PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Ongoing removals of invasive lionfish in Honduras and their effect on native Caribbean prey fishes
items: lncRNA H19 is involved in TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT Signaling Pathway
items: MGST2 and WNT2 are candidate genes for comitant strabismus susceptibility in Japanese patients
items: Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils
items: How to normalize metatranscriptomic count data for differential expression analysis
items: Exploring the psychological health of emergency dispatch centre operatives: a systematic review and narrative synthesis
items: Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI
items: Tolerance: the forgotten child of plant resistance
items: L1 and L2 reading skills in Dutch adolescents with a familial risk of dyslexia
items: Investigating the level of agreement of two positioning protocols when using dual energy X-ray absorptiometry in the assessment of body composition

Ongoing removals of invasive lionfish in Honduras and their effect on native Caribbean prey fishes
type: item
type: AcademicArticle
description: The invasion of Indo-Pacific lionfish is one of the most pressing concerns in the context of coral reef conservation throughout the Caribbean. Invasive lionfish threaten Caribbean fish communities by feeding on a wide range of native prey species, some of which have high ecological and economic value. In Roatan (Honduras) a local non-governmental organisation (i.e. Roatan Marine Park) trains residents and tourists in the use of spears to remove invasive lionfish. Here, we assess the effectiveness of local removal efforts in reducing lionfish populations. We ask whether reefs subject to relatively frequent removals support more diverse and abundant native fish assemblages compared to sites were no removals take place. Lionfish biomass, as well as density and diversity of native prey species were quantified on reefs subject to regular and no removal efforts. Reefs subject to regular lionfish removals (two to three removals month−1) with a mean catch per unit effort of 2.76 ± 1.72 lionfish fisher−1 h−1 had 95% lower lionfish biomass compared to non-removal sites. Sites subject to lionfish removals supported 30% higher densities of native prey-sized fishes compared to sites subject to no removal efforts. We found no evidence that species richness and diversity of native fish communities differ between removal and non-removal sites. We conclude that opportunistic voluntary removals are an effective management intervention to reduce lionfish populations locally and might alleviate negative impacts of lionfish predation. We recommend that local management and the diving industry cooperate to cost-effectively extend the spatial scale at which removal regimes are currently sustained.
format: application/pdf
format: text/html
creator: Friederike Peiffer
creator: Sonia Bejarano
creator: Giacomo Palavicini de Witte
creator: Christian Wild
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.3818
publisher: PeerJ Inc.
rights: © 2017 Peiffer et al.
abstract: The invasion of Indo-Pacific lionfish is one of the most pressing concerns in the context of coral reef conservation throughout the Caribbean. Invasive lionfish threaten Caribbean fish communities by feeding on a wide range of native prey species, some of which have high ecological and economic value. In Roatan (Honduras) a local non-governmental organisation (i.e. Roatan Marine Park) trains residents and tourists in the use of spears to remove invasive lionfish. Here, we assess the effectiveness of local removal efforts in reducing lionfish populations. We ask whether reefs subject to relatively frequent removals support more diverse and abundant native fish assemblages compared to sites were no removals take place. Lionfish biomass, as well as density and diversity of native prey species were quantified on reefs subject to regular and no removal efforts. Reefs subject to regular lionfish removals (two to three removals month−1) with a mean catch per unit effort of 2.76 ± 1.72 lionfish fisher−1 h−1 had 95% lower lionfish biomass compared to non-removal sites. Sites subject to lionfish removals supported 30% higher densities of native prey-sized fishes compared to sites subject to no removal efforts. We found no evidence that species richness and diversity of native fish communities differ between removal and non-removal sites. We conclude that opportunistic voluntary removals are an effective management intervention to reduce lionfish populations locally and might alleviate negative impacts of lionfish predation. We recommend that local management and the diving industry cooperate to cost-effectively extend the spatial scale at which removal regimes are currently sustained.
bibliographic citation: Peiffer et al. (2017) Ongoing removals of invasive lionfish in Honduras and their effect on native Caribbean prey fishes. PeerJ 5:e3818 https://doi.org/10.7717/peerj.3818
date submitted: 2017-04-08
date accepted: 2017-08-26
issued: 2017-10-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peiffer
  given name: Friederike
author list: Agent
  family name: Bejarano
  given name: Sonia
author list: Agent
  family name: Palavicini de Witte
  given name: Giacomo
author list: Agent
  family name: Wild
  given name: Christian
doi: 10.7717/peerj.3818
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-18
copyright: © 2017 Peiffer et al.
attribution name: Peiffer et al.

lncRNA H19 is involved in TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT Signaling Pathway
type: item
type: AcademicArticle
description: Increased levels of long noncoding RNA H19 (H19) have been observed in many inflammatory and organ fibrosis diseases including ulcerative colitis, osteoarthritis, liver fibrosis, renal fibrosis and pulmonary fibrosis. However, the role of H19 in bovine mastitis and mastitis-caused fibrosis is still unclear. In our study, H19 was characterized as a novel regulator of EMT induced by transforming growth factor-β1 (TGF-β1) in bovine mammary alveolar cell-T (MAC-T) cell line. We found that H19 was highly expressed in bovine mastitis tissues and inflammatory MAC-T cells induced by virulence factors of pathogens. TGF-β1 was also highly expressed in inflammatory MAC-T cells, and exogenous TGF-β1 could induce EMT, enhance extracellular matrix protein expression, and upregulate H19 expression in epithelial cells. Stable expression of H19 significantly promotes EMT progression and expression of ECM protein induced by TGF-β1 in MAC-T cells. Furthermore, by using a specific inhibitor of the PI3K/AKT pathway, we demonstrated that TGF-β1 upregulated H19 expression through PI3K/AKT pathway. All these observations imply that the lncRNA H19 modulated TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT signaling pathway, which suggests that mammary epithelial cells might be one source for myofibroblasts in vivo in the mammary glands under an inflammatory condition, thereby contributing to mammary gland fibrosis.
format: application/pdf
format: text/html
creator: Wei Yang
creator: Xuezhong Li
creator: Shaopei Qi
creator: Xueru Li
creator: Kun Zhou
creator: Suzhu Qing
creator: Yong Zhang
creator: Ming-Qing Gao
subject: Biochemistry
subject: Cell Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.3950
publisher: PeerJ Inc.
rights: © 2017 Yang et al.
abstract: Increased levels of long noncoding RNA H19 (H19) have been observed in many inflammatory and organ fibrosis diseases including ulcerative colitis, osteoarthritis, liver fibrosis, renal fibrosis and pulmonary fibrosis. However, the role of H19 in bovine mastitis and mastitis-caused fibrosis is still unclear. In our study, H19 was characterized as a novel regulator of EMT induced by transforming growth factor-β1 (TGF-β1) in bovine mammary alveolar cell-T (MAC-T) cell line. We found that H19 was highly expressed in bovine mastitis tissues and inflammatory MAC-T cells induced by virulence factors of pathogens. TGF-β1 was also highly expressed in inflammatory MAC-T cells, and exogenous TGF-β1 could induce EMT, enhance extracellular matrix protein expression, and upregulate H19 expression in epithelial cells. Stable expression of H19 significantly promotes EMT progression and expression of ECM protein induced by TGF-β1 in MAC-T cells. Furthermore, by using a specific inhibitor of the PI3K/AKT pathway, we demonstrated that TGF-β1 upregulated H19 expression through PI3K/AKT pathway. All these observations imply that the lncRNA H19 modulated TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT signaling pathway, which suggests that mammary epithelial cells might be one source for myofibroblasts in vivo in the mammary glands under an inflammatory condition, thereby contributing to mammary gland fibrosis.
bibliographic citation: Yang et al. (2017) lncRNA H19 is involved in TGF-β1-induced epithelial to mesenchymal transition in bovine epithelial cells through PI3K/AKT Signaling Pathway. PeerJ 5:e3950 https://doi.org/10.7717/peerj.3950
date submitted: 2017-07-25
date accepted: 2017-10-01
issued: 2017-10-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Wei
author list: Agent
  family name: Li
  given name: Xuezhong
author list: Agent
  family name: Qi
  given name: Shaopei
author list: Agent
  family name: Li
  given name: Xueru
author list: Agent
  family name: Zhou
  given name: Kun
author list: Agent
  family name: Qing
  given name: Suzhu
author list: Agent
  family name: Zhang
  given name: Yong
author list: Agent
  family name: Gao
  given name: Ming-Qing
doi: 10.7717/peerj.3950
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-17
copyright: ©2017 Yang et al.
attribution name: Yang et al.

MGST2 and WNT2 are candidate genes for comitant strabismus susceptibility in Japanese patients
type: item
type: AcademicArticle
description: Background/Aim Strabismus is a common condition with misalignment between two eyes that may lead to decrease of visual acuity, lack of binocularity, and diplopia. It is caused by heterogeneous environmental and genetic risk factors. Our previous research has identified new chromosomal susceptibility loci in 4q28.3 and 7q31.2 regions for comitant strabismus in Japanese families. We conducted a verification study by linkage analysis to narrow the chromosomal loci down to a single gene. Methods From Japanese and U.S. databases, 24 rsSNPs and 233 rsSNPs were chosen from the 4q28.3 and 7q31.2 region, respectively, and were typed in 108 affected subjects and 96 unaffected subjects of 58 families with primary and non-syndromic comitant strabismus. Three major analytical methods were used: transmission disequilibrium test (TDT), TDT allowing for errors (TDTae), and linkage analysis under dominant and recessive inheritance. Results The SNPs with significant P values in TDT and TDTae were located solely at the gene, microsomal glutathione S-transferase 2 (MGST2), on chromosome 4q28.3 locus. In contrast, significant SNPs were dispersed in a few genes, containing wingless-type MMTV integration site family member 2 (WNT2), on chromosome 7q31.2 locus. The distribution of significant SNPs on the 7q31.2 locus showed that only the ST7 to WNT2 region in the same big haplotype block contained significant SNPs for all three methods of linkage analysis. Conclusions This study suggests that MGST2 and WNT2 are potential candidates for comitant strabismus in Japanese population.
format: application/pdf
format: text/html
creator: Jingjing Zhang
creator: Toshihiko Matsuo
subject: Genetics
subject: Genomics
subject: Ophthalmology
subject: Medical Genetics
description: doi:10.7717/peerj.3935
publisher: PeerJ Inc.
rights: © 2017 Zhang and Matsuo
abstract: Background/Aim Strabismus is a common condition with misalignment between two eyes that may lead to decrease of visual acuity, lack of binocularity, and diplopia. It is caused by heterogeneous environmental and genetic risk factors. Our previous research has identified new chromosomal susceptibility loci in 4q28.3 and 7q31.2 regions for comitant strabismus in Japanese families. We conducted a verification study by linkage analysis to narrow the chromosomal loci down to a single gene. Methods From Japanese and U.S. databases, 24 rsSNPs and 233 rsSNPs were chosen from the 4q28.3 and 7q31.2 region, respectively, and were typed in 108 affected subjects and 96 unaffected subjects of 58 families with primary and non-syndromic comitant strabismus. Three major analytical methods were used: transmission disequilibrium test (TDT), TDT allowing for errors (TDTae), and linkage analysis under dominant and recessive inheritance. Results The SNPs with significant P values in TDT and TDTae were located solely at the gene, microsomal glutathione S-transferase 2 (MGST2), on chromosome 4q28.3 locus. In contrast, significant SNPs were dispersed in a few genes, containing wingless-type MMTV integration site family member 2 (WNT2), on chromosome 7q31.2 locus. The distribution of significant SNPs on the 7q31.2 locus showed that only the ST7 to WNT2 region in the same big haplotype block contained significant SNPs for all three methods of linkage analysis. Conclusions This study suggests that MGST2 and WNT2 are potential candidates for comitant strabismus in Japanese population.
bibliographic citation: Zhang et al. (2017) MGST2 and WNT2 are candidate genes for comitant strabismus susceptibility in Japanese patients. PeerJ 5:e3935 https://doi.org/10.7717/peerj.3935
date submitted: 2017-06-02
date accepted: 2017-09-26
issued: 2017-10-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Jingjing
author list: Agent
  family name: Matsuo
  given name: Toshihiko
doi: 10.7717/peerj.3935
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-17
copyright: ©2017 Zhang and Matsuo
attribution name: Zhang and Matsuo

Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils
type: item
type: AcademicArticle
description: In arable cropping systems, reduced or conservation tillage practices are linked with improved soil quality, C retention and higher microbial biomass, but most long-term studies rarely focus on depths greater than 15 cm nor allow comparison of microbial community responses to agricultural practices. We investigated microbial community structure in a long-term field trial (12-years, Lincoln, New Zealand) established in a silt-loam soil over four depth ranges down to 30 cm. Our objectives were to investigate the degree of homogenisation of soil biological and chemical properties with depth, and to determine the main drivers of microbial community response to tillage. We hypothesised that soil microbiological responses would depend on tillage depth, observed by a homogenisation of microbial community composition within the tilled zone. Tillage treatments were mouldboard plough and disc harrow, impacting soil to ∼20 and ∼10 cm depth, respectively. These treatments were compared to a no-tillage treatment and two control treatments, both permanent pasture and permanent fallow. Bacterial and fungal communities collected from the site were not impacted by the spatial location of sampling across the study area but were affected by physicochemical changes associated with tillage induced soil homogenisation and plant presence. Tillage treatment effects on both species richness and composition were more evident for bacterial communities than fungal communities, and were greater at depths <15 cm. Homogenisation of soil and changing land management appears to redistribute both microbiota and nutrients deeper in the soil profile while consequences for soil biogeochemical functioning remain poorly understood.
format: application/pdf
format: text/html
creator: Craig Anderson
creator: Mike Beare
creator: Hannah L. Buckley
creator: Gavin Lear
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.3930
publisher: PeerJ Inc.
rights: © 2017 Anderson et al.
abstract: In arable cropping systems, reduced or conservation tillage practices are linked with improved soil quality, C retention and higher microbial biomass, but most long-term studies rarely focus on depths greater than 15 cm nor allow comparison of microbial community responses to agricultural practices. We investigated microbial community structure in a long-term field trial (12-years, Lincoln, New Zealand) established in a silt-loam soil over four depth ranges down to 30 cm. Our objectives were to investigate the degree of homogenisation of soil biological and chemical properties with depth, and to determine the main drivers of microbial community response to tillage. We hypothesised that soil microbiological responses would depend on tillage depth, observed by a homogenisation of microbial community composition within the tilled zone. Tillage treatments were mouldboard plough and disc harrow, impacting soil to ∼20 and ∼10 cm depth, respectively. These treatments were compared to a no-tillage treatment and two control treatments, both permanent pasture and permanent fallow. Bacterial and fungal communities collected from the site were not impacted by the spatial location of sampling across the study area but were affected by physicochemical changes associated with tillage induced soil homogenisation and plant presence. Tillage treatment effects on both species richness and composition were more evident for bacterial communities than fungal communities, and were greater at depths <15 cm. Homogenisation of soil and changing land management appears to redistribute both microbiota and nutrients deeper in the soil profile while consequences for soil biogeochemical functioning remain poorly understood.
bibliographic citation: Anderson et al. (2017) Bacterial and fungal communities respond differently to varying tillage depth in agricultural soils. PeerJ 5:e3930 https://doi.org/10.7717/peerj.3930
date submitted: 2017-07-26
date accepted: 2017-09-26
issued: 2017-10-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Anderson
  given name: Craig
author list: Agent
  family name: Beare
  given name: Mike
author list: Agent
  family name: Buckley
  given name: Hannah L.
author list: Agent
  family name: Lear
  given name: Gavin
doi: 10.7717/peerj.3930
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-17
copyright: ©2017 Anderson et al.
attribution name: Anderson et al.

How to normalize metatranscriptomic count data for differential expression analysis
type: item
type: AcademicArticle
description: Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. Methods We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count data. For taxon-specific scaling and recombination of scaled counts we provide a simple R script. Results When applying transcriptomic tools for differential expression analysis directly to metatranscriptomic data with an organism-independent (global) scaling of counts the resulting differences may be difficult to interpret. The differences may correspond to changing functional profiles of the contributing organisms but may also result from a variation of taxonomic abundances. Taxon-specific scaling eliminates this variation and therefore the resulting differences actually reflect a different behavior of organisms under changing conditions. In simulation studies we show that the divergence between results from global and taxon-specific scaling can be drastic. In particular, the variation of organism abundances can imply a considerable increase of significant differences with global scaling. Also, on real metatranscriptomic data, the predictions from taxon-specific and…
format: application/pdf
format: text/html
creator: Heiner Klingenberg
creator: Peter Meinicke
subject: Bioinformatics
subject: Statistics
description: doi:10.7717/peerj.3859
publisher: PeerJ Inc.
rights: © 2017 Klingenberg and Meinicke
abstract: Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. Methods We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count data. For taxon-specific scaling and recombination of scaled counts we provide a simple R script. Results When applying transcriptomic tools for differential expression analysis directly to metatranscriptomic data with an organism-independent (global) scaling of counts the resulting differences may be difficult to interpret. The differences may correspond to changing functional profiles of the contributing organisms but may also result from a variation of taxonomic abundances. Taxon-specific scaling eliminates this variation and therefore the resulting differences actually reflect a different behavior of organisms under changing conditions. In simulation studies we show that the divergence between results from global and taxon-specific scaling can be drastic. In particular, the variation of organism abundances can imply a considerable increase of significant differences with global scaling. Also, on real metatranscriptomic data, the predictions from taxon-specific and…
bibliographic citation: Klingenberg et al. (2017) How to normalize metatranscriptomic count data for differential expression analysis. PeerJ 5:e3859 https://doi.org/10.7717/peerj.3859
date submitted: 2017-05-10
date accepted: 2017-09-06
issued: 2017-10-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klingenberg
  given name: Heiner
author list: Agent
  family name: Meinicke
  given name: Peter
doi: 10.7717/peerj.3859
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-17
copyright: ©2017 Klingenberg and Meinicke
attribution name: Klingenberg and Meinicke

Exploring the psychological health of emergency dispatch centre operatives: a systematic review and narrative synthesis
type: item
type: AcademicArticle
description: Background The study objective was to investigate and synthesize available evidence relating to the psychological health of Emergency Dispatch Centre (EDC) operatives, and to identify key stressors experienced by EDC operatives. Methods Eight electronic databases (Embase, PubMed, Medline, CINAHL, PsycInfo, PsycArticles, The Psychology and Behavioural Sciences Collection, and Google Scholar) were searched. All study designs were included, and no date limits were set. Studies were included if they were published in English, and explored the psychological health of any EDC operatives, across fire, police, and emergency medical services. Studies were excluded if they related solely to other emergency workers, such as police officers or paramedics. Methodological quality of included studies was assessed using checklists adapted from the Critical Appraisal Skills Programme. A narrative synthesis was conducted, using thematic analysis. Results A total of 16 articles were included in the review. Two overarching themes were identified during the narrative synthesis: ‘Organisational and Operational Factors’ and ‘Interactions with Others’. Stressors identified included being exposed to traumatic calls, lacking control over high workload, and working in under-resourced and pressured environments. Lack of support from management and providing an emotionally demanding service were additional sources of stress. Peer support and social support from friends and family were helpful in managing work-related stress. Discussion EDC operatives experience stress as a result of their work, which appears to be related to negative psychological health outcomes. Future research should explore the long-term effects of this stress, and the potential for workplace interventions to alleviate the negative impacts on psychological health. PROSPERO Registration Number CRD42014010806.
format: application/pdf
format: text/html
creator: Sarah E. Golding
creator: Claire Horsfield
creator: Annette Davies
creator: Bernadette Egan
creator: Martyn Jones
creator: Mary Raleigh
creator: Patricia Schofield
creator: Allison Squires
creator: Kath Start
creator: Tom Quinn
creator: Mark Cropley
subject: Emergency and Critical Care
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3735
publisher: PeerJ Inc.
rights: © 2017 Golding et al.
abstract: Background The study objective was to investigate and synthesize available evidence relating to the psychological health of Emergency Dispatch Centre (EDC) operatives, and to identify key stressors experienced by EDC operatives. Methods Eight electronic databases (Embase, PubMed, Medline, CINAHL, PsycInfo, PsycArticles, The Psychology and Behavioural Sciences Collection, and Google Scholar) were searched. All study designs were included, and no date limits were set. Studies were included if they were published in English, and explored the psychological health of any EDC operatives, across fire, police, and emergency medical services. Studies were excluded if they related solely to other emergency workers, such as police officers or paramedics. Methodological quality of included studies was assessed using checklists adapted from the Critical Appraisal Skills Programme. A narrative synthesis was conducted, using thematic analysis. Results A total of 16 articles were included in the review. Two overarching themes were identified during the narrative synthesis: ‘Organisational and Operational Factors’ and ‘Interactions with Others’. Stressors identified included being exposed to traumatic calls, lacking control over high workload, and working in under-resourced and pressured environments. Lack of support from management and providing an emotionally demanding service were additional sources of stress. Peer support and social support from friends and family were helpful in managing work-related stress. Discussion EDC operatives experience stress as a result of their work, which appears to be related to negative psychological health outcomes. Future research should explore the long-term effects of this stress, and the potential for workplace interventions to alleviate the negative impacts on psychological health. PROSPERO Registration Number CRD42014010806.
bibliographic citation: Golding et al. (2017) Exploring the psychological health of emergency dispatch centre operatives: a systematic review and narrative synthesis. PeerJ 5:e3735 https://doi.org/10.7717/peerj.3735
date submitted: 2017-04-08
date accepted: 2017-08-04
issued: 2017-10-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Golding
  given name: Sarah E.
author list: Agent
  family name: Horsfield
  given name: Claire
author list: Agent
  family name: Davies
  given name: Annette
author list: Agent
  family name: Egan
  given name: Bernadette
author list: Agent
  family name: Jones
  given name: Martyn
author list: Agent
  family name: Raleigh
  given name: Mary
author list: Agent
  family name: Schofield
  given name: Patricia
author list: Agent
  family name: Squires
  given name: Allison
author list: Agent
  family name: Start
  given name: Kath
author list: Agent
  family name: Quinn
  given name: Tom
author list: Agent
  family name: Cropley
  given name: Mark
doi: 10.7717/peerj.3735
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-17
copyright: ©2017 Golding et al.
attribution name: Golding et al.

Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI
type: item
type: AcademicArticle
description: Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island.
format: application/pdf
format: text/html
creator: Miranda H. Hengy
creator: Dean J. Horton
creator: Donald G. Uzarski
creator: Deric R. Learman
subject: Biodiversity
subject: Ecology
subject: Environmental Sciences
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.3937
publisher: PeerJ Inc.
rights: © 2017 Hengy et al.
abstract: Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island.
bibliographic citation: Hengy et al. (2017) Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI. PeerJ 5:e3937 https://doi.org/10.7717/peerj.3937
date submitted: 2017-06-13
date accepted: 2017-09-26
issued: 2017-10-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hengy
  given name: Miranda H.
author list: Agent
  family name: Horton
  given name: Dean J.
author list: Agent
  family name: Uzarski
  given name: Donald G.
author list: Agent
  family name: Learman
  given name: Deric R.
doi: 10.7717/peerj.3937
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-16
copyright: ©2017 Hengy et al.
attribution name: Hengy et al.

Tolerance: the forgotten child of plant resistance
type: item
type: AcademicArticle
description: Plant resistance against insect herbivory has greatly focused on antibiosis, whereby the plant has a deleterious effect on the herbivore, and antixenosis, whereby the plant is able to direct the herbivore away from it. Although these two types of resistance may reduce injury and yield loss, they can produce selection pressures on insect herbivores that lead to pest resistance. Tolerance, on the other hand, is a more sustainable pest management strategy because it involves only a plant response and therefore does not cause evolution of resistance in target pest populations. Despite its attractive attributes, tolerance has been poorly studied and understood. In this critical, interpretive review, we discuss tolerance to insect herbivory and the biological and socioeconomic factors that have limited its use in plant resistance and integrated pest management. First, tolerance is difficult to identify, and the mechanisms conferring it are poorly understood. Second, the genetics of tolerance are mostly unknown. Third, several obstacles hinder the establishment of high-throughput phenotyping methods for large-scale screening of tolerance. Fourth, tolerance has received little attention from entomologists because, for most, their primary interest, research training, and funding opportunities are in mechanisms which affect pest biology, not plant biology. Fifth, the efforts of plant resistance are directed at controlling pest populations rather than managing plant stress. We conclude this paper by discussing future research and development activities.
format: application/pdf
format: text/html
creator: Robert K.D. Peterson
creator: Andrea C. Varella
creator: Leon G. Higley
subject: Agricultural Science
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.3934
publisher: PeerJ Inc.
rights: © 2017 Peterson et al.
abstract: Plant resistance against insect herbivory has greatly focused on antibiosis, whereby the plant has a deleterious effect on the herbivore, and antixenosis, whereby the plant is able to direct the herbivore away from it. Although these two types of resistance may reduce injury and yield loss, they can produce selection pressures on insect herbivores that lead to pest resistance. Tolerance, on the other hand, is a more sustainable pest management strategy because it involves only a plant response and therefore does not cause evolution of resistance in target pest populations. Despite its attractive attributes, tolerance has been poorly studied and understood. In this critical, interpretive review, we discuss tolerance to insect herbivory and the biological and socioeconomic factors that have limited its use in plant resistance and integrated pest management. First, tolerance is difficult to identify, and the mechanisms conferring it are poorly understood. Second, the genetics of tolerance are mostly unknown. Third, several obstacles hinder the establishment of high-throughput phenotyping methods for large-scale screening of tolerance. Fourth, tolerance has received little attention from entomologists because, for most, their primary interest, research training, and funding opportunities are in mechanisms which affect pest biology, not plant biology. Fifth, the efforts of plant resistance are directed at controlling pest populations rather than managing plant stress. We conclude this paper by discussing future research and development activities.
bibliographic citation: Peterson et al. (2017) Tolerance: the forgotten child of plant resistance. PeerJ 5:e3934 https://doi.org/10.7717/peerj.3934
date submitted: 2017-07-20
date accepted: 2017-09-26
issued: 2017-10-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peterson
  given name: Robert K.D.
author list: Agent
  family name: Varella
  given name: Andrea C.
author list: Agent
  family name: Higley
  given name: Leon G.
doi: 10.7717/peerj.3934
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-16
copyright: ©2017 Peterson et al.
attribution name: Peterson et al.

L1 and L2 reading skills in Dutch adolescents with a familial risk of dyslexia
type: item
type: AcademicArticle
description: Background The present study investigated differences in reading and spelling outcomes in Dutch and English as a second language (ESL) in adolescents with a high familial risk of dyslexia, of whom some have developed dyslexia (HRDys) while others have not (HRnonDys), in comparison to a low familial risk control group without dyslexia (LRnonDys). This allowed us to investigate the persistence of dyslexia in the first language (L1) and the effect of dyslexia on the second language (L2), which has, in this case, a lower orthographic transparency. Furthermore, the inclusion of the HRnonDys group allowed us to investigate the continuity of the familial risk of dyslexia, as previous studies observed that the HRnonDys group often scores in between the HRDys and LRnonDys group, and whether these readers without reading deficits in Dutch, have more reading difficulties in ESL. Methods The data of three groups of adolescents were analyzed; 27 LRnonDys, 25 HRdys 25 HRnonDys. The mean age was 14;1 years; months, and 37 were male. All were native speakers of Dutch, attended regular secondary education (grade 7–10), and were non-native speakers of English. Using MANOVA the groups were compared on Dutch and English word reading fluency (WRF), spelling and vocabulary, Dutch pseudoword and loanword reading fluency, phonological awareness (PA), rapid automatized naming (RAN), and verbal short term and working memory. A repeated measures ANOVA was used to compare English and Dutch WRF, spelling and vocabulary directly within the three groups. Results The analyses revealed that the HRDys group had a deficit in both reading and spelling in Dutch and ESL. They also performed poorer than the LRnonDys group on all other measures. Effect sizes were especially large for pseudoword reading and the reaction times during the PA task. The HRnonDys group scored generally poorer than the LRnonDys group but this difference was only significant for Dutch pseudoword reading, PA reaction times and ver…
format: application/pdf
format: text/html
creator: Ellie R.H. van Setten
creator: Wim Tops
creator: Britt E. Hakvoort
creator: Aryan van der Leij
creator: Natasha M. Maurits
creator: Ben A.M. Maassen
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3895
publisher: PeerJ Inc.
rights: © 2017 van Setten et al.
abstract: Background The present study investigated differences in reading and spelling outcomes in Dutch and English as a second language (ESL) in adolescents with a high familial risk of dyslexia, of whom some have developed dyslexia (HRDys) while others have not (HRnonDys), in comparison to a low familial risk control group without dyslexia (LRnonDys). This allowed us to investigate the persistence of dyslexia in the first language (L1) and the effect of dyslexia on the second language (L2), which has, in this case, a lower orthographic transparency. Furthermore, the inclusion of the HRnonDys group allowed us to investigate the continuity of the familial risk of dyslexia, as previous studies observed that the HRnonDys group often scores in between the HRDys and LRnonDys group, and whether these readers without reading deficits in Dutch, have more reading difficulties in ESL. Methods The data of three groups of adolescents were analyzed; 27 LRnonDys, 25 HRdys 25 HRnonDys. The mean age was 14;1 years; months, and 37 were male. All were native speakers of Dutch, attended regular secondary education (grade 7–10), and were non-native speakers of English. Using MANOVA the groups were compared on Dutch and English word reading fluency (WRF), spelling and vocabulary, Dutch pseudoword and loanword reading fluency, phonological awareness (PA), rapid automatized naming (RAN), and verbal short term and working memory. A repeated measures ANOVA was used to compare English and Dutch WRF, spelling and vocabulary directly within the three groups. Results The analyses revealed that the HRDys group had a deficit in both reading and spelling in Dutch and ESL. They also performed poorer than the LRnonDys group on all other measures. Effect sizes were especially large for pseudoword reading and the reaction times during the PA task. The HRnonDys group scored generally poorer than the LRnonDys group but this difference was only significant for Dutch pseudoword reading, PA reaction times and ver…
bibliographic citation: van Setten et al. (2017) L1 and L2 reading skills in Dutch adolescents with a familial risk of dyslexia. PeerJ 5:e3895 https://doi.org/10.7717/peerj.3895
date submitted: 2017-04-25
date accepted: 2017-09-15
issued: 2017-10-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: van Setten
  given name: Ellie R.H.
author list: Agent
  family name: Tops
  given name: Wim
author list: Agent
  family name: Hakvoort
  given name: Britt E.
author list: Agent
  family name: van der Leij
  given name: Aryan
author list: Agent
  family name: Maurits
  given name: Natasha M.
author list: Agent
  family name: Maassen
  given name: Ben A.M.
doi: 10.7717/peerj.3895
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-16
copyright: ©2017 van Setten et al.
attribution name: van Setten et al.

Investigating the level of agreement of two positioning protocols when using dual energy X-ray absorptiometry in the assessment of body composition
type: item
type: AcademicArticle
description: Background Dual energy X-ray absorptiometry (DXA) is a commonly used instrument for analysing segmental body composition (BC). The information from the scan guides the clinician in the treatment of conditions such as obesity and can be used to monitor recovery of lean mass following injury. Two commonly used DXA positioning protocols have been identified—the Nana positioning protocol and the National Health and Nutrition Examination Survey (NHANES). Both protocols have been shown to be reliable. However, only one study has assessed the level of agreement between the protocols and ascertained the participants’ preference of protocol based upon comfort. Given the paucity of research in the field and the growing use of DXA in both healthy and pathological populations further research determining the most appropriate positioning protocol is warranted. Therefore, the aims of this study were to assess the level of agreement between results from the NHANES protocol and Nana protocol, and the participants’ preference of protocol based on comfort. Methods Thirty healthy participants (15 males, 15 females, aged 23–59 years) volunteered to participate in this study. These participants underwent two whole body DXA scans in a single morning (Nana positioning protocol and NHANES positioning protocol), in a randomised order. Each participant attended for scanning wearing minimal clothing and having fasted overnight, refrained from exercise in the past 24 h and voided their bladders. Level of agreement, comparing NAHNES to Nana protocol was assessed using an intra-class correlation coefficient (ICC), concordance correlation coefficient (CCC) and percentage change in mean. Limit of agreement comparing the two protocols were assessed using plots, mean difference and confidence limits. Participants were asked to indicate the protocol they found most comfortable. Results When assessing level of agreement between protocols both the ICC and CCC scores were very high and ranged from 0.987…
format: application/pdf
format: text/html
creator: Flinn Shiel
creator: Carl Persson
creator: Vini Simas
creator: James Furness
creator: Mike Climstein
creator: Ben Schram
subject: Drugs and Devices
subject: Epidemiology
subject: Kinesiology
subject: Nutrition
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.3880
publisher: PeerJ Inc.
rights: © 2017 Shiel et al.
abstract: Background Dual energy X-ray absorptiometry (DXA) is a commonly used instrument for analysing segmental body composition (BC). The information from the scan guides the clinician in the treatment of conditions such as obesity and can be used to monitor recovery of lean mass following injury. Two commonly used DXA positioning protocols have been identified—the Nana positioning protocol and the National Health and Nutrition Examination Survey (NHANES). Both protocols have been shown to be reliable. However, only one study has assessed the level of agreement between the protocols and ascertained the participants’ preference of protocol based upon comfort. Given the paucity of research in the field and the growing use of DXA in both healthy and pathological populations further research determining the most appropriate positioning protocol is warranted. Therefore, the aims of this study were to assess the level of agreement between results from the NHANES protocol and Nana protocol, and the participants’ preference of protocol based on comfort. Methods Thirty healthy participants (15 males, 15 females, aged 23–59 years) volunteered to participate in this study. These participants underwent two whole body DXA scans in a single morning (Nana positioning protocol and NHANES positioning protocol), in a randomised order. Each participant attended for scanning wearing minimal clothing and having fasted overnight, refrained from exercise in the past 24 h and voided their bladders. Level of agreement, comparing NAHNES to Nana protocol was assessed using an intra-class correlation coefficient (ICC), concordance correlation coefficient (CCC) and percentage change in mean. Limit of agreement comparing the two protocols were assessed using plots, mean difference and confidence limits. Participants were asked to indicate the protocol they found most comfortable. Results When assessing level of agreement between protocols both the ICC and CCC scores were very high and ranged from 0.987…
bibliographic citation: Shiel et al. (2017) Investigating the level of agreement of two positioning protocols when using dual energy X-ray absorptiometry in the assessment of body composition. PeerJ 5:e3880 https://doi.org/10.7717/peerj.3880
date submitted: 2017-05-16
date accepted: 2017-09-12
issued: 2017-10-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shiel
  given name: Flinn
author list: Agent
  family name: Persson
  given name: Carl
author list: Agent
  family name: Simas
  given name: Vini
author list: Agent
  family name: Furness
  given name: James
author list: Agent
  family name: Climstein
  given name: Mike
author list: Agent
  family name: Schram
  given name: Ben
doi: 10.7717/peerj.3880
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-16
copyright: ©2017 Shiel et al.
attribution name: Shiel et al.

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