PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Primate occurrence across a human-impacted landscape in Guinea-Bissau and neighbouring regions in West Africa: using a systematic literature review to highlight the next conservation steps
items: Impact of crop residue management on crop production and soil chemistry after seven years of crop rotation in temperate climate, loamy soils
items: Predicting the potential distributions of the invasive cycad scale Aulacaspis yasumatsui (Hemiptera: Diaspididae) under different climate change scenarios and the implications for management
items: Taxonomic monograph of Oxygyne (Thismiaceae), rare achlorophyllous mycoheterotrophs with strongly disjunct distribution
items: Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota
items: Evidence-based economic analysis demonstrates that ecosystem service benefits of water hyacinth management greatly exceed research and control costs
items: Immunogenicity evaluation of MS2 phage-mediated chimeric nanoparticle displaying an immunodominant B cell epitope of foot-and-mouth disease virus
items: Sample entropy analysis for the estimating depth of anaesthesia through human EEG signal at different levels of unconsciousness during surgeries
items: An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region
items: Endozoochory by mallard in New Zealand: what seeds are dispersed and how far?

Primate occurrence across a human-impacted landscape in Guinea-Bissau and neighbouring regions in West Africa: using a systematic literature review to highlight the next conservation steps
type: item
type: AcademicArticle
description: Background West African landscapes are largely characterised by complex agroforest mosaics. Although the West African forests are considered a nonhuman primate hotspot, knowledge on the distribution of many species is often lacking and out-of-date. Considering the fast-changing nature of the landscapes in this region, up-to-date information on primate occurrence is urgently needed, particularly of taxa such as colobines, which may be more sensitive to habitat modification than others. Understanding wildlife occurrence and mechanisms of persistence in these human-dominated landscapes is fundamental for developing effective conservation strategies. Methods In this paper, we aim to review current knowledge on the distribution of three threatened primates in Guinea-Bissau and neighbouring regions, highlighting research gaps and identifying priority research and conservation action. We conducted a systematic literature review of primate studies from 1976 to 2016 in Guinea-Bissau, southern Senegal and western Guinea (Boké Region). We mapped historical observation records of chimpanzee (Pan troglodytes verus), Temminck’s red colobus (Pilicolobus badius temminckii) and king colobus (Colobus polykomos), including our preliminary survey data from Dulombi, a newly established National Park (NP) in Guinea-Bissau. Results We found 151 documents, including 87 journal articles, that contained field data on primates in this region. In Guinea-Bissau, nearly all studies focussed south of the Corubal River, including mainly Cantanhez, Cufada, and Boé NP’s. In Senegal, most of the data came from Fongoli and Niokolo-Koba NP. In Boké (Guinea) studies are few, with the most recent data coming from Sangarédi. In Dulombi NP we recorded eight primate species, including chimpanzees, red colobus and king colobus. Across the selected region, chimpanzees, red colobus and king colobus were reported in eleven, twelve and seven protected areas, respectively. Discussion Our study demonstrates large …
format: application/pdf
format: text/html
creator: Elena Bersacola
creator: Joana Bessa
creator: Amélia Frazão-Moreira
creator: Dora Biro
creator: Cláudia Sousa
creator: Kimberley Jane Hockings
subject: Anthropology
subject: Conservation Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.4847
publisher: PeerJ Inc.
rights: © 2018 Bersacola et al.
abstract: Background West African landscapes are largely characterised by complex agroforest mosaics. Although the West African forests are considered a nonhuman primate hotspot, knowledge on the distribution of many species is often lacking and out-of-date. Considering the fast-changing nature of the landscapes in this region, up-to-date information on primate occurrence is urgently needed, particularly of taxa such as colobines, which may be more sensitive to habitat modification than others. Understanding wildlife occurrence and mechanisms of persistence in these human-dominated landscapes is fundamental for developing effective conservation strategies. Methods In this paper, we aim to review current knowledge on the distribution of three threatened primates in Guinea-Bissau and neighbouring regions, highlighting research gaps and identifying priority research and conservation action. We conducted a systematic literature review of primate studies from 1976 to 2016 in Guinea-Bissau, southern Senegal and western Guinea (Boké Region). We mapped historical observation records of chimpanzee (Pan troglodytes verus), Temminck’s red colobus (Pilicolobus badius temminckii) and king colobus (Colobus polykomos), including our preliminary survey data from Dulombi, a newly established National Park (NP) in Guinea-Bissau. Results We found 151 documents, including 87 journal articles, that contained field data on primates in this region. In Guinea-Bissau, nearly all studies focussed south of the Corubal River, including mainly Cantanhez, Cufada, and Boé NP’s. In Senegal, most of the data came from Fongoli and Niokolo-Koba NP. In Boké (Guinea) studies are few, with the most recent data coming from Sangarédi. In Dulombi NP we recorded eight primate species, including chimpanzees, red colobus and king colobus. Across the selected region, chimpanzees, red colobus and king colobus were reported in eleven, twelve and seven protected areas, respectively. Discussion Our study demonstrates large …
bibliographic citation: Bersacola et al. (2018) Primate occurrence across a human-impacted landscape in Guinea-Bissau and neighbouring regions in West Africa: using a systematic literature review to highlight the next conservation steps. PeerJ 6:e4847 https://doi.org/10.7717/peerj.4847
date submitted: 2018-03-02
date accepted: 2018-05-06
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bersacola
  given name: Elena
author list: Agent
  family name: Bessa
  given name: Joana
author list: Agent
  family name: Frazão-Moreira
  given name: Amélia
author list: Agent
  family name: Biro
  given name: Dora
author list: Agent
  family name: Sousa
  given name: Cláudia
author list: Agent
  family name: Hockings
  given name: Kimberley Jane
doi: 10.7717/peerj.4847
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: ©2018 Bersacola et al.
attribution name: Bersacola et al.

Impact of crop residue management on crop production and soil chemistry after seven years of crop rotation in temperate climate, loamy soils
type: item
type: AcademicArticle
description: Society is increasingly demanding a more sustainable management of agro-ecosystems in a context of climate change and an ever growing global population. The fate of crop residues is one of the important management aspects under debate, since it represents an unneglectable quantity of organic matter which can be kept in or removed from the agro-ecosystem. The topic of residue management is not new, but the need for global conclusion on the impact of crop residue management on the agro-ecosystem linked to local pedo-climatic conditions has become apparent with an increasing amount of studies showing a diversity of conclusions. This study specifically focusses on temperate climate and loamy soil using a seven-year data set. Between 2008 and 2016, we compared four contrasting residue management strategies differing in the amount of crop residues returned to the soil (incorporation vs. exportation of residues) and in the type of tillage (reduced tillage (10 cm depth) vs. conventional tillage (ploughing at 25 cm depth)) in a field experiment. We assessed the impact of the crop residue management on crop production (three crops—winter wheat, faba bean and maize—cultivated over six cropping seasons), soil organic carbon content, nitrate ( ${\mathrm{NO}}_{3}^{-}$ NO 3 − ), phosphorus (P) and potassium (K) soil content and uptake by the crops. The main differences came primarily from the tillage practice and less from the restitution or removal of residues. All years and crops combined, conventional tillage resulted in a yield advantage of 3.4% as compared to reduced tillage, which can be partly explained by a lower germination rate observed under reduced tillage, especially during drier years. On average, only small differences were observed for total organic carbon (TOC) content of the soil, but reduced tillage resulted in a very clear stratification of TOC and also of P and K content as compared to conventional tillage. We observed no effect of residue management on the ${…
format: application/pdf
format: text/html
creator: Marie-Pierre Hiel
creator: Sophie Barbieux
creator: Jérôme Pierreux
creator: Claire Olivier
creator: Guillaume Lobet
creator: Christian Roisin
creator: Sarah Garré
creator: Gilles Colinet
creator: Bernard Bodson
creator: Benjamin Dumont
subject: Agricultural Science
subject: Soil Science
subject: Natural Resource Management
description: doi:10.7717/peerj.4836
publisher: PeerJ Inc.
rights: © 2018 Hiel et al.
abstract: Society is increasingly demanding a more sustainable management of agro-ecosystems in a context of climate change and an ever growing global population. The fate of crop residues is one of the important management aspects under debate, since it represents an unneglectable quantity of organic matter which can be kept in or removed from the agro-ecosystem. The topic of residue management is not new, but the need for global conclusion on the impact of crop residue management on the agro-ecosystem linked to local pedo-climatic conditions has become apparent with an increasing amount of studies showing a diversity of conclusions. This study specifically focusses on temperate climate and loamy soil using a seven-year data set. Between 2008 and 2016, we compared four contrasting residue management strategies differing in the amount of crop residues returned to the soil (incorporation vs. exportation of residues) and in the type of tillage (reduced tillage (10 cm depth) vs. conventional tillage (ploughing at 25 cm depth)) in a field experiment. We assessed the impact of the crop residue management on crop production (three crops—winter wheat, faba bean and maize—cultivated over six cropping seasons), soil organic carbon content, nitrate ( ${\mathrm{NO}}_{3}^{-}$ NO 3 − ), phosphorus (P) and potassium (K) soil content and uptake by the crops. The main differences came primarily from the tillage practice and less from the restitution or removal of residues. All years and crops combined, conventional tillage resulted in a yield advantage of 3.4% as compared to reduced tillage, which can be partly explained by a lower germination rate observed under reduced tillage, especially during drier years. On average, only small differences were observed for total organic carbon (TOC) content of the soil, but reduced tillage resulted in a very clear stratification of TOC and also of P and K content as compared to conventional tillage. We observed no effect of residue management on the ${…
bibliographic citation: Hiel et al. (2018) Impact of crop residue management on crop production and soil chemistry after seven years of crop rotation in temperate climate, loamy soils. PeerJ 6:e4836 https://doi.org/10.7717/peerj.4836
date submitted: 2017-10-03
date accepted: 2018-05-04
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hiel
  given name: Marie-Pierre
author list: Agent
  family name: Barbieux
  given name: Sophie
author list: Agent
  family name: Pierreux
  given name: Jérôme
author list: Agent
  family name: Olivier
  given name: Claire
author list: Agent
  family name: Lobet
  given name: Guillaume
author list: Agent
  family name: Roisin
  given name: Christian
author list: Agent
  family name: Garré
  given name: Sarah
author list: Agent
  family name: Colinet
  given name: Gilles
author list: Agent
  family name: Bodson
  given name: Bernard
author list: Agent
  family name: Dumont
  given name: Benjamin
doi: 10.7717/peerj.4836
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: ©2018 Hiel et al.
attribution name: Hiel et al.

Predicting the potential distributions of the invasive cycad scale Aulacaspis yasumatsui (Hemiptera: Diaspididae) under different climate change scenarios and the implications for management
type: item
type: AcademicArticle
description: Cycads are an ancient group of gymnosperms that are popular as landscaping plants, though nearly all of them are threatened or endangered in the wild. The cycad aulacaspis scale (CAS), Aulacaspis yasumatsui Takagi (Hemiptera: Diaspididae), has become one of the most serious pests of cycads in recent years; however, the potential distribution range and the management approach for this pest are unclear. A potential risk map of cycad aulacaspis scale was created based on occurrence data under different climatic conditions and topology factors in this study. Furthermore, the future potential distributions of CAS were projected for the periods 2050s and 2070s under three different climate change scenarios (GFDL-CM3, HADGEM2-AO and MIROC5) described in the Special Report on Emissions Scenarios of the IPCC (Intergovernmental Panel on Climate Change). The model suggested high environmental suitability for the continents of Asia and North America, where the species has already been recorded. The potential distribution expansions or reductions were also predicted under different climate change conditions. Temperature of Driest Quarter (Bio9) was the most important factor, explaining 48.1% of the distribution of the species. The results also suggested that highly suitable habitat for CAS would exist in the study area if the mean temperature of 15–20 °C in the driest quarter and a mean temperature of 25–28 °C the wettest quarter. This research provides a theoretical reference framework for developing policy to manage and control this invasive pest.
format: application/pdf
format: text/html
creator: Jiufeng Wei
creator: Qing Zhao
creator: Wanqing Zhao
creator: Hufang Zhang
subject: Agricultural Science
subject: Entomology
subject: Zoology
subject: Climate Change Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.4832
publisher: PeerJ Inc.
rights: © 2018 Wei et al.
abstract: Cycads are an ancient group of gymnosperms that are popular as landscaping plants, though nearly all of them are threatened or endangered in the wild. The cycad aulacaspis scale (CAS), Aulacaspis yasumatsui Takagi (Hemiptera: Diaspididae), has become one of the most serious pests of cycads in recent years; however, the potential distribution range and the management approach for this pest are unclear. A potential risk map of cycad aulacaspis scale was created based on occurrence data under different climatic conditions and topology factors in this study. Furthermore, the future potential distributions of CAS were projected for the periods 2050s and 2070s under three different climate change scenarios (GFDL-CM3, HADGEM2-AO and MIROC5) described in the Special Report on Emissions Scenarios of the IPCC (Intergovernmental Panel on Climate Change). The model suggested high environmental suitability for the continents of Asia and North America, where the species has already been recorded. The potential distribution expansions or reductions were also predicted under different climate change conditions. Temperature of Driest Quarter (Bio9) was the most important factor, explaining 48.1% of the distribution of the species. The results also suggested that highly suitable habitat for CAS would exist in the study area if the mean temperature of 15–20 °C in the driest quarter and a mean temperature of 25–28 °C the wettest quarter. This research provides a theoretical reference framework for developing policy to manage and control this invasive pest.
bibliographic citation: Wei et al. (2018) Predicting the potential distributions of the invasive cycad scale Aulacaspis yasumatsui (Hemiptera: Diaspididae) under different climate change scenarios and the implications for management. PeerJ 6:e4832 https://doi.org/10.7717/peerj.4832
date submitted: 2017-11-24
date accepted: 2018-05-03
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Jiufeng
author list: Agent
  family name: Zhao
  given name: Qing
author list: Agent
  family name: Zhao
  given name: Wanqing
author list: Agent
  family name: Zhang
  given name: Hufang
doi: 10.7717/peerj.4832
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: ©2018 Wei et al.
attribution name: Wei et al.

Taxonomic monograph of Oxygyne (Thismiaceae), rare achlorophyllous mycoheterotrophs with strongly disjunct distribution
type: item
type: AcademicArticle
description: Oxygyne Schltr. (Thismiaceae) is a rare and little-known genus of achlorophyllous mycoheterotrophic perennial herbs with one of the most remarkable distributions of all angiosperm plant genera globally, being disjunct between Japan and West–Central Africa. Each species is known only from a single location, and in most cases from a single specimen. This monographic study names, describes and maps two new species, Oxygyne duncanii Cheek from cloud forest in SW Region Cameroon and O. frankei Cheek from gallery forest in the Central African Republic, representing the first new Oxygyne species described from Africa in 112 years, and raising the number of described Oxygyne species from four to six. Oxygyne duncanii is remarkable for sharing more morphological characters with two of the three Japanese species (O. hyodoi C.Abe & Akasawa, O. shinzatoi (H. Ohashi) Tsukaya) than with the geographically much closer type species of the genus, O. triandra from Mt Cameroon. Based mainly on herbarium specimens and field observations made in Cameroon and Japan during a series of botanical surveys, we provide descriptions, synonymy, mapping and extinction risk assessments for each species of Oxygyne, together with keys to the genera of Thismiaceae and the species of Oxygyne. The subterranean structures of African Oxygyne are described for the first time, and found to be consistent with those of the Japanese species. We review and reject an earlier proposal that the Japanese species should be segregated from the African species as a separate genus, Saionia Hatus. The only character that separates the two disjunct species groups is now flower colour: blue or partly-blue in the Japanese species compared with orange-brown in the African species. Studies of the pollination biology and mycorrhizal partners of Oxygyne are still lacking. Two of the six species, O. triandra Schltr. and O. hyodoi, appear to be extinct, and the remaining four are assessed as Critically Endangered using the IUCN…
format: application/pdf
format: text/html
creator: Martin Cheek
creator: Hirokazu Tsukaya
creator: Paula J. Rudall
creator: Kenji Suetsugu
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.4828
publisher: PeerJ Inc.
rights: © 2018 Cheek et al.
abstract: Oxygyne Schltr. (Thismiaceae) is a rare and little-known genus of achlorophyllous mycoheterotrophic perennial herbs with one of the most remarkable distributions of all angiosperm plant genera globally, being disjunct between Japan and West–Central Africa. Each species is known only from a single location, and in most cases from a single specimen. This monographic study names, describes and maps two new species, Oxygyne duncanii Cheek from cloud forest in SW Region Cameroon and O. frankei Cheek from gallery forest in the Central African Republic, representing the first new Oxygyne species described from Africa in 112 years, and raising the number of described Oxygyne species from four to six. Oxygyne duncanii is remarkable for sharing more morphological characters with two of the three Japanese species (O. hyodoi C.Abe & Akasawa, O. shinzatoi (H. Ohashi) Tsukaya) than with the geographically much closer type species of the genus, O. triandra from Mt Cameroon. Based mainly on herbarium specimens and field observations made in Cameroon and Japan during a series of botanical surveys, we provide descriptions, synonymy, mapping and extinction risk assessments for each species of Oxygyne, together with keys to the genera of Thismiaceae and the species of Oxygyne. The subterranean structures of African Oxygyne are described for the first time, and found to be consistent with those of the Japanese species. We review and reject an earlier proposal that the Japanese species should be segregated from the African species as a separate genus, Saionia Hatus. The only character that separates the two disjunct species groups is now flower colour: blue or partly-blue in the Japanese species compared with orange-brown in the African species. Studies of the pollination biology and mycorrhizal partners of Oxygyne are still lacking. Two of the six species, O. triandra Schltr. and O. hyodoi, appear to be extinct, and the remaining four are assessed as Critically Endangered using the IUCN…
bibliographic citation: Cheek et al. (2018) Taxonomic monograph of Oxygyne (Thismiaceae), rare achlorophyllous mycoheterotrophs with strongly disjunct distribution. PeerJ 6:e4828 https://doi.org/10.7717/peerj.4828
date submitted: 2017-12-22
date accepted: 2018-05-02
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheek
  given name: Martin
author list: Agent
  family name: Tsukaya
  given name: Hirokazu
author list: Agent
  family name: Rudall
  given name: Paula J.
author list: Agent
  family name: Suetsugu
  given name: Kenji
doi: 10.7717/peerj.4828
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: ©2018 Cheek et al.
attribution name: Cheek et al.

Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota
type: item
type: AcademicArticle
description: Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25 °C, 4 °C, and −80 °C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on Days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value = 6.87, DF = 3, P < 0.001), storage temperature (F-value=1.77, DF = 3, P = 0.037), and duration of sample storage (F-value = 3.68, DF = 3, P < 0.001). Changes in bacterial composition were observed in samples stored in −80 °C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF = 8.57, P < 0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome…
format: application/pdf
format: text/html
creator: Katti R. Horng
creator: Holly H. Ganz
creator: Jonathan A. Eisen
creator: Stanley L. Marks
subject: Biodiversity
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.4827
publisher: PeerJ Inc.
rights: © 2018 Horng et al.
abstract: Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25 °C, 4 °C, and −80 °C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on Days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value = 6.87, DF = 3, P < 0.001), storage temperature (F-value=1.77, DF = 3, P = 0.037), and duration of sample storage (F-value = 3.68, DF = 3, P < 0.001). Changes in bacterial composition were observed in samples stored in −80 °C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF = 8.57, P < 0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome…
bibliographic citation: Horng et al. (2018) Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota. PeerJ 6:e4827 https://doi.org/10.7717/peerj.4827
date submitted: 2017-10-24
date accepted: 2018-04-30
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Horng
  given name: Katti R.
author list: Agent
  family name: Ganz
  given name: Holly H.
author list: Agent
  family name: Eisen
  given name: Jonathan A.
author list: Agent
  family name: Marks
  given name: Stanley L.
doi: 10.7717/peerj.4827
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: ©2018 Horng et al.
attribution name: Horng et al.

Evidence-based economic analysis demonstrates that ecosystem service benefits of water hyacinth management greatly exceed research and control costs
type: item
type: AcademicArticle
description: Invasive species management can be a victim of its own success when decades of effective control cause memories of past harm to fade and raise questions of whether programs should continue. Economic analysis can be used to assess the efficiency of investing in invasive species control by comparing ecosystem service benefits to program costs, but only if appropriate data exist. We used a case study of water hyacinth (Eichhornia crassipes (Mart.) Solms), a nuisance floating aquatic plant, in Louisiana to demonstrate how comprehensive record-keeping supports economic analysis. Using long-term data sets, we developed empirical and spatio-temporal simulation models of intermediate complexity to project invasive species growth for control and no-control scenarios. For Louisiana, we estimated that peak plant cover would be 76% higher without the substantial growth rate suppression (84% reduction) that appeared due primarily to biological control agents. Our economic analysis revealed that combined biological and herbicide control programs, monitored over an unusually long time period (1975–2013), generated a benefit-cost ratio of about 34:1 derived from the relatively modest costs of $124 million ($2013) compared to the $4.2 billion ($2013) in benefits to anglers, waterfowl hunters, boating-dependent businesses, and water treatment facilities over the 38-year analysis period. This work adds to the literature by: (1) providing evidence of the effectiveness of water hyacinth biological control; (2) demonstrating use of parsimonious spatio-temporal models to estimate benefits of invasive species control; and (3) incorporating activity substitution into economic benefit transfer to avoid overstating benefits. Our study suggests that robust and cost-effective economic analysis is enabled by good record keeping and generalizable models that can demonstrate management effectiveness and promote social efficiency of invasive species control.
format: application/pdf
format: text/html
creator: Lisa A. Wainger
creator: Nathan E. Harms
creator: Cedric Magen
creator: Dong Liang
creator: Genevieve M. Nesslage
creator: Anna M. McMurray
creator: Al F. Cofrancesco
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
description: doi:10.7717/peerj.4824
publisher: PeerJ Inc.
rights: © 2018
abstract: Invasive species management can be a victim of its own success when decades of effective control cause memories of past harm to fade and raise questions of whether programs should continue. Economic analysis can be used to assess the efficiency of investing in invasive species control by comparing ecosystem service benefits to program costs, but only if appropriate data exist. We used a case study of water hyacinth (Eichhornia crassipes (Mart.) Solms), a nuisance floating aquatic plant, in Louisiana to demonstrate how comprehensive record-keeping supports economic analysis. Using long-term data sets, we developed empirical and spatio-temporal simulation models of intermediate complexity to project invasive species growth for control and no-control scenarios. For Louisiana, we estimated that peak plant cover would be 76% higher without the substantial growth rate suppression (84% reduction) that appeared due primarily to biological control agents. Our economic analysis revealed that combined biological and herbicide control programs, monitored over an unusually long time period (1975–2013), generated a benefit-cost ratio of about 34:1 derived from the relatively modest costs of $124 million ($2013) compared to the $4.2 billion ($2013) in benefits to anglers, waterfowl hunters, boating-dependent businesses, and water treatment facilities over the 38-year analysis period. This work adds to the literature by: (1) providing evidence of the effectiveness of water hyacinth biological control; (2) demonstrating use of parsimonious spatio-temporal models to estimate benefits of invasive species control; and (3) incorporating activity substitution into economic benefit transfer to avoid overstating benefits. Our study suggests that robust and cost-effective economic analysis is enabled by good record keeping and generalizable models that can demonstrate management effectiveness and promote social efficiency of invasive species control.
bibliographic citation: Wainger et al. (2018) Evidence-based economic analysis demonstrates that ecosystem service benefits of water hyacinth management greatly exceed research and control costs. PeerJ 6:e4824 https://doi.org/10.7717/peerj.4824
date submitted: 2018-03-02
date accepted: 2018-05-02
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Wainger
  given name: Lisa A.
author list: Agent
  family name: Harms
  given name: Nathan E.
author list: Agent
  family name: Magen
  given name: Cedric
author list: Agent
  family name: Liang
  given name: Dong
author list: Agent
  family name: Nesslage
  given name: Genevieve M.
author list: Agent
  family name: McMurray
  given name: Anna M.
author list: Agent
  family name: Cofrancesco
  given name: Al F.
doi: 10.7717/peerj.4824
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23

Immunogenicity evaluation of MS2 phage-mediated chimeric nanoparticle displaying an immunodominant B cell epitope of foot-and-mouth disease virus
type: item
type: AcademicArticle
description: Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals that has caused tremendous economic losses worldwide. In this study, we designed a chimeric nanoparticles (CNPs) vaccine that displays the predominant epitope of the serotype O foot-and-mouth disease virus (FMDV) VP1 131-160 on the surface of MS2 phage. The recombinant protein was expressed in Escherichia Coli and can self-assemble into CNPs with diameter at 25–30 nm in vitro. A tandem repeat peptide epitopes (TRE) was prepared as control. Mice were immunized with CNPs, TRE and commercialized synthetic peptide vaccines (PepVac), respectively. The ELISA results showed that CNPs stimulated a little higher specific antibody levels to PepVac, but was significantly higher than the TRE groups. Moreover, the results from specific IFN-γ responses and lymphocyte proliferation test indicated that CNP immunized mice exhibited significantly enhanced cellular immune response compared to TRE. These results suggested that the CNPs constructed in current study could be a potential alternative vaccine in future FMDV control.
format: application/pdf
format: text/html
creator: Guoqiang Wang
creator: Yunchao Liu
creator: Hua Feng
creator: Yumei Chen
creator: Suzhen Yang
creator: Qiang Wei
creator: Juan Wang
creator: Dongmin Liu
creator: Gaiping Zhang
subject: Bioengineering
subject: Biotechnology
subject: Immunology
description: doi:10.7717/peerj.4823
publisher: PeerJ Inc.
rights: © 2018 Wang et al.
abstract: Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals that has caused tremendous economic losses worldwide. In this study, we designed a chimeric nanoparticles (CNPs) vaccine that displays the predominant epitope of the serotype O foot-and-mouth disease virus (FMDV) VP1 131-160 on the surface of MS2 phage. The recombinant protein was expressed in Escherichia Coli and can self-assemble into CNPs with diameter at 25–30 nm in vitro. A tandem repeat peptide epitopes (TRE) was prepared as control. Mice were immunized with CNPs, TRE and commercialized synthetic peptide vaccines (PepVac), respectively. The ELISA results showed that CNPs stimulated a little higher specific antibody levels to PepVac, but was significantly higher than the TRE groups. Moreover, the results from specific IFN-γ responses and lymphocyte proliferation test indicated that CNP immunized mice exhibited significantly enhanced cellular immune response compared to TRE. These results suggested that the CNPs constructed in current study could be a potential alternative vaccine in future FMDV control.
bibliographic citation: Wang et al. (2018) Immunogenicity evaluation of MS2 phage-mediated chimeric nanoparticle displaying an immunodominant B cell epitope of foot-and-mouth disease virus. PeerJ 6:e4823 https://doi.org/10.7717/peerj.4823
date submitted: 2018-01-16
date accepted: 2018-05-02
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Guoqiang
author list: Agent
  family name: Liu
  given name: Yunchao
author list: Agent
  family name: Feng
  given name: Hua
author list: Agent
  family name: Chen
  given name: Yumei
author list: Agent
  family name: Yang
  given name: Suzhen
author list: Agent
  family name: Wei
  given name: Qiang
author list: Agent
  family name: Wang
  given name: Juan
author list: Agent
  family name: Liu
  given name: Dongmin
author list: Agent
  family name: Zhang
  given name: Gaiping
doi: 10.7717/peerj.4823
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: ©2018 Wang et al.
attribution name: Wang et al.

Sample entropy analysis for the estimating depth of anaesthesia through human EEG signal at different levels of unconsciousness during surgeries
type: item
type: AcademicArticle
description: Estimating the depth of anaesthesia (DoA) in operations has always been a challenging issue due to the underlying complexity of the brain mechanisms. Electroencephalogram (EEG) signals are undoubtedly the most widely used signals for measuring DoA. In this paper, a novel EEG-based index is proposed to evaluate DoA for 24 patients receiving general anaesthesia with different levels of unconsciousness. Sample Entropy (SampEn) algorithm was utilised in order to acquire the chaotic features of the signals. After calculating the SampEn from the EEG signals, Random Forest was utilised for developing learning regression models with Bispectral index (BIS) as the target. Correlation coefficient, mean absolute error, and area under the curve (AUC) were used to verify the perioperative performance of the proposed method. Validation comparisons with typical nonstationary signal analysis methods (i.e., recurrence analysis and permutation entropy) and regression methods (i.e., neural network and support vector machine) were conducted. To further verify the accuracy and validity of the proposed methodology, the data is divided into four unconsciousness-level groups on the basis of BIS levels. Subsequently, analysis of variance (ANOVA) was applied to the corresponding index (i.e., regression output). Results indicate that the correlation coefficient improved to 0.72 ± 0.09 after filtering and to 0.90 ± 0.05 after regression from the initial values of 0.51 ± 0.17. Similarly, the final mean absolute error dramatically declined to 5.22 ± 2.12. In addition, the ultimate AUC increased to 0.98 ± 0.02, and the ANOVA analysis indicates that each of the four groups of different anaesthetic levels demonstrated significant difference from the nearest levels. Furthermore, the Random Forest output was extensively linear in relation to BIS, thus with better DoA prediction accuracy. In conclusion, the proposed method provides a concrete basis for monitoring patients’ anaesthetic level during surg…
format: application/pdf
format: text/html
creator: Quan Liu
creator: Li Ma
creator: Shou-Zen Fan
creator: Maysam F. Abbod
creator: Jiann-Shing Shieh
subject: Anesthesiology and Pain Management
subject: Statistics
subject: Computational Science
description: doi:10.7717/peerj.4817
publisher: PeerJ Inc.
rights: © 2018 Liu et al.
abstract: Estimating the depth of anaesthesia (DoA) in operations has always been a challenging issue due to the underlying complexity of the brain mechanisms. Electroencephalogram (EEG) signals are undoubtedly the most widely used signals for measuring DoA. In this paper, a novel EEG-based index is proposed to evaluate DoA for 24 patients receiving general anaesthesia with different levels of unconsciousness. Sample Entropy (SampEn) algorithm was utilised in order to acquire the chaotic features of the signals. After calculating the SampEn from the EEG signals, Random Forest was utilised for developing learning regression models with Bispectral index (BIS) as the target. Correlation coefficient, mean absolute error, and area under the curve (AUC) were used to verify the perioperative performance of the proposed method. Validation comparisons with typical nonstationary signal analysis methods (i.e., recurrence analysis and permutation entropy) and regression methods (i.e., neural network and support vector machine) were conducted. To further verify the accuracy and validity of the proposed methodology, the data is divided into four unconsciousness-level groups on the basis of BIS levels. Subsequently, analysis of variance (ANOVA) was applied to the corresponding index (i.e., regression output). Results indicate that the correlation coefficient improved to 0.72 ± 0.09 after filtering and to 0.90 ± 0.05 after regression from the initial values of 0.51 ± 0.17. Similarly, the final mean absolute error dramatically declined to 5.22 ± 2.12. In addition, the ultimate AUC increased to 0.98 ± 0.02, and the ANOVA analysis indicates that each of the four groups of different anaesthetic levels demonstrated significant difference from the nearest levels. Furthermore, the Random Forest output was extensively linear in relation to BIS, thus with better DoA prediction accuracy. In conclusion, the proposed method provides a concrete basis for monitoring patients’ anaesthetic level during surg…
bibliographic citation: Liu et al. (2018) Sample entropy analysis for the estimating depth of anaesthesia through human EEG signal at different levels of unconsciousness during surgeries. PeerJ 6:e4817 https://doi.org/10.7717/peerj.4817
date submitted: 2017-11-15
date accepted: 2018-05-01
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Quan
author list: Agent
  family name: Ma
  given name: Li
author list: Agent
  family name: Fan
  given name: Shou-Zen
author list: Agent
  family name: Abbod
  given name: Maysam F.
author list: Agent
  family name: Shieh
  given name: Jiann-Shing
doi: 10.7717/peerj.4817
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: ©2018 Liu et al.
attribution name: Liu et al.

An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region
type: item
type: AcademicArticle
description: The Internal Transcribed Spacer 2 (ITS2) rRNA gene is a commonly targeted genetic marker to assess diversity of Symbiodinium, a dinoflagellate genus of algal endosymbionts that is pervasively associated with marine invertebrates, and notably reef-building corals. Here we tested three commonly used ITS2 primer pairs (SYM_VAR_5.8S2/SYM_VAR_REV, ITSintfor2/ITSReverse, and ITS-DINO/ITS2Rev2) with regard to amplification specificity and sensitivity towards Symbiodinium, as well as sub-genera taxonomic bias. We tested these primers over a range of sample types including three coral species, coral surrounding water, reef surface water, and open ocean water to assess their suitability for use in large-scale next generation sequencing projects and to develop a standardised PCR protocol. We found the SYM_VAR_5.8S2/SYM_VAR_REV primers to perform superior to the other tested ITS2 primers. We therefore used this primer pair to develop a standardised PCR protocol. To do this, we tested the effect of PCR-to-PCR variation, annealing temperature, cycle number, and different polymerase systems on the PCR efficacy. The Symbiodinium ITS2 PCR protocol developed here delivers improved specificity and sensitivity towards Symbiodinium with apparent minimal sub-genera taxonomic bias across all sample types. In particular, the protocol’s ability to amplify Symbiodinium from a range of environmental sources will facilitate the study of Symbiodinium populations across biomes.
format: application/pdf
format: text/html
creator: Benjamin C.C. Hume
creator: Maren Ziegler
creator: Julie Poulain
creator: Xavier Pochon
creator: Sarah Romac
creator: Emilie Boissin
creator: Colomban de Vargas
creator: Serge Planes
creator: Patrick Wincker
creator: Christian R. Voolstra
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Molecular Biology
subject: Climate Change Biology
description: doi:10.7717/peerj.4816
publisher: PeerJ Inc.
rights: © 2018 Hume et al.
abstract: The Internal Transcribed Spacer 2 (ITS2) rRNA gene is a commonly targeted genetic marker to assess diversity of Symbiodinium, a dinoflagellate genus of algal endosymbionts that is pervasively associated with marine invertebrates, and notably reef-building corals. Here we tested three commonly used ITS2 primer pairs (SYM_VAR_5.8S2/SYM_VAR_REV, ITSintfor2/ITSReverse, and ITS-DINO/ITS2Rev2) with regard to amplification specificity and sensitivity towards Symbiodinium, as well as sub-genera taxonomic bias. We tested these primers over a range of sample types including three coral species, coral surrounding water, reef surface water, and open ocean water to assess their suitability for use in large-scale next generation sequencing projects and to develop a standardised PCR protocol. We found the SYM_VAR_5.8S2/SYM_VAR_REV primers to perform superior to the other tested ITS2 primers. We therefore used this primer pair to develop a standardised PCR protocol. To do this, we tested the effect of PCR-to-PCR variation, annealing temperature, cycle number, and different polymerase systems on the PCR efficacy. The Symbiodinium ITS2 PCR protocol developed here delivers improved specificity and sensitivity towards Symbiodinium with apparent minimal sub-genera taxonomic bias across all sample types. In particular, the protocol’s ability to amplify Symbiodinium from a range of environmental sources will facilitate the study of Symbiodinium populations across biomes.
bibliographic citation: Hume et al. (2018) An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region. PeerJ 6:e4816 https://doi.org/10.7717/peerj.4816
date submitted: 2018-03-05
date accepted: 2018-05-01
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hume
  given name: Benjamin C.C.
author list: Agent
  family name: Ziegler
  given name: Maren
author list: Agent
  family name: Poulain
  given name: Julie
author list: Agent
  family name: Pochon
  given name: Xavier
author list: Agent
  family name: Romac
  given name: Sarah
author list: Agent
  family name: Boissin
  given name: Emilie
author list: Agent
  family name: de Vargas
  given name: Colomban
author list: Agent
  family name: Planes
  given name: Serge
author list: Agent
  family name: Wincker
  given name: Patrick
author list: Agent
  family name: Voolstra
  given name: Christian R.
doi: 10.7717/peerj.4816
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: © 2018 Hume et al.
attribution name: Hume et al.

Endozoochory by mallard in New Zealand: what seeds are dispersed and how far?
type: item
type: AcademicArticle
description: In Europe and North America waterfowl are major dispersers of aquatic and terrestrial plants, but in New Zealand their role has yet to be investigated. Mallards were introduced to New Zealand in the late 1800s, and today they are the most abundant and widespread waterfowl in the country. To assess seed dispersal, we radiomarked 284 female mallards from two study sites during the pre-breeding (June–August) and breeding (August–December) periods in 2014–2015, and examined movements that occurred within 24, 48 or 72 h when seed dispersal by endozoochory is considered likely. During June and July 2015, we collected 29 faecal samples from individual female mallards during radiomarking and 24 samples from mallard flocks. We recovered 69 intact seeds from the faecal samples and identified 12 plant taxa. Of the plant seeds identified and dispersed by mallards in this study, 40% were members of the Asteraceae family, nine plant species were alien to New Zealand, and the indigenous-status of three unidentified taxa could not be determined. Two taxa (and 9% of seeds) were germinated following gut passage: an unidentified Asteraceae and Solanum nigrum. During the pre-breeding and breeding periods, movement of females within 24 h averaged 394 m (SD = 706 m) and 222 m (SD = 605 m) respectively, with maximum distances of 3,970 m and 8,028 m. Maxima extended to 19,230 m within 48 h. Most plant species recorded are generally assumed to be self-dispersed or dispersed by water; mechanisms that provide a much lower maximum dispersal distance than mallards. The ability of mallards to disperse viable seeds up to 19 km within 48 h suggests they have an important and previously overlooked role as vectors for a variety of wetland or grassland plant species in New Zealand.
format: application/pdf
format: text/html
creator: Riley D. Bartel
creator: Jennifer L. Sheppard
creator: Ádám Lovas-Kiss
creator: Andy J. Green
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.4811
publisher: PeerJ Inc.
rights: © 2018 Bartel et al.
abstract: In Europe and North America waterfowl are major dispersers of aquatic and terrestrial plants, but in New Zealand their role has yet to be investigated. Mallards were introduced to New Zealand in the late 1800s, and today they are the most abundant and widespread waterfowl in the country. To assess seed dispersal, we radiomarked 284 female mallards from two study sites during the pre-breeding (June–August) and breeding (August–December) periods in 2014–2015, and examined movements that occurred within 24, 48 or 72 h when seed dispersal by endozoochory is considered likely. During June and July 2015, we collected 29 faecal samples from individual female mallards during radiomarking and 24 samples from mallard flocks. We recovered 69 intact seeds from the faecal samples and identified 12 plant taxa. Of the plant seeds identified and dispersed by mallards in this study, 40% were members of the Asteraceae family, nine plant species were alien to New Zealand, and the indigenous-status of three unidentified taxa could not be determined. Two taxa (and 9% of seeds) were germinated following gut passage: an unidentified Asteraceae and Solanum nigrum. During the pre-breeding and breeding periods, movement of females within 24 h averaged 394 m (SD = 706 m) and 222 m (SD = 605 m) respectively, with maximum distances of 3,970 m and 8,028 m. Maxima extended to 19,230 m within 48 h. Most plant species recorded are generally assumed to be self-dispersed or dispersed by water; mechanisms that provide a much lower maximum dispersal distance than mallards. The ability of mallards to disperse viable seeds up to 19 km within 48 h suggests they have an important and previously overlooked role as vectors for a variety of wetland or grassland plant species in New Zealand.
bibliographic citation: Bartel et al. (2018) Endozoochory by mallard in New Zealand: what seeds are dispersed and how far?. PeerJ 6:e4811 https://doi.org/10.7717/peerj.4811
date submitted: 2018-03-05
date accepted: 2018-04-30
issued: 2018-05-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bartel
  given name: Riley D.
author list: Agent
  family name: Sheppard
  given name: Jennifer L.
author list: Agent
  family name: Lovas-Kiss
  given name: Ádám
author list: Agent
  family name: Green
  given name: Andy J.
doi: 10.7717/peerj.4811
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-23
copyright: ©2018 Bartel et al.
attribution name: Bartel et al.

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