PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Application of open field, tonic immobility, and attention bias tests to hens with different ranging patterns
items: Introducing a new tool to navigate, understand and use International Codes of Nomenclature
items: Peripheral blood bovine lymphocytes and MAP show distinctly different proteome changes and immune pathways in host-pathogen interaction
items: Mapping theme trends and recognizing hot spots in postmenopausal osteoporosis research: a bibliometric analysis
items: Molecular characterization of G-protein-coupled receptor (GPCR) and protein kinase A (PKA) cDNA in Perinereis aibuhitensis and expression during benzo(a)pyrene exposure
items: Oral toxicity of arjunolic acid on hematological, biochemical and histopathological investigations in female Sprague Dawley rats
items: Lymph node detection in MR Lymphography: false positive reduction using multi-view convolutional neural networks
items: Long-term study of behaviors of two cohabiting sea urchin species, Mesocentrotus nudus and Strongylocentrotus intermedius, under conditions of high food quantity and predation risk in situ
items: Munidopsis species (Crustacea: Decapoda: Munidopsidae) from carcass falls in Weijia Guyot, West Pacific, with recognition of a new species based on integrative taxonomy
items: Comprehensive analysis of differentially expressed microRNAs and mRNAs in MDBK cells expressing bovine papillomavirus E5 oncogene

Application of open field, tonic immobility, and attention bias tests to hens with different ranging patterns
type: item
type: AcademicArticle
description: Assessment of negative affective states is a key component of animal welfare research. In laying hens, excessive fearfulness results in reduced production and increased sensitivity to stress. Fearfulness can be defined as a response to a known threat, but anxiety is a response to an unknown threat and may have similar negative consequences. The open field test and tonic immobility test are commonly applied to measure fearfulness in laying hens. An attention bias test that measured individual hen’s responses to playback of a conspecific alarm call in the presence of food was recently pharmacologically validated using an anxiogenic drug but was confounded by the hen’s typical motionless response in a novel environment. The current study used 56-week old free-range layers to further assess the validity of an attention bias test to differentiate ranging treatment groups in comparison with the open field and tonic immobility tests. The selected hens varied in their range use patterns as tracked by radio-frequency identification technology. ‘Indoor’ hens did not access the range and ‘outdoor’ hens ranged daily; previous research has confirmed higher fearfulness in hens that remain indoors. The tonic immobility test did not differentiate ranging groups (P = 0.34), but indoor birds were slower to first step (P = 0.03) and stepped less (P = 0.02) in the open field test. The attention bias test occurred in an isolated wooden box using a conspecific alarm call playback (a threat) and mixed grain (a positive stimulus). The behavioural response of latency to resume eating following playback of the alarm call was measured to differentiate the anxiety states of the indoor and outdoor ranging birds. Before the attention bias test could occur, birds had to be habituated to the test box across three separate 5-minute sessions to increase the willingness to feed within the novel test environment. All birds ate faster across time (P < 0.001) but the indoor birds were slower to eat than…
format: application/pdf
format: text/html
creator: Dana L.M. Campbell
creator: Emily J. Dickson
creator: Caroline Lee
subject: Agricultural Science
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.8122
publisher: PeerJ Inc.
rights: © 2019 Campbell et al.
abstract: Assessment of negative affective states is a key component of animal welfare research. In laying hens, excessive fearfulness results in reduced production and increased sensitivity to stress. Fearfulness can be defined as a response to a known threat, but anxiety is a response to an unknown threat and may have similar negative consequences. The open field test and tonic immobility test are commonly applied to measure fearfulness in laying hens. An attention bias test that measured individual hen’s responses to playback of a conspecific alarm call in the presence of food was recently pharmacologically validated using an anxiogenic drug but was confounded by the hen’s typical motionless response in a novel environment. The current study used 56-week old free-range layers to further assess the validity of an attention bias test to differentiate ranging treatment groups in comparison with the open field and tonic immobility tests. The selected hens varied in their range use patterns as tracked by radio-frequency identification technology. ‘Indoor’ hens did not access the range and ‘outdoor’ hens ranged daily; previous research has confirmed higher fearfulness in hens that remain indoors. The tonic immobility test did not differentiate ranging groups (P = 0.34), but indoor birds were slower to first step (P = 0.03) and stepped less (P = 0.02) in the open field test. The attention bias test occurred in an isolated wooden box using a conspecific alarm call playback (a threat) and mixed grain (a positive stimulus). The behavioural response of latency to resume eating following playback of the alarm call was measured to differentiate the anxiety states of the indoor and outdoor ranging birds. Before the attention bias test could occur, birds had to be habituated to the test box across three separate 5-minute sessions to increase the willingness to feed within the novel test environment. All birds ate faster across time (P < 0.001) but the indoor birds were slower to eat than…
bibliographic citation: Campbell et al. (2019) Application of open field, tonic immobility, and attention bias tests to hens with different ranging patterns. PeerJ 7:e8122 https://doi.org/10.7717/peerj.8122
date submitted: 2019-09-04
date accepted: 2019-10-30
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Campbell
  given name: Dana L.M.
author list: Agent
  family name: Dickson
  given name: Emily J.
author list: Agent
  family name: Lee
  given name: Caroline
doi: 10.7717/peerj.8122
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Campbell et al.
attribution name: Campbell et al.

Introducing a new tool to navigate, understand and use International Codes of Nomenclature
type: item
type: AcademicArticle
description: Background In order to designate the various concepts of taxa in biology, evolution and paleontology, scientists have developed various rules on how to create unique names for taxa. Different Codes of Nomenclature have been developed for animals, plants, fungi, bacteria etc., with standard sets of Rules that govern the formation, publication and application of the nomina of extant and extinct species. These Codes are the result of decades of discussions, workshops, publications and revisions. The structure and complexity of these Codes have been criticized many times by zoologists. This project aims, using the International Code of Zoological Nomenclature as a case study, to show that the structure of these Codes is better reflected and understood as networks. Methods The majority of the text of the Code has been divided into hundreds of Nodes of different types, connected to each other with different types of Edges to form a network. The various mathematical descriptors of the entire system, as well as for the elements of the network, have been conceptually framed to help describing and understanding the Code as a network. Results The network of the Code comprises 1,379 Nodes, which are connected with 11,276 Edges. The structure of the Code can be accurately described as a network, a mathematical structure that is better suited than any kind of linear text publication to reflect its structure. Discussion Thinking of the Code as a network allows a better, in-depth understanding of the Code itself, as the user can navigate in a more efficient way, as well as to depict and analyze all the implied connections between the various parts of the Code that are not visible immediately. The network of the Code is an open access tool that could also help teaching, using and disseminating the Code. More importantly, this network is a powerful tool that allows identifying a priori the parts of the Code that could be potentially affected by upcoming amendment and revisions. This …
format: application/pdf
format: text/html
creator: Evangelos Vlachos
subject: Taxonomy
subject: Zoology
subject: Computational Science
description: doi:10.7717/peerj.8127
publisher: PeerJ Inc.
rights: © 2019 Vlachos
abstract: Background In order to designate the various concepts of taxa in biology, evolution and paleontology, scientists have developed various rules on how to create unique names for taxa. Different Codes of Nomenclature have been developed for animals, plants, fungi, bacteria etc., with standard sets of Rules that govern the formation, publication and application of the nomina of extant and extinct species. These Codes are the result of decades of discussions, workshops, publications and revisions. The structure and complexity of these Codes have been criticized many times by zoologists. This project aims, using the International Code of Zoological Nomenclature as a case study, to show that the structure of these Codes is better reflected and understood as networks. Methods The majority of the text of the Code has been divided into hundreds of Nodes of different types, connected to each other with different types of Edges to form a network. The various mathematical descriptors of the entire system, as well as for the elements of the network, have been conceptually framed to help describing and understanding the Code as a network. Results The network of the Code comprises 1,379 Nodes, which are connected with 11,276 Edges. The structure of the Code can be accurately described as a network, a mathematical structure that is better suited than any kind of linear text publication to reflect its structure. Discussion Thinking of the Code as a network allows a better, in-depth understanding of the Code itself, as the user can navigate in a more efficient way, as well as to depict and analyze all the implied connections between the various parts of the Code that are not visible immediately. The network of the Code is an open access tool that could also help teaching, using and disseminating the Code. More importantly, this network is a powerful tool that allows identifying a priori the parts of the Code that could be potentially affected by upcoming amendment and revisions. This …
bibliographic citation: Vlachos (2019) Introducing a new tool to navigate, understand and use International Codes of Nomenclature. PeerJ 7:e8127 https://doi.org/10.7717/peerj.8127
date submitted: 2019-06-12
date accepted: 2019-10-30
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vlachos
  given name: Evangelos
doi: 10.7717/peerj.8127
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Vlachos
attribution name: Vlachos

Peripheral blood bovine lymphocytes and MAP show distinctly different proteome changes and immune pathways in host-pathogen interaction
type: item
type: AcademicArticle
description: Mycobacterium avium subsp. paratuberculosis (MAP) is a pathogen causing paratuberculosis in cattle and small ruminants. During the long asymptomatic subclinical stage, high numbers of MAP are excreted and can be transmitted to food for human consumption, where they survive many of the standard techniques of food decontamination. Whether MAP is a human pathogen is currently under debate. The aim of this study was a better understanding of the host-pathogen response by analyzing the interaction of peripheral blood lymphocytes (PBL) from cattle with MAP in their exoproteomes/secretomes to gain more information about the pathogenic mechanisms of MAP. Because in other mycobacterial infections, the immune phenotype correlates with susceptibility, we additionally tested the interaction of MAP with recently detected cattle with a different immune capacity referred as immune deviant (ID) cows. In PBL, different biological pathways were enhanced in response to MAP dependent on the immune phenotype of the host. PBL of control cows activated members of cell activation and chemotaxis of leukocytes pathway as well as IL-12 mediated signaling. In contrast, in ID cows CNOT1 was detected as highly abundant protein, pointing to a different immune response, which could be favorable for MAP. Additionally, MAP exoproteomes differed in either GroEL1 or DnaK abundance, depending on the interacting host immune response. These finding point to an interdependent, tightly regulated response of the bovine immune system to MAP and vise versa.
format: application/pdf
format: text/html
creator: Kristina J.H. Kleinwort
creator: Stefanie M. Hauck
creator: Roxane L. Degroote
creator: Armin M. Scholz
creator: Christina Hölzel
creator: Erwin P. Maertlbauer
creator: Cornelia Deeg
subject: Food Science and Technology
subject: Microbiology
subject: Veterinary Medicine
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.8130
publisher: PeerJ Inc.
rights: © 2019 Kleinwort et al.
abstract: Mycobacterium avium subsp. paratuberculosis (MAP) is a pathogen causing paratuberculosis in cattle and small ruminants. During the long asymptomatic subclinical stage, high numbers of MAP are excreted and can be transmitted to food for human consumption, where they survive many of the standard techniques of food decontamination. Whether MAP is a human pathogen is currently under debate. The aim of this study was a better understanding of the host-pathogen response by analyzing the interaction of peripheral blood lymphocytes (PBL) from cattle with MAP in their exoproteomes/secretomes to gain more information about the pathogenic mechanisms of MAP. Because in other mycobacterial infections, the immune phenotype correlates with susceptibility, we additionally tested the interaction of MAP with recently detected cattle with a different immune capacity referred as immune deviant (ID) cows. In PBL, different biological pathways were enhanced in response to MAP dependent on the immune phenotype of the host. PBL of control cows activated members of cell activation and chemotaxis of leukocytes pathway as well as IL-12 mediated signaling. In contrast, in ID cows CNOT1 was detected as highly abundant protein, pointing to a different immune response, which could be favorable for MAP. Additionally, MAP exoproteomes differed in either GroEL1 or DnaK abundance, depending on the interacting host immune response. These finding point to an interdependent, tightly regulated response of the bovine immune system to MAP and vise versa.
bibliographic citation: Kleinwort et al. (2019) Peripheral blood bovine lymphocytes and MAP show distinctly different proteome changes and immune pathways in host-pathogen interaction. PeerJ 7:e8130 https://doi.org/10.7717/peerj.8130
date submitted: 2019-08-14
date accepted: 2019-10-31
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kleinwort
  given name: Kristina J.H.
author list: Agent
  family name: Hauck
  given name: Stefanie M.
author list: Agent
  family name: Degroote
  given name: Roxane L.
author list: Agent
  family name: Scholz
  given name: Armin M.
author list: Agent
  family name: Hölzel
  given name: Christina
author list: Agent
  family name: Maertlbauer
  given name: Erwin P.
author list: Agent
  family name: Deeg
  given name: Cornelia
doi: 10.7717/peerj.8130
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: © 2019 Kleinwort et al.
attribution name: Kleinwort et al.

Mapping theme trends and recognizing hot spots in postmenopausal osteoporosis research: a bibliometric analysis
type: item
type: AcademicArticle
description: Background This study aimed to draw a series of scientific maps to quantitatively and qualitatively evaluate hot spots and trends in postmenopausal osteoporosis research using bibliometric analysis. Methods Scientific papers published on postmenopausal osteoporosis were extracted from the Web of Science Core Collection and PubMed database. Extracted information was analyzed quantitatively with bibliometric analysis by CiteSpace, the Online Analysis Platform of Literature Metrology and Bibliographic Item Co-Occurrence Matrix Builder (BICOMB). To explore the hot spots in this field, co-word biclustering analysis was conducted by gCLUTO based on the major MeSH terms/MeSH subheading terms-source literatures matrix. Results We identified that a total of 5,247 publications related to postmenopausal osteoporosis were published between 2013 and 2017. The overall trend decreased from 1,071 literatures in 2013 to 1,048 literatures in 2017. Osteoporosis International is the leading journal in the field of postmenopausal osteoporosis research, both in terms of impact factor score (3.819) and H-index value (157). The United States has retained a top position and has exerted a pivotal influence in this field. The University of California, San Francisco was identified as a leading institution for research collaboration, and Professors Reginster and Kanis have made great achievements in this area. Eight research hot spots were identified. Conclusions Our study found that in the past few years, the etiology and drug treatment of postmenopausal osteoporosis have been research hot spots. They provide a basis for the study of the pathogenesis of osteoporosis and guidelines for the drug treatment of osteoporosis.
format: application/pdf
format: text/html
creator: Siming Zhou
creator: Zhengbo Tao
creator: Yue Zhu
creator: Lin Tao
subject: Diabetes and Endocrinology
subject: Global Health
subject: Orthopedics
subject: Women’s Health
subject: Statistics
description: doi:10.7717/peerj.8145
publisher: PeerJ Inc.
rights: © 2019 Zhou et al.
abstract: Background This study aimed to draw a series of scientific maps to quantitatively and qualitatively evaluate hot spots and trends in postmenopausal osteoporosis research using bibliometric analysis. Methods Scientific papers published on postmenopausal osteoporosis were extracted from the Web of Science Core Collection and PubMed database. Extracted information was analyzed quantitatively with bibliometric analysis by CiteSpace, the Online Analysis Platform of Literature Metrology and Bibliographic Item Co-Occurrence Matrix Builder (BICOMB). To explore the hot spots in this field, co-word biclustering analysis was conducted by gCLUTO based on the major MeSH terms/MeSH subheading terms-source literatures matrix. Results We identified that a total of 5,247 publications related to postmenopausal osteoporosis were published between 2013 and 2017. The overall trend decreased from 1,071 literatures in 2013 to 1,048 literatures in 2017. Osteoporosis International is the leading journal in the field of postmenopausal osteoporosis research, both in terms of impact factor score (3.819) and H-index value (157). The United States has retained a top position and has exerted a pivotal influence in this field. The University of California, San Francisco was identified as a leading institution for research collaboration, and Professors Reginster and Kanis have made great achievements in this area. Eight research hot spots were identified. Conclusions Our study found that in the past few years, the etiology and drug treatment of postmenopausal osteoporosis have been research hot spots. They provide a basis for the study of the pathogenesis of osteoporosis and guidelines for the drug treatment of osteoporosis.
bibliographic citation: Zhou et al. (2019) Mapping theme trends and recognizing hot spots in postmenopausal osteoporosis research: a bibliometric analysis. PeerJ 7:e8145 https://doi.org/10.7717/peerj.8145
date submitted: 2019-08-01
date accepted: 2019-11-03
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Siming
author list: Agent
  family name: Tao
  given name: Zhengbo
author list: Agent
  family name: Zhu
  given name: Yue
author list: Agent
  family name: Tao
  given name: Lin
doi: 10.7717/peerj.8145
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: © 2019 Zhou et al.
attribution name: Zhou et al.

Molecular characterization of G-protein-coupled receptor (GPCR) and protein kinase A (PKA) cDNA in Perinereis aibuhitensis and expression during benzo(a)pyrene exposure
type: item
type: AcademicArticle
description: Background G-protein-coupled receptors (GPCRs) are one of the most important molecules that transfer signals across the plasma membrane, and play central roles in physiological systems. The molecular architecture of GPCRs allows them to bind to diverse chemicals, including environmental contaminants. Methods To investigate the effects of benzo(a)pyrene (B(a)P) on GPCR signaling, GPCR and the protein kinase A (PKA) catalytic subunit of Perinereis aibuhitensis were cloned. The expression patterns of these two genes during B(a)P exposure were determined with real-time fluorescence quantitative PCR. The PKA content in P. aibuhitensis under B(a)P exposure was examined. Results The full-length cDNAs of PaGPCR and the PaPKA catalytic subunit were 1,514 and 2,662 nucleotides, respectively, encoding 338 and 350 amino acids, respectively. Multiple sequence alignments indicated that the deduced amino acid sequence of PaGPCR shared a low level of similarity with the orphan GPCRs of polychaetes and echinoderms, whereas PaPKA shared a high level of identify with the PKA catalytic subunits of other invertebrates. B(a)P exposure time-dependently elevated the expression of PaGPCR and PaPKA. The expression of both PaGPCR and PaPKA was also dose-dependent, except at a dose of 10 μg/L B(a)P. The PKA content in concentration group was elevated on day 4, with time prolonging the PKA content was down-regulated to control level. Discussion These results suggested that GPCR signaling in P. aibuhitensis was involved in the polychaete’s response to environmental contaminants.
format: application/pdf
format: text/html
creator: Yi Huang
creator: Jia Sun
creator: Ping Han
creator: Heling Zhao
creator: Mengting Wang
creator: Yibing Zhou
creator: Dazuo Yang
creator: Huan Zhao
subject: Marine Biology
subject: Molecular Biology
subject: Ecotoxicology
description: doi:10.7717/peerj.8044
publisher: PeerJ Inc.
rights: © 2019 Huang et al.
abstract: Background G-protein-coupled receptors (GPCRs) are one of the most important molecules that transfer signals across the plasma membrane, and play central roles in physiological systems. The molecular architecture of GPCRs allows them to bind to diverse chemicals, including environmental contaminants. Methods To investigate the effects of benzo(a)pyrene (B(a)P) on GPCR signaling, GPCR and the protein kinase A (PKA) catalytic subunit of Perinereis aibuhitensis were cloned. The expression patterns of these two genes during B(a)P exposure were determined with real-time fluorescence quantitative PCR. The PKA content in P. aibuhitensis under B(a)P exposure was examined. Results The full-length cDNAs of PaGPCR and the PaPKA catalytic subunit were 1,514 and 2,662 nucleotides, respectively, encoding 338 and 350 amino acids, respectively. Multiple sequence alignments indicated that the deduced amino acid sequence of PaGPCR shared a low level of similarity with the orphan GPCRs of polychaetes and echinoderms, whereas PaPKA shared a high level of identify with the PKA catalytic subunits of other invertebrates. B(a)P exposure time-dependently elevated the expression of PaGPCR and PaPKA. The expression of both PaGPCR and PaPKA was also dose-dependent, except at a dose of 10 μg/L B(a)P. The PKA content in concentration group was elevated on day 4, with time prolonging the PKA content was down-regulated to control level. Discussion These results suggested that GPCR signaling in P. aibuhitensis was involved in the polychaete’s response to environmental contaminants.
bibliographic citation: Huang et al. (2019) Molecular characterization of G-protein-coupled receptor (GPCR) and protein kinase A (PKA) cDNA in Perinereis aibuhitensis and expression during benzo(a)pyrene exposure. PeerJ 7:e8044 https://doi.org/10.7717/peerj.8044
date submitted: 2019-07-10
date accepted: 2019-10-16
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Yi
author list: Agent
  family name: Sun
  given name: Jia
author list: Agent
  family name: Han
  given name: Ping
author list: Agent
  family name: Zhao
  given name: Heling
author list: Agent
  family name: Wang
  given name: Mengting
author list: Agent
  family name: Zhou
  given name: Yibing
author list: Agent
  family name: Yang
  given name: Dazuo
author list: Agent
  family name: Zhao
  given name: Huan
doi: 10.7717/peerj.8044
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: © 2019 Huang et al.
attribution name: Huang et al.

Oral toxicity of arjunolic acid on hematological, biochemical and histopathological investigations in female Sprague Dawley rats
type: item
type: AcademicArticle
description: Background Arjunolic acid (AA) is a potent phytochemical with wider pharmacological activities. Despite potential medicinal properties on various in vitro and in vivo studies, there is still a dearth of scientific data related to its safety profile and toxicological parameters. The current study aimed to investigate acute toxicity of AA in normal female Sprague Dawley rats. Methods In this study, AA was administered orally at an individual dose of 300 and 2000 mg/kg body weight to group 1 and 2 respectively, while group 3 served as normal control. All the animals were observed for 2 weeks to determine any behavioral and physical changes. On day 15, blood was collected for hematological and biochemical investigation, later animals from all the three groups were euthanized to harvest and store essential organs for histopathological analysis. Four different staining techniques; hematoxylin and eosin, Masson trichrome, Periodic acid Schiff and Oil O Red were used to investigate any alterations in different tissues through microscopical observation. Results The results of the study showed no morbidity and mortality at two different dosage of AA treatment. Daily food & water intake, body weight, relative organ weight, hematological and biochemical parameters were detected to be normal with no severe alteration seen through microscopical investigation in the structure of harvested tissues. Our findings support the safety profile of AA, which was well tolerated at higher dose. Thus, an in-detail study on the subacute disease model is warranted.
format: application/pdf
format: text/html
creator: Khurram Aamir
creator: Hidayat Ullah Khan
creator: Chowdhury Faiz Hossain
creator: Mst. Rejina Afrin
creator: Imam Shaik
creator: Naguib Salleh
creator: Nelli Giribabu
creator: Aditya Arya
subject: Biochemistry
subject: Toxicology
subject: Hematology
subject: Histology
description: doi:10.7717/peerj.8045
publisher: PeerJ Inc.
rights: © 2019 Aamir et al.
abstract: Background Arjunolic acid (AA) is a potent phytochemical with wider pharmacological activities. Despite potential medicinal properties on various in vitro and in vivo studies, there is still a dearth of scientific data related to its safety profile and toxicological parameters. The current study aimed to investigate acute toxicity of AA in normal female Sprague Dawley rats. Methods In this study, AA was administered orally at an individual dose of 300 and 2000 mg/kg body weight to group 1 and 2 respectively, while group 3 served as normal control. All the animals were observed for 2 weeks to determine any behavioral and physical changes. On day 15, blood was collected for hematological and biochemical investigation, later animals from all the three groups were euthanized to harvest and store essential organs for histopathological analysis. Four different staining techniques; hematoxylin and eosin, Masson trichrome, Periodic acid Schiff and Oil O Red were used to investigate any alterations in different tissues through microscopical observation. Results The results of the study showed no morbidity and mortality at two different dosage of AA treatment. Daily food & water intake, body weight, relative organ weight, hematological and biochemical parameters were detected to be normal with no severe alteration seen through microscopical investigation in the structure of harvested tissues. Our findings support the safety profile of AA, which was well tolerated at higher dose. Thus, an in-detail study on the subacute disease model is warranted.
bibliographic citation: Aamir et al. (2019) Oral toxicity of arjunolic acid on hematological, biochemical and histopathological investigations in female Sprague Dawley rats. PeerJ 7:e8045 https://doi.org/10.7717/peerj.8045
date submitted: 2019-07-29
date accepted: 2019-10-16
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aamir
  given name: Khurram
author list: Agent
  family name: Khan
  given name: Hidayat Ullah
author list: Agent
  family name: Hossain
  given name: Chowdhury Faiz
author list: Agent
  family name: Afrin
  given name: Mst. Rejina
author list: Agent
  family name: Shaik
  given name: Imam
author list: Agent
  family name: Salleh
  given name: Naguib
author list: Agent
  family name: Giribabu
  given name: Nelli
author list: Agent
  family name: Arya
  given name: Aditya
doi: 10.7717/peerj.8045
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: © 2019 Aamir et al.
attribution name: Aamir et al.

Lymph node detection in MR Lymphography: false positive reduction using multi-view convolutional neural networks
type: item
type: AcademicArticle
description: Purpose To investigate whether multi-view convolutional neural networks can improve a fully automated lymph node detection system for pelvic MR Lymphography (MRL) images of patients with prostate cancer. Methods A fully automated computer-aided detection (CAD) system had been previously developed to detect lymph nodes in MRL studies. The CAD system was extended with three types of 2D multi-view convolutional neural networks (CNN) aiming to reduce false positives (FP). A 2D multi-view CNN is an efficient approximation of a 3D CNN, and three types were evaluated: a 1-view, 3-view, and 9-view 2D CNN. The three deep learning CNN architectures were trained and configured on retrospective data of 240 prostate cancer patients that received MRL images as the standard of care between January 2008 and April 2010. The MRL used ferumoxtran-10 as a contrast agent and comprised at least two imaging sequences: a 3D T1-weighted and a 3D T2*-weighted sequence. A total of 5089 lymph nodes were annotated by two expert readers, reading in consensus. A first experiment compared the performance with and without CNNs and a second experiment compared the individual contribution of the 1-view, 3-view, or 9-view architecture to the performance. The performances were visually compared using free-receiver operating characteristic (FROC) analysis and statistically compared using partial area under the FROC curve analysis. Training and analysis were performed using bootstrapped FROC and 5-fold cross-validation. Results Adding multi-view CNNs significantly (p < 0.01) reduced false positive detections. The 3-view and 9-view CNN outperformed (p < 0.01) the 1-view CNN, reducing FP from 20.6 to 7.8/image at 80% sensitivity. Conclusion Multi-view convolutional neural networks significantly reduce false positives in a lymph node detection system for MRL images, and three orthogonal views are sufficient. At the achieved level of performance, CAD for MRL may help speed up finding lymph nodes and assessin…
format: application/pdf
format: text/html
creator: Oscar A. Debats
creator: Geert J.S. Litjens
creator: Henkjan J. Huisman
subject: Oncology
subject: Radiology and Medical Imaging
subject: Urology
description: doi:10.7717/peerj.8052
publisher: PeerJ Inc.
rights: © 2019 Debats et al.
abstract: Purpose To investigate whether multi-view convolutional neural networks can improve a fully automated lymph node detection system for pelvic MR Lymphography (MRL) images of patients with prostate cancer. Methods A fully automated computer-aided detection (CAD) system had been previously developed to detect lymph nodes in MRL studies. The CAD system was extended with three types of 2D multi-view convolutional neural networks (CNN) aiming to reduce false positives (FP). A 2D multi-view CNN is an efficient approximation of a 3D CNN, and three types were evaluated: a 1-view, 3-view, and 9-view 2D CNN. The three deep learning CNN architectures were trained and configured on retrospective data of 240 prostate cancer patients that received MRL images as the standard of care between January 2008 and April 2010. The MRL used ferumoxtran-10 as a contrast agent and comprised at least two imaging sequences: a 3D T1-weighted and a 3D T2*-weighted sequence. A total of 5089 lymph nodes were annotated by two expert readers, reading in consensus. A first experiment compared the performance with and without CNNs and a second experiment compared the individual contribution of the 1-view, 3-view, or 9-view architecture to the performance. The performances were visually compared using free-receiver operating characteristic (FROC) analysis and statistically compared using partial area under the FROC curve analysis. Training and analysis were performed using bootstrapped FROC and 5-fold cross-validation. Results Adding multi-view CNNs significantly (p < 0.01) reduced false positive detections. The 3-view and 9-view CNN outperformed (p < 0.01) the 1-view CNN, reducing FP from 20.6 to 7.8/image at 80% sensitivity. Conclusion Multi-view convolutional neural networks significantly reduce false positives in a lymph node detection system for MRL images, and three orthogonal views are sufficient. At the achieved level of performance, CAD for MRL may help speed up finding lymph nodes and assessin…
bibliographic citation: Debats et al. (2019) Lymph node detection in MR Lymphography: false positive reduction using multi-view convolutional neural networks. PeerJ 7:e8052 https://doi.org/10.7717/peerj.8052
date submitted: 2018-12-13
date accepted: 2019-10-17
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Debats
  given name: Oscar A.
author list: Agent
  family name: Litjens
  given name: Geert J.S.
author list: Agent
  family name: Huisman
  given name: Henkjan J.
doi: 10.7717/peerj.8052
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: ©2019 Debats et al.
attribution name: Debats et al.

Long-term study of behaviors of two cohabiting sea urchin species, Mesocentrotus nudus and Strongylocentrotus intermedius, under conditions of high food quantity and predation risk in situ
type: item
type: AcademicArticle
description: Background In the predator–sea urchin–macrophyte trophic cascade, the ecological effect of sea urchins as grazers depends both on their density and the changes in foraging activity, which are influenced by various disturbing factors. However, the complete duration of the alarm reactions of echinoids has not been studied until now. Here, we tested a hypothesis that two cohabiting sea urchins, Mesocentrotus nudus and Strongylocentrotus intermedius, which differ morphologically, might display different behavioral responses to high hydrodynamic activity and predation. Methods We used continuous time-lapse video recording to clarify behavioral patterns of M. nudus and S. intermedius in presence of a large quantity of food (the kelp Saccharina japonica) but under different weather conditions and different types of predation threat: (1) calm weather conditions, (2) stormy weather conditions, (3) predation risk associated with the presence of several sea star species and (4) predation risk associated with an alarm stimulus (crushed conspecifics or heterospecifics). Three separate video recording experiments (134 days in total) were conducted under field conditions. Video recording analysis was performed to determine the number of specimens of each sea urchin species in the cameras’ field of view, size of sea urchins’ groups, movement patterns and the duration of the alarm responses of both sea urchin species. Results We showed that in the presence of kelp, M. nudus and S. intermedius exhibited both similar and different behavioral responses to hydrodynamics and predation threat. Under calm weather, movement patterns of both echinoids were similar but M. nudus exhibited the higher locomotion speed and distance traveled. Furthermore, S. intermedius but not M. nudus tended to group near the food substrate. The stormy weather caused a sharp decrease in movement activity followed by escape response in both echinoids. Six starfish species failed to predate on healthy sea urchins …
format: application/pdf
format: text/html
creator: Peter M. Zhadan
creator: Marina A. Vaschenko
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.8087
publisher: PeerJ Inc.
rights: © 2019 Zhadan and Vaschenko
abstract: Background In the predator–sea urchin–macrophyte trophic cascade, the ecological effect of sea urchins as grazers depends both on their density and the changes in foraging activity, which are influenced by various disturbing factors. However, the complete duration of the alarm reactions of echinoids has not been studied until now. Here, we tested a hypothesis that two cohabiting sea urchins, Mesocentrotus nudus and Strongylocentrotus intermedius, which differ morphologically, might display different behavioral responses to high hydrodynamic activity and predation. Methods We used continuous time-lapse video recording to clarify behavioral patterns of M. nudus and S. intermedius in presence of a large quantity of food (the kelp Saccharina japonica) but under different weather conditions and different types of predation threat: (1) calm weather conditions, (2) stormy weather conditions, (3) predation risk associated with the presence of several sea star species and (4) predation risk associated with an alarm stimulus (crushed conspecifics or heterospecifics). Three separate video recording experiments (134 days in total) were conducted under field conditions. Video recording analysis was performed to determine the number of specimens of each sea urchin species in the cameras’ field of view, size of sea urchins’ groups, movement patterns and the duration of the alarm responses of both sea urchin species. Results We showed that in the presence of kelp, M. nudus and S. intermedius exhibited both similar and different behavioral responses to hydrodynamics and predation threat. Under calm weather, movement patterns of both echinoids were similar but M. nudus exhibited the higher locomotion speed and distance traveled. Furthermore, S. intermedius but not M. nudus tended to group near the food substrate. The stormy weather caused a sharp decrease in movement activity followed by escape response in both echinoids. Six starfish species failed to predate on healthy sea urchins …
bibliographic citation: Zhadan et al. (2019) Long-term study of behaviors of two cohabiting sea urchin species, Mesocentrotus nudus and Strongylocentrotus intermedius, under conditions of high food quantity and predation risk in situ. PeerJ 7:e8087 https://doi.org/10.7717/peerj.8087
date submitted: 2019-06-05
date accepted: 2019-10-23
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhadan
  given name: Peter M.
author list: Agent
  family name: Vaschenko
  given name: Marina A.
doi: 10.7717/peerj.8087
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: © 2019 Zhadan and Vaschenko
attribution name: Zhadan and Vaschenko

Munidopsis species (Crustacea: Decapoda: Munidopsidae) from carcass falls in Weijia Guyot, West Pacific, with recognition of a new species based on integrative taxonomy
type: item
type: AcademicArticle
description: Several squat lobster specimens of the genus Munidopsis were collected from an artificially placed carcass fall (cow bones) on Weijia Guyot in the western Pacific Ocean. Based on morphological comparisons and molecular analysis, three specimens were confirmed as juveniles of M. albatrossae Pequegnat & Pequegnat, 1973, which represents the first record of this species in the western Pacific. The other specimens collected are newly described as Munidopsis spinifrons sp. nov., which is distinguished from the closely related species in having a spinose rostrum and basal lateral eyespine on the eyestalk. The M. albatrossae from Weijia Guyot exhibited very low genetic distances when compared with a conspecific sample from Monterey Bay, USA, and the closely related species M. aries (A. Milne Edwards, 1880) from the northeastern Atlantic. A phylogenetic tree based on the mtCOI gene shows M. spinifrons sp. nov. as sister to M. vrijenhoeki Jones & Macpherson, 2007 and M. nitida (A. Milne Edwards, 1880), although M. vrijenhoeki presents a complex relationship with other species in the clade. The systematic status of the new species and the closely related species are discussed.
format: application/pdf
format: text/html
creator: Dong Dong
creator: Peng Xu
creator: Xin-Zheng Li
creator: Chunsheng Wang
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.8089
publisher: PeerJ Inc.
rights: © 2019 Dong et al.
abstract: Several squat lobster specimens of the genus Munidopsis were collected from an artificially placed carcass fall (cow bones) on Weijia Guyot in the western Pacific Ocean. Based on morphological comparisons and molecular analysis, three specimens were confirmed as juveniles of M. albatrossae Pequegnat & Pequegnat, 1973, which represents the first record of this species in the western Pacific. The other specimens collected are newly described as Munidopsis spinifrons sp. nov., which is distinguished from the closely related species in having a spinose rostrum and basal lateral eyespine on the eyestalk. The M. albatrossae from Weijia Guyot exhibited very low genetic distances when compared with a conspecific sample from Monterey Bay, USA, and the closely related species M. aries (A. Milne Edwards, 1880) from the northeastern Atlantic. A phylogenetic tree based on the mtCOI gene shows M. spinifrons sp. nov. as sister to M. vrijenhoeki Jones & Macpherson, 2007 and M. nitida (A. Milne Edwards, 1880), although M. vrijenhoeki presents a complex relationship with other species in the clade. The systematic status of the new species and the closely related species are discussed.
bibliographic citation: Dong et al. (2019) Munidopsis species (Crustacea: Decapoda: Munidopsidae) from carcass falls in Weijia Guyot, West Pacific, with recognition of a new species based on integrative taxonomy. PeerJ 7:e8089 https://doi.org/10.7717/peerj.8089
date submitted: 2019-09-18
date accepted: 2019-10-23
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Dong
author list: Agent
  family name: Xu
  given name: Peng
author list: Agent
  family name: Li
  given name: Xin-Zheng
author list: Agent
  family name: Wang
  given name: Chunsheng
doi: 10.7717/peerj.8089
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: ©2019 Dong et al.
attribution name: Dong et al.

Comprehensive analysis of differentially expressed microRNAs and mRNAs in MDBK cells expressing bovine papillomavirus E5 oncogene
type: item
type: AcademicArticle
description: Delta bovine papillomaviruses (δBPVs) causes fibropapillomas or bladder cancer in cattle. E5 is the major oncogene of δBPVs; however, the influence that E5 oncogene has on host microRNA (miRNA) and mRNA expression profiles remains little elucidated. In the present study, small RNA sequencing and RNA sequencing were used to explore alterations in miRNAs and mRNAs in E5 over-expressing Madin-Darby bovine kidney (MDBK) cells compared with controls. In total, 77 miRNAs (including 30 bovine-derived miRNAs) and 223 genes were differentially expressed (DE) following E5 overexpression. The dysregulated genes were mainly involved in metabolic and biosynthetic processes. We constructed a potential miRNA-gene regulatory network from the differentially expressed genes (DEGs) and DE miRNAs. Finally, 22 DEGs and nine DE miRNAs were selected for RT-qPCR validation. Of these, downregulation of six miRNAs, bta-miR-34c, bta-miR-122, bta-miR-195, bta-miR-449b, bta-miR-2425-5p, and bta-miR-2428-3p were confirmed; In addition, upregulation of 16 genes, ACSS2, DDIT4, INHBE, INSIG1, PNRC1, PSAT1, PSPH, PYCR1, SC4MOL, SLC34A2, SCD, SPARC, IDI1, PCK2, HMGCS1, and SMIM14 and downregulation of two genes, BATF3 and WFDC2 were confirmed. Specially, bta-miR-34c and bta-miR-449b potentially regulated PYCR1 and DDIT4, which were involved in cancer progression and angiogenesis. Our study presented for the first time the comprehensive miRNA and mRNA alterations in MDBK cells expressing the BPV E5 oncogene, providing new insights into the tumorigenesis induced by BPV E5.
format: application/pdf
format: text/html
creator: Feng Pang
creator: Zhen Chen
creator: Chengqiang Wang
creator: Mengmeng Zhang
creator: Zhenxing Zhang
creator: Xiaohong Yang
creator: Yiying Zheng
creator: Ang Liu
creator: Yiwen Cheng
creator: Jie Chen
creator: Bin Li
creator: Li Du
creator: Fengyang Wang
subject: Bioinformatics
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.8098
publisher: PeerJ Inc.
rights: © 2019 Pang et al.
abstract: Delta bovine papillomaviruses (δBPVs) causes fibropapillomas or bladder cancer in cattle. E5 is the major oncogene of δBPVs; however, the influence that E5 oncogene has on host microRNA (miRNA) and mRNA expression profiles remains little elucidated. In the present study, small RNA sequencing and RNA sequencing were used to explore alterations in miRNAs and mRNAs in E5 over-expressing Madin-Darby bovine kidney (MDBK) cells compared with controls. In total, 77 miRNAs (including 30 bovine-derived miRNAs) and 223 genes were differentially expressed (DE) following E5 overexpression. The dysregulated genes were mainly involved in metabolic and biosynthetic processes. We constructed a potential miRNA-gene regulatory network from the differentially expressed genes (DEGs) and DE miRNAs. Finally, 22 DEGs and nine DE miRNAs were selected for RT-qPCR validation. Of these, downregulation of six miRNAs, bta-miR-34c, bta-miR-122, bta-miR-195, bta-miR-449b, bta-miR-2425-5p, and bta-miR-2428-3p were confirmed; In addition, upregulation of 16 genes, ACSS2, DDIT4, INHBE, INSIG1, PNRC1, PSAT1, PSPH, PYCR1, SC4MOL, SLC34A2, SCD, SPARC, IDI1, PCK2, HMGCS1, and SMIM14 and downregulation of two genes, BATF3 and WFDC2 were confirmed. Specially, bta-miR-34c and bta-miR-449b potentially regulated PYCR1 and DDIT4, which were involved in cancer progression and angiogenesis. Our study presented for the first time the comprehensive miRNA and mRNA alterations in MDBK cells expressing the BPV E5 oncogene, providing new insights into the tumorigenesis induced by BPV E5.
bibliographic citation: Pang et al. (2019) Comprehensive analysis of differentially expressed microRNAs and mRNAs in MDBK cells expressing bovine papillomavirus E5 oncogene. PeerJ 7:e8098 https://doi.org/10.7717/peerj.8098
date submitted: 2019-07-13
date accepted: 2019-10-24
issued: 2019-11-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pang
  given name: Feng
author list: Agent
  family name: Chen
  given name: Zhen
author list: Agent
  family name: Wang
  given name: Chengqiang
author list: Agent
  family name: Zhang
  given name: Mengmeng
author list: Agent
  family name: Zhang
  given name: Zhenxing
author list: Agent
  family name: Yang
  given name: Xiaohong
author list: Agent
  family name: Zheng
  given name: Yiying
author list: Agent
  family name: Liu
  given name: Ang
author list: Agent
  family name: Cheng
  given name: Yiwen
author list: Agent
  family name: Chen
  given name: Jie
author list: Agent
  family name: Li
  given name: Bin
author list: Agent
  family name: Du
  given name: Li
author list: Agent
  family name: Wang
  given name: Fengyang
doi: 10.7717/peerj.8098
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-22
copyright: © 2019 Pang et al.
attribution name: Pang et al.

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