PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications
items: Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research
items: Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference
items: Familiarity with visual stimuli boosts recency bias in macaques
items: Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry
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

Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications
type: item
type: AcademicArticle
description: The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.
format: application/pdf
format: text/html
creator: Siuli Mitra
creator: Vaishnavi Kunteepuram
creator: Klaus-Peter Koepfli
creator: Neha Mehra
creator: Wajeeda Tabasum
creator: Ara Sreenivas
creator: Ajay Gaur
subject: Conservation Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.8033
publisher: PeerJ Inc.
rights: © 2019 Mitra et al.
abstract: The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.
bibliographic citation: Mitra et al. (2019) Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications. PeerJ 7:e8033 https://doi.org/10.7717/peerj.8033
date submitted: 2019-02-07
date accepted: 2019-10-14
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mitra
  given name: Siuli
author list: Agent
  family name: Kunteepuram
  given name: Vaishnavi
author list: Agent
  family name: Koepfli
  given name: Klaus-Peter
author list: Agent
  family name: Mehra
  given name: Neha
author list: Agent
  family name: Tabasum
  given name: Wajeeda
author list: Agent
  family name: Sreenivas
  given name: Ara
author list: Agent
  family name: Gaur
  given name: Ajay
doi: 10.7717/peerj.8033
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Mitra et al.
attribution name: Mitra et al.

Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research
type: item
type: AcademicArticle
description: Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number o…
format: application/pdf
format: text/html
creator: Neil S. Cobb
creator: Lawrence F. Gall
creator: Jennifer M. Zaspel
creator: Nicolas J. Dowdy
creator: Lindsie M. McCabe
creator: Akito Y. Kawahara
subject: Biodiversity
subject: Entomology
description: doi:10.7717/peerj.8086
publisher: PeerJ Inc.
rights: © 2019 Cobb et al.
abstract: Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number o…
bibliographic citation: Cobb et al. (2019) Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research. PeerJ 7:e8086 https://doi.org/10.7717/peerj.8086
date submitted: 2019-08-02
date accepted: 2019-10-23
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cobb
  given name: Neil S.
author list: Agent
  family name: Gall
  given name: Lawrence F.
author list: Agent
  family name: Zaspel
  given name: Jennifer M.
author list: Agent
  family name: Dowdy
  given name: Nicolas J.
author list: Agent
  family name: McCabe
  given name: Lindsie M.
author list: Agent
  family name: Kawahara
  given name: Akito Y.
doi: 10.7717/peerj.8086
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Cobb et al.
attribution name: Cobb et al.

Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference
type: item
type: AcademicArticle
description: Background The exoskeleton of an insect could be an important factor in the success of its evolutionary process. This reaches its maximum expression in beetles, which constitute the most diversified animal taxon. The involvement in the management of environmental radiation could be one of the most important functions of the exoskeleton due to the passive contributions to the thermoregulation of body temperature. We study whether the elytra of two sympatric and closely related beetle species respond differentially to the radiation of distinct wavelengths in agreement with their ecological preferences. Methods Onthophagus coenobita (Herbst) and O. medius (Kugelaan) occupy different habitats and environmental conditions (shaded vs. unshaded from solar radiation). The potential adaptive variations to thermoregulation under these different ecological conditions were studied using the responses of their exoskeletons to radiation of different wavelengths (ultraviolet, visible and near-infrared). For these two species, the amounts of the three wavelengths that were reflected, transmitted or absorbed by the exoskeleton were measured using of a spectrophotometer. In addition, the darkness and thickness of the elytra were examined to determine whether these two features influence the management of radiation by the exoskeleton. Results Both species differ in the management of visible and near-infrared radiation. In agreement with habitat preferences, the species inhabiting shaded conditions would allow infrared and visible radiation to penetrate the elytra more easily to heat internal body parts, while the elytra of the heliophilous species would have increased absorbance of these same types of radiation. An increase in body size (and therefore in elytron thickness) and the quantity of dark spots may serve as barriers against exogenous heat gain. However, the maintenance of between-species differences independent of the effects of these two morphological features led us to susp…
format: application/pdf
format: text/html
creator: Eva Cuesta
creator: Jorge M. Lobo
subject: Biophysics
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.8104
publisher: PeerJ Inc.
rights: © 2019 Cuesta and Lobo
abstract: Background The exoskeleton of an insect could be an important factor in the success of its evolutionary process. This reaches its maximum expression in beetles, which constitute the most diversified animal taxon. The involvement in the management of environmental radiation could be one of the most important functions of the exoskeleton due to the passive contributions to the thermoregulation of body temperature. We study whether the elytra of two sympatric and closely related beetle species respond differentially to the radiation of distinct wavelengths in agreement with their ecological preferences. Methods Onthophagus coenobita (Herbst) and O. medius (Kugelaan) occupy different habitats and environmental conditions (shaded vs. unshaded from solar radiation). The potential adaptive variations to thermoregulation under these different ecological conditions were studied using the responses of their exoskeletons to radiation of different wavelengths (ultraviolet, visible and near-infrared). For these two species, the amounts of the three wavelengths that were reflected, transmitted or absorbed by the exoskeleton were measured using of a spectrophotometer. In addition, the darkness and thickness of the elytra were examined to determine whether these two features influence the management of radiation by the exoskeleton. Results Both species differ in the management of visible and near-infrared radiation. In agreement with habitat preferences, the species inhabiting shaded conditions would allow infrared and visible radiation to penetrate the elytra more easily to heat internal body parts, while the elytra of the heliophilous species would have increased absorbance of these same types of radiation. An increase in body size (and therefore in elytron thickness) and the quantity of dark spots may serve as barriers against exogenous heat gain. However, the maintenance of between-species differences independent of the effects of these two morphological features led us to susp…
bibliographic citation: Cuesta et al. (2019) Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference. PeerJ 7:e8104 https://doi.org/10.7717/peerj.8104
date submitted: 2019-06-14
date accepted: 2019-10-25
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cuesta
  given name: Eva
author list: Agent
  family name: Lobo
  given name: Jorge M.
doi: 10.7717/peerj.8104
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: © 2019 Cuesta and Lobo
attribution name: Cuesta and Lobo

Familiarity with visual stimuli boosts recency bias in macaques
type: item
type: AcademicArticle
description: To probe how non-human primates (NHPs) decode temporal dynamic stimuli, we used a two-alternative forced choice task (2AFC), where the cue was dynamic: a movie snippet drawn from an animation that transforms one image into another. When the cue was drawn from either the beginning or end of the animation, thus heavily weighted towards one (the target) of both images (the choice pair), then primates performed at high levels of accuracy. For a subset of trials, however, the cue was ambiguous, drawn from the middle of the animation, containing information that could be associated to either image. Those trials, rewarded randomly and independent of choice, offered an opportunity to study the strategy the animals used trying to decode the cue. Despite being ambiguous, the primates exhibited a clear strategy, suggesting they were not aware that reward was given non-differentially. More specifically, they relied more on information provided at the end than at the beginning of those cues, consistent with the recency effect reported by numerous serial position studies. Interestingly and counterintuitively, this effect became stronger for sessions where the primates were already familiar with the stimuli. In other words, despite having rehearsed with the same stimuli in a previous session, the animals relied even more on a decision strategy that did not yield any benefits during a previous session. In the discussion section we speculate on what might cause this behavioral shift towards stronger bias, as well as why this behavior shows similarities with a repetition bias in humans known as the illusory truth effect.
format: application/pdf
format: text/html
creator: Nicolas Brunet
creator: Bharathi Jagadeesh
subject: Animal Behavior
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.8105
publisher: PeerJ Inc.
rights: © 2019 Brunet and Jagadeesh
abstract: To probe how non-human primates (NHPs) decode temporal dynamic stimuli, we used a two-alternative forced choice task (2AFC), where the cue was dynamic: a movie snippet drawn from an animation that transforms one image into another. When the cue was drawn from either the beginning or end of the animation, thus heavily weighted towards one (the target) of both images (the choice pair), then primates performed at high levels of accuracy. For a subset of trials, however, the cue was ambiguous, drawn from the middle of the animation, containing information that could be associated to either image. Those trials, rewarded randomly and independent of choice, offered an opportunity to study the strategy the animals used trying to decode the cue. Despite being ambiguous, the primates exhibited a clear strategy, suggesting they were not aware that reward was given non-differentially. More specifically, they relied more on information provided at the end than at the beginning of those cues, consistent with the recency effect reported by numerous serial position studies. Interestingly and counterintuitively, this effect became stronger for sessions where the primates were already familiar with the stimuli. In other words, despite having rehearsed with the same stimuli in a previous session, the animals relied even more on a decision strategy that did not yield any benefits during a previous session. In the discussion section we speculate on what might cause this behavioral shift towards stronger bias, as well as why this behavior shows similarities with a repetition bias in humans known as the illusory truth effect.
bibliographic citation: Brunet et al. (2019) Familiarity with visual stimuli boosts recency bias in macaques. PeerJ 7:e8105 https://doi.org/10.7717/peerj.8105
date submitted: 2019-06-11
date accepted: 2019-10-26
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brunet
  given name: Nicolas
author list: Agent
  family name: Jagadeesh
  given name: Bharathi
doi: 10.7717/peerj.8105
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Brunet and Jagadeesh
attribution name: Brunet and Jagadeesh

Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry
type: item
type: AcademicArticle
description: Background The production of photocatalytic nanoparticles such as TiO2 has received increasing interest for biomedical and wastewater treatment applications. However, the conventional synthesis of such materials faces several environmental concerns. Methods In this work, green synthesis is addressed to prepare TiO2 nanoparticles at large scale using Lemongrass (Cymbopogon citratus) and titanium isopropoxide (TTIP). This process was designed and modeled using computer-aided process engineering (CAPE) in order to obtain the extended mass/energy balances, as well as operating parameters. Process simulation was carried out using the commercial software Aspen Plus®. In addition, energy performance of large-scale nanoparticle production was analyzed to identify alternatives for process improvement from an exergetic point of view. Results The production capacity of the plant was estimated as 1,496 t/y of TiO2 nanoparticles by the conversion of 32,675 t/y lemongrass and 5,724 t/y TTIP. Hence, the overall production yield is 0.26 kg TiO2/kg TTIP. Exergy analysis reported an overall exergy efficiency of 0.27% and an exergy loss of 159,824.80 MJ/h. These results suggest that such a process requires the implementation of process improvement strategies to reach a more sustainable design from energy and thermodynamic viewpoints.
format: application/pdf
format: text/html
creator: Samir Meramo-Hurtado
creator: Kariana Moreno-Sader
creator: Ángel D. González-Delgado
subject: Green Chemistry
description: doi:10.7717/peerj.8113
publisher: PeerJ Inc.
rights: © 2019 Meramo-Hurtado et al.
abstract: Background The production of photocatalytic nanoparticles such as TiO2 has received increasing interest for biomedical and wastewater treatment applications. However, the conventional synthesis of such materials faces several environmental concerns. Methods In this work, green synthesis is addressed to prepare TiO2 nanoparticles at large scale using Lemongrass (Cymbopogon citratus) and titanium isopropoxide (TTIP). This process was designed and modeled using computer-aided process engineering (CAPE) in order to obtain the extended mass/energy balances, as well as operating parameters. Process simulation was carried out using the commercial software Aspen Plus®. In addition, energy performance of large-scale nanoparticle production was analyzed to identify alternatives for process improvement from an exergetic point of view. Results The production capacity of the plant was estimated as 1,496 t/y of TiO2 nanoparticles by the conversion of 32,675 t/y lemongrass and 5,724 t/y TTIP. Hence, the overall production yield is 0.26 kg TiO2/kg TTIP. Exergy analysis reported an overall exergy efficiency of 0.27% and an exergy loss of 159,824.80 MJ/h. These results suggest that such a process requires the implementation of process improvement strategies to reach a more sustainable design from energy and thermodynamic viewpoints.
bibliographic citation: Meramo-Hurtado et al. (2019) Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry. PeerJ 7:e8113 https://doi.org/10.7717/peerj.8113
date submitted: 2019-05-21
date accepted: 2019-10-28
issued: 2019-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meramo-Hurtado
  given name: Samir
author list: Agent
  family name: Moreno-Sader
  given name: Kariana
author list: Agent
  family name: González-Delgado
  given name: Ángel D.
doi: 10.7717/peerj.8113
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-11-25
copyright: ©2019 Meramo-Hurtado et al.
attribution name: Meramo-Hurtado et al.

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.

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