PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Heparin-binding protein as a novel biomarker for sepsis-related acute kidney injury
items: Association of pre-pregnancy body mass index with adverse pregnancy outcome among first-time mothers
items: Long non-coding RNA LINC01234 regulates proliferation, migration and invasion via HIF-2α pathways in clear cell renal cell carcinoma cells
items: Belowground fungal community diversity, composition and ecological functionality associated with winter wheat in conventional and organic agricultural systems
items: Differentially expressed transcripts and associated protein pathways in basilar artery smooth muscle cells of the high-salt intake–induced hypertensive rat
items: Data sharing policies of journals in life, health, and physical sciences indexed in Journal Citation Reports
items: Plasma miRNA profiles associated with stable warfarin dosage in Chinese patients
items: Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils
items: Utilising one minute and four minute recovery when employing the resistance training contrast method does not negatively affect subsequent jump performance in the presence of concurrent training
items: Plastome structure and adaptive evolution of Calanthe s.l. species

Heparin-binding protein as a novel biomarker for sepsis-related acute kidney injury
type: item
type: AcademicArticle
description: Background Sepsis-related acute kidney injury (AKI) is associated with high morbidity and mortality among patients. Underlying pathomechanisms include capillary leakage and fluid loss into the interstitial tissue and constant exposure to pathogens results in activation of inflammatory cascades, organ dysfunction and subsequently organ damage. Methods To identify novel factors that trigger sepsis-related acute kidney injury, plasma levels of Granzyme A, as representative of a lymphocyte-derived protease, and heparin-binding protein as indicator for neutrophil-derived mediators, were investigated retrospectively in 60 sepsis patients. Results While no association was found between plasma levels of lymphocyte-derived Granzyme A and the incidence of sepsis-related AKI, sepsis patients with AKI had significantly higher plasma levels of heparin-binding protein compared to those without AKI. This applies both to heparin-binding protein peak values (43.30 ± 23.34 vs. 30.25 ± 15.63 pg/mL; p = 0.005) as well as mean values (27.93 ± 14.39 vs. 22.02 ± 7.65 pg/mL; p = 0.021). Furthermore, a heparin-binding protein cut-off value of 23.89 pg/mL was established for AKI diagnosis. Conclusion This study identifies the neutrophil-derived heparin-binding protein as a valuable new biomarker for AKI in sepsis. Beyond the diagnostic perspective, this offers prospect for further research on pathogenesis of AKI and novel therapeutic approaches.
format: application/pdf
format: text/html
creator: Sahra Pajenda
creator: Andreja Figurek
creator: Ludwig Wagner
creator: Daniela Gerges
creator: Alice Schmidt
creator: Harald Herkner
creator: Wolfgang Winnicki
subject: Biochemistry
subject: Emergency and Critical Care
subject: Internal Medicine
subject: Nephrology
description: doi:10.7717/peerj.10122
publisher: PeerJ Inc.
rights: © 2020 Pajenda et al.
abstract: Background Sepsis-related acute kidney injury (AKI) is associated with high morbidity and mortality among patients. Underlying pathomechanisms include capillary leakage and fluid loss into the interstitial tissue and constant exposure to pathogens results in activation of inflammatory cascades, organ dysfunction and subsequently organ damage. Methods To identify novel factors that trigger sepsis-related acute kidney injury, plasma levels of Granzyme A, as representative of a lymphocyte-derived protease, and heparin-binding protein as indicator for neutrophil-derived mediators, were investigated retrospectively in 60 sepsis patients. Results While no association was found between plasma levels of lymphocyte-derived Granzyme A and the incidence of sepsis-related AKI, sepsis patients with AKI had significantly higher plasma levels of heparin-binding protein compared to those without AKI. This applies both to heparin-binding protein peak values (43.30 ± 23.34 vs. 30.25 ± 15.63 pg/mL; p = 0.005) as well as mean values (27.93 ± 14.39 vs. 22.02 ± 7.65 pg/mL; p = 0.021). Furthermore, a heparin-binding protein cut-off value of 23.89 pg/mL was established for AKI diagnosis. Conclusion This study identifies the neutrophil-derived heparin-binding protein as a valuable new biomarker for AKI in sepsis. Beyond the diagnostic perspective, this offers prospect for further research on pathogenesis of AKI and novel therapeutic approaches.
bibliographic citation: Pajenda et al. (2020) Heparin-binding protein as a novel biomarker for sepsis-related acute kidney injury. PeerJ 8:e10122 https://doi.org/10.7717/peerj.10122
date submitted: 2020-06-10
date accepted: 2020-09-16
issued: 2020-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pajenda
  given name: Sahra
author list: Agent
  family name: Figurek
  given name: Andreja
author list: Agent
  family name: Wagner
  given name: Ludwig
author list: Agent
  family name: Gerges
  given name: Daniela
author list: Agent
  family name: Schmidt
  given name: Alice
author list: Agent
  family name: Herkner
  given name: Harald
author list: Agent
  family name: Winnicki
  given name: Wolfgang
doi: 10.7717/peerj.10122
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-14
copyright: ©2020 Pajenda et al.
attribution name: Pajenda et al.

Association of pre-pregnancy body mass index with adverse pregnancy outcome among first-time mothers
type: item
type: AcademicArticle
description: Background Studies have reported an increased risk of adverse pregnancy outcome associated with pre-pregnancy body mass index (BMI). However, the data on such associations in urban areas of southern Chinese women is limited, which drive us to clarify the associations of pre-pregnancy BMI and the risks of adverse pregnancy outcomes (preterm birth (PTB) and low birth weight (LBW)) and maternal health outcomes (gestational hypertension and cesarean delivery). Methods We performed a hospital-based case-control study including 3,864 Southern Chinese women who gave first birth to a live singleton infant from January 2015 to December 2015. PTB was stratified into three subgroups according to gestational age (extremely PTB, very PTB and moderate PTB). Besides, we combined birth weight and gestational age to dichotomise as being small for gestational age (SGA, less than the tenth percentile of weight for gestation) and non-small for gestational age (NSGA, large than the tenth percentile of weight for gestation), gestational week was also classified into categories of term, 34-36 week and below 34 week.. We then divided newborns into six groups: (1) term and NSGA; (2) 34–36 week gestation and NSGA; (3) below 34 week gestation and NSGA; (4) term and SAG; (5) 34–36 week gestation and SAG; (6) below 34 week gestation and SAG. Adjusted logistic regression models was used to estimate the odds ratios of adverse outcomes. Results Underweight women were more likely to give LBW (AOR = 1.44, 95% CI [1.11–1.89]), the similar result was seen in term and SAG as compared with term and NSAG (AOR = 1.78, 95% CI [1.45–2.17]), whereas underweight was significantly associated with a lower risk of gestational hypertension (AOR = 0.45, 95% CI [0.25–0.82) and caesarean delivery (AOR = 0.74, 95% CI [0.62–0.90]). The risk of extremely PTB is relatively higher among overweight and obese mothers in a subgroup analysis of PTB (AOR = 8.12, 95% CI [1.11–59.44]; AOR = 15.06, 95% CI [1.32–172.13], respecti…
format: application/pdf
format: text/html
creator: Li Li
creator: Yanhong Chen
creator: Zhifeng Lin
creator: Weiyan Lin
creator: Yangqi Liu
creator: Weilin Ou
creator: Chengli Zeng
creator: Li Ke
subject: Epidemiology
subject: Gynecology and Obstetrics
subject: Health Policy
subject: Women’s Health
description: doi:10.7717/peerj.10123
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Background Studies have reported an increased risk of adverse pregnancy outcome associated with pre-pregnancy body mass index (BMI). However, the data on such associations in urban areas of southern Chinese women is limited, which drive us to clarify the associations of pre-pregnancy BMI and the risks of adverse pregnancy outcomes (preterm birth (PTB) and low birth weight (LBW)) and maternal health outcomes (gestational hypertension and cesarean delivery). Methods We performed a hospital-based case-control study including 3,864 Southern Chinese women who gave first birth to a live singleton infant from January 2015 to December 2015. PTB was stratified into three subgroups according to gestational age (extremely PTB, very PTB and moderate PTB). Besides, we combined birth weight and gestational age to dichotomise as being small for gestational age (SGA, less than the tenth percentile of weight for gestation) and non-small for gestational age (NSGA, large than the tenth percentile of weight for gestation), gestational week was also classified into categories of term, 34-36 week and below 34 week.. We then divided newborns into six groups: (1) term and NSGA; (2) 34–36 week gestation and NSGA; (3) below 34 week gestation and NSGA; (4) term and SAG; (5) 34–36 week gestation and SAG; (6) below 34 week gestation and SAG. Adjusted logistic regression models was used to estimate the odds ratios of adverse outcomes. Results Underweight women were more likely to give LBW (AOR = 1.44, 95% CI [1.11–1.89]), the similar result was seen in term and SAG as compared with term and NSAG (AOR = 1.78, 95% CI [1.45–2.17]), whereas underweight was significantly associated with a lower risk of gestational hypertension (AOR = 0.45, 95% CI [0.25–0.82) and caesarean delivery (AOR = 0.74, 95% CI [0.62–0.90]). The risk of extremely PTB is relatively higher among overweight and obese mothers in a subgroup analysis of PTB (AOR = 8.12, 95% CI [1.11–59.44]; AOR = 15.06, 95% CI [1.32–172.13], respecti…
bibliographic citation: Li et al. (2020) Association of pre-pregnancy body mass index with adverse pregnancy outcome among first-time mothers. PeerJ 8:e10123 https://doi.org/10.7717/peerj.10123
date submitted: 2020-04-21
date accepted: 2020-09-16
issued: 2020-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Li
author list: Agent
  family name: Chen
  given name: Yanhong
author list: Agent
  family name: Lin
  given name: Zhifeng
author list: Agent
  family name: Lin
  given name: Weiyan
author list: Agent
  family name: Liu
  given name: Yangqi
author list: Agent
  family name: Ou
  given name: Weilin
author list: Agent
  family name: Zeng
  given name: Chengli
author list: Agent
  family name: Ke
  given name: Li
doi: 10.7717/peerj.10123
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-14
copyright: ©2020 Li et al.
attribution name: Li et al.

Long non-coding RNA LINC01234 regulates proliferation, migration and invasion via HIF-2α pathways in clear cell renal cell carcinoma cells
type: item
type: AcademicArticle
description: Long non-coding RNAs (lncRNAs) have been proved to have an important role in different malignancies including clear cell renal cell carcinoma (ccRCC). However, their role in disease progression is still not clear. The objective of the study was to identify lncRNA-based prognostic biomarkers and further to investigate the role of one lncRNA LINC01234 in progression of ccRCC cells. We found that six adverse prognostic lncRNA biomarkers including LINC01234 were identified in ccRCC patients by bioinformatic analysis using The Cancer Genome Atlas database. LINC01234 knockdown impaired cell proliferation, migration and invasion in vitro as compared to negative control. Furthermore, the epithelial-mesenchymal transition was inhibited after LINC01234 knockdown. Additionally, LINC01234 knockdown impaired hypoxia-inducible factor-2a (HIF-2α) pathways, including a suppression of the expression of HIF-2α, vascular endothelial growth factor A, epidermal growth factor receptor, c-Myc, Cyclin D1 and MET. Together, these datas showed that LINC01234 was likely to regulate the progression of ccRCC by HIF-2α pathways, and LINC01234 was both a promising prognostic biomarker and a potential therapeutic target for ccRCC.
format: application/pdf
format: text/html
creator: Feilong Yang
creator: Cheng Liu
creator: Guojiang Zhao
creator: Liyuan Ge
creator: Yimeng Song
creator: Zhigang Chen
creator: Zhuo Liu
creator: Kai Hong
creator: Lulin Ma
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.10149
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Long non-coding RNAs (lncRNAs) have been proved to have an important role in different malignancies including clear cell renal cell carcinoma (ccRCC). However, their role in disease progression is still not clear. The objective of the study was to identify lncRNA-based prognostic biomarkers and further to investigate the role of one lncRNA LINC01234 in progression of ccRCC cells. We found that six adverse prognostic lncRNA biomarkers including LINC01234 were identified in ccRCC patients by bioinformatic analysis using The Cancer Genome Atlas database. LINC01234 knockdown impaired cell proliferation, migration and invasion in vitro as compared to negative control. Furthermore, the epithelial-mesenchymal transition was inhibited after LINC01234 knockdown. Additionally, LINC01234 knockdown impaired hypoxia-inducible factor-2a (HIF-2α) pathways, including a suppression of the expression of HIF-2α, vascular endothelial growth factor A, epidermal growth factor receptor, c-Myc, Cyclin D1 and MET. Together, these datas showed that LINC01234 was likely to regulate the progression of ccRCC by HIF-2α pathways, and LINC01234 was both a promising prognostic biomarker and a potential therapeutic target for ccRCC.
bibliographic citation: Yang et al. (2020) Long non-coding RNA LINC01234 regulates proliferation, migration and invasion via HIF-2α pathways in clear cell renal cell carcinoma cells. PeerJ 8:e10149 https://doi.org/10.7717/peerj.10149
date submitted: 2020-06-03
date accepted: 2020-09-21
issued: 2020-10-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Feilong
author list: Agent
  family name: Liu
  given name: Cheng
author list: Agent
  family name: Zhao
  given name: Guojiang
author list: Agent
  family name: Ge
  given name: Liyuan
author list: Agent
  family name: Song
  given name: Yimeng
author list: Agent
  family name: Chen
  given name: Zhigang
author list: Agent
  family name: Liu
  given name: Zhuo
author list: Agent
  family name: Hong
  given name: Kai
author list: Agent
  family name: Ma
  given name: Lulin
doi: 10.7717/peerj.10149
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-14
copyright: © 2020 Yang et al.
attribution name: Yang et al.

Belowground fungal community diversity, composition and ecological functionality associated with winter wheat in conventional and organic agricultural systems
type: item
type: AcademicArticle
description: Understanding the impacts of agricultural practices on belowground fungal communities is crucial in order to preserve biological diversity in agricultural soils and enhance their role in agroecosystem functioning. Although fungal communities are widely distributed, relatively few studies have correlated agricultural production practices. We investigated the diversity, composition and ecological functionality of fungal communities in roots of winter wheat (Triticum aestivum) growing in conventional and organic farming systems. Direct and nested polymerase chain reaction (PCR) amplifications spanning the internal transcribed spacer (ITS) region of the rDNA from pooled fine root samples were performed with two different sets of fungal specific primers. Fungal identification was carried out through similarity searches against validated reference sequences (RefSeq). The R package ‘picante’ and FUNGuild were used to analyse fungal community composition and trophic mode, respectively. Either by direct or cloning sequencing, 130 complete ITS sequences were clustered into 39 operational taxonomic units (OTUs) (25 singletons), belonging to the Ascomycota (24), the Basidiomycota (14) and to the Glomeromycota (1). Fungal communities from conventional farming sites are phylogenetically more related than expected by chance. Constrained ordination analysis identified total N, total S and Pcal that had a significant effect on the OTU’s abundance and distribution, and a further correlation with the diversity of the co-occurring vegetation could be hypothesised. The functional predictions based on FUNGuild suggested that conventional farming increased the presence of plant pathogenic fungi compared with organic farming. Based on diversity, OTU distribution, nutrition mode and the significant phylogenetic clustering of fungal communities, this study shows that fungal communities differ across sampling sites, depending on agricultural practices. Although it is not fully clear which fac…
format: application/pdf
format: text/html
creator: Sigisfredo Garnica
creator: Ronja Rosenstein
creator: Max Emil Schön
subject: Agricultural Science
subject: Ecology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.9732
publisher: PeerJ Inc.
rights: © 2020 Garnica et al.
abstract: Understanding the impacts of agricultural practices on belowground fungal communities is crucial in order to preserve biological diversity in agricultural soils and enhance their role in agroecosystem functioning. Although fungal communities are widely distributed, relatively few studies have correlated agricultural production practices. We investigated the diversity, composition and ecological functionality of fungal communities in roots of winter wheat (Triticum aestivum) growing in conventional and organic farming systems. Direct and nested polymerase chain reaction (PCR) amplifications spanning the internal transcribed spacer (ITS) region of the rDNA from pooled fine root samples were performed with two different sets of fungal specific primers. Fungal identification was carried out through similarity searches against validated reference sequences (RefSeq). The R package ‘picante’ and FUNGuild were used to analyse fungal community composition and trophic mode, respectively. Either by direct or cloning sequencing, 130 complete ITS sequences were clustered into 39 operational taxonomic units (OTUs) (25 singletons), belonging to the Ascomycota (24), the Basidiomycota (14) and to the Glomeromycota (1). Fungal communities from conventional farming sites are phylogenetically more related than expected by chance. Constrained ordination analysis identified total N, total S and Pcal that had a significant effect on the OTU’s abundance and distribution, and a further correlation with the diversity of the co-occurring vegetation could be hypothesised. The functional predictions based on FUNGuild suggested that conventional farming increased the presence of plant pathogenic fungi compared with organic farming. Based on diversity, OTU distribution, nutrition mode and the significant phylogenetic clustering of fungal communities, this study shows that fungal communities differ across sampling sites, depending on agricultural practices. Although it is not fully clear which fac…
bibliographic citation: Garnica et al. (2020) Belowground fungal community diversity, composition and ecological functionality associated with winter wheat in conventional and organic agricultural systems. PeerJ 8:e9732 https://doi.org/10.7717/peerj.9732
date submitted: 2020-03-04
date accepted: 2020-07-24
issued: 2020-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garnica
  given name: Sigisfredo
author list: Agent
  family name: Rosenstein
  given name: Ronja
author list: Agent
  family name: Schön
  given name: Max Emil
doi: 10.7717/peerj.9732
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-13
copyright: © 2020 Garnica et al.
attribution name: Garnica et al.

Differentially expressed transcripts and associated protein pathways in basilar artery smooth muscle cells of the high-salt intake–induced hypertensive rat
type: item
type: AcademicArticle
description: The pathology of cerebrovascular disorders, such as hypertension, is associated with genetic changes and dysfunction of basilar artery smooth muscle cells (BASMCs). Long-term high-salt diets have been associated with the development of hypertension. However, the molecular mechanisms underlying salt-sensitive hypertension-induced BASMC modifications have not been well defined, especially at the level of variations in gene transcription. Here, we utilized high-throughput sequencing and subsequent signaling pathway analyses to find a two–fold change or greater upregulated expression of 203 transcripts and downregulated expression of 165 transcripts in BASMCs derived from rats fed a high-salt diet compared with those from control rats. These differentially expressed transcripts were enriched in pathways involved in cellular, morphological, and structural plasticity, autophagy, and endocrine regulation. These transcripts changes in the BASMCs derived from high-salt intake–induced hypertensive rats may provide critical information about multiple cellular processes and biological functions that occur during the development of cerebrovascular disorders and provide potential new targets to help control or block the development of hypertension.
format: application/pdf
format: text/html
creator: Junhao Huang
creator: Lesha Zhang
creator: Yang Fang
creator: Wan Jiang
creator: Juan Du
creator: Jinhang Zhu
creator: Min Hu
creator: Bing Shen
subject: Bioinformatics
subject: Anatomy and Physiology
subject: Neurology
description: doi:10.7717/peerj.9849
publisher: PeerJ Inc.
rights: © 2020 Huang et al.
abstract: The pathology of cerebrovascular disorders, such as hypertension, is associated with genetic changes and dysfunction of basilar artery smooth muscle cells (BASMCs). Long-term high-salt diets have been associated with the development of hypertension. However, the molecular mechanisms underlying salt-sensitive hypertension-induced BASMC modifications have not been well defined, especially at the level of variations in gene transcription. Here, we utilized high-throughput sequencing and subsequent signaling pathway analyses to find a two–fold change or greater upregulated expression of 203 transcripts and downregulated expression of 165 transcripts in BASMCs derived from rats fed a high-salt diet compared with those from control rats. These differentially expressed transcripts were enriched in pathways involved in cellular, morphological, and structural plasticity, autophagy, and endocrine regulation. These transcripts changes in the BASMCs derived from high-salt intake–induced hypertensive rats may provide critical information about multiple cellular processes and biological functions that occur during the development of cerebrovascular disorders and provide potential new targets to help control or block the development of hypertension.
bibliographic citation: Huang et al. (2020) Differentially expressed transcripts and associated protein pathways in basilar artery smooth muscle cells of the high-salt intake–induced hypertensive rat. PeerJ 8:e9849 https://doi.org/10.7717/peerj.9849
date submitted: 2020-04-03
date accepted: 2020-08-11
issued: 2020-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Junhao
author list: Agent
  family name: Zhang
  given name: Lesha
author list: Agent
  family name: Fang
  given name: Yang
author list: Agent
  family name: Jiang
  given name: Wan
author list: Agent
  family name: Du
  given name: Juan
author list: Agent
  family name: Zhu
  given name: Jinhang
author list: Agent
  family name: Hu
  given name: Min
author list: Agent
  family name: Shen
  given name: Bing
doi: 10.7717/peerj.9849
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-13
copyright: ©2020 Huang et al.
attribution name: Huang et al.

Data sharing policies of journals in life, health, and physical sciences indexed in Journal Citation Reports
type: item
type: AcademicArticle
description: Background Many scholarly journals have established their own data-related policies, which specify their enforcement of data sharing, the types of data to be submitted, and their procedures for making data available. However, except for the journal impact factor and the subject area, the factors associated with the overall strength of the data sharing policies of scholarly journals remain unknown. This study examines how factors, including impact factor, subject area, type of journal publisher, and geographical location of the publisher are related to the strength of the data sharing policy. Methods From each of the 178 categories of the Web of Science’s 2017 edition of Journal Citation Reports, the top journals in each quartile (Q1, Q2, Q3, and Q4) were selected in December 2018. Of the resulting 709 journals (5%), 700 in the fields of life, health, and physical sciences were selected for analysis. Four of the authors independently reviewed the results of the journal website searches, categorized the journals’ data sharing policies, and extracted the characteristics of individual journals. Univariable multinomial logistic regression analyses were initially conducted to determine whether there was a relationship between each factor and the strength of the data sharing policy. Based on the univariable analyses, a multivariable model was performed to further investigate the factors related to the presence and/or strength of the policy. Results Of the 700 journals, 308 (44.0%) had no data sharing policy, 125 (17.9%) had a weak policy, and 267 (38.1%) had a strong policy (expecting or mandating data sharing). The impact factor quartile was positively associated with the strength of the data sharing policies. Physical science journals were less likely to have a strong policy relative to a weak policy than Life science journals (relative risk ratio [RRR], 0.36; 95% CI [0.17–0.78]). Life science journals had a greater probability of having a weak policy relative to no poli…
format: application/pdf
format: text/html
creator: Jihyun Kim
creator: Soon Kim
creator: Hye-Min Cho
creator: Jae Hwa Chang
creator: Soo Young Kim
subject: Ethical Issues
subject: Science and Medical Education
subject: Science Policy
subject: Statistics
description: doi:10.7717/peerj.9924
publisher: PeerJ Inc.
rights: © 2020 Kim et al.
abstract: Background Many scholarly journals have established their own data-related policies, which specify their enforcement of data sharing, the types of data to be submitted, and their procedures for making data available. However, except for the journal impact factor and the subject area, the factors associated with the overall strength of the data sharing policies of scholarly journals remain unknown. This study examines how factors, including impact factor, subject area, type of journal publisher, and geographical location of the publisher are related to the strength of the data sharing policy. Methods From each of the 178 categories of the Web of Science’s 2017 edition of Journal Citation Reports, the top journals in each quartile (Q1, Q2, Q3, and Q4) were selected in December 2018. Of the resulting 709 journals (5%), 700 in the fields of life, health, and physical sciences were selected for analysis. Four of the authors independently reviewed the results of the journal website searches, categorized the journals’ data sharing policies, and extracted the characteristics of individual journals. Univariable multinomial logistic regression analyses were initially conducted to determine whether there was a relationship between each factor and the strength of the data sharing policy. Based on the univariable analyses, a multivariable model was performed to further investigate the factors related to the presence and/or strength of the policy. Results Of the 700 journals, 308 (44.0%) had no data sharing policy, 125 (17.9%) had a weak policy, and 267 (38.1%) had a strong policy (expecting or mandating data sharing). The impact factor quartile was positively associated with the strength of the data sharing policies. Physical science journals were less likely to have a strong policy relative to a weak policy than Life science journals (relative risk ratio [RRR], 0.36; 95% CI [0.17–0.78]). Life science journals had a greater probability of having a weak policy relative to no poli…
bibliographic citation: Kim et al. (2020) Data sharing policies of journals in life, health, and physical sciences indexed in Journal Citation Reports. PeerJ 8:e9924 https://doi.org/10.7717/peerj.9924
date submitted: 2020-01-06
date accepted: 2020-08-21
issued: 2020-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Jihyun
author list: Agent
  family name: Kim
  given name: Soon
author list: Agent
  family name: Cho
  given name: Hye-Min
author list: Agent
  family name: Chang
  given name: Jae Hwa
author list: Agent
  family name: Kim
  given name: Soo Young
doi: 10.7717/peerj.9924
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-13
copyright: ©2020 Kim et al.
attribution name: Kim et al.

Plasma miRNA profiles associated with stable warfarin dosage in Chinese patients
type: item
type: AcademicArticle
description: Background We used bioinformatic analysis and quantitative reverse transcription polymerase chain reaction (RT-qPCR) assays to investigate the association between plasma microRNAs (miRNAs) and stable warfarin dosage in a Chinese Han population. Methods Bioinformatics analysis was used to screen out potential warfarin dose-associated miRNAs. Three plasma miRNAs were validated in 99 samples by RT-qPCR. Kruskal–Wallis test and multivariate logistic regression were used to compare differences in plasma miRNAs expression levels between three warfarin dosage groups. Results There were significant between-group differences among the three dose groups for hsa-miR-133b expression (p = 0.005), but we observed an “n-shaped” dose-dependent curve rather than a linear relationship. Expression levels of hsa-miR-24-3p (p = 0.475) and hsa-miR-1276 (p = 0.558) were not significantly different in the multivariate logistic regression. Conclusion miRNAs have received extensive attention as ideal biomarkers and possible therapeutic targets for various diseases. However, they are not yet widely used in precision medicine. Our results indicate that hsa-miR-133b may be a possible reference factor for the warfarin dosage algorithm. These findings emphasize the importance of a comprehensive evaluation of complex relationships in warfarin dose prediction models and provide new avenues for future pharmacogenomics studies.
format: application/pdf
format: text/html
creator: Li Zhao
creator: Jin Wang
creator: Shaoxin Shi
creator: Yuan Wu
creator: Jumei Liu
creator: Shiwei He
creator: Yue Zou
creator: Huabin Xie
creator: Shengxiang Ge
creator: Huiming Ye
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Evidence Based Medicine
subject: Hematology
description: doi:10.7717/peerj.9995
publisher: PeerJ Inc.
rights: © 2020 Zhao et al.
abstract: Background We used bioinformatic analysis and quantitative reverse transcription polymerase chain reaction (RT-qPCR) assays to investigate the association between plasma microRNAs (miRNAs) and stable warfarin dosage in a Chinese Han population. Methods Bioinformatics analysis was used to screen out potential warfarin dose-associated miRNAs. Three plasma miRNAs were validated in 99 samples by RT-qPCR. Kruskal–Wallis test and multivariate logistic regression were used to compare differences in plasma miRNAs expression levels between three warfarin dosage groups. Results There were significant between-group differences among the three dose groups for hsa-miR-133b expression (p = 0.005), but we observed an “n-shaped” dose-dependent curve rather than a linear relationship. Expression levels of hsa-miR-24-3p (p = 0.475) and hsa-miR-1276 (p = 0.558) were not significantly different in the multivariate logistic regression. Conclusion miRNAs have received extensive attention as ideal biomarkers and possible therapeutic targets for various diseases. However, they are not yet widely used in precision medicine. Our results indicate that hsa-miR-133b may be a possible reference factor for the warfarin dosage algorithm. These findings emphasize the importance of a comprehensive evaluation of complex relationships in warfarin dose prediction models and provide new avenues for future pharmacogenomics studies.
bibliographic citation: Zhao et al. (2020) Plasma miRNA profiles associated with stable warfarin dosage in Chinese patients. PeerJ 8:e9995 https://doi.org/10.7717/peerj.9995
date submitted: 2020-04-06
date accepted: 2020-08-28
issued: 2020-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Li
author list: Agent
  family name: Wang
  given name: Jin
author list: Agent
  family name: Shi
  given name: Shaoxin
author list: Agent
  family name: Wu
  given name: Yuan
author list: Agent
  family name: Liu
  given name: Jumei
author list: Agent
  family name: He
  given name: Shiwei
author list: Agent
  family name: Zou
  given name: Yue
author list: Agent
  family name: Xie
  given name: Huabin
author list: Agent
  family name: Ge
  given name: Shengxiang
author list: Agent
  family name: Ye
  given name: Huiming
doi: 10.7717/peerj.9995
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-13
copyright: ©2020 Zhao et al.
attribution name: Zhao et al.

Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils
type: item
type: AcademicArticle
description: Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3′ end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in T…
format: application/pdf
format: text/html
creator: Raden Pramesa Narakusumo
creator: Alexander Riedel
creator: Joan Pons
subject: Entomology
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.10017
publisher: PeerJ Inc.
rights: © 2020 Narakusumo et al.
abstract: Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3′ end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in T…
bibliographic citation: Narakusumo et al. (2020) Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils. PeerJ 8:e10017 https://doi.org/10.7717/peerj.10017
date submitted: 2020-04-24
date accepted: 2020-09-01
issued: 2020-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0/
author list: Agent
  family name: Narakusumo
  given name: Raden Pramesa
author list: Agent
  family name: Riedel
  given name: Alexander
author list: Agent
  family name: Pons
  given name: Joan
doi: 10.7717/peerj.10017
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-13
copyright: ©2020 Narakusumo et al.
attribution name: Narakusumo et al.

Utilising one minute and four minute recovery when employing the resistance training contrast method does not negatively affect subsequent jump performance in the presence of concurrent training
type: item
type: AcademicArticle
description: Background Little is known about contrast training and post-activation performance enhancement (PAPE) in a same day concurrent training model. The aim of the current study was to examine the use of two short duration (1-min and 4-min) recovery periods on drop jump performance in same day concurrently trained athletes. Methods Ten professional Australian Rules footballers (age, 20.6 ± 1.9 yr; height, 184.8 ± 6.9 cm; body mass, 85.8 ± 8.4 kg) completed two resistance training sessions with different PAPE recovery durations; 1-min and 4-min, 1 h following a field-based endurance session. Baseline (pre) drop jumps were compared to post-test maximal drop jumps, performed after each set of three squats (where each participant was encouraged to lift as heavy as they could), to determine changes between 1-min and 4-min recovery periods. Data were analysed by fitting a mixed model (significance was set at P ≤ 0.05). Corrected Hedges’ g standardised effect sizes ±95% confidence limits were calculated using group means ± SDs. Results There were no significant differences between baseline and experimental sets 1, 2 and 3 for reactive strength index (RSI), flight time, and total and relative impulse for either recovery duration. However, for contact time, 1-min baseline was significantly different from set 2 (mean difference; 95% CI [0.029; 0.000–0.057 s], P = 0.047, ES; 95% CI [−0.27; −1.20 to 0.66]). For RSI and flight time, 1-min was significantly higher than 4-min (RSI: 0.367; 0.091 to 0.642, P = 0.010, ES; 95% CI [0.52; −0.37 to 1.42]; flight time: 0.033; 0.003 to 0.063 s, P = 0.027, ES; 95% CI [0.86; −0.06 to 1.78]). Discussion Short recovery periods of 1-min may be a time-efficient form of prescribing strength-power exercise in contrast loading schemes. Longer recovery periods do not appear to benefit immediate, subsequent performance.
format: application/pdf
format: text/html
creator: Dean Ritchie
creator: Justin W.L. Keogh
creator: Peter Reaburn
creator: Jonathan D. Bartlett
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.10031
publisher: PeerJ Inc.
rights: © 2020 Ritchie et al.
abstract: Background Little is known about contrast training and post-activation performance enhancement (PAPE) in a same day concurrent training model. The aim of the current study was to examine the use of two short duration (1-min and 4-min) recovery periods on drop jump performance in same day concurrently trained athletes. Methods Ten professional Australian Rules footballers (age, 20.6 ± 1.9 yr; height, 184.8 ± 6.9 cm; body mass, 85.8 ± 8.4 kg) completed two resistance training sessions with different PAPE recovery durations; 1-min and 4-min, 1 h following a field-based endurance session. Baseline (pre) drop jumps were compared to post-test maximal drop jumps, performed after each set of three squats (where each participant was encouraged to lift as heavy as they could), to determine changes between 1-min and 4-min recovery periods. Data were analysed by fitting a mixed model (significance was set at P ≤ 0.05). Corrected Hedges’ g standardised effect sizes ±95% confidence limits were calculated using group means ± SDs. Results There were no significant differences between baseline and experimental sets 1, 2 and 3 for reactive strength index (RSI), flight time, and total and relative impulse for either recovery duration. However, for contact time, 1-min baseline was significantly different from set 2 (mean difference; 95% CI [0.029; 0.000–0.057 s], P = 0.047, ES; 95% CI [−0.27; −1.20 to 0.66]). For RSI and flight time, 1-min was significantly higher than 4-min (RSI: 0.367; 0.091 to 0.642, P = 0.010, ES; 95% CI [0.52; −0.37 to 1.42]; flight time: 0.033; 0.003 to 0.063 s, P = 0.027, ES; 95% CI [0.86; −0.06 to 1.78]). Discussion Short recovery periods of 1-min may be a time-efficient form of prescribing strength-power exercise in contrast loading schemes. Longer recovery periods do not appear to benefit immediate, subsequent performance.
bibliographic citation: Ritchie et al. (2020) Utilising one minute and four minute recovery when employing the resistance training contrast method does not negatively affect subsequent jump performance in the presence of concurrent training. PeerJ 8:e10031 https://doi.org/10.7717/peerj.10031
date submitted: 2020-06-26
date accepted: 2020-09-03
issued: 2020-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ritchie
  given name: Dean
author list: Agent
  family name: Keogh
  given name: Justin W.L.
author list: Agent
  family name: Reaburn
  given name: Peter
author list: Agent
  family name: Bartlett
  given name: Jonathan D.
doi: 10.7717/peerj.10031
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-13
copyright: © 2020 Ritchie et al.
attribution name: Ritchie et al.

Plastome structure and adaptive evolution of Calanthe s.l. species
type: item
type: AcademicArticle
description: Calanthe s.l. is the most diverse group in the tribe Collabieae (Orchidaceae), which are pantropical in distribution. Illumina sequencing followed by de novo assembly was used in this study, and the plastid genetic information of Calanthe s.l. was used to investigate the adaptive evolution of this taxon. Herein, the complete plastome of five Calanthe s.l. species (Calanthe davidii, Styloglossum lyroglossa, Preptanthe rubens, Cephalantheropsis obcordata, and Phaius tankervilliae) were determined, and the two other published plastome sequences of Calanthe s.l. were added for comparative analyses to examine the evolutionary pattern of the plastome in the alliance. The seven plastomes ranged from 150,181 bp (C. delavayi) to 159,014 bp (C. davidii) in length and were all mapped as circular structures. Except for the three ndh genes (ndhC, ndhF, and ndhK) lost in C. delavayi, the remaining six species contain identical gene orders and numbers (115 gene). Nucleotide diversity was detected across the plastomes, and we screened 14 mutational hotspot regions, including 12 non-coding regions and two gene regions. For the adaptive evolution investigation, three species showed positive selected genes compared with others, C. obcordata (cemA), S. lyroglossa (infA, ycf1 and ycf2) and C. delavayi (nad6 and ndhB). Six genes were under site-specific positive selection in Calanthe s.l., namely, accD, ndhB, ndhD, rpoC2, ycf1, and ycf2, most of which are involved in photosynthesis. These results, including the new plastomes, provide resources for the comparative plastome, breeding, and plastid genetic engineering of orchids and flowering plants.
format: application/pdf
format: text/html
creator: Yanqiong Chen
creator: Hui Zhong
creator: Yating Zhu
creator: Yuanzhen Huang
creator: Shasha Wu
creator: Zhongjian Liu
creator: Siren Lan
creator: Junwen Zhai
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10051
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Calanthe s.l. is the most diverse group in the tribe Collabieae (Orchidaceae), which are pantropical in distribution. Illumina sequencing followed by de novo assembly was used in this study, and the plastid genetic information of Calanthe s.l. was used to investigate the adaptive evolution of this taxon. Herein, the complete plastome of five Calanthe s.l. species (Calanthe davidii, Styloglossum lyroglossa, Preptanthe rubens, Cephalantheropsis obcordata, and Phaius tankervilliae) were determined, and the two other published plastome sequences of Calanthe s.l. were added for comparative analyses to examine the evolutionary pattern of the plastome in the alliance. The seven plastomes ranged from 150,181 bp (C. delavayi) to 159,014 bp (C. davidii) in length and were all mapped as circular structures. Except for the three ndh genes (ndhC, ndhF, and ndhK) lost in C. delavayi, the remaining six species contain identical gene orders and numbers (115 gene). Nucleotide diversity was detected across the plastomes, and we screened 14 mutational hotspot regions, including 12 non-coding regions and two gene regions. For the adaptive evolution investigation, three species showed positive selected genes compared with others, C. obcordata (cemA), S. lyroglossa (infA, ycf1 and ycf2) and C. delavayi (nad6 and ndhB). Six genes were under site-specific positive selection in Calanthe s.l., namely, accD, ndhB, ndhD, rpoC2, ycf1, and ycf2, most of which are involved in photosynthesis. These results, including the new plastomes, provide resources for the comparative plastome, breeding, and plastid genetic engineering of orchids and flowering plants.
bibliographic citation: Chen et al. (2020) Plastome structure and adaptive evolution of Calanthe s.l. species. PeerJ 8:e10051 https://doi.org/10.7717/peerj.10051
date submitted: 2020-06-09
date accepted: 2020-09-07
issued: 2020-10-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yanqiong
author list: Agent
  family name: Zhong
  given name: Hui
author list: Agent
  family name: Zhu
  given name: Yating
author list: Agent
  family name: Huang
  given name: Yuanzhen
author list: Agent
  family name: Wu
  given name: Shasha
author list: Agent
  family name: Liu
  given name: Zhongjian
author list: Agent
  family name: Lan
  given name: Siren
author list: Agent
  family name: Zhai
  given name: Junwen
doi: 10.7717/peerj.10051
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-13
copyright: ©2020 Chen et al.
attribution name: Chen et al.

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