0.001) at the time of switching and stabilized at 48 weeks after switching to TAF (93.47 mL/min/1.73m², P = 1.000). The body weight decreased from 69.2 ± 12.2 kg at TDF start to 67.4 ± 12.1 kg (P < 0.001) at the time of switching to TAF and returned to 68.7 ± 12.7 kg (P < 0.001) 48 weeks thereafter. The body mass index (BMI) decreased from 25 ± 3.3 kg/m² at TDF start to 24.5 ± 3.3 kg/m² (P = 0.002) at the time of switching to TAF and returned to 25.1 ± 3.6 kg/m² (P < 0.001) 48 weeks thereafter. Conclusions Our study showed that switching to TAF from TDF had good an…
bibliographic citation: Su et al. (2021) Real-world experience of switching from tenofovir disoproxil fumarate to tenofovir alafenamide in patients with chronic hepatitis B: a retrospective study. PeerJ 9:e12527 https://doi.org/10.7717/peerj.12527
date submitted: 2021-08-18
date accepted: 2021-11-01
issued: 2021-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Pei-Yuan
author list: Agent
  family name: Su
  given name: Wei-Wen
author list: Agent
  family name: Hsu
  given name: Yu-Chun
author list: Agent
  family name: Huang
  given name: Siou-Ping
author list: Agent
  family name: Yen
  given name: Hsu-Heng
doi: 10.7717/peerj.12527
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-19
copyright: © 2021 Su et al.
attribution name: Su et al.

UBE2E3 regulates cellular senescence and osteogenic differentiation of BMSCs during aging
type: item
type: AcademicArticle
description: Background Osteoporosis has gradually become a public health problem in the world. However, the exact molecular mechanism of osteoporosis still remains unclear. Senescence and osteogenic differentiation inhibition of bone marrow mesenchymal stem cells (BMSCs ) are supposed to play an important part in osteoporosis. Methods We used two gene expression profiles (GSE35956 and GSE35958) associated with osteoporosis and selected the promising gene Ubiquitin-conjugating enzyme E2 E3 (UBE2E3). We then verified its function and mechanism by in vitro experiments. Results UBE2E3 was highly expressed in the bone marrow and positively associated with osteogenesis related genes. Besides, UBE2E3 expression reduced in old BMSCs compared with that in young BMSCs. In in vitro experiments, knockdown of UBE2E3 accelerated cellular senescence and inhibited osteogenic differentiation of young BMSCs. On the other hand, overexpression of UBE2E3 attenuated cellular senescence as well as enhanced osteogenic differentiation of old BMSCs. Mechanistically, UBE2E3 might regulate the nuclear factor erythroid 2-related factor (Nrf2) and control its function, thus affecting the senescence and osteogenic differentiation of BMSCs. Conclusion UBE2E3 may be potentially involved in the pathogenesis of osteoporosis by regulating cellular senescence and osteogenic differentiation of BMSCs.
format: application/pdf
format: text/html
creator: Yalin Liu
creator: Guangping Cai
creator: Peng Chen
creator: Tiejian Jiang
creator: Zhuying Xia
subject: Geriatrics
subject: Orthopedics
subject: Metabolic Sciences
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.12253
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Background Osteoporosis has gradually become a public health problem in the world. However, the exact molecular mechanism of osteoporosis still remains unclear. Senescence and osteogenic differentiation inhibition of bone marrow mesenchymal stem cells (BMSCs ) are supposed to play an important part in osteoporosis. Methods We used two gene expression profiles (GSE35956 and GSE35958) associated with osteoporosis and selected the promising gene Ubiquitin-conjugating enzyme E2 E3 (UBE2E3). We then verified its function and mechanism by in vitro experiments. Results UBE2E3 was highly expressed in the bone marrow and positively associated with osteogenesis related genes. Besides, UBE2E3 expression reduced in old BMSCs compared with that in young BMSCs. In in vitro experiments, knockdown of UBE2E3 accelerated cellular senescence and inhibited osteogenic differentiation of young BMSCs. On the other hand, overexpression of UBE2E3 attenuated cellular senescence as well as enhanced osteogenic differentiation of old BMSCs. Mechanistically, UBE2E3 might regulate the nuclear factor erythroid 2-related factor (Nrf2) and control its function, thus affecting the senescence and osteogenic differentiation of BMSCs. Conclusion UBE2E3 may be potentially involved in the pathogenesis of osteoporosis by regulating cellular senescence and osteogenic differentiation of BMSCs.
bibliographic citation: Liu et al. (2021) UBE2E3 regulates cellular senescence and osteogenic differentiation of BMSCs during aging. PeerJ 9:e12253 https://doi.org/10.7717/peerj.12253
date submitted: 2021-06-27
date accepted: 2021-09-14
issued: 2021-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yalin
author list: Agent
  family name: Cai
  given name: Guangping
author list: Agent
  family name: Chen
  given name: Peng
author list: Agent
  family name: Jiang
  given name: Tiejian
author list: Agent
  family name: Xia
  given name: Zhuying
doi: 10.7717/peerj.12253
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-18
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Misinformation effects in an online sample: results of an experimental study with a five day retention interval
type: item
type: AcademicArticle
description: Traditional face-to-face laboratory studies have contributed greatly to our understanding of how misinformation effects develop. However, an area of emerging concern that has been relatively under-researched is the impact of misinformation following exposure to traumatic events that are viewed online. Here we describe a novel method for investigating misinformation effects in an online context. Participants (N = 99) completed the study online. They first watched a 10-min video of a fictional school shooting. Between 5 and 10 days later, they were randomly assigned to receive misinformation or no misinformation about the video before completing a recognition test. Misinformed participants were less accurate at discriminating between misinformation and true statements than control participants. This effect was most strongly supported by ROC analyses (Cohen’s d = 0.59, BF10 = 8.34). Misinformation effects can be established in an online experiment using candid violent viral-style video stimuli.
format: application/pdf
format: text/html
creator: Olivia Sievwright
creator: Michael Philipp
creator: Aaron Drummond
creator: Katie Knapp
creator: Kirsty Ross
subject: Psychiatry and Psychology
subject: Legal Issues
description: doi:10.7717/peerj.12299
publisher: PeerJ Inc.
rights: © 2021 Sievwright et al.
abstract: Traditional face-to-face laboratory studies have contributed greatly to our understanding of how misinformation effects develop. However, an area of emerging concern that has been relatively under-researched is the impact of misinformation following exposure to traumatic events that are viewed online. Here we describe a novel method for investigating misinformation effects in an online context. Participants (N = 99) completed the study online. They first watched a 10-min video of a fictional school shooting. Between 5 and 10 days later, they were randomly assigned to receive misinformation or no misinformation about the video before completing a recognition test. Misinformed participants were less accurate at discriminating between misinformation and true statements than control participants. This effect was most strongly supported by ROC analyses (Cohen’s d = 0.59, BF10 = 8.34). Misinformation effects can be established in an online experiment using candid violent viral-style video stimuli.
bibliographic citation: Sievwright et al. (2021) Misinformation effects in an online sample: results of an experimental study with a five day retention interval. PeerJ 9:e12299 https://doi.org/10.7717/peerj.12299
date submitted: 2021-03-16
date accepted: 2021-09-21
issued: 2021-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sievwright
  given name: Olivia
author list: Agent
  family name: Philipp
  given name: Michael
author list: Agent
  family name: Drummond
  given name: Aaron
author list: Agent
  family name: Knapp
  given name: Katie
author list: Agent
  family name: Ross
  given name: Kirsty
doi: 10.7717/peerj.12299
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-18
copyright: © 2021 Sievwright et al.
attribution name: Sievwright et al.

De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins
type: item
type: AcademicArticle
description: The aim of this study was to generate and analyze the atlas of the loggerhead turtle blood transcriptome by RNA-seq, as well as identify and characterize thioredoxin (Tnxs) and peroxiredoxin (Prdxs) antioxidant enzymes of the greatest interest in the control of peroxide levels and other biological functions. The transcriptome of loggerhead turtle was sequenced using the Illumina Hiseq 2000 platform and de novo assembly was performed using the Trinity pipeline. The assembly comprised 515,597 contigs with an N50 of 2,631 bp. Contigs were analyzed with CD-Hit obtaining 374,545 unigenes, of which 165,676 had ORFs encoding putative proteins longer than 100 amino acids. A total of 52,147 (31.5%) of these transcripts had significant homology matches in at least one of the five databases used. From the enrichment of GO terms, 180 proteins with antioxidant activity were identified, among these 28 Prdxs and 50 putative Tnxs. The putative proteins of loggerhead turtles encoded by the genes Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip were predicted and characterized in silico. When comparing Prdxs and Txns of loggerhead turtle with homologous human proteins, they showed 18 (9%), 52 (18%) 94 (43%), 36 (16%), 35 (33%) and 74 (19%) amino acid mutations respectively. However, they showed high conservation in active sites and structural motifs (98%), with few specific modifications. Of these, Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip presented 0, 25, 18, three, six and two deleterious changes. This study provides a high quality blood transcriptome and functional annotation of loggerhead sea turtles.
format: application/pdf
format: text/html
creator: Javier Hernández-Fernández
creator: Andrés Mauricio Pinzón Velasco
creator: Ellie Anne López Barrera
creator: María Del Pilar Rodríguez Becerra
creator: José Luis Villanueva-Cañas
creator: M. Mar Alba
creator: Leonardo Mariño Ramírez
subject: Bioinformatics
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
subject: Ecotoxicology
description: doi:10.7717/peerj.12395
publisher: PeerJ Inc.
rights: © 2021 Hernández-Fernández et al.
abstract: The aim of this study was to generate and analyze the atlas of the loggerhead turtle blood transcriptome by RNA-seq, as well as identify and characterize thioredoxin (Tnxs) and peroxiredoxin (Prdxs) antioxidant enzymes of the greatest interest in the control of peroxide levels and other biological functions. The transcriptome of loggerhead turtle was sequenced using the Illumina Hiseq 2000 platform and de novo assembly was performed using the Trinity pipeline. The assembly comprised 515,597 contigs with an N50 of 2,631 bp. Contigs were analyzed with CD-Hit obtaining 374,545 unigenes, of which 165,676 had ORFs encoding putative proteins longer than 100 amino acids. A total of 52,147 (31.5%) of these transcripts had significant homology matches in at least one of the five databases used. From the enrichment of GO terms, 180 proteins with antioxidant activity were identified, among these 28 Prdxs and 50 putative Tnxs. The putative proteins of loggerhead turtles encoded by the genes Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip were predicted and characterized in silico. When comparing Prdxs and Txns of loggerhead turtle with homologous human proteins, they showed 18 (9%), 52 (18%) 94 (43%), 36 (16%), 35 (33%) and 74 (19%) amino acid mutations respectively. However, they showed high conservation in active sites and structural motifs (98%), with few specific modifications. Of these, Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip presented 0, 25, 18, three, six and two deleterious changes. This study provides a high quality blood transcriptome and functional annotation of loggerhead sea turtles.
bibliographic citation: Hernández-Fernández et al. (2021) De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins. PeerJ 9:e12395 https://doi.org/10.7717/peerj.12395
date submitted: 2021-01-14
date accepted: 2021-10-06
issued: 2021-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernández-Fernández
  given name: Javier
author list: Agent
  family name: Pinzón Velasco
  given name: Andrés Mauricio
author list: Agent
  family name: López Barrera
  given name: Ellie Anne
author list: Agent
  family name: Rodríguez Becerra
  given name: María Del Pilar
author list: Agent
  family name: Villanueva-Cañas
  given name: José Luis
author list: Agent
  family name: Alba
  given name: M. Mar
author list: Agent
  family name: Mariño Ramírez
  given name: Leonardo
doi: 10.7717/peerj.12395
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-18
copyright: ©2021 Hernández-Fernández et al.
attribution name: Hernández-Fernández et al.

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