PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genome-wide identification of the rubber tree superoxide dismutase (SOD) gene family and analysis of its expression under abiotic stress
items: Scientists’ warning of the impacts of climate change on mountains
items: Rolling circle amplification (RCA) -based biosensor system for the fluorescent detection of miR-129-2-3p miRNA
items: Screening and identification of miRNAs regulating Tbx4/5 genes of Pampus argenteus
items: ArVirInd—a database of arboviral antigenic proteins from the Indian subcontinent
items: Knowledge of safe handling, administration, and waste management of chemotherapeutic drugs among oncology nurses working at Khartoum Oncology Hospital, Sudan
items: Spatiotemporal Bayesian estimation of the number of under-reported COVID-19 cases in Victoria Australia
items: Ontogenetic growth in the crania of Exaeretodon argentinus (Synapsida: Cynodontia) captures a dietary shift
items: Telomerase reverse transcriptase promotes angiogenesis in neonatal rats after hypoxic-ischemic brain damage
items: Effects of carbodiimide combined with ethanol–wet bonding pretreatment on dentin bonding properties: an in vitro study

Genome-wide identification of the rubber tree superoxide dismutase (SOD) gene family and analysis of its expression under abiotic stress
type: item
type: AcademicArticle
description: Background The rubber tree (Hevea brasiliensis) is the only species capable of producing high-quality natural rubber for commercial use, and is often subjected to various abiotic stresses in non-traditional rubber plantation areas. Superoxide dismutase (SOD) is a vital metalloenzyme translated by a SOD gene family member and acts as a first-line of protection in plant cells by catalysing the disproportionation of reactive oxygen species (ROS) to produce H2O2 and O2. However, the SOD gene family is not reported in rubber trees. Methods Here, we used hidden markov model (HMM) and BLASTP methods to identify SOD genes in the H. brasiliensis genome. Phylogenetic tree, conserved motifs, gene structures, cis elements, and gene ontology annotation (GO) analyses were performed using MEGA 6.0, MEME, TBtools, PlantCARE, and eggNOG database, respectively. HbSOD gene expression profiles were analysed using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results We identified nine HbSOD genes in the rubber tree genome, including five HbCSDs, two HbFSDs, and two HbMSDs. Phylogenetic relationship analysis classified the SOD proteins from the rubber tree and other related species into three subfamilies. The results of gene structure and conserved motif analysis illustrated that most HbSOD genes have similar exon-intron numbers and conserved motifs in the same evolutionary branch. Five hormone-related, four stress-related, and light-responsive elements were detected in the HbSODs’ promoters. HbSODs were expressed in different tissues, gradually increased with leaf development, and were abundantly expressed in mature leaves. HbCSD2 and HbCSD4 was significantly upregulated under low and high temperatures, and salt stress, except for HbCSD2, by heat. Furthermore, most HbSOD genes were significantly upregulated by drought, except HbMSD2. These findings imply that these genes may play vital roles in rubber tree stress resistance. Our results provide a basis for fur…
format: application/pdf
format: text/html
creator: Wencai Yu
creator: Guanghong Kong
creator: Jinquan Chao
creator: Tuo Yin
creator: Hai Tian
creator: Huajin Ya
creator: Ligang He
creator: Hanyao Zhang
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Mathematical Biology
subject: Plant Science
description: doi:10.7717/peerj.14251
publisher: PeerJ Inc.
rights: © 2022 Yu et al.
abstract: Background The rubber tree (Hevea brasiliensis) is the only species capable of producing high-quality natural rubber for commercial use, and is often subjected to various abiotic stresses in non-traditional rubber plantation areas. Superoxide dismutase (SOD) is a vital metalloenzyme translated by a SOD gene family member and acts as a first-line of protection in plant cells by catalysing the disproportionation of reactive oxygen species (ROS) to produce H2O2 and O2. However, the SOD gene family is not reported in rubber trees. Methods Here, we used hidden markov model (HMM) and BLASTP methods to identify SOD genes in the H. brasiliensis genome. Phylogenetic tree, conserved motifs, gene structures, cis elements, and gene ontology annotation (GO) analyses were performed using MEGA 6.0, MEME, TBtools, PlantCARE, and eggNOG database, respectively. HbSOD gene expression profiles were analysed using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Results We identified nine HbSOD genes in the rubber tree genome, including five HbCSDs, two HbFSDs, and two HbMSDs. Phylogenetic relationship analysis classified the SOD proteins from the rubber tree and other related species into three subfamilies. The results of gene structure and conserved motif analysis illustrated that most HbSOD genes have similar exon-intron numbers and conserved motifs in the same evolutionary branch. Five hormone-related, four stress-related, and light-responsive elements were detected in the HbSODs’ promoters. HbSODs were expressed in different tissues, gradually increased with leaf development, and were abundantly expressed in mature leaves. HbCSD2 and HbCSD4 was significantly upregulated under low and high temperatures, and salt stress, except for HbCSD2, by heat. Furthermore, most HbSOD genes were significantly upregulated by drought, except HbMSD2. These findings imply that these genes may play vital roles in rubber tree stress resistance. Our results provide a basis for fur…
bibliographic citation: Yu et al. (2022) Genome-wide identification of the rubber tree superoxide dismutase (SOD) gene family and analysis of its expression under abiotic stress. PeerJ 10:e14251 https://doi.org/10.7717/peerj.14251
date submitted: 2022-06-24
date accepted: 2022-09-26
issued: 2022-10-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Wencai
author list: Agent
  family name: Kong
  given name: Guanghong
author list: Agent
  family name: Chao
  given name: Jinquan
author list: Agent
  family name: Yin
  given name: Tuo
author list: Agent
  family name: Tian
  given name: Hai
author list: Agent
  family name: Ya
  given name: Huajin
author list: Agent
  family name: He
  given name: Ligang
author list: Agent
  family name: Zhang
  given name: Hanyao
doi: 10.7717/peerj.14251
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-24
copyright: © 2022 Yu et al.
attribution name: Yu et al.

Scientists’ warning of the impacts of climate change on mountains
type: item
type: AcademicArticle
description: Mountains are highly diverse in areal extent, geological and climatic context, ecosystems and human activity. As such, mountain environments worldwide are particularly sensitive to the effects of anthropogenic climate change (global warming) as a result of their unique heat balance properties and the presence of climatically-sensitive snow, ice, permafrost and ecosystems. Consequently, mountain systems—in particular cryospheric ones—are currently undergoing unprecedented changes in the Anthropocene. This study identifies and discusses four of the major properties of mountains upon which anthropogenic climate change can impact, and indeed is already doing so. These properties are: the changing mountain cryosphere of glaciers and permafrost; mountain hazards and risk; mountain ecosystems and their services; and mountain communities and infrastructure. It is notable that changes in these different mountain properties do not follow a predictable trajectory of evolution in response to anthropogenic climate change. This demonstrates that different elements of mountain systems exhibit different sensitivities to forcing. The interconnections between these different properties highlight that mountains should be considered as integrated biophysical systems, of which human activity is part. Interrelationships between these mountain properties are discussed through a model of mountain socio-biophysical systems, which provides a framework for examining climate impacts and vulnerabilities. Managing the risks associated with ongoing climate change in mountains requires an integrated approach to climate change impacts monitoring and management.
format: application/pdf
format: text/html
creator: Jasper Knight
subject: Ecology
subject: Ecosystem Science
subject: Climate Change Biology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.14253
publisher: PeerJ Inc.
rights: © 2022 Knight
abstract: Mountains are highly diverse in areal extent, geological and climatic context, ecosystems and human activity. As such, mountain environments worldwide are particularly sensitive to the effects of anthropogenic climate change (global warming) as a result of their unique heat balance properties and the presence of climatically-sensitive snow, ice, permafrost and ecosystems. Consequently, mountain systems—in particular cryospheric ones—are currently undergoing unprecedented changes in the Anthropocene. This study identifies and discusses four of the major properties of mountains upon which anthropogenic climate change can impact, and indeed is already doing so. These properties are: the changing mountain cryosphere of glaciers and permafrost; mountain hazards and risk; mountain ecosystems and their services; and mountain communities and infrastructure. It is notable that changes in these different mountain properties do not follow a predictable trajectory of evolution in response to anthropogenic climate change. This demonstrates that different elements of mountain systems exhibit different sensitivities to forcing. The interconnections between these different properties highlight that mountains should be considered as integrated biophysical systems, of which human activity is part. Interrelationships between these mountain properties are discussed through a model of mountain socio-biophysical systems, which provides a framework for examining climate impacts and vulnerabilities. Managing the risks associated with ongoing climate change in mountains requires an integrated approach to climate change impacts monitoring and management.
bibliographic citation: Knight (2022) Scientists’ warning of the impacts of climate change on mountains. PeerJ 10:e14253 https://doi.org/10.7717/peerj.14253
date submitted: 2022-06-09
date accepted: 2022-09-26
issued: 2022-10-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Knight
  given name: Jasper
doi: 10.7717/peerj.14253
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-24
copyright: © 2022 Knight
attribution name: Knight

Rolling circle amplification (RCA) -based biosensor system for the fluorescent detection of miR-129-2-3p miRNA
type: item
type: AcademicArticle
description: Herein, a versatile fluorescent bioanalysis platform for sensitive and specific screening of target miRNA (miR-129-2-3p) was innovatively designed by applying target-induced rolling circle amplification (RCA) for efficient signal amplification. Specifically, miR-129-2-3p was used as a ligation template to facilitate its ligation with padlock probes, followed by an RCA reaction in the presence of phi29 DNA polymerase. The dsDNA fragments and products were stained by SYBR Green I and then detected by fluorescence spectrophotometry. As a result, miR-129-2-3p concentrations as low as 50 nM could be detected. Furthermore, the expression of miR-129-2-3p in breast cancer patients was about twice that in healthy people. Therefore, the results indicated that the RCA-based biosensor system could be a valuable platform for miRNA detection in clinical diagnosis and biomedical study.
format: application/pdf
format: text/html
creator: Yan Ye
creator: Yao Lin
creator: Zilin Chi
creator: Jiasheng Zhang
creator: Fan Cai
creator: Youzhi Zhu
creator: Dianping Tang
creator: Qingqiang Lin
subject: Biochemistry
subject: Biotechnology
subject: Molecular Biology
description: doi:10.7717/peerj.14257
publisher: PeerJ Inc.
rights: © 2022 Ye et al.
abstract: Herein, a versatile fluorescent bioanalysis platform for sensitive and specific screening of target miRNA (miR-129-2-3p) was innovatively designed by applying target-induced rolling circle amplification (RCA) for efficient signal amplification. Specifically, miR-129-2-3p was used as a ligation template to facilitate its ligation with padlock probes, followed by an RCA reaction in the presence of phi29 DNA polymerase. The dsDNA fragments and products were stained by SYBR Green I and then detected by fluorescence spectrophotometry. As a result, miR-129-2-3p concentrations as low as 50 nM could be detected. Furthermore, the expression of miR-129-2-3p in breast cancer patients was about twice that in healthy people. Therefore, the results indicated that the RCA-based biosensor system could be a valuable platform for miRNA detection in clinical diagnosis and biomedical study.
bibliographic citation: Ye et al. (2022) Rolling circle amplification (RCA) -based biosensor system for the fluorescent detection of miR-129-2-3p miRNA. PeerJ 10:e14257 https://doi.org/10.7717/peerj.14257
date submitted: 2022-03-28
date accepted: 2022-09-27
issued: 2022-10-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Yan
author list: Agent
  family name: Lin
  given name: Yao
author list: Agent
  family name: Chi
  given name: Zilin
author list: Agent
  family name: Zhang
  given name: Jiasheng
author list: Agent
  family name: Cai
  given name: Fan
author list: Agent
  family name: Zhu
  given name: Youzhi
author list: Agent
  family name: Tang
  given name: Dianping
author list: Agent
  family name: Lin
  given name: Qingqiang
doi: 10.7717/peerj.14257
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-24
copyright: ©2022 Ye et al.
attribution name: Ye et al.

Screening and identification of miRNAs regulating Tbx4/5 genes of Pampus argenteus
type: item
type: AcademicArticle
description: Background Silver pomfret (Pampus argenteus) is one of the most widely distributed and economically important pelagic fish species. However, an unique morphological feature of P. argenteus is the loss of pelvic fins, which can increase the energy requirement during food capture to some extent and is therefore not conducive to artificial culture. Tbx4/5 genes are highly conserved regulatory factors that regulate limb development in vertebrates and are in turn regulated by microRNAs (miRNAs). However, the miRNAs that directly regulate the Tbx4/5 genes in P. argenteus remain to be elucidated. Methods The Tbx4/5 genes of P. argenteus were first cloned, and the small RNA transcriptomes were sequenced by high-throughput sequencing during the critical period of the fin development at days 1, 7, and 13 of hatching. The miRNAs regulating the Tbx4/5 genes of P. argenteus were subsequently predicted by bioinformatics analysis, and the related miRNAs were verified in vitro using a dual fluorescence reporter system. Results A total of 662 miRNAs were identified, of which 257 were known miRNAs and 405 were novel miRNAs were identified. Compared to day 1, 182 miRNAs were differentially expressed (DE) on day 7, of which 77 and 105 miRNAs were downregulated and upregulated, respectively, while 278 miRNAs were DE on day 13, of which 136 and 142 miRNAs were downregulated and upregulated, respectively. Compared to day 13, four miRNAs were DE on day 7, of which three miRNAs were downregulated and one miRNA was upregulated. The results of hierarchical clustering of the miRNAs revealed that the DE genes were inversely expressed between days 1 and 7, and between days 1 and 13 of larval development, indicating that the larvae were in the peak stage of differentiation. However, the number of DE genes between days 7 and 13 of larval development was relatively small, suggesting the initiation of development. The potential target genes of the DE miRNAs were subsequently predicted, and Gene Onto…
format: application/pdf
format: text/html
creator: Cheng Zhang
creator: Shun Zhang
creator: Mengdi Liu
creator: Yajun Wang
creator: Danli Wang
creator: Shanliang Xu
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.14300
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Silver pomfret (Pampus argenteus) is one of the most widely distributed and economically important pelagic fish species. However, an unique morphological feature of P. argenteus is the loss of pelvic fins, which can increase the energy requirement during food capture to some extent and is therefore not conducive to artificial culture. Tbx4/5 genes are highly conserved regulatory factors that regulate limb development in vertebrates and are in turn regulated by microRNAs (miRNAs). However, the miRNAs that directly regulate the Tbx4/5 genes in P. argenteus remain to be elucidated. Methods The Tbx4/5 genes of P. argenteus were first cloned, and the small RNA transcriptomes were sequenced by high-throughput sequencing during the critical period of the fin development at days 1, 7, and 13 of hatching. The miRNAs regulating the Tbx4/5 genes of P. argenteus were subsequently predicted by bioinformatics analysis, and the related miRNAs were verified in vitro using a dual fluorescence reporter system. Results A total of 662 miRNAs were identified, of which 257 were known miRNAs and 405 were novel miRNAs were identified. Compared to day 1, 182 miRNAs were differentially expressed (DE) on day 7, of which 77 and 105 miRNAs were downregulated and upregulated, respectively, while 278 miRNAs were DE on day 13, of which 136 and 142 miRNAs were downregulated and upregulated, respectively. Compared to day 13, four miRNAs were DE on day 7, of which three miRNAs were downregulated and one miRNA was upregulated. The results of hierarchical clustering of the miRNAs revealed that the DE genes were inversely expressed between days 1 and 7, and between days 1 and 13 of larval development, indicating that the larvae were in the peak stage of differentiation. However, the number of DE genes between days 7 and 13 of larval development was relatively small, suggesting the initiation of development. The potential target genes of the DE miRNAs were subsequently predicted, and Gene Onto…
bibliographic citation: Zhang et al. (2022) Screening and identification of miRNAs regulating Tbx4/5 genes of Pampus argenteus. PeerJ 10:e14300 https://doi.org/10.7717/peerj.14300
date submitted: 2022-03-08
date accepted: 2022-10-05
issued: 2022-10-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Cheng
author list: Agent
  family name: Zhang
  given name: Shun
author list: Agent
  family name: Liu
  given name: Mengdi
author list: Agent
  family name: Wang
  given name: Yajun
author list: Agent
  family name: Wang
  given name: Danli
author list: Agent
  family name: Xu
  given name: Shanliang
doi: 10.7717/peerj.14300
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-24
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

ArVirInd—a database of arboviral antigenic proteins from the Indian subcontinent
type: item
type: AcademicArticle
description: Background Studies on antigenic proteins for arboviruses are important for providing diagnostics and vaccine development. India and its neighboring countries have a huge burden of arboviral diseases. Data mining for country-specific sequences from existing bioinformatics databases is cumbersome and time-consuming. This necessitated the development of a database of antigenic proteins from arboviruses isolated from the countries of the Indian subcontinent. Methods Arboviral antigenic protein sequences were obtained from the NCBI and other databases. In silico antigenic characterization was performed (Epitope predictions) and data was incorporated into the database. The front end was designed and developed using HTML, CSS, and PHP. For the backend of the database, we have used MySQL. Results A database, named ArVirInd, is created as a repository of information on curated antigenic proteins. This enlists sequences by country and year of outbreak or origin of the viral strain. For each entry, antigenic information is provided along with functional sites, etc. Researchers can search this database by virus/protein name, country, and year of collection (or in combination) as well as peptide search for epitopes. It is available publicly via the Internet at http://www.arvirind.co.in. ArVirInd will be useful in the study of immune informatics, diagnostics, and vaccinology for arboviruses.
format: application/pdf
format: text/html
creator: Nitin Motilal Atre
creator: Kalichamy Alagarasu
creator: Pratip Shil
subject: Bioinformatics
subject: Virology
subject: Immunology
description: doi:10.7717/peerj.13851
publisher: PeerJ Inc.
rights: © 2022 Atre et al.
abstract: Background Studies on antigenic proteins for arboviruses are important for providing diagnostics and vaccine development. India and its neighboring countries have a huge burden of arboviral diseases. Data mining for country-specific sequences from existing bioinformatics databases is cumbersome and time-consuming. This necessitated the development of a database of antigenic proteins from arboviruses isolated from the countries of the Indian subcontinent. Methods Arboviral antigenic protein sequences were obtained from the NCBI and other databases. In silico antigenic characterization was performed (Epitope predictions) and data was incorporated into the database. The front end was designed and developed using HTML, CSS, and PHP. For the backend of the database, we have used MySQL. Results A database, named ArVirInd, is created as a repository of information on curated antigenic proteins. This enlists sequences by country and year of outbreak or origin of the viral strain. For each entry, antigenic information is provided along with functional sites, etc. Researchers can search this database by virus/protein name, country, and year of collection (or in combination) as well as peptide search for epitopes. It is available publicly via the Internet at http://www.arvirind.co.in. ArVirInd will be useful in the study of immune informatics, diagnostics, and vaccinology for arboviruses.
bibliographic citation: Atre et al. (2022) ArVirInd—a database of arboviral antigenic proteins from the Indian subcontinent. PeerJ 10:e13851 https://doi.org/10.7717/peerj.13851
date submitted: 2022-04-05
date accepted: 2022-07-16
issued: 2022-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Atre
  given name: Nitin Motilal
author list: Agent
  family name: Alagarasu
  given name: Kalichamy
author list: Agent
  family name: Shil
  given name: Pratip
doi: 10.7717/peerj.13851
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-21
copyright: ©2022 Atre et al.
attribution name: Atre et al.

Knowledge of safe handling, administration, and waste management of chemotherapeutic drugs among oncology nurses working at Khartoum Oncology Hospital, Sudan
type: item
type: AcademicArticle
description: Introduction Knowledge of chemotherapeutic drug (CD) handling, administration, and waste disposal are important among nurses involved in cancer therapy. Inadequate knowledge of the management of CD could cause environmental contamination and potential harm to patients and nurses. To assess the knowledge of safe handling, administration, and waste management of CD among oncology nurses working at Khartoum Oncology Hospital, Sudan. Methods A questionnaire was developed by a team of experts to assess the knowledge in three domains of oncology nursing practice (handling, administration, and disposal). The study involved 78 oncology nurses working in Khartoum Oncology Hospital in Sudan from April 2020. Results The mean CD knowledge score of nurses was 12.7 ± 3.9 out of 26 items in the questionnaire. For each domain, their knowledge showed poor scores related to safe handling (mean = 2.0 ± 1.5 out of eight knowledge items) and good scores for administration (mean = 6.2 ± 1.7 out of 10) and poor scores for waste disposal (mean = 4.4 ± 1.5 out of eight). Simple linear regression indicated that education level (β = 3.715, p = .008) and training (β = 0.969, p = .004) significantly predicted knowledge among nurses. Conclusion There is a significant need to enhance the knowledge and safe handling skills of CD among oncology nurses in Sudan. Implementation of strict guidelines to manage cytotoxic waste to reduce health risks and hospital contamination.
format: application/pdf
format: text/html
creator: Abdelgayoom Alhag Warsha Sargidy
creator: Amira Yahia
creator: Mehrunnisha Ahmad
creator: Adel Abdalla
creator: Suhail Naser Khalil
creator: Sharifa Alasiry
creator: Mohammad Abu Shaphe
creator: Shabir Ahmad Mir
creator: Faizan Z. Kashoo
subject: Drugs and Devices
subject: Nursing
subject: Oncology
subject: Science and Medical Education
subject: Palliative Care
description: doi:10.7717/peerj.14173
publisher: PeerJ Inc.
rights: © 2022 Sargidy et al.
abstract: Introduction Knowledge of chemotherapeutic drug (CD) handling, administration, and waste disposal are important among nurses involved in cancer therapy. Inadequate knowledge of the management of CD could cause environmental contamination and potential harm to patients and nurses. To assess the knowledge of safe handling, administration, and waste management of CD among oncology nurses working at Khartoum Oncology Hospital, Sudan. Methods A questionnaire was developed by a team of experts to assess the knowledge in three domains of oncology nursing practice (handling, administration, and disposal). The study involved 78 oncology nurses working in Khartoum Oncology Hospital in Sudan from April 2020. Results The mean CD knowledge score of nurses was 12.7 ± 3.9 out of 26 items in the questionnaire. For each domain, their knowledge showed poor scores related to safe handling (mean = 2.0 ± 1.5 out of eight knowledge items) and good scores for administration (mean = 6.2 ± 1.7 out of 10) and poor scores for waste disposal (mean = 4.4 ± 1.5 out of eight). Simple linear regression indicated that education level (β = 3.715, p = .008) and training (β = 0.969, p = .004) significantly predicted knowledge among nurses. Conclusion There is a significant need to enhance the knowledge and safe handling skills of CD among oncology nurses in Sudan. Implementation of strict guidelines to manage cytotoxic waste to reduce health risks and hospital contamination.
bibliographic citation: Sargidy et al. (2022) Knowledge of safe handling, administration, and waste management of chemotherapeutic drugs among oncology nurses working at Khartoum Oncology Hospital, Sudan. PeerJ 10:e14173 https://doi.org/10.7717/peerj.14173
date submitted: 2022-06-02
date accepted: 2022-09-12
issued: 2022-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sargidy
  given name: Abdelgayoom Alhag Warsha
author list: Agent
  family name: Yahia
  given name: Amira
author list: Agent
  family name: Ahmad
  given name: Mehrunnisha
author list: Agent
  family name: Abdalla
  given name: Adel
author list: Agent
  family name: Khalil
  given name: Suhail Naser
author list: Agent
  family name: Alasiry
  given name: Sharifa
author list: Agent
  family name: Shaphe
  given name: Mohammad Abu
author list: Agent
  family name: Mir
  given name: Shabir Ahmad
author list: Agent
  family name: Kashoo
  given name: Faizan Z.
doi: 10.7717/peerj.14173
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-21
copyright: ©2022 Sargidy et al.
attribution name: Sargidy et al.

Spatiotemporal Bayesian estimation of the number of under-reported COVID-19 cases in Victoria Australia
type: item
type: AcademicArticle
description: Having an estimate of the number of under-reported cases is crucial in determining the true burden of a disease. In the COVID-19 pandemic, there is a great need to quantify the true disease burden by capturing the true incidence rate to establish appropriate measures and strategies to combat the disease. This study investigates the under-reporting of COVID-19 cases in Victoria, Australia, during the third wave of the pandemic as a result of variation in geographic area and time. It is aimed to determine potential under-reported areas and generate the true picture of the disease in terms of the number of cases. A two-tiered Bayesian hierarchical model approach is employed to estimate the true incidence and detection rates through Bayesian model averaging. The proposed model goes beyond testing inequality across areas by looking into other covariates such as weather, vaccination rates, and access to vaccination and testing centres, including interactions and variations between space and time. This model aims for parsimony yet allows a broader range of scope to capture the underlying dynamic of the reported COVID-19 cases. Moreover, it is a data-driven, flexible, and generalisable model to a global context such as cross-country estimation and across time points under strict pandemic conditions.
format: application/pdf
format: text/html
creator: Dinah Jane Lope
creator: Haydar Demirhan
subject: Epidemiology
subject: Infectious Diseases
subject: Statistics
subject: COVID-19
description: doi:10.7717/peerj.14184
publisher: PeerJ Inc.
rights: © 2022 Lope and Demirhan
abstract: Having an estimate of the number of under-reported cases is crucial in determining the true burden of a disease. In the COVID-19 pandemic, there is a great need to quantify the true disease burden by capturing the true incidence rate to establish appropriate measures and strategies to combat the disease. This study investigates the under-reporting of COVID-19 cases in Victoria, Australia, during the third wave of the pandemic as a result of variation in geographic area and time. It is aimed to determine potential under-reported areas and generate the true picture of the disease in terms of the number of cases. A two-tiered Bayesian hierarchical model approach is employed to estimate the true incidence and detection rates through Bayesian model averaging. The proposed model goes beyond testing inequality across areas by looking into other covariates such as weather, vaccination rates, and access to vaccination and testing centres, including interactions and variations between space and time. This model aims for parsimony yet allows a broader range of scope to capture the underlying dynamic of the reported COVID-19 cases. Moreover, it is a data-driven, flexible, and generalisable model to a global context such as cross-country estimation and across time points under strict pandemic conditions.
bibliographic citation: Lope et al. (2022) Spatiotemporal Bayesian estimation of the number of under-reported COVID-19 cases in Victoria Australia. PeerJ 10:e14184 https://doi.org/10.7717/peerj.14184
date submitted: 2022-06-21
date accepted: 2022-09-14
issued: 2022-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lope
  given name: Dinah Jane
author list: Agent
  family name: Demirhan
  given name: Haydar
doi: 10.7717/peerj.14184
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-21
copyright: ©2022 Lope and Demirhan
attribution name: Lope and Demirhan

Ontogenetic growth in the crania of Exaeretodon argentinus (Synapsida: Cynodontia) captures a dietary shift
type: item
type: AcademicArticle
description: Background An ontogenetic niche shift in vertebrates is a common occurrence where ecology shifts with morphological changes throughout growth. How ecology shifts over a vertebrate’s lifetime is often reconstructed in extant species—by combining observational and skeletal data from growth series of the same species—because interactions between organisms and their environment can be observed directly. However, reconstructing shifts using extinct vertebrates is difficult and requires well-sampled growth series, specimens with relatively complete preservation, and easily observable skeletal traits associated with ecologies suspected to change throughout growth, such as diet. Methods To reconstruct ecological changes throughout the growth of a stem-mammal, we describe changes associated with dietary ecology in a growth series of crania of the large-bodied (∼2 m in length) and herbivorous form, Exaeretodon argentinus (Cynodontia: Traversodontidae) from the Late Triassic Ischigualasto Formation, San Juan, Argentina. Nearly all specimens were deformed by taphonomic processes, so we reconstructed allometric slope using a generalized linear mixed effects model with distortion as a random effect. Results Under a mixed effects model, we find that throughout growth, E. argentinus reduced the relative length of the palate, postcanine series, orbits, and basicranium, and expanded the relative length of the temporal region and the height of the zygomatic arch. The allometric relationship between the zygomatic arch and temporal region with the total length of the skull approximate the rate of growth for feeding musculature. Based on a higher allometric slope, the zygoma height is growing relatively faster than the length of the temporal region. The higher rate of change in the zygoma may suggest that smaller individuals had a crushing-dominated feeding style that transitioned into a chewing-dominated feeding style in larger individuals, suggesting a dietary shift from possible fauni…
format: application/pdf
format: text/html
creator: Brenen Wynd
creator: Fernando Abdala
creator: Sterling J. Nesbitt
subject: Developmental Biology
subject: Ecology
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.14196
publisher: PeerJ Inc.
rights: © 2022 Wynd et al.
abstract: Background An ontogenetic niche shift in vertebrates is a common occurrence where ecology shifts with morphological changes throughout growth. How ecology shifts over a vertebrate’s lifetime is often reconstructed in extant species—by combining observational and skeletal data from growth series of the same species—because interactions between organisms and their environment can be observed directly. However, reconstructing shifts using extinct vertebrates is difficult and requires well-sampled growth series, specimens with relatively complete preservation, and easily observable skeletal traits associated with ecologies suspected to change throughout growth, such as diet. Methods To reconstruct ecological changes throughout the growth of a stem-mammal, we describe changes associated with dietary ecology in a growth series of crania of the large-bodied (∼2 m in length) and herbivorous form, Exaeretodon argentinus (Cynodontia: Traversodontidae) from the Late Triassic Ischigualasto Formation, San Juan, Argentina. Nearly all specimens were deformed by taphonomic processes, so we reconstructed allometric slope using a generalized linear mixed effects model with distortion as a random effect. Results Under a mixed effects model, we find that throughout growth, E. argentinus reduced the relative length of the palate, postcanine series, orbits, and basicranium, and expanded the relative length of the temporal region and the height of the zygomatic arch. The allometric relationship between the zygomatic arch and temporal region with the total length of the skull approximate the rate of growth for feeding musculature. Based on a higher allometric slope, the zygoma height is growing relatively faster than the length of the temporal region. The higher rate of change in the zygoma may suggest that smaller individuals had a crushing-dominated feeding style that transitioned into a chewing-dominated feeding style in larger individuals, suggesting a dietary shift from possible fauni…
bibliographic citation: Wynd et al. (2022) Ontogenetic growth in the crania of Exaeretodon argentinus (Synapsida: Cynodontia) captures a dietary shift. PeerJ 10:e14196 https://doi.org/10.7717/peerj.14196
date submitted: 2021-12-17
date accepted: 2022-09-15
issued: 2022-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wynd
  given name: Brenen
author list: Agent
  family name: Abdala
  given name: Fernando
author list: Agent
  family name: Nesbitt
  given name: Sterling J.
doi: 10.7717/peerj.14196
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-21
copyright: ©2022 Wynd et al.
attribution name: Wynd et al.

Telomerase reverse transcriptase promotes angiogenesis in neonatal rats after hypoxic-ischemic brain damage
type: item
type: AcademicArticle
description: Background Angiogenesis is an endogenous repair mechanism following hypoxic-ischemic brain damage (HIBD). Interestingly, recent studies have shown that angiogenesis can be regulated by telomerase reverse transcriptase (TERT), a critical component of telomerase. As telomerase reverse transcriptase can promote angiogenesis after stroke, we hypothesized that it could also promote angiogenesis after HIBD. To test this hypothesis, we developed in vivo and in vitro HIBD models in neonatal rats. Methods TERT was overexpressed by lentivirus and adenovirus infection, and levels were measured using quantitative real-time polymerase chain reaction. We used a cell counting kit to quantify the proliferation rate of brain microvascular endothelial cells (BMECs), and immunofluorescence staining to measure CD34 expression levels. A microvessel formation assay was used to evaluate angiogenesis. Blood-brain barrier (BBB) integrity was assessed using immunohistochemical staining for ZO-1 and Evans Blue staining. Lastly, the expression level of Notch-1 was measured by western blotting. Results Overexpression of TERT promoted the proliferation of BMECs after hypoxic-ischemic damage in vitro. TERT overexpression increased the formation of microvessels in the neonatal brain after HIBD both in vivo and in vitro. Overexpression of TERT improved BBB integrity in the brains of neonatal rats after HIBD. In addition, the expression level of Notch-1 was increased in BMECs following oxygen glucose deprivation, and overexpression of TERT further increased Notch-1 expression levels in BMECs following oxygen glucose deprivation. Discussion Our results reveal that telomerase reverse transcriptase promotes angiogenesis and maintains the integrity of the blood-brain barrier after neonatal hypoxic-ischemic brain damage. Furthermore, the Notch-1 signaling pathway appears to contribute to the angiogenic function of telomerase reverse transcriptase. This protective effect of telomerase reverse transcriptas…
format: application/pdf
format: text/html
creator: Jiao Li
creator: Yi Feng
creator: Jing Zhao
creator: Zhi Fang
creator: Haiting Liu
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Histology
description: doi:10.7717/peerj.14220
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background Angiogenesis is an endogenous repair mechanism following hypoxic-ischemic brain damage (HIBD). Interestingly, recent studies have shown that angiogenesis can be regulated by telomerase reverse transcriptase (TERT), a critical component of telomerase. As telomerase reverse transcriptase can promote angiogenesis after stroke, we hypothesized that it could also promote angiogenesis after HIBD. To test this hypothesis, we developed in vivo and in vitro HIBD models in neonatal rats. Methods TERT was overexpressed by lentivirus and adenovirus infection, and levels were measured using quantitative real-time polymerase chain reaction. We used a cell counting kit to quantify the proliferation rate of brain microvascular endothelial cells (BMECs), and immunofluorescence staining to measure CD34 expression levels. A microvessel formation assay was used to evaluate angiogenesis. Blood-brain barrier (BBB) integrity was assessed using immunohistochemical staining for ZO-1 and Evans Blue staining. Lastly, the expression level of Notch-1 was measured by western blotting. Results Overexpression of TERT promoted the proliferation of BMECs after hypoxic-ischemic damage in vitro. TERT overexpression increased the formation of microvessels in the neonatal brain after HIBD both in vivo and in vitro. Overexpression of TERT improved BBB integrity in the brains of neonatal rats after HIBD. In addition, the expression level of Notch-1 was increased in BMECs following oxygen glucose deprivation, and overexpression of TERT further increased Notch-1 expression levels in BMECs following oxygen glucose deprivation. Discussion Our results reveal that telomerase reverse transcriptase promotes angiogenesis and maintains the integrity of the blood-brain barrier after neonatal hypoxic-ischemic brain damage. Furthermore, the Notch-1 signaling pathway appears to contribute to the angiogenic function of telomerase reverse transcriptase. This protective effect of telomerase reverse transcriptas…
bibliographic citation: Li et al. (2022) Telomerase reverse transcriptase promotes angiogenesis in neonatal rats after hypoxic-ischemic brain damage. PeerJ 10:e14220 https://doi.org/10.7717/peerj.14220
date submitted: 2022-06-08
date accepted: 2022-09-20
issued: 2022-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jiao
author list: Agent
  family name: Feng
  given name: Yi
author list: Agent
  family name: Zhao
  given name: Jing
author list: Agent
  family name: Fang
  given name: Zhi
author list: Agent
  family name: Liu
  given name: Haiting
doi: 10.7717/peerj.14220
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-21
copyright: ©2022 Li et al.
attribution name: Li et al.

Effects of carbodiimide combined with ethanol–wet bonding pretreatment on dentin bonding properties: an in vitro study
type: item
type: AcademicArticle
description: Purpose This study evaluated the combined effects of Carbodiimide (EDC) and ethanol–wet bonding (EWB) pretreatment on the bond strength and resin–dentin surface. Methods Phosphoric acid-etched dentin specimens were randomly divided into five groups based on the following pretreatments: deionized water (control), EWB, 0.3M EDC in water (EDCw), EDC water solution combined EWB (EDCw + EWB), and 0.3M EDC in ethanol (EDCe). A scanning electron microscope (SEM) was used to observe the morphology of collagen fibrils on the demineralized dentin matrix in each group after pretreatment. The adhesives Prime & Bond NT (PB) (Dentsply De trey, Konstanz, Germany) or Single bond 2 (SB) (3M ESPE, St. Paul, MN, USA) was applied after pretreatments, and a confocal laser scanning microscope (CLSM) was used to evaluate the quality of resin tags. The degree of conversion (DC) of the adhesive was investigated by Fourier transform infrared spectroscopy (ATR-FTIR). The dentin was first bonded with resin and bathed in water at 37 °C for 24 h. Half of them were subjected to 10, 000 cycles in a thermocycler between 5 °C and 55 °C before a microshear bond strength (µSBS) test. The statistical methods were Analysis of Variance (ANOVA) and a Tukey post hoc test at α = 0.05. Results The µSBS was significantly affected by pretreatments (p < 0.001), adhesives (p < 0.001), and aging conditions (p < 0.001) as revealed by the three-way ANOVA. The EDCw, EDCw + EWB, and EDCe groups significantly increased the µSBS; the EDCw + EWB and EDCe groups produced the highest µSBS. In the EDC-containing groups, the SEM showed at the collagen fibrils in the dentin matrix formed a three-dimensional network structure in the tubules after cross-linking into sheets, and the hybrid layer formed thicker resin tags under a CLSM. In the EDC-containing groups, the CLSM observed an increase in the length of resin tags. PB showed a higher DC and bonding strength than SB, and the five pretreatment groups tested did not affect …
format: application/pdf
format: text/html
creator: Xiaoxiao You
creator: Long Chen
creator: Jie Xu
creator: Sihui Li
creator: Zhenghao Zhang
creator: Ling Guo
subject: Dentistry
description: doi:10.7717/peerj.14238
publisher: PeerJ Inc.
rights: © 2022 You et al.
abstract: Purpose This study evaluated the combined effects of Carbodiimide (EDC) and ethanol–wet bonding (EWB) pretreatment on the bond strength and resin–dentin surface. Methods Phosphoric acid-etched dentin specimens were randomly divided into five groups based on the following pretreatments: deionized water (control), EWB, 0.3M EDC in water (EDCw), EDC water solution combined EWB (EDCw + EWB), and 0.3M EDC in ethanol (EDCe). A scanning electron microscope (SEM) was used to observe the morphology of collagen fibrils on the demineralized dentin matrix in each group after pretreatment. The adhesives Prime & Bond NT (PB) (Dentsply De trey, Konstanz, Germany) or Single bond 2 (SB) (3M ESPE, St. Paul, MN, USA) was applied after pretreatments, and a confocal laser scanning microscope (CLSM) was used to evaluate the quality of resin tags. The degree of conversion (DC) of the adhesive was investigated by Fourier transform infrared spectroscopy (ATR-FTIR). The dentin was first bonded with resin and bathed in water at 37 °C for 24 h. Half of them were subjected to 10, 000 cycles in a thermocycler between 5 °C and 55 °C before a microshear bond strength (µSBS) test. The statistical methods were Analysis of Variance (ANOVA) and a Tukey post hoc test at α = 0.05. Results The µSBS was significantly affected by pretreatments (p < 0.001), adhesives (p < 0.001), and aging conditions (p < 0.001) as revealed by the three-way ANOVA. The EDCw, EDCw + EWB, and EDCe groups significantly increased the µSBS; the EDCw + EWB and EDCe groups produced the highest µSBS. In the EDC-containing groups, the SEM showed at the collagen fibrils in the dentin matrix formed a three-dimensional network structure in the tubules after cross-linking into sheets, and the hybrid layer formed thicker resin tags under a CLSM. In the EDC-containing groups, the CLSM observed an increase in the length of resin tags. PB showed a higher DC and bonding strength than SB, and the five pretreatment groups tested did not affect …
bibliographic citation: You et al. (2022) Effects of carbodiimide combined with ethanol–wet bonding pretreatment on dentin bonding properties: an in vitro study. PeerJ 10:e14238 https://doi.org/10.7717/peerj.14238
date submitted: 2022-07-19
date accepted: 2022-09-23
issued: 2022-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: You
  given name: Xiaoxiao
author list: Agent
  family name: Chen
  given name: Long
author list: Agent
  family name: Xu
  given name: Jie
author list: Agent
  family name: Li
  given name: Sihui
author list: Agent
  family name: Zhang
  given name: Zhenghao
author list: Agent
  family name: Guo
  given name: Ling
doi: 10.7717/peerj.14238
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-21
copyright: ©2022 You et al.
attribution name: You et al.

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