PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Size dimorphism and sexual segregation in pheasants: tests of three competing hypotheses
items: Biosorption potential of natural, pyrolysed and acid-assisted pyrolysed sugarcane bagasse for the removal of lead from contaminated water
items: New mud dragons from Svalbard: three new species of Cristaphyes and the first Arctic species of Pycnophyes (Kinorhyncha: Allomalorhagida: Pycnophyidae)
items: Closing the gap: mixed stock analysis of three foraging populations of green turtles (Chelonia mydas) on the Great Barrier Reef
items: Xeno-miRNet: a comprehensive database and analytics platform to explore xeno-miRNAs and their potential targets
items: Molecular analysis of oral microflora in patients with primary Sjögren’s syndrome by using high-throughput sequencing
items: Dynamics of nitrogen and active nitrogen components across seasons under varying stand densities in a Larix principis-rupprechtii (Pinaceae) plantation
items: Functional responses of a cosmopolitan invader demonstrate intraspecific variability in consumer-resource dynamics
items: Finding wolf homesites: improving the efficacy of howl surveys to study wolves
items: E-cigarettes versus nicotine patches for perioperative smoking cessation: a pilot randomized trial

Size dimorphism and sexual segregation in pheasants: tests of three competing hypotheses
type: item
type: AcademicArticle
description: Fine scale sexual segregation outside of the mating season is common in sexually dimorphic and polygamous species, particularly in ungulates. A number of hypotheses predict sexual segregation but these are often contradictory with no agreement as to a common cause, perhaps because they are species specific. We explicitly tested three of these hypotheses which are commonly linked by a dependence on sexual dimorphism for animals which exhibit fine-scale sexual segregation; the Predation Risk Hypothesis, the Forage Selection Hypothesis, and the Activity Budget Hypothesis, in a single system the pheasant, Phasianus colchicus; a large, sedentary bird that is predominantly terrestrial and therefore analogous to ungulates rather than many avian species which sexually segregate. Over four years we reared 2,400 individually tagged pheasants from one day old and after a period of 8–10 weeks we released them into the wild. We then followed the birds for 7 months, during the period that they sexually segregate, determined their fate and collected behavioural and morphological measures pertinent to the hypotheses. Pheasants are sexually dimorphic during the entire period that they sexually segregate in the wild; males are larger than females in both body size and gut measurements. However, this did not influence predation risk and predation rates (as predicted by the Predation Risk Hypothesis), diet choice (as predicted by the Forage Selection Hypothesis), or the amount of time spent foraging, resting or walking (as predicted by the Activity Budget Hypothesis). We conclude that adult sexual size dimorphism is not responsible for sexual segregation in the pheasant in the wild. Instead, we consider that segregation may be mediated by other, perhaps social, factors. We highlight the importance of studies on a wide range of taxa to help further the knowledge of sexual segregation.
format: application/pdf
format: text/html
creator: Mark A. Whiteside
creator: Jayden O. van Horik
creator: Ellis J.G. Langley
creator: Christine E. Beardsworth
creator: Joah R. Madden
subject: Animal Behavior
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.5674
publisher: PeerJ Inc.
rights: © 2018 Whiteside et al.
abstract: Fine scale sexual segregation outside of the mating season is common in sexually dimorphic and polygamous species, particularly in ungulates. A number of hypotheses predict sexual segregation but these are often contradictory with no agreement as to a common cause, perhaps because they are species specific. We explicitly tested three of these hypotheses which are commonly linked by a dependence on sexual dimorphism for animals which exhibit fine-scale sexual segregation; the Predation Risk Hypothesis, the Forage Selection Hypothesis, and the Activity Budget Hypothesis, in a single system the pheasant, Phasianus colchicus; a large, sedentary bird that is predominantly terrestrial and therefore analogous to ungulates rather than many avian species which sexually segregate. Over four years we reared 2,400 individually tagged pheasants from one day old and after a period of 8–10 weeks we released them into the wild. We then followed the birds for 7 months, during the period that they sexually segregate, determined their fate and collected behavioural and morphological measures pertinent to the hypotheses. Pheasants are sexually dimorphic during the entire period that they sexually segregate in the wild; males are larger than females in both body size and gut measurements. However, this did not influence predation risk and predation rates (as predicted by the Predation Risk Hypothesis), diet choice (as predicted by the Forage Selection Hypothesis), or the amount of time spent foraging, resting or walking (as predicted by the Activity Budget Hypothesis). We conclude that adult sexual size dimorphism is not responsible for sexual segregation in the pheasant in the wild. Instead, we consider that segregation may be mediated by other, perhaps social, factors. We highlight the importance of studies on a wide range of taxa to help further the knowledge of sexual segregation.
bibliographic citation: Whiteside et al. (2018) Size dimorphism and sexual segregation in pheasants: tests of three competing hypotheses. PeerJ 6:e5674 https://doi.org/10.7717/peerj.5674
date submitted: 2018-03-07
date accepted: 2018-08-30
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Whiteside
  given name: Mark A.
author list: Agent
  family name: van Horik
  given name: Jayden O.
author list: Agent
  family name: Langley
  given name: Ellis J.G.
author list: Agent
  family name: Beardsworth
  given name: Christine E.
author list: Agent
  family name: Madden
  given name: Joah R.
doi: 10.7717/peerj.5674
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Whiteside et al.
attribution name: Whiteside et al.

Biosorption potential of natural, pyrolysed and acid-assisted pyrolysed sugarcane bagasse for the removal of lead from contaminated water
type: item
type: AcademicArticle
description: Lead (Pb) is a ubiquitous pollutant which poses serious threats to plants, animals and humans once entered into the food chain via contaminated industrial effluents on their discharge into the surface of water bodies and/or geological materials. This study aimed to examine and compare the biosorption potential of natural sugarcane bagasse (NB), pyrolysed sugarcane bagasse (PB) and acid assisted pyrolysed sugarcane bagasse (APB) for the removal of Pb from contaminated water. To explore this objective, a series of batch experiments were conducted at various adsorbent mass (0.25, 0.5, 0.75, 1.0 g per 100 ml contaminated water), initial Pb concentration (7, 15, 30, 60 and 120 ppm), and contact time (7, 15, 30, 60 and 120 min). Results revealed that all the tested bio-sorbents have potential to adsorb and remove Pb ions from the contaminated water. In this regard, APB proved more effective since it removed 98% of Pb from aqueous solution at initial Pb concentration of 7 ppm and mass of 0.25 g per 100 ml of aqueous solution. The respective values in case of NB and PB were 90 and 95%. For a given adsorbent type, Pb adsorption decreased by increasing the mass from 0.25 to 1.0 g per 100 ml of aqueous solution. However, the greatest Pb removal occurred at adsorbent mass of 1.0 g per 100 ml of aqueous solution. Initial Pb concentration had a great impact on Pb adsorption and removal by adsorbent. The former increased and the latter decreased with the increase in initial Pb concentration from seven to 120 ppm. At seven ppm Pb concentration, maximum Pb removal took place irrespective to the adsorbent type. Out of the total Pb adsorption and removal, maximum contribution occurred within 15 min of contact time between the adsorbate and adsorbent, which slightly increased till 30 min, thereafter, it reached to equilibrium. Application of equilibrium isotherm models revealed that our results were better fitted with Freundlich adsorption isotherm model. Overall, and for the reasons d…
format: application/pdf
format: text/html
creator: Ghulam Mustafa Shah
creator: Muhammad Nasir
creator: Muhammad Imran
creator: Hafiz Faiq Bakhat
creator: Faiz Rabbani
creator: Muhammad Sajjad
creator: Abu Bakr Umer Farooq
creator: Sajjad Ahmad
creator: Lifen Song
subject: Natural Resource Management
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.5672
publisher: PeerJ Inc.
rights: © 2018 Shah et al.
abstract: Lead (Pb) is a ubiquitous pollutant which poses serious threats to plants, animals and humans once entered into the food chain via contaminated industrial effluents on their discharge into the surface of water bodies and/or geological materials. This study aimed to examine and compare the biosorption potential of natural sugarcane bagasse (NB), pyrolysed sugarcane bagasse (PB) and acid assisted pyrolysed sugarcane bagasse (APB) for the removal of Pb from contaminated water. To explore this objective, a series of batch experiments were conducted at various adsorbent mass (0.25, 0.5, 0.75, 1.0 g per 100 ml contaminated water), initial Pb concentration (7, 15, 30, 60 and 120 ppm), and contact time (7, 15, 30, 60 and 120 min). Results revealed that all the tested bio-sorbents have potential to adsorb and remove Pb ions from the contaminated water. In this regard, APB proved more effective since it removed 98% of Pb from aqueous solution at initial Pb concentration of 7 ppm and mass of 0.25 g per 100 ml of aqueous solution. The respective values in case of NB and PB were 90 and 95%. For a given adsorbent type, Pb adsorption decreased by increasing the mass from 0.25 to 1.0 g per 100 ml of aqueous solution. However, the greatest Pb removal occurred at adsorbent mass of 1.0 g per 100 ml of aqueous solution. Initial Pb concentration had a great impact on Pb adsorption and removal by adsorbent. The former increased and the latter decreased with the increase in initial Pb concentration from seven to 120 ppm. At seven ppm Pb concentration, maximum Pb removal took place irrespective to the adsorbent type. Out of the total Pb adsorption and removal, maximum contribution occurred within 15 min of contact time between the adsorbate and adsorbent, which slightly increased till 30 min, thereafter, it reached to equilibrium. Application of equilibrium isotherm models revealed that our results were better fitted with Freundlich adsorption isotherm model. Overall, and for the reasons d…
bibliographic citation: Shah et al. (2018) Biosorption potential of natural, pyrolysed and acid-assisted pyrolysed sugarcane bagasse for the removal of lead from contaminated water. PeerJ 6:e5672 https://doi.org/10.7717/peerj.5672
date submitted: 2018-03-29
date accepted: 2018-08-29
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shah
  given name: Ghulam Mustafa
author list: Agent
  family name: Nasir
  given name: Muhammad
author list: Agent
  family name: Imran
  given name: Muhammad
author list: Agent
  family name: Bakhat
  given name: Hafiz Faiq
author list: Agent
  family name: Rabbani
  given name: Faiz
author list: Agent
  family name: Sajjad
  given name: Muhammad
author list: Agent
  family name: Umer Farooq
  given name: Abu Bakr
author list: Agent
  family name: Ahmad
  given name: Sajjad
author list: Agent
  family name: Song
  given name: Lifen
doi: 10.7717/peerj.5672
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Shah et al.
attribution name: Shah et al.

New mud dragons from Svalbard: three new species of Cristaphyes and the first Arctic species of Pycnophyes (Kinorhyncha: Allomalorhagida: Pycnophyidae)
type: item
type: AcademicArticle
description: Background Kinorhynchs are marine, microscopic invertebrates inhabiting the seafloors. Their segmented trunk equipped with spines and processes has inspired scientists to give them the common name “mud dragons.” Even though kinorhynchs have been known since the 19th century, less than 300 species are known to science, and it is still considered a largely understudied animal group—in particular in the Arctic, from which only 23 species are known so far. Methods Samples were collected at eight stations around Svalbard and in the fjords of Spitsbergen. Meiofauna was extracted from the sediment cores with LUDOX centrifugation method, and kinorhynchs were picked up and mounted for light- and scanning electron microscopy. Results Four new species of the kinorhynch family Pycnophyidae are described from Svalbard: Cristaphyes dordaidelosensis sp. nov., C. glaurung sp. nov., C. scatha sp. nov., and Pycnophyes ancalagon sp. nov. The new species are generally recognized by their distribution of setae along the trunk segments. Discussion After the discovery of the new species, Pycnophyidae becomes with 14 species the most diverse kinorhynch genus in the Arctic, closely followed by Echinoderidae with 13 species. So far, these are the only kinorhynch families with an Arctic distribution.
format: application/pdf
format: text/html
creator: Martin Vinther Sørensen
creator: Katarzyna Grzelak
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.5653
publisher: PeerJ Inc.
rights: © 2018 Sørensen and Grzelak
abstract: Background Kinorhynchs are marine, microscopic invertebrates inhabiting the seafloors. Their segmented trunk equipped with spines and processes has inspired scientists to give them the common name “mud dragons.” Even though kinorhynchs have been known since the 19th century, less than 300 species are known to science, and it is still considered a largely understudied animal group—in particular in the Arctic, from which only 23 species are known so far. Methods Samples were collected at eight stations around Svalbard and in the fjords of Spitsbergen. Meiofauna was extracted from the sediment cores with LUDOX centrifugation method, and kinorhynchs were picked up and mounted for light- and scanning electron microscopy. Results Four new species of the kinorhynch family Pycnophyidae are described from Svalbard: Cristaphyes dordaidelosensis sp. nov., C. glaurung sp. nov., C. scatha sp. nov., and Pycnophyes ancalagon sp. nov. The new species are generally recognized by their distribution of setae along the trunk segments. Discussion After the discovery of the new species, Pycnophyidae becomes with 14 species the most diverse kinorhynch genus in the Arctic, closely followed by Echinoderidae with 13 species. So far, these are the only kinorhynch families with an Arctic distribution.
bibliographic citation: Sørensen et al. (2018) New mud dragons from Svalbard: three new species of Cristaphyes and the first Arctic species of Pycnophyes (Kinorhyncha: Allomalorhagida: Pycnophyidae). PeerJ 6:e5653 https://doi.org/10.7717/peerj.5653
date submitted: 2018-07-09
date accepted: 2018-08-24
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sørensen
  given name: Martin Vinther
author list: Agent
  family name: Grzelak
  given name: Katarzyna
doi: 10.7717/peerj.5653
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: © 2018 Sørensen and Grzelak
attribution name: Sørensen and Grzelak

Closing the gap: mixed stock analysis of three foraging populations of green turtles (Chelonia mydas) on the Great Barrier Reef
type: item
type: AcademicArticle
description: A solid understanding of the spatial ecology of green turtles (Chelonia mydas) is fundamental to their effective conservation. Yet this species, like many marine migratory species, is challenging to monitor and manage because they utilise a variety of habitats that span wide spatio-temporal scales. To further elucidate the connectivity between green turtle rookeries and foraging populations, we sequenced the mtDNA control region of 278 turtles across three foraging sites from the northern Great Barrier Reef (GBR) spanning more than 330 km: Cockle Bay, Green Island and Low Isles. This was performed with a newly developed assay, which targets a longer fragment of mtDNA than previous studies. We used a mixed stock analysis (MSA), which utilises genetic data to estimate the relative proportion of genetically distinct breeding populations found at a given foraging ground. Haplotype and nucleotide diversity was also assessed. A total of 35 haplotypes were identified across all sites, 13 of which had not been found previously in any rookery. The MSA showed that the northern GBR (nGBR), Coral Sea (CS), southern GBR (sGBR) and New Caledonia (NC) stocks supplied the bulk of the turtles at all three sites, with small contributions from other rookeries in the region. Stock contribution shifted gradually from north to south, although sGBR/CS stock dominated at all three sites. The major change in composition occured between Cockle Bay and Low Isles. Our findings, together with other recent studies in this field, show that stock composition shifts with latitude as a natural progression along a coastal gradient. This phenomenon is likely to be the result of ocean currents influencing both post-hatchling dispersal and subsequent juvenile recruitment to diverse coastal foraging sites.
format: application/pdf
format: text/html
creator: Karina Jones
creator: Michael Jensen
creator: Graham Burgess
creator: Johanna Leonhardt
creator: Lynne van Herwerden
creator: Julia Hazel
creator: Mark Hamann
creator: Ian Bell
creator: Ellen Ariel
subject: Conservation Biology
subject: Marine Biology
subject: Molecular Biology
subject: Natural Resource Management
subject: Population Biology
description: doi:10.7717/peerj.5651
publisher: PeerJ Inc.
rights: © 2018 Jones et al.
abstract: A solid understanding of the spatial ecology of green turtles (Chelonia mydas) is fundamental to their effective conservation. Yet this species, like many marine migratory species, is challenging to monitor and manage because they utilise a variety of habitats that span wide spatio-temporal scales. To further elucidate the connectivity between green turtle rookeries and foraging populations, we sequenced the mtDNA control region of 278 turtles across three foraging sites from the northern Great Barrier Reef (GBR) spanning more than 330 km: Cockle Bay, Green Island and Low Isles. This was performed with a newly developed assay, which targets a longer fragment of mtDNA than previous studies. We used a mixed stock analysis (MSA), which utilises genetic data to estimate the relative proportion of genetically distinct breeding populations found at a given foraging ground. Haplotype and nucleotide diversity was also assessed. A total of 35 haplotypes were identified across all sites, 13 of which had not been found previously in any rookery. The MSA showed that the northern GBR (nGBR), Coral Sea (CS), southern GBR (sGBR) and New Caledonia (NC) stocks supplied the bulk of the turtles at all three sites, with small contributions from other rookeries in the region. Stock contribution shifted gradually from north to south, although sGBR/CS stock dominated at all three sites. The major change in composition occured between Cockle Bay and Low Isles. Our findings, together with other recent studies in this field, show that stock composition shifts with latitude as a natural progression along a coastal gradient. This phenomenon is likely to be the result of ocean currents influencing both post-hatchling dispersal and subsequent juvenile recruitment to diverse coastal foraging sites.
bibliographic citation: Jones et al. (2018) Closing the gap: mixed stock analysis of three foraging populations of green turtles (Chelonia mydas) on the Great Barrier Reef. PeerJ 6:e5651 https://doi.org/10.7717/peerj.5651
date submitted: 2018-03-05
date accepted: 2018-08-28
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jones
  given name: Karina
author list: Agent
  family name: Jensen
  given name: Michael
author list: Agent
  family name: Burgess
  given name: Graham
author list: Agent
  family name: Leonhardt
  given name: Johanna
author list: Agent
  family name: van Herwerden
  given name: Lynne
author list: Agent
  family name: Hazel
  given name: Julia
author list: Agent
  family name: Hamann
  given name: Mark
author list: Agent
  family name: Bell
  given name: Ian
author list: Agent
  family name: Ariel
  given name: Ellen
doi: 10.7717/peerj.5651
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Jones et al.
attribution name: Jones et al.

Xeno-miRNet: a comprehensive database and analytics platform to explore xeno-miRNAs and their potential targets
type: item
type: AcademicArticle
description: Xeno-miRNAs are microRNAs originating from exogenous species detected in host biofluids. A growing number of studies have suggested that many of these xeno-miRNAs may be involved in cross-species interactions and manipulations. To date, hundreds of xeno-miRNAs have been reported in different hosts at various abundance levels. Based on computational predictions, many more miRNAs could be potentially transferred to human circulation system. There is a clear need for bioinformatics resources and tools dedicated to xeno-miRNA annotations and their potential functions. To address this need, we have systematically curated xeno-miRNAs from multiple sources, performed target predictions using well-established algorithms, and developed a user-friendly web-based tool—Xeno-miRNet—to allow researchers to search and explore xeno-miRNAs and their potential targets within different host species. Xeno-miRNet currently contains 1,702 (including both detected and predicted) xeno-miRNAs from 54 species and 98,053 potential gene targets in six hosts. The web application is freely available at http://xeno.mirnet.ca.
format: application/pdf
format: text/html
creator: Yannan Fan
creator: Maria Habib
creator: Jianguo Xia
subject: Bioinformatics
subject: Computational Biology
subject: Genetics
subject: Genomics
subject: Parasitology
description: doi:10.7717/peerj.5650
publisher: PeerJ Inc.
rights: © 2018 Fan et al.
abstract: Xeno-miRNAs are microRNAs originating from exogenous species detected in host biofluids. A growing number of studies have suggested that many of these xeno-miRNAs may be involved in cross-species interactions and manipulations. To date, hundreds of xeno-miRNAs have been reported in different hosts at various abundance levels. Based on computational predictions, many more miRNAs could be potentially transferred to human circulation system. There is a clear need for bioinformatics resources and tools dedicated to xeno-miRNA annotations and their potential functions. To address this need, we have systematically curated xeno-miRNAs from multiple sources, performed target predictions using well-established algorithms, and developed a user-friendly web-based tool—Xeno-miRNet—to allow researchers to search and explore xeno-miRNAs and their potential targets within different host species. Xeno-miRNet currently contains 1,702 (including both detected and predicted) xeno-miRNAs from 54 species and 98,053 potential gene targets in six hosts. The web application is freely available at http://xeno.mirnet.ca.
bibliographic citation: Fan et al. (2018) Xeno-miRNet: a comprehensive database and analytics platform to explore xeno-miRNAs and their potential targets. PeerJ 6:e5650 https://doi.org/10.7717/peerj.5650
date submitted: 2018-04-24
date accepted: 2018-08-24
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Yannan
author list: Agent
  family name: Habib
  given name: Maria
author list: Agent
  family name: Xia
  given name: Jianguo
doi: 10.7717/peerj.5650
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Fan et al.
attribution name: Fan et al.

Molecular analysis of oral microflora in patients with primary Sjögren’s syndrome by using high-throughput sequencing
type: item
type: AcademicArticle
description: Background The objective of this study was to characterize the oral microflora profile of primary Sjögren’s syndrome (pSS) patients, thereby revealing the connection between oral bacterial composition and dental caries, and to identify the “core microbiome” in the oral cavities of pSS patients and systemic healthy individuals by using a high-throughput sequencing technique. Methods Twenty-two pSS patients and 23 healthy controls were enrolled in this study. Their clinical data and oral rinse samples were collected. The V3–V4 hypervariable regions of the bacterial 16S rRNA gene of samples were amplified and analyzed by high-throughput sequencing on the Illumina Miseq PE300 platform. Results Both two groups were age- and sex-matched. There were significantly higher decayed, missing and filled teeth (DMFT) and decayed, missing and filled surfaces (DMFS) in the pSS group than in the control group (p < 0.01). Alpha diversity was depleted in pSS patients, compared with healthy controls (p < 0.01), while beta diversity between the two groups was not significantly different. Seven discriminative genera (LDA > 4) were found between the two groups in LEfSe (LDA Effect Size) analysis. The relative abundance of Veillonella in pSS patients was fourfold higher, while Actinomyces, Haemophilus, Neisseria, Rothia, Porphyromonas and Peptostreptococcus were significantly lower in pSS patients than in healthy controls. However, the correlation between Veillonella and DMFT/DMFS was not significant (p > 0.05). In Venn diagram analysis, nine genera shared by all samples of two groups, which comprised 71.88% and 67.64% in pSS patients and controls, respectively. Discussion These findings indicate a microbial dysbiosis in pSS patients; notably, Veillonella might be recognized as a biomarker in pSS patients. The core microbiome in pSS patients was similar to the systemic healthy population. These provide insight regarding advanced microbial prevention and treatment of severe dental caries in…
format: application/pdf
format: text/html
creator: Zhifang Zhou
creator: Guanghui Ling
creator: Ning Ding
creator: Zhe Xun
creator: Ce Zhu
creator: Hong Hua
creator: Xiaochi Chen
subject: Microbiology
subject: Molecular Biology
subject: Allergy and Clinical Immunology
subject: Dentistry
description: doi:10.7717/peerj.5649
publisher: PeerJ Inc.
rights: © 2018 Zhou et al.
abstract: Background The objective of this study was to characterize the oral microflora profile of primary Sjögren’s syndrome (pSS) patients, thereby revealing the connection between oral bacterial composition and dental caries, and to identify the “core microbiome” in the oral cavities of pSS patients and systemic healthy individuals by using a high-throughput sequencing technique. Methods Twenty-two pSS patients and 23 healthy controls were enrolled in this study. Their clinical data and oral rinse samples were collected. The V3–V4 hypervariable regions of the bacterial 16S rRNA gene of samples were amplified and analyzed by high-throughput sequencing on the Illumina Miseq PE300 platform. Results Both two groups were age- and sex-matched. There were significantly higher decayed, missing and filled teeth (DMFT) and decayed, missing and filled surfaces (DMFS) in the pSS group than in the control group (p < 0.01). Alpha diversity was depleted in pSS patients, compared with healthy controls (p < 0.01), while beta diversity between the two groups was not significantly different. Seven discriminative genera (LDA > 4) were found between the two groups in LEfSe (LDA Effect Size) analysis. The relative abundance of Veillonella in pSS patients was fourfold higher, while Actinomyces, Haemophilus, Neisseria, Rothia, Porphyromonas and Peptostreptococcus were significantly lower in pSS patients than in healthy controls. However, the correlation between Veillonella and DMFT/DMFS was not significant (p > 0.05). In Venn diagram analysis, nine genera shared by all samples of two groups, which comprised 71.88% and 67.64% in pSS patients and controls, respectively. Discussion These findings indicate a microbial dysbiosis in pSS patients; notably, Veillonella might be recognized as a biomarker in pSS patients. The core microbiome in pSS patients was similar to the systemic healthy population. These provide insight regarding advanced microbial prevention and treatment of severe dental caries in…
bibliographic citation: Zhou et al. (2018) Molecular analysis of oral microflora in patients with primary Sjögren’s syndrome by using high-throughput sequencing. PeerJ 6:e5649 https://doi.org/10.7717/peerj.5649
date submitted: 2018-04-24
date accepted: 2018-08-26
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Zhifang
author list: Agent
  family name: Ling
  given name: Guanghui
author list: Agent
  family name: Ding
  given name: Ning
author list: Agent
  family name: Xun
  given name: Zhe
author list: Agent
  family name: Zhu
  given name: Ce
author list: Agent
  family name: Hua
  given name: Hong
author list: Agent
  family name: Chen
  given name: Xiaochi
doi: 10.7717/peerj.5649
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Zhou et al.
attribution name: Zhou et al.

Dynamics of nitrogen and active nitrogen components across seasons under varying stand densities in a Larix principis-rupprechtii (Pinaceae) plantation
type: item
type: AcademicArticle
description: Changes in the concentration of soil nitrogen (N) or its components may directly affect ecosystem functioning in forestry. Thinning of forest stands, a widely used forestry management practice, may transform soil nutrients directly by altering the soil environment, or indirectly by changing above- or belowground plant biomass. The study objectives were to determine how tree stem density affects the soil N pool and what mechanisms drive any potential changes. In this study, N and its active components were measured in the soil of a Larix principis-rupprechtii plantation across two full growing seasons, in 12 (25 × 25 m) plots: (low thinning, removal of 15% of the trees, three plot repetitions), moderate thinning (MT) (35% removal) and heavy thinning (HT) (50% removal) and no thinning control. Environmental indices, like the light condition, soil respiration, soil temperatures, and prescription, were measured in the plots also. Results indicated that soil total nitrogen (STN) was affected by tree stem density adjustments in the short-term; STN generally increased with decreasing tree stem density, reaching its highest concentration in the MT treatment before decreasing in HT. This pattern was echoed by the DON/STN ratio dissolved organic nitrogen (DON) under MT. A lower DON/STN was measured across the seasons. Microbial biomass nitrogen (MBN) and the SOC/STN (soil organic carbon (SOC)) ratio and density treatments influenced MBN concentration and inhibited SOC/STN. MT tended to accumulate more STN, produce lower DON/STN and had a generally higher microbial activity, which may be partly ascribed to the higher MBN value, MBN/STN ratio and lower DON/STN. The water conditions (soil moisture), light and soil temperatures could partly be responsible for the N pool dynamic in the different density treatments.
format: application/pdf
format: text/html
creator: Junyong Ma
creator: Hairong Han
creator: Wenwen Zhang
creator: Xiaoqin Cheng
subject: Ecosystem Science
subject: Soil Science
subject: Biogeochemistry
subject: Forestry
description: doi:10.7717/peerj.5647
publisher: PeerJ Inc.
rights: © 2018 Ma et al.
abstract: Changes in the concentration of soil nitrogen (N) or its components may directly affect ecosystem functioning in forestry. Thinning of forest stands, a widely used forestry management practice, may transform soil nutrients directly by altering the soil environment, or indirectly by changing above- or belowground plant biomass. The study objectives were to determine how tree stem density affects the soil N pool and what mechanisms drive any potential changes. In this study, N and its active components were measured in the soil of a Larix principis-rupprechtii plantation across two full growing seasons, in 12 (25 × 25 m) plots: (low thinning, removal of 15% of the trees, three plot repetitions), moderate thinning (MT) (35% removal) and heavy thinning (HT) (50% removal) and no thinning control. Environmental indices, like the light condition, soil respiration, soil temperatures, and prescription, were measured in the plots also. Results indicated that soil total nitrogen (STN) was affected by tree stem density adjustments in the short-term; STN generally increased with decreasing tree stem density, reaching its highest concentration in the MT treatment before decreasing in HT. This pattern was echoed by the DON/STN ratio dissolved organic nitrogen (DON) under MT. A lower DON/STN was measured across the seasons. Microbial biomass nitrogen (MBN) and the SOC/STN (soil organic carbon (SOC)) ratio and density treatments influenced MBN concentration and inhibited SOC/STN. MT tended to accumulate more STN, produce lower DON/STN and had a generally higher microbial activity, which may be partly ascribed to the higher MBN value, MBN/STN ratio and lower DON/STN. The water conditions (soil moisture), light and soil temperatures could partly be responsible for the N pool dynamic in the different density treatments.
bibliographic citation: Ma et al. (2018) Dynamics of nitrogen and active nitrogen components across seasons under varying stand densities in a Larix principis-rupprechtii (Pinaceae) plantation. PeerJ 6:e5647 https://doi.org/10.7717/peerj.5647
date submitted: 2018-05-02
date accepted: 2018-08-27
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Junyong
author list: Agent
  family name: Han
  given name: Hairong
author list: Agent
  family name: Zhang
  given name: Wenwen
author list: Agent
  family name: Cheng
  given name: Xiaoqin
doi: 10.7717/peerj.5647
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: © 2018 Ma et al.
attribution name: Ma et al.

Functional responses of a cosmopolitan invader demonstrate intraspecific variability in consumer-resource dynamics
type: item
type: AcademicArticle
description: Background Variability in the ecological impacts of invasive species across their geographical ranges may decrease the accuracy of risk assessments. Comparative functional response analysis can be used to estimate invasive consumer-resource dynamics, explain impact variability, and thus potentially inform impact predictions. The European green crab (Carcinus maenas) has been introduced on multiple continents beyond its native range, although its ecological impacts appear to vary among populations and regions. Our aim was to test whether consumer-resource dynamics under standardized conditions are similarly variable across the current geographic distribution of green crab, and to identify correlated morphological features. Methods Crabs were collected from multiple populations within both native (Northern Ireland) and invasive regions (South Africa and Canada). Their functional responses to local mussels (Mytilus spp.) were tested. Attack rates and handling times were compared among green crab populations within each region, and among regions (Pacific Canada, Atlantic Canada, South Africa, and Northern Ireland). The effect of predator and prey morphology on prey consumption was investigated. Results Across regions, green crabs consumed prey according to a Type II (hyperbolic) functional response curve. Attack rates (i.e., the rate at which a predator finds and attacks prey), handling times and maximum feeding rates differed among regions. There was a trend toward higher attack rates in invasive than in native populations. Green crabs from Canada had lower handling times and thus higher maximum feeding rates than those from South Africa and Northern Ireland. Canadian and Northern Ireland crabs had significantly larger claws than South African crabs. Claw size was a more important predictor of the proportion of mussels killed than prey shell strength. Discussion The differences in functional response between regions reflect observed impacts of green crabs in the wild. …
format: application/pdf
format: text/html
creator: Brett R. Howard
creator: Daniel Barrios-O’Neill
creator: Mhairi E. Alexander
creator: Jaimie T.A. Dick
creator: Thomas W. Therriault
creator: Tamara B. Robinson
creator: Isabelle M. Côté
subject: Animal Behavior
subject: Biogeography
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.5634
publisher: PeerJ Inc.
rights: ©
abstract: Background Variability in the ecological impacts of invasive species across their geographical ranges may decrease the accuracy of risk assessments. Comparative functional response analysis can be used to estimate invasive consumer-resource dynamics, explain impact variability, and thus potentially inform impact predictions. The European green crab (Carcinus maenas) has been introduced on multiple continents beyond its native range, although its ecological impacts appear to vary among populations and regions. Our aim was to test whether consumer-resource dynamics under standardized conditions are similarly variable across the current geographic distribution of green crab, and to identify correlated morphological features. Methods Crabs were collected from multiple populations within both native (Northern Ireland) and invasive regions (South Africa and Canada). Their functional responses to local mussels (Mytilus spp.) were tested. Attack rates and handling times were compared among green crab populations within each region, and among regions (Pacific Canada, Atlantic Canada, South Africa, and Northern Ireland). The effect of predator and prey morphology on prey consumption was investigated. Results Across regions, green crabs consumed prey according to a Type II (hyperbolic) functional response curve. Attack rates (i.e., the rate at which a predator finds and attacks prey), handling times and maximum feeding rates differed among regions. There was a trend toward higher attack rates in invasive than in native populations. Green crabs from Canada had lower handling times and thus higher maximum feeding rates than those from South Africa and Northern Ireland. Canadian and Northern Ireland crabs had significantly larger claws than South African crabs. Claw size was a more important predictor of the proportion of mussels killed than prey shell strength. Discussion The differences in functional response between regions reflect observed impacts of green crabs in the wild. …
bibliographic citation: Howard et al. (2018) Functional responses of a cosmopolitan invader demonstrate intraspecific variability in consumer-resource dynamics. PeerJ 6:e5634 https://doi.org/10.7717/peerj.5634
date submitted: 2018-03-10
date accepted: 2018-08-24
issued: 2018-09-28
is part of: PeerJ
license: open-government-licence
author list: Agent
  family name: Howard
  given name: Brett R.
author list: Agent
  family name: Barrios-O’Neill
  given name: Daniel
author list: Agent
  family name: Alexander
  given name: Mhairi E.
author list: Agent
  family name: Dick
  given name: Jaimie T.A.
author list: Agent
  family name: Therriault
  given name: Thomas W.
author list: Agent
  family name: Robinson
  given name: Tamara B.
author list: Agent
  family name: Côté
  given name: Isabelle M.
doi: 10.7717/peerj.5634
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28

Finding wolf homesites: improving the efficacy of howl surveys to study wolves
type: item
type: AcademicArticle
description: Locating wolf (Canis lupus) homesites is valuable for understanding the foraging behavior, population dynamics, and reproductive ecology of wolves during summer. During this period wolf pack members (adults and pups) readily respond to simulated wolf howls (i.e., howl surveys), which allows researchers to estimate the location of the homesite via triangulation. Confirming the actual locations of homesites via ground truthing is labor intensive because of the error surrounding estimated locations. Our objectives were (1) to quantify observer error during howl surveys and compare amongst experience levels, (2) provide a simple method for locating homesites in the field by incorporating observer error, and (3) further document the value of this method for monitoring wolf packs throughout the summer. We located 17 homesites by howl surveys during 2015–2017 in the Greater Voyageurs Ecosystem, Minnesota, USA. Of 62 bearings taken by observers during howl surveys, bearings erred by an average of 7.6° ± 6.3° (SD). There was no difference in observer error between novice and experienced observers. A simple way to increase efficiency when searching for homesites is to search concentric areas (bands) based on estimated observer error, specifically by: (1) adding ±10° error bands around howl survey bearings when ≥3 bearings can be obtained, (2) ±10° and ±20° error bands when 2 bearings are obtained, and (3) ±10° and ±26° error bands when 1 bearing is obtained. By incorporating observer error and understanding how frequently and how far wolves move homesites, it is possible to monitor wolf packs and confirm most, if not all, homesites used by a pack from at least June until August without having a collared individual in a pack.
format: application/pdf
format: text/html
creator: Thomas D. Gable
creator: Steve K. Windels
creator: Joseph K. Bump
subject: Animal Behavior
subject: Ecology
subject: Natural Resource Management
description: doi:10.7717/peerj.5629
publisher: PeerJ Inc.
rights: © 2018 Gable et al.
abstract: Locating wolf (Canis lupus) homesites is valuable for understanding the foraging behavior, population dynamics, and reproductive ecology of wolves during summer. During this period wolf pack members (adults and pups) readily respond to simulated wolf howls (i.e., howl surveys), which allows researchers to estimate the location of the homesite via triangulation. Confirming the actual locations of homesites via ground truthing is labor intensive because of the error surrounding estimated locations. Our objectives were (1) to quantify observer error during howl surveys and compare amongst experience levels, (2) provide a simple method for locating homesites in the field by incorporating observer error, and (3) further document the value of this method for monitoring wolf packs throughout the summer. We located 17 homesites by howl surveys during 2015–2017 in the Greater Voyageurs Ecosystem, Minnesota, USA. Of 62 bearings taken by observers during howl surveys, bearings erred by an average of 7.6° ± 6.3° (SD). There was no difference in observer error between novice and experienced observers. A simple way to increase efficiency when searching for homesites is to search concentric areas (bands) based on estimated observer error, specifically by: (1) adding ±10° error bands around howl survey bearings when ≥3 bearings can be obtained, (2) ±10° and ±20° error bands when 2 bearings are obtained, and (3) ±10° and ±26° error bands when 1 bearing is obtained. By incorporating observer error and understanding how frequently and how far wolves move homesites, it is possible to monitor wolf packs and confirm most, if not all, homesites used by a pack from at least June until August without having a collared individual in a pack.
bibliographic citation: Gable et al. (2018) Finding wolf homesites: improving the efficacy of howl surveys to study wolves. PeerJ 6:e5629 https://doi.org/10.7717/peerj.5629
date submitted: 2018-05-23
date accepted: 2018-08-23
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gable
  given name: Thomas D.
author list: Agent
  family name: Windels
  given name: Steve K.
author list: Agent
  family name: Bump
  given name: Joseph K.
doi: 10.7717/peerj.5629
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Gable et al.
attribution name: Gable et al.

E-cigarettes versus nicotine patches for perioperative smoking cessation: a pilot randomized trial
type: item
type: AcademicArticle
description: Introduction Cigarette smoking by surgical patients is associated with increased complications. E-cigarettes have emerged as a potential smoking cessation tool. We sought to determine the feasibility and acceptability of e-cigarettes, compared to nicotine patch, for perioperative smoking cessation in veterans. Methods Preoperative patients were randomized to either the nicotine patch group (n = 10) or the e-cigarette group (n = 20). Both groups were given a free 6-week supply in a tapering dose. All patients received brief counseling, a brochure on perioperative smoking cessation, and referral to the California Smokers’ Helpline. The primary outcome was rate of smoking cessation on day of surgery confirmed by exhaled carbon monoxide. Secondary outcomes included smoking habits, pulmonary function, adverse events, and satisfaction with the products on day of surgery and at 8-weeks follow-up. Results Biochemically verified smoking cessation on day of surgery was similar in both groups. Change in forced expiratory volume in one second (FEV1) was 592 ml greater in the e-cigarette group (95% CI [153–1,031] ml, p = 0.01) and change in forced expiratory volume in one second to forced vital capacity ratio (FEV1/FVC ratio) was 40.1% greater in the e-cigarette group (95% CI [18.2%–78.4%], p = 0.04). Satisfaction with the product was similar in both groups. Discussion E-cigarettes are a feasible tool for perioperative smoking cessation in veterans with quit rates comparable to nicotine replacement patch. Spirometry appears to be improved 8-weeks after initiating e-cigarettes compared to nicotine patch, possibly due to worse baseline spirometry and more smoking reduction in the e-cigarette group. An adequately powered study is recommended to determine if these results can be duplicated.
format: application/pdf
format: text/html
creator: Susan M. Lee
creator: Rachel Tenney
creator: Arthur W. Wallace
creator: Mehrdad Arjomandi
subject: Anesthesiology and Pain Management
subject: Clinical Trials
subject: Public Health
subject: Respiratory Medicine
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.5609
publisher: PeerJ Inc.
rights: © 2018 Lee et al.
abstract: Introduction Cigarette smoking by surgical patients is associated with increased complications. E-cigarettes have emerged as a potential smoking cessation tool. We sought to determine the feasibility and acceptability of e-cigarettes, compared to nicotine patch, for perioperative smoking cessation in veterans. Methods Preoperative patients were randomized to either the nicotine patch group (n = 10) or the e-cigarette group (n = 20). Both groups were given a free 6-week supply in a tapering dose. All patients received brief counseling, a brochure on perioperative smoking cessation, and referral to the California Smokers’ Helpline. The primary outcome was rate of smoking cessation on day of surgery confirmed by exhaled carbon monoxide. Secondary outcomes included smoking habits, pulmonary function, adverse events, and satisfaction with the products on day of surgery and at 8-weeks follow-up. Results Biochemically verified smoking cessation on day of surgery was similar in both groups. Change in forced expiratory volume in one second (FEV1) was 592 ml greater in the e-cigarette group (95% CI [153–1,031] ml, p = 0.01) and change in forced expiratory volume in one second to forced vital capacity ratio (FEV1/FVC ratio) was 40.1% greater in the e-cigarette group (95% CI [18.2%–78.4%], p = 0.04). Satisfaction with the product was similar in both groups. Discussion E-cigarettes are a feasible tool for perioperative smoking cessation in veterans with quit rates comparable to nicotine replacement patch. Spirometry appears to be improved 8-weeks after initiating e-cigarettes compared to nicotine patch, possibly due to worse baseline spirometry and more smoking reduction in the e-cigarette group. An adequately powered study is recommended to determine if these results can be duplicated.
bibliographic citation: Lee et al. (2018) E-cigarettes versus nicotine patches for perioperative smoking cessation: a pilot randomized trial. PeerJ 6:e5609 https://doi.org/10.7717/peerj.5609
date submitted: 2018-04-09
date accepted: 2018-08-19
issued: 2018-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Susan M.
author list: Agent
  family name: Tenney
  given name: Rachel
author list: Agent
  family name: Wallace
  given name: Arthur W.
author list: Agent
  family name: Arjomandi
  given name: Mehrdad
doi: 10.7717/peerj.5609
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-28
copyright: ©2018 Lee et al.
attribution name: Lee et al.

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