PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Towards a pragmatic use of statistics in ecology
items: The bioinformatics and experimental analysis of AlkB family for prognosis and immune cell infiltration in hepatocellular carcinoma
items: Geographic disparities and socio-demographic predictors of pertussis risk in Florida
items: Exploring private land conservation non-adopters’ attendance at outreach events in the Chesapeake Bay watershed, USA
items: https://peerj.com/articles/12028
items: COVID-19 and regional differences in the timeliness of hip-fracture surgery: an interrupted time-series analysis
items: Germline mutation analyses of malignant ground glass opacity nodules in non-smoking lung adenocarcinoma patients
items: Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea
items: Transcriptome analysis reveals gene expression differences in Liriomyza trifolii exposed to combined heat and abamectin exposure
items: Investigation of inhibition effect of daidzein on osteosarcoma cells based on experimental validation and systematic pharmacology analysis

Towards a pragmatic use of statistics in ecology
type: item
type: AcademicArticle
description: Although null hypothesis testing (NHT) is the primary method for analyzing data in many natural sciences, it has been increasingly criticized. Recently, approaches based on information theory (IT) have become popular and were held by many to be superior because it enables researchers to properly assess the strength of the evidence that data provide for competing hypotheses. Many studies have compared IT and NHT in the context of model selection and stepwise regression, but a systematic comparison of the most basic uses of statistics by ecologists is still lacking. We used computer simulations to compare how both approaches perform in four basic test designs (t-test, ANOVA, correlation tests, and multiple linear regression). Performance was measured by the proportion of simulated samples for which each method provided the correct conclusion (power), the proportion of detected effects with a wrong sign (S-error), and the mean ratio of the estimated effect to the true effect (M-error). We also checked if the p-value from significance tests correlated to a measure of strength of evidence, the Akaike weight. In general both methods performed equally well. The concordance is explained by the monotonic relationship between p-values and evidence weights in simple designs, which agree with analytic results. Our results show that researchers can agree on the conclusions drawn from a data set even when they are using different statistical approaches. By focusing on the practical consequences of inferences, such a pragmatic view of statistics can promote insightful dialogue among researchers on how to find a common ground from different pieces of evidence. A less dogmatic view of statistical inference can also help to broaden the debate about the role of statistics in science to the entire path that leads from a research hypothesis to a statistical hypothesis.
format: application/pdf
format: text/html
creator: Leonardo Braga Castilho
creator: Paulo Inácio Prado
subject: Ecology
subject: Statistics
description: doi:10.7717/peerj.12090
publisher: PeerJ Inc.
rights: © 2021 Castilho and Prado
abstract: Although null hypothesis testing (NHT) is the primary method for analyzing data in many natural sciences, it has been increasingly criticized. Recently, approaches based on information theory (IT) have become popular and were held by many to be superior because it enables researchers to properly assess the strength of the evidence that data provide for competing hypotheses. Many studies have compared IT and NHT in the context of model selection and stepwise regression, but a systematic comparison of the most basic uses of statistics by ecologists is still lacking. We used computer simulations to compare how both approaches perform in four basic test designs (t-test, ANOVA, correlation tests, and multiple linear regression). Performance was measured by the proportion of simulated samples for which each method provided the correct conclusion (power), the proportion of detected effects with a wrong sign (S-error), and the mean ratio of the estimated effect to the true effect (M-error). We also checked if the p-value from significance tests correlated to a measure of strength of evidence, the Akaike weight. In general both methods performed equally well. The concordance is explained by the monotonic relationship between p-values and evidence weights in simple designs, which agree with analytic results. Our results show that researchers can agree on the conclusions drawn from a data set even when they are using different statistical approaches. By focusing on the practical consequences of inferences, such a pragmatic view of statistics can promote insightful dialogue among researchers on how to find a common ground from different pieces of evidence. A less dogmatic view of statistical inference can also help to broaden the debate about the role of statistics in science to the entire path that leads from a research hypothesis to a statistical hypothesis.
bibliographic citation: Castilho et al. (2021) Towards a pragmatic use of statistics in ecology. PeerJ 9:e12090 https://doi.org/10.7717/peerj.12090
date submitted: 2021-04-29
date accepted: 2021-08-08
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Castilho
  given name: Leonardo Braga
author list: Agent
  family name: Prado
  given name: Paulo Inácio
doi: 10.7717/peerj.12090
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: © 2021 Castilho and Prado
attribution name: Castilho and Prado

The bioinformatics and experimental analysis of AlkB family for prognosis and immune cell infiltration in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Serving as N6-methyladenosine demethylases, the AlkB family is involved in the tumorigenesis of hepatocellular carcinoma (HCC). However, the molecular profiles and clinical values of the AlkB family in HCC are not well known. Methods Several bioinformatics tools and in vitro experiments were used to identify the immune-related profiles and prognostic values of AlkB family in HCC. Results In this study expression levels of ALKBH1/2/3/4/7 were all remarkably increased in HCC tissues when compared with normal tissues. Quantitative PCR (qPCR) and immunohistochemistry were used to validate the expression of AlkB family members in HCC tissues and normal liver tissues. In addition, high expression levels of ALKBH4 were negatively correlated with overall survival (OS) and disease-free survival (DFS) in patients with HCC. Increased ALKBH4 was also associated with pathological stage in HCC patients. The molecular profiles of AlkB family in HCC were mainly associated with peptidyl-serine modification, peptidyl-tyrosine modification, regulation of metal ion transport, etc. Furthermore, tumor-infiltrating immune cell analysis indicated that ALKBH1/2/3/4/5/6/7/8 and FTO were related to the infiltration of different immune cell, such as CD8+ T cells, macrophages, neutrophils, dendritic cells and CD4+ T cells. We also discovered that the methylation levels of ALKBH1/2/4/5/6/8 and FTO were remarkably reduced in HCC tissues. Conclusions Collectively, our findings may deepen the understanding of specific molecular profiles of the AlkB family in HCC pathology. In particular, ALKBH4 could serve as a promising prognostic candidate for treating HCC, and these results might potentiate the development of more reliable therapeutic strategies for patients with HCC.
format: application/pdf
format: text/html
creator: Bi Peng
creator: Yuanliang Yan
creator: Zhijie Xu
subject: Bioinformatics
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.12123
publisher: PeerJ Inc.
rights: © 2021 Peng et al.
abstract: Background Serving as N6-methyladenosine demethylases, the AlkB family is involved in the tumorigenesis of hepatocellular carcinoma (HCC). However, the molecular profiles and clinical values of the AlkB family in HCC are not well known. Methods Several bioinformatics tools and in vitro experiments were used to identify the immune-related profiles and prognostic values of AlkB family in HCC. Results In this study expression levels of ALKBH1/2/3/4/7 were all remarkably increased in HCC tissues when compared with normal tissues. Quantitative PCR (qPCR) and immunohistochemistry were used to validate the expression of AlkB family members in HCC tissues and normal liver tissues. In addition, high expression levels of ALKBH4 were negatively correlated with overall survival (OS) and disease-free survival (DFS) in patients with HCC. Increased ALKBH4 was also associated with pathological stage in HCC patients. The molecular profiles of AlkB family in HCC were mainly associated with peptidyl-serine modification, peptidyl-tyrosine modification, regulation of metal ion transport, etc. Furthermore, tumor-infiltrating immune cell analysis indicated that ALKBH1/2/3/4/5/6/7/8 and FTO were related to the infiltration of different immune cell, such as CD8+ T cells, macrophages, neutrophils, dendritic cells and CD4+ T cells. We also discovered that the methylation levels of ALKBH1/2/4/5/6/8 and FTO were remarkably reduced in HCC tissues. Conclusions Collectively, our findings may deepen the understanding of specific molecular profiles of the AlkB family in HCC pathology. In particular, ALKBH4 could serve as a promising prognostic candidate for treating HCC, and these results might potentiate the development of more reliable therapeutic strategies for patients with HCC.
bibliographic citation: Peng et al. (2021) The bioinformatics and experimental analysis of AlkB family for prognosis and immune cell infiltration in hepatocellular carcinoma. PeerJ 9:e12123 https://doi.org/10.7717/peerj.12123
date submitted: 2021-07-09
date accepted: 2021-08-16
issued: 2021-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peng
  given name: Bi
author list: Agent
  family name: Yan
  given name: Yuanliang
author list: Agent
  family name: Xu
  given name: Zhijie
doi: 10.7717/peerj.12123
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-09-01
copyright: ©2021 Peng et al.
attribution name: Peng et al.

Geographic disparities and socio-demographic predictors of pertussis risk in Florida
type: item
type: AcademicArticle
description: Background Pertussis is a toxin-mediated respiratory illness caused by Bordetella pertussis that can result in severe complications and death, particularly in infants. Between 2008 and 2011, children less than 3 months old accounted for 83% of the pertussis deaths in the United States. Understanding the geographic disparities in the distribution of pertussis risk and identifying high risk geographic areas is necessary for guiding resource allocation and public health control strategies. Therefore, this study investigated geographic disparities and temporal changes in pertussis risk in Florida from 2010 to 2018. It also investigated socioeconomic and demographic predictors of the identified disparities. Methods Pertussis data covering the time period 2010–2018 were obtained from Florida HealthCHARTS web interface. Spatial patterns and temporal changes in geographic distribution of pertussis risk were assessed using county-level choropleth maps for the time periods 2010–2012, 2013–2015, 2016–2018 and 2010–2018. Tango’s flexible spatial scan statistics were used to identify high-risk spatial clusters which were displayed in maps. Ordinary least squares (OLS) regression was used to identify significant predictors of county-level risk. Residuals of the OLS model were assessed for model assumptions including spatial autocorrelation. Results County-level pertussis risk varied from 0 to 116.31 cases per 100,000 people during the study period. A total of 11 significant (p < 0.05) spatial clusters were identified with risk ratios ranging from 1.5 to 5.8. Geographic distribution remained relatively consistent over time with areas of high risk persisting in the western panhandle, northeastern coast, and along the western coast. Although county level pertussis risks generally increased from 2010–2012 to 2013–2015, risk tended to be lower during the 2016–2018 time period. Significant predictors of county-level pertussis risk were rurality, percentage of females, and median income…
format: application/pdf
format: text/html
creator: Corinne B. Tandy
creator: Agricola Odoi
subject: Epidemiology
subject: Global Health
subject: Infectious Diseases
subject: Public Health
subject: Respiratory Medicine
description: doi:10.7717/peerj.11902
publisher: PeerJ Inc.
rights: © 2021 Tandy and Odoi
abstract: Background Pertussis is a toxin-mediated respiratory illness caused by Bordetella pertussis that can result in severe complications and death, particularly in infants. Between 2008 and 2011, children less than 3 months old accounted for 83% of the pertussis deaths in the United States. Understanding the geographic disparities in the distribution of pertussis risk and identifying high risk geographic areas is necessary for guiding resource allocation and public health control strategies. Therefore, this study investigated geographic disparities and temporal changes in pertussis risk in Florida from 2010 to 2018. It also investigated socioeconomic and demographic predictors of the identified disparities. Methods Pertussis data covering the time period 2010–2018 were obtained from Florida HealthCHARTS web interface. Spatial patterns and temporal changes in geographic distribution of pertussis risk were assessed using county-level choropleth maps for the time periods 2010–2012, 2013–2015, 2016–2018 and 2010–2018. Tango’s flexible spatial scan statistics were used to identify high-risk spatial clusters which were displayed in maps. Ordinary least squares (OLS) regression was used to identify significant predictors of county-level risk. Residuals of the OLS model were assessed for model assumptions including spatial autocorrelation. Results County-level pertussis risk varied from 0 to 116.31 cases per 100,000 people during the study period. A total of 11 significant (p < 0.05) spatial clusters were identified with risk ratios ranging from 1.5 to 5.8. Geographic distribution remained relatively consistent over time with areas of high risk persisting in the western panhandle, northeastern coast, and along the western coast. Although county level pertussis risks generally increased from 2010–2012 to 2013–2015, risk tended to be lower during the 2016–2018 time period. Significant predictors of county-level pertussis risk were rurality, percentage of females, and median income…
bibliographic citation: Tandy et al. (2021) Geographic disparities and socio-demographic predictors of pertussis risk in Florida. PeerJ 9:e11902 https://doi.org/10.7717/peerj.11902
date submitted: 2021-03-25
date accepted: 2021-07-13
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tandy
  given name: Corinne B.
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.11902
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: © 2021 Tandy and Odoi
attribution name: Tandy and Odoi

Exploring private land conservation non-adopters’ attendance at outreach events in the Chesapeake Bay watershed, USA
type: item
type: AcademicArticle
description: Background Outreach events such as trainings, demonstrations, and workshops are important opportunities for encouraging private land operators to adopt voluntary conservation practices. However, the ability to understand the effectiveness of such events at influencing conservation behavior is confounded by the likelihood that attendees are already interested in conservation and may already be adopters. Understanding characteristics of events that draw non-adopters can aid in designing events and messaging that are better able to reach beyond those already interested in conservation. Methods For this study, we interviewed 101 operators of private agricultural lands in Maryland, USA, and used descriptive statistics and qualitative comparative analysis to investigate differences between the kinds of outreach events that adopters and non-adopters attended. Results Our results suggested that non-adopters, as compared to adopters, attended events that provided production-relevant information and were logistically easy to attend. Further, non-adopters were more selective when reading advertisements, generally preferring simplicity. Future research and outreach can build on these findings by experimentally testing the effectiveness of messages that are simple and relevant to farmers’ production priorities.
format: application/pdf
format: text/html
creator: Daniel J. Read
creator: Alexandra Carroll
creator: Lisa A. Wainger
subject: Conservation Biology
subject: Science and Medical Education
subject: Science Policy
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
description: doi:10.7717/peerj.11959
publisher: PeerJ Inc.
rights: © 2021 Read et al.
abstract: Background Outreach events such as trainings, demonstrations, and workshops are important opportunities for encouraging private land operators to adopt voluntary conservation practices. However, the ability to understand the effectiveness of such events at influencing conservation behavior is confounded by the likelihood that attendees are already interested in conservation and may already be adopters. Understanding characteristics of events that draw non-adopters can aid in designing events and messaging that are better able to reach beyond those already interested in conservation. Methods For this study, we interviewed 101 operators of private agricultural lands in Maryland, USA, and used descriptive statistics and qualitative comparative analysis to investigate differences between the kinds of outreach events that adopters and non-adopters attended. Results Our results suggested that non-adopters, as compared to adopters, attended events that provided production-relevant information and were logistically easy to attend. Further, non-adopters were more selective when reading advertisements, generally preferring simplicity. Future research and outreach can build on these findings by experimentally testing the effectiveness of messages that are simple and relevant to farmers’ production priorities.
bibliographic citation: Read et al. (2021) Exploring private land conservation non-adopters’ attendance at outreach events in the Chesapeake Bay watershed, USA. PeerJ 9:e11959 https://doi.org/10.7717/peerj.11959
date submitted: 2021-05-24
date accepted: 2021-07-21
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Read
  given name: Daniel J.
author list: Agent
  family name: Carroll
  given name: Alexandra
author list: Agent
  family name: Wainger
  given name: Lisa A.
doi: 10.7717/peerj.11959
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: ©2021 Read et al.
attribution name: Read et al.

https://peerj.com/articles/12028
type: item
type: AcademicArticle
title: Impact of dietary level and ratio of n-6 and n-3 fatty acids on disease progression and mRNA expression of immune and inflammatory markers in Atlantic salmon (Salmo salar) challenged with Paramoeba perurans
description: The aim of the study was to investigate the influence of dietary level and ratio of n-6/n-3 fatty acids (FA) on growth, disease progression and expression of immune and inflammatory markers in Atlantic salmon (Salmo salar) following challenge with Paramoeba perurans. Fish (80 g) were fed four different diets with different ratios of n-6/n-3 FA; at 1.3, 2.4 and 6.0 and one diet with ratio of 1.3 combined with a higher level of n-3 FA and n-6 FA. The diet with the n-6/n-3 FA ratio of 6.0 was included to ensure potential n-6 FA effects were revealed, while the three other diets were more commercially relevant n-6/n-3 FA ratios and levels. After a pre-feeding period of 3 months, fish from each diet regime were challenged with a standardized laboratory challenge using a clonal culture of P. perurans at the concentration of 1,000 cells L−1. The subsequent development of the disease was monitored (by gross gill score), and sampling conducted before challenge and at weekly sampling points for 5 weeks post-challenge. Challenge with P. perurans did not have a significant impact on the growth of the fish during the challenge period, but fish given the feed with the highest n-6/n-3 FA ratio had reduced growth compared to the other groups. Total gill score for all surfaces showed a significant increase with time, reaching a maximum at 21 days post-challenge and declined thereafter, irrespective of diet groups. Challenge with P. perurans influenced the mRNA expression of examined genes involved in immune and inflammatory response (TNF-α, iNOS, IL4-13b, GATA-3, IL-1β, p53, COX2 and PGE2-EP4), but diet did not influence the gene expression. In conclusion, an increase in dietary n-6/n-3 FA ratio influenced the growth of Atlantic salmon challenged with P. perurans; however, it did not alter the mRNA expression of immune genes or progression of the disease.
format: application/pdf
format: text/html
creator: Chandrasekar Selvam
creator: Mark D. Powell
creator: Nina S. Liland
creator: Grethe Rosenlund
creator: Nini H. Sissener
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Parasitology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12028
publisher: PeerJ Inc.
rights: © 2021 Selvam et al.
abstract: The aim of the study was to investigate the influence of dietary level and ratio of n-6/n-3 fatty acids (FA) on growth, disease progression and expression of immune and inflammatory markers in Atlantic salmon (Salmo salar) following challenge with Paramoeba perurans. Fish (80 g) were fed four different diets with different ratios of n-6/n-3 FA; at 1.3, 2.4 and 6.0 and one diet with ratio of 1.3 combined with a higher level of n-3 FA and n-6 FA. The diet with the n-6/n-3 FA ratio of 6.0 was included to ensure potential n-6 FA effects were revealed, while the three other diets were more commercially relevant n-6/n-3 FA ratios and levels. After a pre-feeding period of 3 months, fish from each diet regime were challenged with a standardized laboratory challenge using a clonal culture of P. perurans at the concentration of 1,000 cells L−1. The subsequent development of the disease was monitored (by gross gill score), and sampling conducted before challenge and at weekly sampling points for 5 weeks post-challenge. Challenge with P. perurans did not have a significant impact on the growth of the fish during the challenge period, but fish given the feed with the highest n-6/n-3 FA ratio had reduced growth compared to the other groups. Total gill score for all surfaces showed a significant increase with time, reaching a maximum at 21 days post-challenge and declined thereafter, irrespective of diet groups. Challenge with P. perurans influenced the mRNA expression of examined genes involved in immune and inflammatory response (TNF-α, iNOS, IL4-13b, GATA-3, IL-1β, p53, COX2 and PGE2-EP4), but diet did not influence the gene expression. In conclusion, an increase in dietary n-6/n-3 FA ratio influenced the growth of Atlantic salmon challenged with P. perurans; however, it did not alter the mRNA expression of immune genes or progression of the disease.
bibliographic citation: Selvam et al. (2021) Impact of dietary level and ratio of n-6 and n-3 fatty acids on disease progression and mRNA expression of immune and inflammatory markers in Atlantic salmon (Salmo salar) challenged with Paramoeba perurans. PeerJ 9:e12028 https://doi.org/10.7717/peerj.12028
date submitted: 2021-06-15
date accepted: 2021-07-30
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Selvam
  given name: Chandrasekar
author list: Agent
  family name: Powell
  given name: Mark D.
author list: Agent
  family name: Liland
  given name: Nina S.
author list: Agent
  family name: Rosenlund
  given name: Grethe
author list: Agent
  family name: Sissener
  given name: Nini H.
doi: 10.7717/peerj.12028
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: © 2021 Selvam et al.
attribution name: Selvam et al.

COVID-19 and regional differences in the timeliness of hip-fracture surgery: an interrupted time-series analysis
type: item
type: AcademicArticle
description: Background It is of great importance to examine the impact of the healthcare reorganization adopted to confront the COVID-19 pandemic on the quality of care provided to non-COVID-19 patients. The aim of this study is to assess the impact of the COVID-19 national lockdown (March 9, 2020) on the quality of care provided to patients with hip fracture (HF) in Piedmont and Emilia-Romagna, two large regions of northern Italy severely hit by the pandemic. Methods We calculated the percentage of HF patients undergoing surgery within 2 days of hospital admission. An interrupted time-series analysis was performed on weekly data from December 11, 2019 to June 9, 2020 (≈6 months), interrupting the series in the 2nd week of March. The same data observed the year before were included as a control time series with no “intervention” (lockdown) in the middle of the observation period. Results Before the lockdown, 2-day surgery was 69.9% in Piedmont and 79.2% in Emilia-Romagna; after the lockdown, these proportions were equal to 69.8% (–0.1%) and 69.3% (–9.9%), respectively. While Piedmont did not experience any drop in the amount of surgery, Emilia-Romagna exhibited a significant decline at a weekly rate of –1.29% (95% CI [−1.71 to −0.88]). Divergent trend patterns in the two study regions reflect local differences in pandemic timing as well as in healthcare services capacity, management, and emergency preparedness.
format: application/pdf
format: text/html
creator: Davide Golinelli
creator: Jacopo Lenzi
creator: Emanuele Adorno
creator: Maria Michela Gianino
creator: Maria Pia Fantini
subject: Epidemiology
subject: Evidence Based Medicine
subject: Health Policy
subject: Orthopedics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.12046
publisher: PeerJ Inc.
rights: © 2021 Golinelli et al.
abstract: Background It is of great importance to examine the impact of the healthcare reorganization adopted to confront the COVID-19 pandemic on the quality of care provided to non-COVID-19 patients. The aim of this study is to assess the impact of the COVID-19 national lockdown (March 9, 2020) on the quality of care provided to patients with hip fracture (HF) in Piedmont and Emilia-Romagna, two large regions of northern Italy severely hit by the pandemic. Methods We calculated the percentage of HF patients undergoing surgery within 2 days of hospital admission. An interrupted time-series analysis was performed on weekly data from December 11, 2019 to June 9, 2020 (≈6 months), interrupting the series in the 2nd week of March. The same data observed the year before were included as a control time series with no “intervention” (lockdown) in the middle of the observation period. Results Before the lockdown, 2-day surgery was 69.9% in Piedmont and 79.2% in Emilia-Romagna; after the lockdown, these proportions were equal to 69.8% (–0.1%) and 69.3% (–9.9%), respectively. While Piedmont did not experience any drop in the amount of surgery, Emilia-Romagna exhibited a significant decline at a weekly rate of –1.29% (95% CI [−1.71 to −0.88]). Divergent trend patterns in the two study regions reflect local differences in pandemic timing as well as in healthcare services capacity, management, and emergency preparedness.
bibliographic citation: Golinelli et al. (2021) COVID-19 and regional differences in the timeliness of hip-fracture surgery: an interrupted time-series analysis. PeerJ 9:e12046 https://doi.org/10.7717/peerj.12046
date submitted: 2021-06-25
date accepted: 2021-08-03
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Golinelli
  given name: Davide
author list: Agent
  family name: Lenzi
  given name: Jacopo
author list: Agent
  family name: Adorno
  given name: Emanuele
author list: Agent
  family name: Gianino
  given name: Maria Michela
author list: Agent
  family name: Fantini
  given name: Maria Pia
doi: 10.7717/peerj.12046
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: ©2021 Golinelli et al.
attribution name: Golinelli et al.

Germline mutation analyses of malignant ground glass opacity nodules in non-smoking lung adenocarcinoma patients
type: item
type: AcademicArticle
description: Background Germline mutations play an important role in the pathogenesis of lung cancer. Nonetheless, research on malignant ground glass opacity (GGO) nodules is limited. Methods A total of 13 participants with malignant GGO nodules were recruited in this study. Peripheral blood was used for exome sequencing, and germline mutations were analyzed using InterVar. The whole exome sequencing dataset was analyzed using a filtering strategy. KOBAS 3.0 was used to analyze KEGG pathway to further identify possible deleterious mutations. Results There were seven potentially deleterious germline mutations. NM_001184790:exon8: c.C1070T in PARD3, NM_001170721:exon4:c.C392T in BCAR1 and NM_001127221:exon46: c.G6587A in CACNA1A were present in three cases each; rs756875895 frameshift in MAX, NM_005732: exon13:c.2165_2166insT in RAD50 and NM_001142316:exon2:c.G203C in LMO2, were present in two cases each; one variant was present in NOTCH3. Conclusions Our results expand the germline mutation spectrum in malignant GGO nodules. Importantly, these findings will potentially help screen the high-risk population, guide their health management, and contribute to their clinical treatment and determination of prognosis.
format: application/pdf
format: text/html
creator: Wenjun Mao
creator: Ruo Chen
creator: Rongguo Lu
creator: Shengfei Wang
creator: Huizhu Song
creator: Dan You
creator: Feng Liu
creator: Yijun He
creator: Mingfeng Zheng
subject: Genetics
subject: Molecular Biology
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.12048
publisher: PeerJ Inc.
rights: © 2021 Mao et al.
abstract: Background Germline mutations play an important role in the pathogenesis of lung cancer. Nonetheless, research on malignant ground glass opacity (GGO) nodules is limited. Methods A total of 13 participants with malignant GGO nodules were recruited in this study. Peripheral blood was used for exome sequencing, and germline mutations were analyzed using InterVar. The whole exome sequencing dataset was analyzed using a filtering strategy. KOBAS 3.0 was used to analyze KEGG pathway to further identify possible deleterious mutations. Results There were seven potentially deleterious germline mutations. NM_001184790:exon8: c.C1070T in PARD3, NM_001170721:exon4:c.C392T in BCAR1 and NM_001127221:exon46: c.G6587A in CACNA1A were present in three cases each; rs756875895 frameshift in MAX, NM_005732: exon13:c.2165_2166insT in RAD50 and NM_001142316:exon2:c.G203C in LMO2, were present in two cases each; one variant was present in NOTCH3. Conclusions Our results expand the germline mutation spectrum in malignant GGO nodules. Importantly, these findings will potentially help screen the high-risk population, guide their health management, and contribute to their clinical treatment and determination of prognosis.
bibliographic citation: Mao et al. (2021) Germline mutation analyses of malignant ground glass opacity nodules in non-smoking lung adenocarcinoma patients. PeerJ 9:e12048 https://doi.org/10.7717/peerj.12048
date submitted: 2021-01-29
date accepted: 2021-08-03
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mao
  given name: Wenjun
author list: Agent
  family name: Chen
  given name: Ruo
author list: Agent
  family name: Lu
  given name: Rongguo
author list: Agent
  family name: Wang
  given name: Shengfei
author list: Agent
  family name: Song
  given name: Huizhu
author list: Agent
  family name: You
  given name: Dan
author list: Agent
  family name: Liu
  given name: Feng
author list: Agent
  family name: He
  given name: Yijun
author list: Agent
  family name: Zheng
  given name: Mingfeng
doi: 10.7717/peerj.12048
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: ©2021 Mao et al.
attribution name: Mao et al.

Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea
type: item
type: AcademicArticle
description: Background Understanding region-wide patterns of larval connectivity and gene flow is crucial for managing and conserving marine biodiversity. Dongsha Atoll National Park (DANP), located in the northern South China Sea (SCS), was established in 2007 to study and conserve this diverse and remote coral atoll. However, the role of Dongsha Atoll in connectivity throughout the SCS is seldom studied. In this study, we aim to evaluate the role of DANP in conserving regional marine biodiversity. Methods In total, 206 samples across nine marine species were collected and sequenced from Dongsha Atoll, and these data were combined with available sequence data from each of these nine species archived in the Genomic Observatories Metadatabase (GEOME). Together, these data provide the most extensive population genetic analysis of a single marine protected area. We evaluate metapopulation structure for each species by using a coalescent sampler, selecting among panmixia, stepping-stone, and island models of connectivity in a likelihood-based framework. We then completed a heuristic graph theoretical analysis based on maximum dispersal distance to get a sense of Dongsha’s centrality within the SCS. Results Our dataset yielded 111 unique haplotypes across all taxa at DANP, 58% of which were not sampled elsewhere. Analysis of metapopulation structure showed that five out of nine species have strong regional connectivity across the SCS such that their gene pools are effectively panmictic (mean pelagic larval duration (PLD) = 78 days, sd = 60 days); while four species have stepping-stone metapopulation structure, indicating that larvae are exchanged primarily between nearby populations (mean PLD = 37 days, sd = 15 days). For all but one species, Dongsha was ranked within the top 15 out of 115 large reefs in the South China Sea for betweenness centrality. Thus, for most species, Dongsha Atoll provides an essential link for maintaining stepping-stone gene flow across the SCS. Conclusions…
format: application/pdf
format: text/html
creator: Shang Yin Vanson Liu
creator: Jacob Green
creator: Dana Briggs
creator: Ruth Hastings
creator: Ylva Jondelius
creator: Skylar Kensinger
creator: Hannah Leever
creator: Sophia Santos
creator: Trevor Throne
creator: Chi Cheng
creator: Hawis Madduppa
creator: Robert J. Toonen
creator: Michelle R. Gaither
creator: Eric D. Crandall
subject: Biodiversity
subject: Conservation Biology
subject: Evolutionary Studies
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.12063
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Background Understanding region-wide patterns of larval connectivity and gene flow is crucial for managing and conserving marine biodiversity. Dongsha Atoll National Park (DANP), located in the northern South China Sea (SCS), was established in 2007 to study and conserve this diverse and remote coral atoll. However, the role of Dongsha Atoll in connectivity throughout the SCS is seldom studied. In this study, we aim to evaluate the role of DANP in conserving regional marine biodiversity. Methods In total, 206 samples across nine marine species were collected and sequenced from Dongsha Atoll, and these data were combined with available sequence data from each of these nine species archived in the Genomic Observatories Metadatabase (GEOME). Together, these data provide the most extensive population genetic analysis of a single marine protected area. We evaluate metapopulation structure for each species by using a coalescent sampler, selecting among panmixia, stepping-stone, and island models of connectivity in a likelihood-based framework. We then completed a heuristic graph theoretical analysis based on maximum dispersal distance to get a sense of Dongsha’s centrality within the SCS. Results Our dataset yielded 111 unique haplotypes across all taxa at DANP, 58% of which were not sampled elsewhere. Analysis of metapopulation structure showed that five out of nine species have strong regional connectivity across the SCS such that their gene pools are effectively panmictic (mean pelagic larval duration (PLD) = 78 days, sd = 60 days); while four species have stepping-stone metapopulation structure, indicating that larvae are exchanged primarily between nearby populations (mean PLD = 37 days, sd = 15 days). For all but one species, Dongsha was ranked within the top 15 out of 115 large reefs in the South China Sea for betweenness centrality. Thus, for most species, Dongsha Atoll provides an essential link for maintaining stepping-stone gene flow across the SCS. Conclusions…
bibliographic citation: Liu et al. (2021) Dongsha Atoll is an important stepping-stone that promotes regional genetic connectivity in the South China Sea. PeerJ 9:e12063 https://doi.org/10.7717/peerj.12063
date submitted: 2021-04-19
date accepted: 2021-08-04
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Shang Yin Vanson
author list: Agent
  family name: Green
  given name: Jacob
author list: Agent
  family name: Briggs
  given name: Dana
author list: Agent
  family name: Hastings
  given name: Ruth
author list: Agent
  family name: Jondelius
  given name: Ylva
author list: Agent
  family name: Kensinger
  given name: Skylar
author list: Agent
  family name: Leever
  given name: Hannah
author list: Agent
  family name: Santos
  given name: Sophia
author list: Agent
  family name: Throne
  given name: Trevor
author list: Agent
  family name: Cheng
  given name: Chi
author list: Agent
  family name: Madduppa
  given name: Hawis
author list: Agent
  family name: Toonen
  given name: Robert J.
author list: Agent
  family name: Gaither
  given name: Michelle R.
author list: Agent
  family name: Crandall
  given name: Eric D.
doi: 10.7717/peerj.12063
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: © 2021 Liu et al.
attribution name: Liu et al.

Transcriptome analysis reveals gene expression differences in Liriomyza trifolii exposed to combined heat and abamectin exposure
type: item
type: AcademicArticle
description: Liriomyza trifolii is an invasive pest of horticultural and vegetable crops that possesses robust competitive advantages that enable it to replace closely-related species. High temperatures often occur concomitantly with insecticide usage during L. trifolii outbreaks. In this study, we compared the transcriptomes of L. trifolii exposed to high temperature (40 °C T40), insecticide (LC50 of technical grade abamectin, I50) and combined high temperature and abamectin exposure (IT5040, I50 followed by T40; and TI4050, T40 followed by I50). RNA-seq generated and revealed 44,633 unigenes with annotation data; these were compared with COG and KEGG databases for functional classification and enrichment analysis. Compared with the I50 treatment, COG classification indicated that ‘post-translational modification, protein turnover, chaperones’ was enriched in the IT5040 treatment. In the TI4050 treatment, ‘carbohydrate transport and metabolism’ was the most abundant group. The most enriched KEGG pathways in the TI4050 and IT5040 treatments were ‘longevity regulating pathway - multiple species’ and ‘protein processing in endoplasmic reticulum’, respectively. Subsequent annotation and enrichment analyses indicated that stress-related genes such as CYP450s and HSPs were differentially expressed in the I50 vs. TI4050 or I50 vs. IT5040 treatment groups. Three commercial insecticide formulations were also used to further verify the expression of selected differentially-expressed genes. This study will be conductive to consider the temperature effect on insecticide tolerance in L. trifolii, and provides a framework for improving the application efficiency of insecticides in hot weather, which will ultimately reduce the overuse of pesticides.
format: application/pdf
format: text/html
creator: Yu-Cheng Wang
creator: Ya-Wen Chang
creator: Yu-Zhou Du
subject: Agricultural Science
subject: Entomology
subject: Molecular Biology
subject: Climate Change Biology
description: doi:10.7717/peerj.12064
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Liriomyza trifolii is an invasive pest of horticultural and vegetable crops that possesses robust competitive advantages that enable it to replace closely-related species. High temperatures often occur concomitantly with insecticide usage during L. trifolii outbreaks. In this study, we compared the transcriptomes of L. trifolii exposed to high temperature (40 °C T40), insecticide (LC50 of technical grade abamectin, I50) and combined high temperature and abamectin exposure (IT5040, I50 followed by T40; and TI4050, T40 followed by I50). RNA-seq generated and revealed 44,633 unigenes with annotation data; these were compared with COG and KEGG databases for functional classification and enrichment analysis. Compared with the I50 treatment, COG classification indicated that ‘post-translational modification, protein turnover, chaperones’ was enriched in the IT5040 treatment. In the TI4050 treatment, ‘carbohydrate transport and metabolism’ was the most abundant group. The most enriched KEGG pathways in the TI4050 and IT5040 treatments were ‘longevity regulating pathway - multiple species’ and ‘protein processing in endoplasmic reticulum’, respectively. Subsequent annotation and enrichment analyses indicated that stress-related genes such as CYP450s and HSPs were differentially expressed in the I50 vs. TI4050 or I50 vs. IT5040 treatment groups. Three commercial insecticide formulations were also used to further verify the expression of selected differentially-expressed genes. This study will be conductive to consider the temperature effect on insecticide tolerance in L. trifolii, and provides a framework for improving the application efficiency of insecticides in hot weather, which will ultimately reduce the overuse of pesticides.
bibliographic citation: Wang et al. (2021) Transcriptome analysis reveals gene expression differences in Liriomyza trifolii exposed to combined heat and abamectin exposure. PeerJ 9:e12064 https://doi.org/10.7717/peerj.12064
date submitted: 2021-04-21
date accepted: 2021-08-04
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wang
  given name: Yu-Cheng
author list: Agent
  family name: Chang
  given name: Ya-Wen
author list: Agent
  family name: Du
  given name: Yu-Zhou
doi: 10.7717/peerj.12064
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Investigation of inhibition effect of daidzein on osteosarcoma cells based on experimental validation and systematic pharmacology analysis
type: item
type: AcademicArticle
description: Objective This study aims to explore the effect of daidzein, which is a natural isoflavone compound mainly extracted from soybeans, on osteosarcoma and the potential molecular mechanism. Material and Methods 143B and U2OS osteosarcoma cells were treated with gradient concentrations of daidzein, and MTT assay was used to determine the cell proliferation capacity and IC50. Hoechst 33342 staining and Annexin V-FITC/PI detection were used to determine apoptosis. Cell cycle was analyzed by flow cytometry, and migration ability were detected by transwell assays and scratch wound assay. An osteosarcoma xenograft mice model was applied to investigate the effect of daidzein on osteosarcoma in vivo. Systematic pharmacology and molecular modeling analysis were applied to predict the target of daidzein to osteosarcoma, and the target Src was verified by western blotting. We also observed the effect of daidzein on cell proliferation and apoptosis of Src-overexpressing osteosarcoma cells. Results In vitro, daidzein significantly inhibited 143B and U2OS osteosarcoma cell proliferation and migration, and induced cell cycle arrest. In vivo, daidzein exerts antitumor effects in osteosarcoma xenograft mice. After systematic screening and analysis, Src-MAPK signaling pathway was predicted as the highest-ranked pathway. Western blot demonstrated that daidzein inhibited phosphorylation of the Src-ERK pathway in osteosarcoma cells. Also, overexpression of Src could partially reverse the inhibitory effects of daidzein on osteosarcoma cell proliferation. Conclusion Daidzein exerts an antitumor effect on osteosarcoma, and the mechanism may be through the Src-ERK pathway.
format: application/pdf
format: text/html
creator: Yufan Zhu
creator: Zhiqiang Yang
creator: Yuanlong Xie
creator: Min Yang
creator: Yufeng Zhang
creator: Zhouming Deng
creator: Lin Cai
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Toxicology
description: doi:10.7717/peerj.12072
publisher: PeerJ Inc.
rights: © 2021 Zhu et al.
abstract: Objective This study aims to explore the effect of daidzein, which is a natural isoflavone compound mainly extracted from soybeans, on osteosarcoma and the potential molecular mechanism. Material and Methods 143B and U2OS osteosarcoma cells were treated with gradient concentrations of daidzein, and MTT assay was used to determine the cell proliferation capacity and IC50. Hoechst 33342 staining and Annexin V-FITC/PI detection were used to determine apoptosis. Cell cycle was analyzed by flow cytometry, and migration ability were detected by transwell assays and scratch wound assay. An osteosarcoma xenograft mice model was applied to investigate the effect of daidzein on osteosarcoma in vivo. Systematic pharmacology and molecular modeling analysis were applied to predict the target of daidzein to osteosarcoma, and the target Src was verified by western blotting. We also observed the effect of daidzein on cell proliferation and apoptosis of Src-overexpressing osteosarcoma cells. Results In vitro, daidzein significantly inhibited 143B and U2OS osteosarcoma cell proliferation and migration, and induced cell cycle arrest. In vivo, daidzein exerts antitumor effects in osteosarcoma xenograft mice. After systematic screening and analysis, Src-MAPK signaling pathway was predicted as the highest-ranked pathway. Western blot demonstrated that daidzein inhibited phosphorylation of the Src-ERK pathway in osteosarcoma cells. Also, overexpression of Src could partially reverse the inhibitory effects of daidzein on osteosarcoma cell proliferation. Conclusion Daidzein exerts an antitumor effect on osteosarcoma, and the mechanism may be through the Src-ERK pathway.
bibliographic citation: Zhu et al. (2021) Investigation of inhibition effect of daidzein on osteosarcoma cells based on experimental validation and systematic pharmacology analysis. PeerJ 9:e12072 https://doi.org/10.7717/peerj.12072
date submitted: 2021-04-07
date accepted: 2021-08-05
issued: 2021-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Yufan
author list: Agent
  family name: Yang
  given name: Zhiqiang
author list: Agent
  family name: Xie
  given name: Yuanlong
author list: Agent
  family name: Yang
  given name: Min
author list: Agent
  family name: Zhang
  given name: Yufeng
author list: Agent
  family name: Deng
  given name: Zhouming
author list: Agent
  family name: Cai
  given name: Lin
doi: 10.7717/peerj.12072
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-08-31
copyright: ©2021 Zhu et al.
attribution name: Zhu et al.

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