PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Therapeutic effect of Bacillus Calmette–Guerin polysaccharide nucleic acid on mast cell at the transcriptional level
items: Diet and wild ungulate preferences of wolves in northwestern Anatolia during winter
items: Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes
items: Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)
items: Delivery of targeted gene therapies using a hybrid cryogel-coated prosthetic vascular graft
items: Twisted tale of the tiger: the case of inappropriate data and deficient science
items: Investigating safety profiles of human papillomavirus vaccine across group differences using VAERS data and MedDRA
items: Effects of digging by a native and introduced ecosystem engineer on soil physical and chemical properties in temperate grassy woodland
items: Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors
items: Movement velocity can be used to estimate the relative load during the bench press and leg press exercises in older women

Therapeutic effect of Bacillus Calmette–Guerin polysaccharide nucleic acid on mast cell at the transcriptional level
type: item
type: AcademicArticle
description: Background Chronic spontaneous urticaria (CSU) is a common and recurrent autoimmune-related disease with unclear pathogenesis. Dysfunction of immune cells, such as T cells, mast cells, and basophils, is involved. Bacillus Calmette–Guerin polysaccharide nucleic acid (BCG–PSN), an immunomodulator partially extracted from BCG, can be used in the combined treatment of CSU with an unknown mechanism. Methods To study the therapeutic effect and mechanism of BCG–PSN on CSU, we initially assessed the clinical efficacy in 110 enrolled CSU patients of 4-week antihistamine monotherapy vs. antihistamine plus BCG–PSN combined therapy. Subsequently, to explore the further mechanism of BCG-PSN, the mast cell line RBL-2H3 pretreated with BCG-PSN was used to evaluate the transcriptional expression profiles via lncRNA sequencing. Real time PCR was conducted to validate the candidate gene expression. Results We found no significant difference in treatment efficacy between the BCG–PSN group (71.7%) and the monotherapy group (71.9%). However, the average time of complete relief in the BCG–PSN group was significantly shorter than that in the monotherapy group (36.77 ± 17.33 vs. 51.27 ± 16.80, p = 0.026). In vitro experiments showed that BCG-PSN inhibited β-hexosaminidase release rates in IgE-sensitized RBL-2H3 cells (p < 0.001). Sequencing data revealed the expression profiles of functional genes, including a significant decrease in Erb-B2 receptor tyrosine kinase 4, which can be regulated by the nuclear factor kappa B (NF-κB) pathway. Discussion CSU is a chronic, recurrent disease with complex pathogenesis. Mast cells and basophils are the primary target cells of the disease. BCG–PSN decrease the β-HEX release rates and regulated IgE-mediated mast cell activation in RBL-2H3 cells by mediating immune-related gene expression including ERBB4. These findings suggest that BCG–PSN may mediate ERBB4 expression via the NF-κB pathway and may have value in the treatment of CSU.
format: application/pdf
format: text/html
creator: Siyu Yan
creator: Runqiu Liu
creator: Manyun Mao
creator: Zhaoqian Liu
creator: Wei Zhang
creator: Yi Zhang
creator: Jie Li
creator: Cong Peng
creator: Xiang Chen
subject: Allergy and Clinical Immunology
subject: Dermatology
description: doi:10.7717/peerj.7404
publisher: PeerJ Inc.
rights: © 2019 Yan et al.
abstract: Background Chronic spontaneous urticaria (CSU) is a common and recurrent autoimmune-related disease with unclear pathogenesis. Dysfunction of immune cells, such as T cells, mast cells, and basophils, is involved. Bacillus Calmette–Guerin polysaccharide nucleic acid (BCG–PSN), an immunomodulator partially extracted from BCG, can be used in the combined treatment of CSU with an unknown mechanism. Methods To study the therapeutic effect and mechanism of BCG–PSN on CSU, we initially assessed the clinical efficacy in 110 enrolled CSU patients of 4-week antihistamine monotherapy vs. antihistamine plus BCG–PSN combined therapy. Subsequently, to explore the further mechanism of BCG-PSN, the mast cell line RBL-2H3 pretreated with BCG-PSN was used to evaluate the transcriptional expression profiles via lncRNA sequencing. Real time PCR was conducted to validate the candidate gene expression. Results We found no significant difference in treatment efficacy between the BCG–PSN group (71.7%) and the monotherapy group (71.9%). However, the average time of complete relief in the BCG–PSN group was significantly shorter than that in the monotherapy group (36.77 ± 17.33 vs. 51.27 ± 16.80, p = 0.026). In vitro experiments showed that BCG-PSN inhibited β-hexosaminidase release rates in IgE-sensitized RBL-2H3 cells (p < 0.001). Sequencing data revealed the expression profiles of functional genes, including a significant decrease in Erb-B2 receptor tyrosine kinase 4, which can be regulated by the nuclear factor kappa B (NF-κB) pathway. Discussion CSU is a chronic, recurrent disease with complex pathogenesis. Mast cells and basophils are the primary target cells of the disease. BCG–PSN decrease the β-HEX release rates and regulated IgE-mediated mast cell activation in RBL-2H3 cells by mediating immune-related gene expression including ERBB4. These findings suggest that BCG–PSN may mediate ERBB4 expression via the NF-κB pathway and may have value in the treatment of CSU.
bibliographic citation: Yan et al. (2019) Therapeutic effect of Bacillus Calmette–Guerin polysaccharide nucleic acid on mast cell at the transcriptional level. PeerJ 7:e7404 https://doi.org/10.7717/peerj.7404
date submitted: 2018-10-24
date accepted: 2019-07-03
issued: 2019-08-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Siyu
author list: Agent
  family name: Liu
  given name: Runqiu
author list: Agent
  family name: Mao
  given name: Manyun
author list: Agent
  family name: Liu
  given name: Zhaoqian
author list: Agent
  family name: Zhang
  given name: Wei
author list: Agent
  family name: Zhang
  given name: Yi
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Peng
  given name: Cong
author list: Agent
  family name: Chen
  given name: Xiang
doi: 10.7717/peerj.7404
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-21
copyright: ©2019 Yan et al.
attribution name: Yan et al.

Diet and wild ungulate preferences of wolves in northwestern Anatolia during winter
type: item
type: AcademicArticle
description: The gray wolf (Canis lupus) is making a comeback in many habitats in central Europe, where it has been once extirpated. Although densities are still low to moderate, this comeback already raises management concerns. In Anatolia, the gray wolf is one of the most common predator species occupying almost all kind of habitats. Although its numbers were reduced in some parts of the country, it has never been extirpated and lived in sympatry with humans. In this study we investigated, for the first time, the winter diet of wolves in north-west Anatolia, where a multispecies wild ungulate community occurs in sympatry with high density livestock. We selected two geographically close but different habitats (steppe and forest) with different wild prey availabilities and compositions. In both areas ungulate contribution to winter diet biomass was more than 90%. Wolf pack size (four to eight wolves) were higher in the study area where livestock numbers and human disturbance were lower and wild prey were more available. In both study areas, wild boar (Sus scrofa) was the main and most preferred food item (Chesson’s α = 0.7 − 0.9) and it occurred at higher density where wolf pack size was smaller. We could not find a high preference (Chesson’s α = 0.3) and high winter predation pressure on the reintroduced Anatolian wild sheep (Ovis gmelinii anatolica) population that occurs in the study area covered by steppe vegetation. Contribution of livestock and food categories other than wild ungulates to wolf diet stayed low. Wolves can help mitigate human-wildlife conflict regulating wild boar numbers, the most common conflict-causing ungulate species in Anatolia. Instead of managing wolf numbers in human dominated landscapes, we recommend reintroduction of wild ungulates to the areas where they became locally extinct and replaced by livestock.
format: application/pdf
format: text/html
creator: Deniz Mengüllüoğlu
creator: Eylül İlaslan
creator: Hasan Emir
creator: Anne Berger
subject: Conservation Biology
subject: Ecology
subject: Population Biology
description: doi:10.7717/peerj.7446
publisher: PeerJ Inc.
rights: © 2019 Mengüllüoğlu et al.
abstract: The gray wolf (Canis lupus) is making a comeback in many habitats in central Europe, where it has been once extirpated. Although densities are still low to moderate, this comeback already raises management concerns. In Anatolia, the gray wolf is one of the most common predator species occupying almost all kind of habitats. Although its numbers were reduced in some parts of the country, it has never been extirpated and lived in sympatry with humans. In this study we investigated, for the first time, the winter diet of wolves in north-west Anatolia, where a multispecies wild ungulate community occurs in sympatry with high density livestock. We selected two geographically close but different habitats (steppe and forest) with different wild prey availabilities and compositions. In both areas ungulate contribution to winter diet biomass was more than 90%. Wolf pack size (four to eight wolves) were higher in the study area where livestock numbers and human disturbance were lower and wild prey were more available. In both study areas, wild boar (Sus scrofa) was the main and most preferred food item (Chesson’s α = 0.7 − 0.9) and it occurred at higher density where wolf pack size was smaller. We could not find a high preference (Chesson’s α = 0.3) and high winter predation pressure on the reintroduced Anatolian wild sheep (Ovis gmelinii anatolica) population that occurs in the study area covered by steppe vegetation. Contribution of livestock and food categories other than wild ungulates to wolf diet stayed low. Wolves can help mitigate human-wildlife conflict regulating wild boar numbers, the most common conflict-causing ungulate species in Anatolia. Instead of managing wolf numbers in human dominated landscapes, we recommend reintroduction of wild ungulates to the areas where they became locally extinct and replaced by livestock.
bibliographic citation: Mengüllüoğlu et al. (2019) Diet and wild ungulate preferences of wolves in northwestern Anatolia during winter. PeerJ 7:e7446 https://doi.org/10.7717/peerj.7446
date submitted: 2018-12-04
date accepted: 2019-07-09
issued: 2019-08-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mengüllüoğlu
  given name: Deniz
author list: Agent
  family name: İlaslan
  given name: Eylül
author list: Agent
  family name: Emir
  given name: Hasan
author list: Agent
  family name: Berger
  given name: Anne
doi: 10.7717/peerj.7446
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-21
copyright: ©2019 Mengüllüoğlu et al.
attribution name: Mengüllüoğlu et al.

Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes
type: item
type: AcademicArticle
description: Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships.
format: application/pdf
format: text/html
creator: Qi Chen
creator: Xiaobo Wu
creator: Dequan Zhang
subject: Genetics
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.7480
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships.
bibliographic citation: Chen et al. (2019) Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes. PeerJ 7:e7480 https://doi.org/10.7717/peerj.7480
date submitted: 2019-04-09
date accepted: 2019-07-15
issued: 2019-08-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Qi
author list: Agent
  family name: Wu
  given name: Xiaobo
author list: Agent
  family name: Zhang
  given name: Dequan
doi: 10.7717/peerj.7480
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-21
copyright: ©2019 Chen et al.
attribution name: Chen et al.

Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max)
type: item
type: AcademicArticle
description: Background VQ proteins, the plant-specific transcription factors, are involved in plant development and multiple stresses; however, only few articles systematic reported the VQ genes in soybean. Methods In total, we identified 75 GmVQ genes, which were classified into 7 groups (I-VII). Conserved domain analysis indicated that VQ gene family members all contain the VQ domains. VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed that cis-elements related to stress responses, phytohormone responses and controlling physical as well as reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were showed expressing in nine tissues, suggesting their putative function in many aspects of plant growth and development as well as response to stress in Glycine max. Results This study aims to understand the roles of VQ genes in various development processes and their expression patterns in responses to stimuli. Our results provide basic information in identification and classification of GmVQ genes. Further experimental analysis will allows us to know the functions of GmVQs participation in plant growth and stress responses.
format: application/pdf
format: text/html
creator: Yongbin Wang
creator: Zhenfeng Jiang
creator: Zhenxiang Li
creator: Yuanling Zhao
creator: Weiwei Tan
creator: Zhaojun Liu
creator: Shaobin Cui
creator: Xiaoguang Yu
creator: Jun Ma
creator: Guangjin Wang
creator: Wenbin Li
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.7509
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background VQ proteins, the plant-specific transcription factors, are involved in plant development and multiple stresses; however, only few articles systematic reported the VQ genes in soybean. Methods In total, we identified 75 GmVQ genes, which were classified into 7 groups (I-VII). Conserved domain analysis indicated that VQ gene family members all contain the VQ domains. VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed that cis-elements related to stress responses, phytohormone responses and controlling physical as well as reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were showed expressing in nine tissues, suggesting their putative function in many aspects of plant growth and development as well as response to stress in Glycine max. Results This study aims to understand the roles of VQ genes in various development processes and their expression patterns in responses to stimuli. Our results provide basic information in identification and classification of GmVQ genes. Further experimental analysis will allows us to know the functions of GmVQs participation in plant growth and stress responses.
bibliographic citation: Wang et al. (2019) Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max). PeerJ 7:e7509 https://doi.org/10.7717/peerj.7509
date submitted: 2019-03-18
date accepted: 2019-07-17
issued: 2019-08-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yongbin
author list: Agent
  family name: Jiang
  given name: Zhenfeng
author list: Agent
  family name: Li
  given name: Zhenxiang
author list: Agent
  family name: Zhao
  given name: Yuanling
author list: Agent
  family name: Tan
  given name: Weiwei
author list: Agent
  family name: Liu
  given name: Zhaojun
author list: Agent
  family name: Cui
  given name: Shaobin
author list: Agent
  family name: Yu
  given name: Xiaoguang
author list: Agent
  family name: Ma
  given name: Jun
author list: Agent
  family name: Wang
  given name: Guangjin
author list: Agent
  family name: Li
  given name: Wenbin
doi: 10.7717/peerj.7509
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-21
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Delivery of targeted gene therapies using a hybrid cryogel-coated prosthetic vascular graft
type: item
type: AcademicArticle
description: Objectives The success of prosthetic vascular grafts in the management of peripheral arterial disease is frequently limited by the development of anastomotic neointimal hyperplasia (ANIH), with the host response to prosthetic grafts beginning soon after implantation. To address this, we combine a platform of polyethylene terephthalate (PET) fabric with an applied cryogel layer containing biologic agents to create a bioactive prosthetic graft system, with the ability to deliver therapeutics targeting modulators of the ANIH-associated transcriptome response, along with antithrombotic agents. Methods Hybrid graft materials were synthesized by cryopolymerization of methacrylated alginate and heparin onto electrospun (ePET), knitted PET (kPET), or woven PET (wPET). Arg-Gly-Asp (RGD) peptides were added to increase cell adhesion. Scanning electron microscopy (SEM) was used to study the microstructure at 1 day, and 2, 4, and 8 weeks. Physical properties such as swelling ratio, pore connectivity, shape recovery, and stiffness were evaluated. Human aortic endothelial cell (HAoEC) adherence was visualized using confocal microscopy after 24 hours and proliferation was evaluated with a resazurin-based assay for 7 days. Confocal microscopy was used to assess delivery of adeno-associated virus (AAV-GFP) after incubation of hybrid grafts with HAoECs. Heparin activity of the materials was measured using an anti-Xa assay. Results SEM demonstrated large interconnected pores throughout the entire structure for all graft types, with minimal degradation of the cryogel after 8 weeks. Hybrid materials showed a trend towards increased shape recovery, increased stiffness, decreased swelling ratio, and no difference in pore connectivity. HAoECs incorporated, adhered, and proliferated over 7 days on all materials. HAoECs were successfully transduced with AAV-GFP from the hybrid graft materials. Anti-Xa assay confirmed continued activity of heparin from all materials for over 7 days. Conclusio…
format: application/pdf
format: text/html
creator: Cindy Huynh
creator: Ting-Yu Shih
creator: Alexander Mammoo
creator: Amruta Samant
creator: Saif Pathan
creator: David W. Nelson
creator: Christiane Ferran
creator: David Mooney
creator: Frank LoGerfo
creator: Leena Pradhan-Nabzdyk
subject: Bioengineering
subject: Drugs and Devices
subject: Hematology
subject: Pharmacology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.7377
publisher: PeerJ Inc.
rights: © 2019 Huynh et al.
abstract: Objectives The success of prosthetic vascular grafts in the management of peripheral arterial disease is frequently limited by the development of anastomotic neointimal hyperplasia (ANIH), with the host response to prosthetic grafts beginning soon after implantation. To address this, we combine a platform of polyethylene terephthalate (PET) fabric with an applied cryogel layer containing biologic agents to create a bioactive prosthetic graft system, with the ability to deliver therapeutics targeting modulators of the ANIH-associated transcriptome response, along with antithrombotic agents. Methods Hybrid graft materials were synthesized by cryopolymerization of methacrylated alginate and heparin onto electrospun (ePET), knitted PET (kPET), or woven PET (wPET). Arg-Gly-Asp (RGD) peptides were added to increase cell adhesion. Scanning electron microscopy (SEM) was used to study the microstructure at 1 day, and 2, 4, and 8 weeks. Physical properties such as swelling ratio, pore connectivity, shape recovery, and stiffness were evaluated. Human aortic endothelial cell (HAoEC) adherence was visualized using confocal microscopy after 24 hours and proliferation was evaluated with a resazurin-based assay for 7 days. Confocal microscopy was used to assess delivery of adeno-associated virus (AAV-GFP) after incubation of hybrid grafts with HAoECs. Heparin activity of the materials was measured using an anti-Xa assay. Results SEM demonstrated large interconnected pores throughout the entire structure for all graft types, with minimal degradation of the cryogel after 8 weeks. Hybrid materials showed a trend towards increased shape recovery, increased stiffness, decreased swelling ratio, and no difference in pore connectivity. HAoECs incorporated, adhered, and proliferated over 7 days on all materials. HAoECs were successfully transduced with AAV-GFP from the hybrid graft materials. Anti-Xa assay confirmed continued activity of heparin from all materials for over 7 days. Conclusio…
bibliographic citation: Huynh et al. (2019) Delivery of targeted gene therapies using a hybrid cryogel-coated prosthetic vascular graft. PeerJ 7:e7377 https://doi.org/10.7717/peerj.7377
date submitted: 2019-02-06
date accepted: 2019-06-28
issued: 2019-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huynh
  given name: Cindy
author list: Agent
  family name: Shih
  given name: Ting-Yu
author list: Agent
  family name: Mammoo
  given name: Alexander
author list: Agent
  family name: Samant
  given name: Amruta
author list: Agent
  family name: Pathan
  given name: Saif
author list: Agent
  family name: Nelson
  given name: David W.
author list: Agent
  family name: Ferran
  given name: Christiane
author list: Agent
  family name: Mooney
  given name: David
author list: Agent
  family name: LoGerfo
  given name: Frank
author list: Agent
  family name: Pradhan-Nabzdyk
  given name: Leena
doi: 10.7717/peerj.7377
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-20
copyright: ©2019 Huynh et al.
attribution name: Huynh et al.

Twisted tale of the tiger: the case of inappropriate data and deficient science
type: item
type: AcademicArticle
description: Publications in peer-reviewed journals are often looked upon as tenets on which future scientific thought is built. Published information is not always flawless and errors in published research should be expediently reported, preferably by a peer-review process. We review a recent publication by Gopalaswamy et al. (10.1111/2041-210X.12351) that challenges the use of “double sampling” in large-scale animal surveys. Double sampling is often resorted to as an established economical and practical approach for large-scale surveys since it calibrates abundance indices against absolute abundance, thereby potentially addressing the statistical shortfalls of indices. Empirical data used by Gopalaswamy et al. (10.1111/2041-210X.12351) to test their theoretical model, relate to tiger sign and tiger abundance referred to as an Index-Calibration experiment (IC-Karanth). These data on tiger abundance and signs should be paired in time and space to qualify as a calibration experiment for double sampling, but original data of IC-Karanth show lags of (up to) several years. Further, data points used in the paper do not match the original sources. We show that by use of inappropriate and incorrect data collected through a faulty experimental design, poor parameterization of their theoretical model, and selectively picked estimates from literature on detection probability, the inferences of this paper are highly questionable. We highlight how the results of Gopalaswamy et al. were further distorted in popular media. If left unaddressed, the paper of Gopalaswamy et al. could have serious implications on statistical design of large-scale animal surveys by propagating unreliable inferences.
format: application/pdf
format: text/html
creator: Qamar Qureshi
creator: Rajesh Gopal
creator: Yadvendradev Jhala
subject: Conservation Biology
subject: Ecology
subject: Ethical Issues
subject: Natural Resource Management
subject: Population Biology
description: doi:10.7717/peerj.7482
publisher: PeerJ Inc.
rights: © 2019 Qureshi et al.
abstract: Publications in peer-reviewed journals are often looked upon as tenets on which future scientific thought is built. Published information is not always flawless and errors in published research should be expediently reported, preferably by a peer-review process. We review a recent publication by Gopalaswamy et al. (10.1111/2041-210X.12351) that challenges the use of “double sampling” in large-scale animal surveys. Double sampling is often resorted to as an established economical and practical approach for large-scale surveys since it calibrates abundance indices against absolute abundance, thereby potentially addressing the statistical shortfalls of indices. Empirical data used by Gopalaswamy et al. (10.1111/2041-210X.12351) to test their theoretical model, relate to tiger sign and tiger abundance referred to as an Index-Calibration experiment (IC-Karanth). These data on tiger abundance and signs should be paired in time and space to qualify as a calibration experiment for double sampling, but original data of IC-Karanth show lags of (up to) several years. Further, data points used in the paper do not match the original sources. We show that by use of inappropriate and incorrect data collected through a faulty experimental design, poor parameterization of their theoretical model, and selectively picked estimates from literature on detection probability, the inferences of this paper are highly questionable. We highlight how the results of Gopalaswamy et al. were further distorted in popular media. If left unaddressed, the paper of Gopalaswamy et al. could have serious implications on statistical design of large-scale animal surveys by propagating unreliable inferences.
bibliographic citation: Qureshi et al. (2019) Twisted tale of the tiger: the case of inappropriate data and deficient science. PeerJ 7:e7482 https://doi.org/10.7717/peerj.7482
date submitted: 2018-11-13
date accepted: 2019-07-15
issued: 2019-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qureshi
  given name: Qamar
author list: Agent
  family name: Gopal
  given name: Rajesh
author list: Agent
  family name: Jhala
  given name: Yadvendradev
doi: 10.7717/peerj.7482
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-20
copyright: © 2019 Qureshi et al.
attribution name: Qureshi et al.

Investigating safety profiles of human papillomavirus vaccine across group differences using VAERS data and MedDRA
type: item
type: AcademicArticle
description: Background The safety of vaccines is a critical factor in maintaining public trust in national vaccination programs. This study aimed to evaluate the safety profiles of human papillomavirus (HPV) vaccines with regard to the distribution of adverse events (AE) across gender and age, and the correlations across various AEs using the Food and Drug Administration/Centers for Disease Control and Prevention Vaccine Adverse Event Reporting System (VAERS). Methods For analyses, 27,348 patients aged between 9 and 25 years old with at least one AE reported in VAERS between the year of 2006 and 2017 were included. AEs were summarized into two levels: the lower level preferred term (PT) and higher level system organ classes (SOCs) based on the structure of Medical Dictionary for Regulatory Activities (MedDRA). A series of statistical analyses were applied on both levels of AEs. Zero-truncated Poisson regression and multivariate logistic regression models were first developed to assess the rate and risk of SOCs across age groups and genders. Pairwise Pearson correlation analyses and hierarchical clustering analyses were then conducted to explore the interrelationships and clustering pattern among AEs. Results We identified 27,337 unique HPV vaccine reports between 2006 and 2017. Disproportional reporting of AEs was observed across age and gender in 21 SOCs (p < 0.05). The correlation analyses found most SOCs demonstrate weak positive correlations except for five pairs which were negatively correlated: skin and subcutaneous tissue disorders + injury poisoning and procedural complications; skin and subcutaneous tissue disorders + nervous system disorders; Skin and subcutaneous tissue disorders + pregnancy, puerperium and perinatal conditions; nervous system disorders + pregnancy, puerperium and perinatal conditions; pregnancy, puerperium and perinatal conditions + general disorders and administration site conditions. Nervous system disorders had the most AEs which contributed to 1…
format: application/pdf
format: text/html
creator: Yuxi Jia
creator: Cong Zhu
creator: Jingcheng Du
creator: Yang Xiang
creator: Yong Chen
creator: Wei Wang
creator: Cui Tao
subject: Neuroscience
subject: Drugs and Devices
subject: Pharmacology
subject: Public Health
subject: Statistics
description: doi:10.7717/peerj.7490
publisher: PeerJ Inc.
rights: © 2019 Jia et al.
abstract: Background The safety of vaccines is a critical factor in maintaining public trust in national vaccination programs. This study aimed to evaluate the safety profiles of human papillomavirus (HPV) vaccines with regard to the distribution of adverse events (AE) across gender and age, and the correlations across various AEs using the Food and Drug Administration/Centers for Disease Control and Prevention Vaccine Adverse Event Reporting System (VAERS). Methods For analyses, 27,348 patients aged between 9 and 25 years old with at least one AE reported in VAERS between the year of 2006 and 2017 were included. AEs were summarized into two levels: the lower level preferred term (PT) and higher level system organ classes (SOCs) based on the structure of Medical Dictionary for Regulatory Activities (MedDRA). A series of statistical analyses were applied on both levels of AEs. Zero-truncated Poisson regression and multivariate logistic regression models were first developed to assess the rate and risk of SOCs across age groups and genders. Pairwise Pearson correlation analyses and hierarchical clustering analyses were then conducted to explore the interrelationships and clustering pattern among AEs. Results We identified 27,337 unique HPV vaccine reports between 2006 and 2017. Disproportional reporting of AEs was observed across age and gender in 21 SOCs (p < 0.05). The correlation analyses found most SOCs demonstrate weak positive correlations except for five pairs which were negatively correlated: skin and subcutaneous tissue disorders + injury poisoning and procedural complications; skin and subcutaneous tissue disorders + nervous system disorders; Skin and subcutaneous tissue disorders + pregnancy, puerperium and perinatal conditions; nervous system disorders + pregnancy, puerperium and perinatal conditions; pregnancy, puerperium and perinatal conditions + general disorders and administration site conditions. Nervous system disorders had the most AEs which contributed to 1…
bibliographic citation: Jia et al. (2019) Investigating safety profiles of human papillomavirus vaccine across group differences using VAERS data and MedDRA. PeerJ 7:e7490 https://doi.org/10.7717/peerj.7490
date submitted: 2019-01-07
date accepted: 2019-07-16
issued: 2019-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jia
  given name: Yuxi
author list: Agent
  family name: Zhu
  given name: Cong
author list: Agent
  family name: Du
  given name: Jingcheng
author list: Agent
  family name: Xiang
  given name: Yang
author list: Agent
  family name: Chen
  given name: Yong
author list: Agent
  family name: Wang
  given name: Wei
author list: Agent
  family name: Tao
  given name: Cui
doi: 10.7717/peerj.7490
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-20
copyright: © 2019 Jia et al.
attribution name: Jia et al.

Effects of digging by a native and introduced ecosystem engineer on soil physical and chemical properties in temperate grassy woodland
type: item
type: AcademicArticle
description: Temperate grasslands and woodlands are the focus of extensive restoration efforts worldwide. Reintroduction of locally extinct soil-foraging and burrowing animals has been suggested as a means to restore soil function in these ecosystems. Yet little is known about the physical and chemical effects of digging on soil over time and how these effects differ between species of digging animal, vegetation types or ecosystems. We compared foraging pits of a native reintroduced marsupial, the eastern bettong (Bettongia gaimardi) and that of the exotic European rabbit (Oryctolagus cuniculus). We simulated pits of these animals and measured pit dimensions and soil chemical properties over a period of 2 years. We showed that bettong and rabbit pits differed in their morphology and longevity, and that pits had a strong moderating effect on soil surface temperatures. Over 75% of the simulated pits were still visible after 2 years, and bettong pits infilled faster than rabbit pits. Bettong pits reduced diurnal temperature range by up to 25 °C compared to the soil surface. We did not find any effects of digging on soil chemistry that were consistent across vegetation types, between bettong and rabbit pits, and with time since digging, which is contrary to studies conducted in arid biomes. Our findings show that animal foraging pits in temperate ecosystems cause physical alteration of the soil surface and microclimatic conditions rather than nutrient changes often observed in arid areas.
format: application/pdf
format: text/html
creator: Catherine E. Ross
creator: Nicola T. Munro
creator: Philip S. Barton
creator: Maldwyn J. Evans
creator: John Gillen
creator: Ben C.T. Macdonald
creator: Sue McIntyre
creator: Saul A. Cunningham
creator: Adrian D. Manning
subject: Conservation Biology
subject: Ecology
subject: Soil Science
description: doi:10.7717/peerj.7506
publisher: PeerJ Inc.
rights: © 2019 Ross et al.
abstract: Temperate grasslands and woodlands are the focus of extensive restoration efforts worldwide. Reintroduction of locally extinct soil-foraging and burrowing animals has been suggested as a means to restore soil function in these ecosystems. Yet little is known about the physical and chemical effects of digging on soil over time and how these effects differ between species of digging animal, vegetation types or ecosystems. We compared foraging pits of a native reintroduced marsupial, the eastern bettong (Bettongia gaimardi) and that of the exotic European rabbit (Oryctolagus cuniculus). We simulated pits of these animals and measured pit dimensions and soil chemical properties over a period of 2 years. We showed that bettong and rabbit pits differed in their morphology and longevity, and that pits had a strong moderating effect on soil surface temperatures. Over 75% of the simulated pits were still visible after 2 years, and bettong pits infilled faster than rabbit pits. Bettong pits reduced diurnal temperature range by up to 25 °C compared to the soil surface. We did not find any effects of digging on soil chemistry that were consistent across vegetation types, between bettong and rabbit pits, and with time since digging, which is contrary to studies conducted in arid biomes. Our findings show that animal foraging pits in temperate ecosystems cause physical alteration of the soil surface and microclimatic conditions rather than nutrient changes often observed in arid areas.
bibliographic citation: Ross et al. (2019) Effects of digging by a native and introduced ecosystem engineer on soil physical and chemical properties in temperate grassy woodland. PeerJ 7:e7506 https://doi.org/10.7717/peerj.7506
date submitted: 2019-04-11
date accepted: 2019-07-17
issued: 2019-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ross
  given name: Catherine E.
author list: Agent
  family name: Munro
  given name: Nicola T.
author list: Agent
  family name: Barton
  given name: Philip S.
author list: Agent
  family name: Evans
  given name: Maldwyn J.
author list: Agent
  family name: Gillen
  given name: John
author list: Agent
  family name: Macdonald
  given name: Ben C.T.
author list: Agent
  family name: McIntyre
  given name: Sue
author list: Agent
  family name: Cunningham
  given name: Saul A.
author list: Agent
  family name: Manning
  given name: Adrian D.
doi: 10.7717/peerj.7506
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-20
copyright: © 2019 Ross et al.
attribution name: Ross et al.

Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors
type: item
type: AcademicArticle
description: Heat shock protein 70 (Hsp70) plays an essential role in plant growth and development, as well as stress response. Rapeseed (Brassica napus L.) originated from recently interspecific hybridization between Brassica rapa and Brassica oleracea. In this study, a total of 47 Hsp70 genes were identified in B. napus (AnAnCnCn genome), including 22 genes from An subgenome and 25 genes from Cn subgenome. Meanwhile, 29 and 20 Hsp70 genes were explored in B. rapa (ArAr genome) and B. oleracea (CoCo genome), respectively. Based on phylogenetic analysis, 114 Hsp70 proteins derived from B. napus, B. rapa, B. oleracea and Arabidopsis thaliana, were divided into 6 subfamilies containing 16 Ar-An and 11 Co-Cn reliable orthologous pairs. The homology and synteny analysis indicated whole genome triplication and segmental duplication may be the major contributor for the expansion of Hsp70 gene family. Intron gain of BnHsp70 genes and domain loss of BnHsp70 proteins also were found in B. napus, associating with intron evolution and module evolution of proteins after allopolyploidization. In addition, transcriptional profiles analyses indicated that expression patterns of most BnHsp70 genes were tissue-specific. Moreover, Hsp70 orthologs exhibited different expression patterns in the same tissue and Cn subgenome biased expression was observed in leaf. These findings contribute to exploration of the evolutionary adaptation of polyploidy and will facilitate further application of BnHsp70 gene functions.
format: application/pdf
format: text/html
creator: Ziwei Liang
creator: Mengdi Li
creator: Zhengyi Liu
creator: Jianbo Wang
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.7511
publisher: PeerJ Inc.
rights: © 2019 Liang et al.
abstract: Heat shock protein 70 (Hsp70) plays an essential role in plant growth and development, as well as stress response. Rapeseed (Brassica napus L.) originated from recently interspecific hybridization between Brassica rapa and Brassica oleracea. In this study, a total of 47 Hsp70 genes were identified in B. napus (AnAnCnCn genome), including 22 genes from An subgenome and 25 genes from Cn subgenome. Meanwhile, 29 and 20 Hsp70 genes were explored in B. rapa (ArAr genome) and B. oleracea (CoCo genome), respectively. Based on phylogenetic analysis, 114 Hsp70 proteins derived from B. napus, B. rapa, B. oleracea and Arabidopsis thaliana, were divided into 6 subfamilies containing 16 Ar-An and 11 Co-Cn reliable orthologous pairs. The homology and synteny analysis indicated whole genome triplication and segmental duplication may be the major contributor for the expansion of Hsp70 gene family. Intron gain of BnHsp70 genes and domain loss of BnHsp70 proteins also were found in B. napus, associating with intron evolution and module evolution of proteins after allopolyploidization. In addition, transcriptional profiles analyses indicated that expression patterns of most BnHsp70 genes were tissue-specific. Moreover, Hsp70 orthologs exhibited different expression patterns in the same tissue and Cn subgenome biased expression was observed in leaf. These findings contribute to exploration of the evolutionary adaptation of polyploidy and will facilitate further application of BnHsp70 gene functions.
bibliographic citation: Liang et al. (2019) Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors. PeerJ 7:e7511 https://doi.org/10.7717/peerj.7511
date submitted: 2019-03-14
date accepted: 2019-07-17
issued: 2019-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Ziwei
author list: Agent
  family name: Li
  given name: Mengdi
author list: Agent
  family name: Liu
  given name: Zhengyi
author list: Agent
  family name: Wang
  given name: Jianbo
doi: 10.7717/peerj.7511
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-20
copyright: ©2019 Liang et al.
attribution name: Liang et al.

Movement velocity can be used to estimate the relative load during the bench press and leg press exercises in older women
type: item
type: AcademicArticle
description: Background Movement velocity has been proposed as an effective tool to prescribe the load during resistance training in young healthy adults. This study aimed to elucidate whether movement velocity could also be used to estimate the relative load (i.e., % of the one-repetition maximum (1RM)) in older women. Methods A total of 22 older women (age = 68.2 ± 3.6 years, bench press 1RM = 22.3 ± 4.7 kg, leg press 1RM = 114.6 ± 15.9 kg) performed an incremental loading test during the free-weight bench press and the leg press exercises on two separate sessions. The mean velocity (MV) was collected with a linear position transducer. Results A strong linear relationship between MV and the relative load was observed for the bench press (%1RM = −130.4 MV + 119.3; r2 = 0.827, standard error of the estimate (SEE) = 6.10%1RM, p < 0.001) and leg press exercises (%1RM = −158.3 MV + 131.4; r2 = 0.913, SEE = 5.63%1RM, p < 0.001). No significant differences were observed between the bench press and leg press exercises for the MV attained against light-medium relative loads (≤70%1RM), while the MV associated with heavy loads (≥80%1RM) was significantly higher for the leg press. Conclusions These results suggest that the monitoring of MV could be useful to prescribe the loads during resistance training in older women. However, it should be noted that the MV associated with a given %1RM is significantly lower in older women compared to young healthy individuals.
format: application/pdf
format: text/html
creator: Pablo Jorge Marcos-Pardo
creator: Jorge Miguel González-Hernández
creator: Amador García-Ramos
creator: Abraham López-Vivancos
creator: Pedro Jiménez-Reyes
subject: Geriatrics
subject: Kinesiology
subject: Women's Health
description: doi:10.7717/peerj.7533
publisher: PeerJ Inc.
rights: © 2019 Marcos-Pardo et al.
abstract: Background Movement velocity has been proposed as an effective tool to prescribe the load during resistance training in young healthy adults. This study aimed to elucidate whether movement velocity could also be used to estimate the relative load (i.e., % of the one-repetition maximum (1RM)) in older women. Methods A total of 22 older women (age = 68.2 ± 3.6 years, bench press 1RM = 22.3 ± 4.7 kg, leg press 1RM = 114.6 ± 15.9 kg) performed an incremental loading test during the free-weight bench press and the leg press exercises on two separate sessions. The mean velocity (MV) was collected with a linear position transducer. Results A strong linear relationship between MV and the relative load was observed for the bench press (%1RM = −130.4 MV + 119.3; r2 = 0.827, standard error of the estimate (SEE) = 6.10%1RM, p < 0.001) and leg press exercises (%1RM = −158.3 MV + 131.4; r2 = 0.913, SEE = 5.63%1RM, p < 0.001). No significant differences were observed between the bench press and leg press exercises for the MV attained against light-medium relative loads (≤70%1RM), while the MV associated with heavy loads (≥80%1RM) was significantly higher for the leg press. Conclusions These results suggest that the monitoring of MV could be useful to prescribe the loads during resistance training in older women. However, it should be noted that the MV associated with a given %1RM is significantly lower in older women compared to young healthy individuals.
bibliographic citation: Marcos-Pardo et al. (2019) Movement velocity can be used to estimate the relative load during the bench press and leg press exercises in older women. PeerJ 7:e7533 https://doi.org/10.7717/peerj.7533
date submitted: 2019-05-01
date accepted: 2019-07-22
issued: 2019-08-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marcos-Pardo
  given name: Pablo Jorge
author list: Agent
  family name: González-Hernández
  given name: Jorge Miguel
author list: Agent
  family name: García-Ramos
  given name: Amador
author list: Agent
  family name: López-Vivancos
  given name: Abraham
author list: Agent
  family name: Jiménez-Reyes
  given name: Pedro
doi: 10.7717/peerj.7533
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-20
copyright: © 2019 Marcos-Pardo et al.
attribution name: Marcos-Pardo et al.

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