PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Massively parallel read mapping on GPUs with the q-group index and PEANUT
items: Effect of obesity and exercise on the expression of the novel myokines, Myonectin and Fibronectin type III domain containing 5
items: Bumblebee size polymorphism and worker response to queen pheromone
items: GroopM: an automated tool for the recovery of population genomes from related metagenomes
items: Eutrophication and the dietary promotion of sea turtle tumors
items: Nest-building behavior of Monk Parakeets and insights into potential mechanisms for reducing damage to utility poles
items: Detailed comparison of two popular variant calling packages for exome and targeted exon studies
items: Multi-decade biomass dynamics in an old-growth hemlock-northern hardwood forest, Michigan, USA
items: Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression
items: One pair of hands is not like another: caudate BOLD response in dogs depends on signal source and canine temperament
items: Spatial genetic structure across a hybrid zone between European rabbit subspecies
items: Fibrochondrogenic potential of synoviocytes from osteoarthritic and normal joints cultured as tensioned bioscaffolds for meniscal tissue engineering in dogs
items: Case based rubella surveillance in Abia State, South East Nigeria, 2007–2011
items: A candidate multimodal functional genetic network for thermal adaptation
items: Factors associated with leisure time physical inactivity in black individuals: hierarchical model
items: Species and size diversity in protective services offered by coral guard-crabs
items: Revision of the Late Jurassic crocodyliform Alligatorellus, and evidence for allopatric speciation driving high diversity in western European atoposaurids
items: The self prefers itself? Self-referential versus parental standards in face attractiveness
items: Chronic playback of boat noise does not impact hatching success or post-hatching larval growth and survival in a cichlid fish
items: Swarm: robust and fast clustering method for amplicon-based studies
items: Habitat creation and biodiversity maintenance in mangrove forests: teredinid bivalves as ecosystem engineers
items: Synergy as a rationale for phage therapy using phage cocktails
items: Fast and accurate estimation of the covariance between pairwise maximum likelihood distances
items: Shared phylogeographic patterns between the ectocommensal flatworm Temnosewellia albata and its host, the endangered freshwater crayfish Euastacus robertsi
items: Bio-inspired design of ice-retardant devices based on benthic marine invertebrates: the effect of surface texture
items: Differences in healthcare expenditures for inflammatory bowel disease by insurance status, income, and clinical care setting
items: A simple non-invasive method for measuring gross brain size in small live fish with semi-transparent heads
items: Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer
items: The impact of atypical early histories on pet or performer chimpanzees
items: Error estimates for the analysis of differential expression from RNA-seq count data
items: Livestock as a potential biological control agent for an invasive wetland plant
items: Removing batch effects for prediction problems with frozen surrogate variable analysis
items: Anopheles gambiae densovirus (AgDNV) has negligible effects on adult survival and transcriptome of its mosquito host
items: MicroRNAs expression profile in CCR6+ regulatory T cells
items: Students distracted by electronic devices perform at the same level as those who are focused on the lecture
items: Turf algae-mediated coral damage in coastal reefs of Belize, Central America
items: What’s for dinner? Undescribed species of porcini in a commercial packet
items: Role of enzymatic activity in muscle damage and cytotoxicity induced by Bothrops asper Asp49 phospholipase A2 myotoxins: are there additional effector mechanisms involved?
items: Nestling activity levels during begging behaviour predicts activity level and body mass in adulthood
items: Translation, adaptation, validation and performance of the American Weight Efficacy Lifestyle Questionnaire Short Form (WEL-SF) to a Norwegian version: a cross-sectional study
items: Population structure and residency patterns of whale sharks, Rhincodon typus, at a provisioning site in Cebu, Philippines
items: Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity
items: Tracheostomy in children with congenital heart disease: a national analysis of the Kids’ Inpatient Database
items: Identification of a truncated splice variant of IL-18 receptor alpha in the human and rat, with evidence of wider evolutionary conservation
items: Modelling foraging movements of diving predators: a theoretical study exploring the effect of heterogeneous landscapes on foraging efficiency
items: Mitochondrial cytochrome b sequence data are not an improvement for species identification in scleractinian corals
items: Estimating the prevalence of researcher misconduct: a study of UK academics within biological sciences
items: Psoralidin induces autophagy through ROS generation which inhibits the proliferation of human lung cancer A549 cells
items: Digging the pupfish out of its hole: risk analyses to guide harvest of Devils Hole pupfish for captive breeding
items: Trace element profiles of the sea anemone Anemonia viridis living nearby a natural CO2 vent
items: Alterations in fiber pathways reveal brain tumor typology: a diffusion tractography study
items: Metagenome fragment classification based on multiple motif-occurrence profiles
items: Protein kinase C in the wood frog, Rana sylvatica: reassessing the tissue-specific regulation of PKC isozymes during freezing
items: Effects of low and high dose intraarticular tiludronate on synovial fluid and clinical variables in healthy horses—a preliminary investigation
items: Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene
items: Benthic primary production in an upwelling-influenced coral reef, Colombian Caribbean
items: Effects of deuterium oxide on cell growth and vesicle speed in RBL-2H3 cells
items: With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase
items: The effect of cigarette smoking habits on the outcome of dental implant treatment
items: Too big to be noticed: cryptic invasion of Asian camel crickets in North American houses
items: Hand infections: a retrospective analysis
items: Exceptionally preserved insect fossils in the Late Jurassic lagoon of Orbagnoux (Rhône Valley, France)

Massively parallel read mapping on GPUs with the q-group index and PEANUT
type: item
type: AcademicArticle
description: We present the q-group index, a novel data structure for read mapping tailored towards graphics processing units (GPUs) with a small memory footprint and efficient parallel algorithms for querying and building. On top of the q-group index we introduce PEANUT, a highly parallel GPU-based read mapper. PEANUT provides the possibility to output both the best hits or all hits of a read. Our benchmarks show that PEANUT outperforms other state-of-the-art read mappers in terms of speed while maintaining or slightly increasing precision, recall and sensitivity.
format: application/pdf
format: text/html
creator: Johannes Köster
creator: Sven Rahmann
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.606
publisher: PeerJ Inc.
rights: © 2014 Köster and Rahmann
abstract: We present the q-group index, a novel data structure for read mapping tailored towards graphics processing units (GPUs) with a small memory footprint and efficient parallel algorithms for querying and building. On top of the q-group index we introduce PEANUT, a highly parallel GPU-based read mapper. PEANUT provides the possibility to output both the best hits or all hits of a read. Our benchmarks show that PEANUT outperforms other state-of-the-art read mappers in terms of speed while maintaining or slightly increasing precision, recall and sensitivity.
bibliographic citation: Köster et al. (2014) Massively parallel read mapping on GPUs with the q-group index and PEANUT. PeerJ 2:e606 https://doi.org/10.7717/peerj.606
date submitted: 2014-07-23
date accepted: 2014-09-11
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Köster
  given name: Johannes
author list: Agent
  family name: Rahmann
  given name: Sven
doi: 10.7717/peerj.606
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Köster and Rahmann
attribution name: Köster and Rahmann

Effect of obesity and exercise on the expression of the novel myokines, Myonectin and Fibronectin type III domain containing 5
type: item
type: AcademicArticle
description: Metabolic dysfunction in skeletal muscle is a major contributor to the development of type 2 diabetes. Endurance exercise training has long been established as an effective means to directly restore skeletal muscle glucose and lipid uptake and metabolism. However, in addition to the direct effects of skeletal muscle on glucose and lipids, there is renewed interest in the ability of skeletal muscle to coordinate metabolic activity of other tissues, such as adipose tissue and liver. The purpose of this study was to examine the effects of endurance exercise on the expression level of two novel muscle-derived secreted factors, or myokines, Myonectin and Fibronectin type III domain containing 5 (FNDC5), the precursor for Irisin. Methods. We performed immunoblot analysis and quantitative real-time PCR analysis of Myonectin and FNDC5 in the diaphragm muscles of obese Zucker rat (OZR) and lean Zucker rat (LZR) with 9 weeks of aerobic training on a motorized treadmill. Results. We show that myonectin gene expression is increased in the OZR model of obesity and decreases with exercise in both lean and obese Zucker rats. Conversely, myonectin protein concentration was elevated with exercise. Similarly, FNDC5 mRNA levels are significantly higher in the OZR, however exercise training had no effect on the expression level of FNDC5 in either the LZR or OZR. We did not observe any difference in muscle protein content of Irisin with obesity or exercise. Conclusion. Our data shows that exercise training does not increase either FNDC5 or myonectin gene expression, indicating that increased transcriptional regulation of these myokines is not induced by exercise. However, our data also indicates a yet to be explored disconnect between myonectin gene expression and protein content. Further, this report highlights the importance of verifying reference genes when completing gene expression analysis. We found that many commonly used reference genes varied significantly by obesity and/or exe…
format: application/pdf
format: text/html
creator: Jonathan M. Peterson
creator: Ryan Mart
creator: Cherie E. Bond
subject: Molecular Biology
subject: Diabetes and Endocrinology
subject: Kinesiology
subject: Metabolic Sciences
description: doi:10.7717/peerj.605
publisher: PeerJ Inc.
rights: © 2014 Peterson et al.
abstract: Metabolic dysfunction in skeletal muscle is a major contributor to the development of type 2 diabetes. Endurance exercise training has long been established as an effective means to directly restore skeletal muscle glucose and lipid uptake and metabolism. However, in addition to the direct effects of skeletal muscle on glucose and lipids, there is renewed interest in the ability of skeletal muscle to coordinate metabolic activity of other tissues, such as adipose tissue and liver. The purpose of this study was to examine the effects of endurance exercise on the expression level of two novel muscle-derived secreted factors, or myokines, Myonectin and Fibronectin type III domain containing 5 (FNDC5), the precursor for Irisin. Methods. We performed immunoblot analysis and quantitative real-time PCR analysis of Myonectin and FNDC5 in the diaphragm muscles of obese Zucker rat (OZR) and lean Zucker rat (LZR) with 9 weeks of aerobic training on a motorized treadmill. Results. We show that myonectin gene expression is increased in the OZR model of obesity and decreases with exercise in both lean and obese Zucker rats. Conversely, myonectin protein concentration was elevated with exercise. Similarly, FNDC5 mRNA levels are significantly higher in the OZR, however exercise training had no effect on the expression level of FNDC5 in either the LZR or OZR. We did not observe any difference in muscle protein content of Irisin with obesity or exercise. Conclusion. Our data shows that exercise training does not increase either FNDC5 or myonectin gene expression, indicating that increased transcriptional regulation of these myokines is not induced by exercise. However, our data also indicates a yet to be explored disconnect between myonectin gene expression and protein content. Further, this report highlights the importance of verifying reference genes when completing gene expression analysis. We found that many commonly used reference genes varied significantly by obesity and/or exe…
bibliographic citation: Peterson et al. (2014) Effect of obesity and exercise on the expression of the novel myokines, Myonectin and Fibronectin type III domain containing 5. PeerJ 2:e605 https://doi.org/10.7717/peerj.605
date submitted: 2014-06-06
date accepted: 2014-09-10
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peterson
  given name: Jonathan M.
author list: Agent
  family name: Mart
  given name: Ryan
author list: Agent
  family name: Bond
  given name: Cherie E.
doi: 10.7717/peerj.605
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Peterson et al.
attribution name: Peterson et al.

Bumblebee size polymorphism and worker response to queen pheromone
type: item
type: AcademicArticle
description: Queen pheromones are chemical signals produced by reproductive individuals in social insect colonies. In many species they are key to the maintenance of reproductive division of labor, with workers beginning to reproduce individually once the queen pheromone disappears. Recently, a queen pheromone that negatively affects worker fecundity was discovered in the bumblebee Bombus terrestris, presenting an exciting opportunity for comparisons with analogous queen pheromones in independently-evolved eusocial lineages such as honey bees, ants, wasps and termites. I set out to replicate this discovery and verify its reproducibility. Using blind, controlled experiments, I found that n-pentacosane (C25) does indeed negatively affect worker ovary development. Moreover, the pheromone affects both large and small workers, and applies to workers from large, mature colonies as well as young colonies. Given that C25 is readily available and that bumblebees are popular study organisms, I hope that this replication will encourage other researchers to tackle the many research questions enabled by the discovery of a queen pheromone.
format: application/pdf
format: text/html
creator: Luke Holman
subject: Animal Behavior
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.604
publisher: PeerJ Inc.
rights: © 2014 Holman
abstract: Queen pheromones are chemical signals produced by reproductive individuals in social insect colonies. In many species they are key to the maintenance of reproductive division of labor, with workers beginning to reproduce individually once the queen pheromone disappears. Recently, a queen pheromone that negatively affects worker fecundity was discovered in the bumblebee Bombus terrestris, presenting an exciting opportunity for comparisons with analogous queen pheromones in independently-evolved eusocial lineages such as honey bees, ants, wasps and termites. I set out to replicate this discovery and verify its reproducibility. Using blind, controlled experiments, I found that n-pentacosane (C25) does indeed negatively affect worker ovary development. Moreover, the pheromone affects both large and small workers, and applies to workers from large, mature colonies as well as young colonies. Given that C25 is readily available and that bumblebees are popular study organisms, I hope that this replication will encourage other researchers to tackle the many research questions enabled by the discovery of a queen pheromone.
bibliographic citation: Holman (2014) Bumblebee size polymorphism and worker response to queen pheromone. PeerJ 2:e604 https://doi.org/10.7717/peerj.604
date submitted: 2014-08-20
date accepted: 2014-09-09
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Holman
  given name: Luke
doi: 10.7717/peerj.604
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Holman
attribution name: Holman

GroopM: an automated tool for the recovery of population genomes from related metagenomes
type: item
type: AcademicArticle
description: Metagenomic binning methods that leverage differential population abundances in microbial communities (differential coverage) are emerging as a complementary approach to conventional composition-based binning. Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. We demonstrate the effectiveness of GroopM using synthetic and real-world metagenomes, and show that GroopM produces results comparable with more time consuming, labor-intensive methods.
format: application/pdf
format: text/html
creator: Michael Imelfort
creator: Donovan Parks
creator: Ben J. Woodcroft
creator: Paul Dennis
creator: Philip Hugenholtz
creator: Gene W. Tyson
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.603
publisher: PeerJ Inc.
rights: © 2014 Imelfort et al.
abstract: Metagenomic binning methods that leverage differential population abundances in microbial communities (differential coverage) are emerging as a complementary approach to conventional composition-based binning. Here we introduce GroopM, an automated binning tool that primarily uses differential coverage to obtain high fidelity population genomes from related metagenomes. We demonstrate the effectiveness of GroopM using synthetic and real-world metagenomes, and show that GroopM produces results comparable with more time consuming, labor-intensive methods.
bibliographic citation: Imelfort et al. (2014) GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ 2:e603 https://doi.org/10.7717/peerj.603
date submitted: 2014-06-09
date accepted: 2014-09-09
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Imelfort
  given name: Michael
author list: Agent
  family name: Parks
  given name: Donovan
author list: Agent
  family name: Woodcroft
  given name: Ben J.
author list: Agent
  family name: Dennis
  given name: Paul
author list: Agent
  family name: Hugenholtz
  given name: Philip
author list: Agent
  family name: Tyson
  given name: Gene W.
doi: 10.7717/peerj.603
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Imelfort et al.
attribution name: Imelfort et al.

Eutrophication and the dietary promotion of sea turtle tumors
type: item
type: AcademicArticle
description: The tumor-forming disease fibropapillomatosis (FP) has afflicted sea turtle populations for decades with no clear cause. A lineage of α-herpesviruses associated with these tumors has existed for millennia, suggesting environmental factors are responsible for its recent epidemiology. In previous work, we described how herpesviruses could cause FP tumors through a metabolic influx of arginine. We demonstrated the disease prevails in chronically eutrophied coastal waters, and that turtles foraging in these sites might consume arginine-enriched macroalgae. Here, we test the idea using High-Performance Liquid Chromatography (HPLC) to describe the amino acid profiles of green turtle (Chelonia mydas) tumors and five common forage species of macroalgae from a range of eutrophic states. Tumors were notably elevated in glycine, proline, alanine, arginine, and serine and depleted in lysine when compared to baseline samples. All macroalgae from eutrophic locations had elevated arginine, and all species preferentially stored environmental nitrogen as arginine even at oligotrophic sites. From these results, we estimate adult turtles foraging at eutrophied sites increase their arginine intake 17–26 g daily, up to 14 times the background level. Arginine nitrogen increased with total macroalgae nitrogen and watershed nitrogen, and the invasive rhodophyte Hypnea musciformis significantly outperformed all other species in this respect. Our results confirm that eutrophication substantially increases the arginine content of macroalgae, which may metabolically promote latent herpesviruses and cause FP tumors in green turtles.
format: application/pdf
format: text/html
creator: Kyle S. Van Houtan
creator: Celia M. Smith
creator: Meghan L. Dailer
creator: Migiwa Kawachi
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Virology
description: doi:10.7717/peerj.602
publisher: PeerJ Inc.
rights: © 2014 Van Houtan et al.
abstract: The tumor-forming disease fibropapillomatosis (FP) has afflicted sea turtle populations for decades with no clear cause. A lineage of α-herpesviruses associated with these tumors has existed for millennia, suggesting environmental factors are responsible for its recent epidemiology. In previous work, we described how herpesviruses could cause FP tumors through a metabolic influx of arginine. We demonstrated the disease prevails in chronically eutrophied coastal waters, and that turtles foraging in these sites might consume arginine-enriched macroalgae. Here, we test the idea using High-Performance Liquid Chromatography (HPLC) to describe the amino acid profiles of green turtle (Chelonia mydas) tumors and five common forage species of macroalgae from a range of eutrophic states. Tumors were notably elevated in glycine, proline, alanine, arginine, and serine and depleted in lysine when compared to baseline samples. All macroalgae from eutrophic locations had elevated arginine, and all species preferentially stored environmental nitrogen as arginine even at oligotrophic sites. From these results, we estimate adult turtles foraging at eutrophied sites increase their arginine intake 17–26 g daily, up to 14 times the background level. Arginine nitrogen increased with total macroalgae nitrogen and watershed nitrogen, and the invasive rhodophyte Hypnea musciformis significantly outperformed all other species in this respect. Our results confirm that eutrophication substantially increases the arginine content of macroalgae, which may metabolically promote latent herpesviruses and cause FP tumors in green turtles.
bibliographic citation: Van Houtan et al. (2014) Eutrophication and the dietary promotion of sea turtle tumors. PeerJ 2:e602 https://doi.org/10.7717/peerj.602
date submitted: 2014-08-14
date accepted: 2014-09-09
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Van Houtan
  given name: Kyle S.
author list: Agent
  family name: Smith
  given name: Celia M.
author list: Agent
  family name: Dailer
  given name: Meghan L.
author list: Agent
  family name: Kawachi
  given name: Migiwa
doi: 10.7717/peerj.602
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Van Houtan et al.
attribution name: Van Houtan et al.

Nest-building behavior of Monk Parakeets and insights into potential mechanisms for reducing damage to utility poles
type: item
type: AcademicArticle
description: The Monk Parakeet (Myiopsitta monachus) commonly uses utility poles as a substrate for building large, bulky nests. These nests often cause fires and electric power outages, creating public safety risks and increasing liability and maintenance costs for electric companies. Previous research has focused on lethal methods and chemical contraception to prevent nesting on utility poles and electrical substations. However, implementation of lethal methods has led to public protests and lawsuits, while chemical contraception may affect other than the targeted species, and must be continually reapplied for effectiveness. One non-lethal alternative, nest removal, is costly and may not be a sustainable measure if Monk Parakeet populations continue to grow. In order to identify cost-effective non-lethal solutions to problems caused by Monk Parakeet nesting, we studied their behavior as they built nests on utility poles. Monk Parakeets initiate nests by attaching sticks at the intersection of the pole and electric lines. We found that parakeets use the electric lines exclusively to gain access to the intersection of lines and pole during nest initiation, and continue to use the lines intensively throughout construction. Monk Parakeets also have more difficulty attaching sticks during the early stages of nest construction than when the nest is nearing completion. These findings suggest that intervention during the earlier stages of nest building, by excluding Monk Parakeets from electric lines adjacent to poles, may be an effective, non-lethal method of reducing or eliminating parakeets nesting on, and damaging, utility poles.
format: application/pdf
format: text/html
creator: Kevin R. Burgio
creator: Margaret A. Rubega
creator: Diego Sustaita
subject: Animal Behavior
subject: Ecology
subject: Zoology
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.601
publisher: PeerJ Inc.
rights: © 2014 Burgio et al.
abstract: The Monk Parakeet (Myiopsitta monachus) commonly uses utility poles as a substrate for building large, bulky nests. These nests often cause fires and electric power outages, creating public safety risks and increasing liability and maintenance costs for electric companies. Previous research has focused on lethal methods and chemical contraception to prevent nesting on utility poles and electrical substations. However, implementation of lethal methods has led to public protests and lawsuits, while chemical contraception may affect other than the targeted species, and must be continually reapplied for effectiveness. One non-lethal alternative, nest removal, is costly and may not be a sustainable measure if Monk Parakeet populations continue to grow. In order to identify cost-effective non-lethal solutions to problems caused by Monk Parakeet nesting, we studied their behavior as they built nests on utility poles. Monk Parakeets initiate nests by attaching sticks at the intersection of the pole and electric lines. We found that parakeets use the electric lines exclusively to gain access to the intersection of lines and pole during nest initiation, and continue to use the lines intensively throughout construction. Monk Parakeets also have more difficulty attaching sticks during the early stages of nest construction than when the nest is nearing completion. These findings suggest that intervention during the earlier stages of nest building, by excluding Monk Parakeets from electric lines adjacent to poles, may be an effective, non-lethal method of reducing or eliminating parakeets nesting on, and damaging, utility poles.
bibliographic citation: Burgio et al. (2014) Nest-building behavior of Monk Parakeets and insights into potential mechanisms for reducing damage to utility poles. PeerJ 2:e601 https://doi.org/10.7717/peerj.601
date submitted: 2014-07-25
date accepted: 2014-09-09
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Burgio
  given name: Kevin R.
author list: Agent
  family name: Rubega
  given name: Margaret A.
author list: Agent
  family name: Sustaita
  given name: Diego
doi: 10.7717/peerj.601
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Burgio et al.
attribution name: Burgio et al.

Detailed comparison of two popular variant calling packages for exome and targeted exon studies
type: item
type: AcademicArticle
description: The Genome Analysis Toolkit (GATK) is commonly used for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome. There have been a number of variant calling comparisons against GATK, but an equally comprehensive comparison for VarScan not yet been performed. More specifically, we compare (1) the effects of different pre-processing steps prior to variant calling with both GATK and VarScan, (2) VarScan variants called with increasingly conservative parameters, and (3) filtered and unfiltered GATK variant calls (for both the UnifiedGenotyper and the HaplotypeCaller). Variant calling was performed on three datasets (1 targeted exon dataset and 2 exome datasets), each with approximately a dozen subjects. In most cases, pre-processing steps (e.g., indel realignment and quality score base recalibration using GATK) had only a modest impact on the variant calls, but the importance of the pre-processing steps varied between datasets and variant callers. Based upon concordance statistics presented in this study, we recommend GATK users focus on “high-quality” GATK variants by filtering out variants flagged as low-quality. We also found that running VarScan with a conservative set of parameters (referred to as “VarScan-Cons”) resulted in a reproducible list of variants, with high concordance (>97%) to high-quality variants called by the GATK UnifiedGenotyper and HaplotypeCaller. These conservative parameters result in decreased sensitivity, but the VarScan-Cons variant list could still recover 84–88% of the high-quality GATK SNPs in the exome datasets. This study also provides limited evidence that VarScan-Cons has a decreased false positive rate among novel variants (relative to high-quality GATK SNPs) and that the GATK HaplotypeCaller has an increased false positive rate for indels (relative to VarScan-Cons and high-quality GATK UnifiedGenotyper indels). More broad…
format: application/pdf
format: text/html
creator: Charles D. Warden
creator: Aaron W. Adamson
creator: Susan L. Neuhausen
creator: Xiwei Wu
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.600
publisher: PeerJ Inc.
rights: © 2014 Warden et al.
abstract: The Genome Analysis Toolkit (GATK) is commonly used for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome. There have been a number of variant calling comparisons against GATK, but an equally comprehensive comparison for VarScan not yet been performed. More specifically, we compare (1) the effects of different pre-processing steps prior to variant calling with both GATK and VarScan, (2) VarScan variants called with increasingly conservative parameters, and (3) filtered and unfiltered GATK variant calls (for both the UnifiedGenotyper and the HaplotypeCaller). Variant calling was performed on three datasets (1 targeted exon dataset and 2 exome datasets), each with approximately a dozen subjects. In most cases, pre-processing steps (e.g., indel realignment and quality score base recalibration using GATK) had only a modest impact on the variant calls, but the importance of the pre-processing steps varied between datasets and variant callers. Based upon concordance statistics presented in this study, we recommend GATK users focus on “high-quality” GATK variants by filtering out variants flagged as low-quality. We also found that running VarScan with a conservative set of parameters (referred to as “VarScan-Cons”) resulted in a reproducible list of variants, with high concordance (>97%) to high-quality variants called by the GATK UnifiedGenotyper and HaplotypeCaller. These conservative parameters result in decreased sensitivity, but the VarScan-Cons variant list could still recover 84–88% of the high-quality GATK SNPs in the exome datasets. This study also provides limited evidence that VarScan-Cons has a decreased false positive rate among novel variants (relative to high-quality GATK SNPs) and that the GATK HaplotypeCaller has an increased false positive rate for indels (relative to VarScan-Cons and high-quality GATK UnifiedGenotyper indels). More broad…
bibliographic citation: Warden et al. (2014) Detailed comparison of two popular variant calling packages for exome and targeted exon studies. PeerJ 2:e600 https://doi.org/10.7717/peerj.600
date submitted: 2014-06-13
date accepted: 2014-09-09
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Warden
  given name: Charles D.
author list: Agent
  family name: Adamson
  given name: Aaron W.
author list: Agent
  family name: Neuhausen
  given name: Susan L.
author list: Agent
  family name: Wu
  given name: Xiwei
doi: 10.7717/peerj.600
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Warden et al.
attribution name: Warden et al.

Multi-decade biomass dynamics in an old-growth hemlock-northern hardwood forest, Michigan, USA
type: item
type: AcademicArticle
description: Trends in living aboveground biomass and inputs to the pool of coarse woody debris (CWD) in an undisturbed, old-growth hemlock-northern hardwood forest in northern MI were estimated from multi-decade observations of permanent plots. Growth and demographic data from seven plot censuses over 47 years (1962–2009), combined with one-time measurement of CWD pools, help assess biomass/carbon status of this landscape. Are trends consistent with traditional notions of late-successional forests as equilibrial ecosystems? Specifically, do biomass pools and CWD inputs show consistent long-term trends and relationships, and can living and dead biomass pools and trends be related to forest composition and history? Aboveground living biomass densities, estimated using standard allometric relationships, range from 360–450 Mg/ha among sampled stands and types; these values are among the highest recorded for northeastern North American forests. Biomass densities showed significant decade-scale variation, but no consistent trends over the full study period (one stand, originating following an 1830 fire, showed an aggrading trend during the first 25 years of the study). Even though total above-ground biomass pools are neither increasing nor decreasing, they have been increasingly dominated, over the full study period, by very large (>70 cm dbh) stems and by the most shade-tolerant species (Acer saccharum and Tsuga canadensis). CWD pools measured in 2007 averaged 151 m3/ha, with highest values in Acer-dominated stands. Snag densities averaged 27/ha, but varied nearly ten-fold with canopy composition (highest in Tsuga-dominated stands, lowest in Acer-dominated); snags constituted 10–50% of CWD biomass. Annualized CWD inputs from tree mortality over the full study period averaged 1.9–3.2 Mg/ha/yr, depending on stand and species composition. CWD input rates tended to increase over the course of the study. Input rates may be expected to increase over longer-term observations because, (a) l…
format: application/pdf
format: text/html
creator: Kerry D. Woods
subject: Climate Change Biology
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
description: doi:10.7717/peerj.598
publisher: PeerJ Inc.
rights: © 2014 Woods
abstract: Trends in living aboveground biomass and inputs to the pool of coarse woody debris (CWD) in an undisturbed, old-growth hemlock-northern hardwood forest in northern MI were estimated from multi-decade observations of permanent plots. Growth and demographic data from seven plot censuses over 47 years (1962–2009), combined with one-time measurement of CWD pools, help assess biomass/carbon status of this landscape. Are trends consistent with traditional notions of late-successional forests as equilibrial ecosystems? Specifically, do biomass pools and CWD inputs show consistent long-term trends and relationships, and can living and dead biomass pools and trends be related to forest composition and history? Aboveground living biomass densities, estimated using standard allometric relationships, range from 360–450 Mg/ha among sampled stands and types; these values are among the highest recorded for northeastern North American forests. Biomass densities showed significant decade-scale variation, but no consistent trends over the full study period (one stand, originating following an 1830 fire, showed an aggrading trend during the first 25 years of the study). Even though total above-ground biomass pools are neither increasing nor decreasing, they have been increasingly dominated, over the full study period, by very large (>70 cm dbh) stems and by the most shade-tolerant species (Acer saccharum and Tsuga canadensis). CWD pools measured in 2007 averaged 151 m3/ha, with highest values in Acer-dominated stands. Snag densities averaged 27/ha, but varied nearly ten-fold with canopy composition (highest in Tsuga-dominated stands, lowest in Acer-dominated); snags constituted 10–50% of CWD biomass. Annualized CWD inputs from tree mortality over the full study period averaged 1.9–3.2 Mg/ha/yr, depending on stand and species composition. CWD input rates tended to increase over the course of the study. Input rates may be expected to increase over longer-term observations because, (a) l…
bibliographic citation: Woods (2014) Multi-decade biomass dynamics in an old-growth hemlock-northern hardwood forest, Michigan, USA. PeerJ 2:e598 https://doi.org/10.7717/peerj.598
date submitted: 2014-07-16
date accepted: 2014-09-06
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Woods
  given name: Kerry D.
doi: 10.7717/peerj.598
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Woods
attribution name: Woods

Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression
type: item
type: AcademicArticle
description: Bacteria from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such as soil. The origin of this behavior is also unknown: it may be biological (that is, dependent on components that sense the environment and regulate growth accordingly) or merely physical. Here we show that B. subtilis, an organism that typically does not respond to media compression, can be induced to do so with two simple and synergistic perturbations: a mutation that maintains cells in the swarming (chained) state, and the addition of EDTA to the growth media, which further increases chain length. EDTA apparently increases chain length by inducing defects in cell separation, as the treatment has only marginal effects on the length of individual cells. These results lead us to three conclusions. First, the wealth of genetic tools available to B. subtilis will provide a new, tractable chassis for engineering compression sensitive organisms. Second, the sensitivity of colony morphology to media compression in Bacillus can be modulated by altering a simple physical property of rod-shaped cells. And third, colony morphology under compression holds promise as a rapid, simple, and low-cost way to screen for changes in the length of rod-shaped cells or chains thereof.
format: application/pdf
format: text/html
creator: Jessica K. Polka
creator: Pamela A. Silver
subject: Cell Biology
subject: Microbiology
description: doi:10.7717/peerj.597
publisher: PeerJ Inc.
rights: © 2014 Polka and Silver
abstract: Bacteria from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such as soil. The origin of this behavior is also unknown: it may be biological (that is, dependent on components that sense the environment and regulate growth accordingly) or merely physical. Here we show that B. subtilis, an organism that typically does not respond to media compression, can be induced to do so with two simple and synergistic perturbations: a mutation that maintains cells in the swarming (chained) state, and the addition of EDTA to the growth media, which further increases chain length. EDTA apparently increases chain length by inducing defects in cell separation, as the treatment has only marginal effects on the length of individual cells. These results lead us to three conclusions. First, the wealth of genetic tools available to B. subtilis will provide a new, tractable chassis for engineering compression sensitive organisms. Second, the sensitivity of colony morphology to media compression in Bacillus can be modulated by altering a simple physical property of rod-shaped cells. And third, colony morphology under compression holds promise as a rapid, simple, and low-cost way to screen for changes in the length of rod-shaped cells or chains thereof.
bibliographic citation: Polka et al. (2014) Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression. PeerJ 2:e597 https://doi.org/10.7717/peerj.597
date submitted: 2014-08-09
date accepted: 2014-09-06
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Polka
  given name: Jessica K.
author list: Agent
  family name: Silver
  given name: Pamela A.
doi: 10.7717/peerj.597
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Polka and Silver
attribution name: Polka and Silver

One pair of hands is not like another: caudate BOLD response in dogs depends on signal source and canine temperament
type: item
type: AcademicArticle
description: Having previously used functional MRI to map the response to a reward signal in the ventral caudate in awake unrestrained dogs, here we examined the importance of signal source to canine caudate activation. Hand signals representing either incipient reward or no reward were presented by a familiar human (each dog’s respective handler), an unfamiliar human, and via illustrated images of hands on a computer screen to 13 dogs undergoing voluntary fMRI. All dogs had received extensive training with the reward and no-reward signals from their handlers and with the computer images and had minimal exposure to the signals from strangers. All dogs showed differentially higher BOLD response in the ventral caudate to the reward versus no reward signals, and there was a robust effect at the group level. Further, differential response to the signal source had a highly significant interaction with a dog’s general aggressivity as measured by the C-BARQ canine personality assessment. Dogs with greater aggressivity showed a higher differential response to the reward signal versus no-reward signal presented by the unfamiliar human and computer, while dogs with lower aggressivity showed a higher differential response to the reward signal versus no-reward signal from their handler. This suggests that specific facets of canine temperament bear more strongly on the perceived reward value of relevant communication signals than does reinforcement history, as each of the dogs were reinforced similarly for each signal, regardless of the source (familiar human, unfamiliar human, or computer). A group-level psychophysiological interaction (PPI) connectivity analysis showed increased functional coupling between the caudate and a region of cortex associated with visual discrimination and learning on reward versus no-reward trials. Our findings emphasize the sensitivity of the domestic dog to human social interaction, and may have other implications and applications pertinent to the training and …
format: application/pdf
format: text/html
creator: Peter F. Cook
creator: Mark Spivak
creator: Gregory S. Berns
subject: Animal Behavior
subject: Neuroscience
subject: Veterinary Medicine
description: doi:10.7717/peerj.596
publisher: PeerJ Inc.
rights: © 2014 Cook et al.
abstract: Having previously used functional MRI to map the response to a reward signal in the ventral caudate in awake unrestrained dogs, here we examined the importance of signal source to canine caudate activation. Hand signals representing either incipient reward or no reward were presented by a familiar human (each dog’s respective handler), an unfamiliar human, and via illustrated images of hands on a computer screen to 13 dogs undergoing voluntary fMRI. All dogs had received extensive training with the reward and no-reward signals from their handlers and with the computer images and had minimal exposure to the signals from strangers. All dogs showed differentially higher BOLD response in the ventral caudate to the reward versus no reward signals, and there was a robust effect at the group level. Further, differential response to the signal source had a highly significant interaction with a dog’s general aggressivity as measured by the C-BARQ canine personality assessment. Dogs with greater aggressivity showed a higher differential response to the reward signal versus no-reward signal presented by the unfamiliar human and computer, while dogs with lower aggressivity showed a higher differential response to the reward signal versus no-reward signal from their handler. This suggests that specific facets of canine temperament bear more strongly on the perceived reward value of relevant communication signals than does reinforcement history, as each of the dogs were reinforced similarly for each signal, regardless of the source (familiar human, unfamiliar human, or computer). A group-level psychophysiological interaction (PPI) connectivity analysis showed increased functional coupling between the caudate and a region of cortex associated with visual discrimination and learning on reward versus no-reward trials. Our findings emphasize the sensitivity of the domestic dog to human social interaction, and may have other implications and applications pertinent to the training and …
bibliographic citation: Cook et al. (2014) One pair of hands is not like another: caudate BOLD response in dogs depends on signal source and canine temperament. PeerJ 2:e596 https://doi.org/10.7717/peerj.596
date submitted: 2014-07-03
date accepted: 2014-09-04
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cook
  given name: Peter F.
author list: Agent
  family name: Spivak
  given name: Mark
author list: Agent
  family name: Berns
  given name: Gregory S.
doi: 10.7717/peerj.596
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Cook et al.
attribution name: Cook et al.

Spatial genetic structure across a hybrid zone between European rabbit subspecies
type: item
type: AcademicArticle
description: The Iberian Peninsula is the only region in the world where the two existing subspecies of the European rabbit (Oryctolagus cuniculus) naturally occur and hybridize. In this study we explore the relative roles of historical and contemporary processes in shaping the spatial genetic structure of the rabbit across its native distribution range, and how they differently affect each subspecies and the hybrid zone. For that purpose we obtained multilocus genotypes and mitochondrial DNA data from 771 rabbits across most of the distribution range of the European rabbit in Spain. Based on the nuclear markers we observed a hierarchical genetic structure firstly comprised by two genetic groups, largely congruent with the mitochondrial lineages and subspecies distributions (O. c. algirus and O. c. cuniculus), which were subsequently subdivided into seven genetic groups. Geographic distance alone emerged as an important factor explaining genetic differentiation across the whole range, without the need to invoke for the effect for geographical barriers. Additionally, the significantly positive spatial correlation up to a distance of only 100 km supported the idea that differentiation at a local level is of greater importance when considering the species overall genetic structure. When looking at the subspecies, northern populations of O. c. cuniculus showed more spatial genetic structure and differentiation than O. c. algirus. This could be due to local geographic barriers, limited resources, soil type and/or social behavior limiting dispersal. The hybrid zone showed similar genetic structure to the southern populations but a larger introgression from the northern lineage genome. These differences have been attributed to selection against the hybrids rather than to behavioral differences between subspecies. Ultimately, the genetic structure of the rabbit in its native distribution range is the result of an ensemble of factors, from geographical and ecological, to behavioral and m…
format: application/pdf
format: text/html
creator: Fernando Alda
creator: Ignacio Doadrio
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.582
publisher: PeerJ Inc.
rights: © 2014 Alda and Doadrio
abstract: The Iberian Peninsula is the only region in the world where the two existing subspecies of the European rabbit (Oryctolagus cuniculus) naturally occur and hybridize. In this study we explore the relative roles of historical and contemporary processes in shaping the spatial genetic structure of the rabbit across its native distribution range, and how they differently affect each subspecies and the hybrid zone. For that purpose we obtained multilocus genotypes and mitochondrial DNA data from 771 rabbits across most of the distribution range of the European rabbit in Spain. Based on the nuclear markers we observed a hierarchical genetic structure firstly comprised by two genetic groups, largely congruent with the mitochondrial lineages and subspecies distributions (O. c. algirus and O. c. cuniculus), which were subsequently subdivided into seven genetic groups. Geographic distance alone emerged as an important factor explaining genetic differentiation across the whole range, without the need to invoke for the effect for geographical barriers. Additionally, the significantly positive spatial correlation up to a distance of only 100 km supported the idea that differentiation at a local level is of greater importance when considering the species overall genetic structure. When looking at the subspecies, northern populations of O. c. cuniculus showed more spatial genetic structure and differentiation than O. c. algirus. This could be due to local geographic barriers, limited resources, soil type and/or social behavior limiting dispersal. The hybrid zone showed similar genetic structure to the southern populations but a larger introgression from the northern lineage genome. These differences have been attributed to selection against the hybrids rather than to behavioral differences between subspecies. Ultimately, the genetic structure of the rabbit in its native distribution range is the result of an ensemble of factors, from geographical and ecological, to behavioral and m…
bibliographic citation: Alda et al. (2014) Spatial genetic structure across a hybrid zone between European rabbit subspecies. PeerJ 2:e582 https://doi.org/10.7717/peerj.582
date submitted: 2014-04-27
date accepted: 2014-08-28
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alda
  given name: Fernando
author list: Agent
  family name: Doadrio
  given name: Ignacio
doi: 10.7717/peerj.582
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Alda and Doadrio
attribution name: Alda and Doadrio

Fibrochondrogenic potential of synoviocytes from osteoarthritic and normal joints cultured as tensioned bioscaffolds for meniscal tissue engineering in dogs
type: item
type: AcademicArticle
description: Meniscal tears are a common cause of stifle lameness in dogs. Use of autologous synoviocytes from the affected stifle is an attractive cell source for tissue engineering replacement fibrocartilage. However, the diseased state of these cells may impede in vitro fibrocartilage formation. Synoviocytes from 12 osteoarthritic (“oaTSB”) and 6 normal joints (“nTSB”) were cultured as tensioned bioscaffolds and compared for their ability to synthesize fibrocartilage sheets. Gene expression of collagens type I and II were higher and expression of interleukin-6 was lower in oaTSB versus nTSB. Compared with nTSB, oaTSB had more glycosaminoglycan and alpha smooth muscle staining and less collagen I and II staining on histologic analysis, whereas collagen and glycosaminoglycan quantities were similar. In conclusion, osteoarthritic joint—origin synoviocytes can produce extracellular matrix components of meniscal fibrocartilage at similar levels to normal joint—origin synoviocytes, which makes them a potential cell source for canine meniscal tissue engineering.
format: application/pdf
format: text/html
creator: Jennifer J. Warnock
creator: Gerd Bobe
creator: Katja F. Duesterdieck-Zellmer
subject: Bioengineering
subject: Cell Biology
subject: Veterinary Medicine
subject: Orthopedics
description: doi:10.7717/peerj.581
publisher: PeerJ Inc.
rights: © 2014 Warnock et al.
abstract: Meniscal tears are a common cause of stifle lameness in dogs. Use of autologous synoviocytes from the affected stifle is an attractive cell source for tissue engineering replacement fibrocartilage. However, the diseased state of these cells may impede in vitro fibrocartilage formation. Synoviocytes from 12 osteoarthritic (“oaTSB”) and 6 normal joints (“nTSB”) were cultured as tensioned bioscaffolds and compared for their ability to synthesize fibrocartilage sheets. Gene expression of collagens type I and II were higher and expression of interleukin-6 was lower in oaTSB versus nTSB. Compared with nTSB, oaTSB had more glycosaminoglycan and alpha smooth muscle staining and less collagen I and II staining on histologic analysis, whereas collagen and glycosaminoglycan quantities were similar. In conclusion, osteoarthritic joint—origin synoviocytes can produce extracellular matrix components of meniscal fibrocartilage at similar levels to normal joint—origin synoviocytes, which makes them a potential cell source for canine meniscal tissue engineering.
bibliographic citation: Warnock et al. (2014) Fibrochondrogenic potential of synoviocytes from osteoarthritic and normal joints cultured as tensioned bioscaffolds for meniscal tissue engineering in dogs. PeerJ 2:e581 https://doi.org/10.7717/peerj.581
date submitted: 2014-06-10
date accepted: 2014-08-26
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Warnock
  given name: Jennifer J.
author list: Agent
  family name: Bobe
  given name: Gerd
author list: Agent
  family name: Duesterdieck-Zellmer
  given name: Katja F.
doi: 10.7717/peerj.581
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Warnock et al.
attribution name: Warnock et al.

Case based rubella surveillance in Abia State, South East Nigeria, 2007–2011
type: item
type: AcademicArticle
description: Introduction. Rubella infection has the potential of causing severe fetal birth defects collectively called congenital rubella syndrome (CRS) if the mother is infected early in pregnancy. However, little is known about rubella and CRS epidemiology in Nigeria and rubella vaccines are still not part of routine childhood immunization in Nigeria. Methods. Analysis of confirmed cases of rubella in Abia State, Nigeria from 2007 to 2011 detected through Abia State Integrated Disease Surveillance and Response system. Results. Of the 757 febrile rash cases, 81(10.7%) tested positive for rubella immunoglobulin M (IgM). New rubella infection decreased from 6.81/1,000,000 population in 2007 to 2.28/1,000,000 in 2009 and increased to 6.34/1,000,000 in 2011. The relative risk of rubella was 1.5 (CI [0.98–2.28]) times as high in females compared to males and 1.6 times (CI [0.90–2.91]) as high in rural areas compared to urban areas. Eighty six percent of rubella infections occurred in children less than 15 years with a high proportion of cases occurring between 5 and 14 years. Conclusion. Rubella infection in Abia State, Nigeria is predominantly in those who are younger than 15 years old. It is also more prevalent in females and in those living in rural areas of the state. Unfortunately, there is no surveillance of CRS in Nigeria and so the public health impact of rubella infection in the state is not known. Efforts should be made to expand the rubella surveillance in Nigeria to incorporate surveillance for CRS.
format: application/pdf
format: text/html
creator: Chukwuemeka Anthony Umeh
creator: Stella Chioma Onyi
subject: Public Health
description: doi:10.7717/peerj.580
publisher: PeerJ Inc.
rights: © 2014 Umeh and Onyi
abstract: Introduction. Rubella infection has the potential of causing severe fetal birth defects collectively called congenital rubella syndrome (CRS) if the mother is infected early in pregnancy. However, little is known about rubella and CRS epidemiology in Nigeria and rubella vaccines are still not part of routine childhood immunization in Nigeria. Methods. Analysis of confirmed cases of rubella in Abia State, Nigeria from 2007 to 2011 detected through Abia State Integrated Disease Surveillance and Response system. Results. Of the 757 febrile rash cases, 81(10.7%) tested positive for rubella immunoglobulin M (IgM). New rubella infection decreased from 6.81/1,000,000 population in 2007 to 2.28/1,000,000 in 2009 and increased to 6.34/1,000,000 in 2011. The relative risk of rubella was 1.5 (CI [0.98–2.28]) times as high in females compared to males and 1.6 times (CI [0.90–2.91]) as high in rural areas compared to urban areas. Eighty six percent of rubella infections occurred in children less than 15 years with a high proportion of cases occurring between 5 and 14 years. Conclusion. Rubella infection in Abia State, Nigeria is predominantly in those who are younger than 15 years old. It is also more prevalent in females and in those living in rural areas of the state. Unfortunately, there is no surveillance of CRS in Nigeria and so the public health impact of rubella infection in the state is not known. Efforts should be made to expand the rubella surveillance in Nigeria to incorporate surveillance for CRS.
bibliographic citation: Umeh et al. (2014) Case based rubella surveillance in Abia State, South East Nigeria, 2007–2011. PeerJ 2:e580 https://doi.org/10.7717/peerj.580
date submitted: 2013-08-03
date accepted: 2014-08-26
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Umeh
  given name: Chukwuemeka Anthony
author list: Agent
  family name: Onyi
  given name: Stella Chioma
doi: 10.7717/peerj.580
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Umeh and Onyi
attribution name: Umeh and Onyi

A candidate multimodal functional genetic network for thermal adaptation
type: item
type: AcademicArticle
description: Vertebrate ectotherms such as reptiles provide ideal organisms for the study of adaptation to environmental thermal change. Comparative genomic and exomic studies can recover markers that diverge between warm and cold adapted lineages, but the genes that are functionally related to thermal adaptation may be difficult to identify. We here used a bioinformatics genome-mining approach to predict and identify functions for suitable candidate markers for thermal adaptation in the chicken. We first established a framework of candidate functions for such markers, and then compiled the literature on genes known to adapt to the thermal environment in different lineages of vertebrates. We then identified them in the genomes of human, chicken, and the lizard Anolis carolinensis, and established a functional genetic interaction network in the chicken. Surprisingly, markers initially identified from diverse lineages of vertebrates such as human and fish were all in close functional relationship with each other and more associated than expected by chance. This indicates that the general genetic functional network for thermoregulation and/or thermal adaptation to the environment might be regulated via similar evolutionarily conserved pathways in different vertebrate lineages. We were able to identify seven functions that were statistically overrepresented in this network, corresponding to four of our originally predicted functions plus three unpredicted functions. We describe this network as multimodal: central regulator genes with the function of relaying thermal signal (1), affect genes with different cellular functions, namely (2) lipoprotein metabolism, (3) membrane channels, (4) stress response, (5) response to oxidative stress, (6) muscle contraction and relaxation, and (7) vasodilation, vasoconstriction and regulation of blood pressure. This network constitutes a novel resource for the study of thermal adaptation in the closely related nonavian reptiles and other vertebrate…
format: application/pdf
format: text/html
creator: Katharina C. Wollenberg Valero
creator: Rachana Pathak
creator: Indira Prajapati
creator: Shannon Bankston
creator: Aprylle Thompson
creator: Jaytriece Usher
creator: Raphael D. Isokpehi
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.578
publisher: PeerJ Inc.
rights: © 2014 Wollenberg Valero et al.
abstract: Vertebrate ectotherms such as reptiles provide ideal organisms for the study of adaptation to environmental thermal change. Comparative genomic and exomic studies can recover markers that diverge between warm and cold adapted lineages, but the genes that are functionally related to thermal adaptation may be difficult to identify. We here used a bioinformatics genome-mining approach to predict and identify functions for suitable candidate markers for thermal adaptation in the chicken. We first established a framework of candidate functions for such markers, and then compiled the literature on genes known to adapt to the thermal environment in different lineages of vertebrates. We then identified them in the genomes of human, chicken, and the lizard Anolis carolinensis, and established a functional genetic interaction network in the chicken. Surprisingly, markers initially identified from diverse lineages of vertebrates such as human and fish were all in close functional relationship with each other and more associated than expected by chance. This indicates that the general genetic functional network for thermoregulation and/or thermal adaptation to the environment might be regulated via similar evolutionarily conserved pathways in different vertebrate lineages. We were able to identify seven functions that were statistically overrepresented in this network, corresponding to four of our originally predicted functions plus three unpredicted functions. We describe this network as multimodal: central regulator genes with the function of relaying thermal signal (1), affect genes with different cellular functions, namely (2) lipoprotein metabolism, (3) membrane channels, (4) stress response, (5) response to oxidative stress, (6) muscle contraction and relaxation, and (7) vasodilation, vasoconstriction and regulation of blood pressure. This network constitutes a novel resource for the study of thermal adaptation in the closely related nonavian reptiles and other vertebrate…
bibliographic citation: Wollenberg Valero et al. (2014) A candidate multimodal functional genetic network for thermal adaptation. PeerJ 2:e578 https://doi.org/10.7717/peerj.578
date submitted: 2014-05-02
date accepted: 2014-08-24
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wollenberg Valero
  given name: Katharina C.
author list: Agent
  family name: Pathak
  given name: Rachana
author list: Agent
  family name: Prajapati
  given name: Indira
author list: Agent
  family name: Bankston
  given name: Shannon
author list: Agent
  family name: Thompson
  given name: Aprylle
author list: Agent
  family name: Usher
  given name: Jaytriece
author list: Agent
  family name: Isokpehi
  given name: Raphael D.
doi: 10.7717/peerj.578
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Wollenberg Valero et al.
attribution name: Wollenberg Valero et al.

Factors associated with leisure time physical inactivity in black individuals: hierarchical model
type: item
type: AcademicArticle
description: Background. A number of studies have shown that the black population exhibits higher levels of leisure-time physical inactivity (LTPI), but few have investigated the factors associated with this behavior. Objective. The aim of this study was to analyze associated factors and the explanatory model proposed for LTPI in black adults. Methods. The design was cross-sectional with a sample of 2,305 adults from 20–96 years of age, 902 (39.1%) men, living in the city of Salvador, Brazil. LTPI was analyzed using the International Physical Activity Questionnaire (IPAQ). A hierarchical model was built with the possible factors associated with LTPI, distributed in distal (age and sex), intermediate 1 (socioeconomic status, educational level and marital status), intermediate 2 (perception of safety/violence in the neighborhood, racial discrimination in private settings and physical activity at work) and proximal blocks (smoking and participation in Carnival block rehearsals). We estimated crude and adjusted odds ratio (OR) using logistic regression. Results. The variables inversely associated with LTPI were male gender, socioeconomic status and secondary/university education, although the proposed model explains only 4.2% of LTPI. Conclusions. We conclude that male gender, higher education and socioeconomic status can reduce LTPI in black adults.
format: application/pdf
format: text/html
creator: Francisco José Gondim Pitanga
creator: Ines Lessa
creator: Paulo José B. Barbosa
creator: Simone Janete O. Barbosa
creator: Maria Cecília Costa
creator: Adair da Silva Lopes
subject: Epidemiology
subject: Global Health
subject: Public Health
subject: Statistics
description: doi:10.7717/peerj.577
publisher: PeerJ Inc.
rights: © 2014 Pitanga et al.
abstract: Background. A number of studies have shown that the black population exhibits higher levels of leisure-time physical inactivity (LTPI), but few have investigated the factors associated with this behavior. Objective. The aim of this study was to analyze associated factors and the explanatory model proposed for LTPI in black adults. Methods. The design was cross-sectional with a sample of 2,305 adults from 20–96 years of age, 902 (39.1%) men, living in the city of Salvador, Brazil. LTPI was analyzed using the International Physical Activity Questionnaire (IPAQ). A hierarchical model was built with the possible factors associated with LTPI, distributed in distal (age and sex), intermediate 1 (socioeconomic status, educational level and marital status), intermediate 2 (perception of safety/violence in the neighborhood, racial discrimination in private settings and physical activity at work) and proximal blocks (smoking and participation in Carnival block rehearsals). We estimated crude and adjusted odds ratio (OR) using logistic regression. Results. The variables inversely associated with LTPI were male gender, socioeconomic status and secondary/university education, although the proposed model explains only 4.2% of LTPI. Conclusions. We conclude that male gender, higher education and socioeconomic status can reduce LTPI in black adults.
bibliographic citation: Pitanga et al. (2014) Factors associated with leisure time physical inactivity in black individuals: hierarchical model. PeerJ 2:e577 https://doi.org/10.7717/peerj.577
date submitted: 2014-07-20
date accepted: 2014-08-25
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pitanga
  given name: Francisco José Gondim
author list: Agent
  family name: Lessa
  given name: Ines
author list: Agent
  family name: Barbosa
  given name: Paulo José B.
author list: Agent
  family name: Barbosa
  given name: Simone Janete O.
author list: Agent
  family name: Costa
  given name: Maria Cecília
author list: Agent
  family name: Lopes
  given name: Adair da Silva
doi: 10.7717/peerj.577
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 Pitanga et al.
attribution name: Pitanga et al.

Species and size diversity in protective services offered by coral guard-crabs
type: item
type: AcademicArticle
description: Coral guard-crabs in the genus Trapezia are well-documented defenders of their pocilloporid coral hosts against coral predators such as the Crown-of-Thorns seastar (Acanthaster planci complex). The objectives of this study were to examine the protective services of six species of Trapezia against corallivory, and the extent of functional diversity among these Trapezia species. Studies conducted in Mo’orea, French Polynesia showed the Trapezia—coral mutualism protected the host corals from multiple predators through functional diversity in the assemblage of crab symbionts. Species differed in their defensive efficacy, but species within similar size classes shared similar abilities. Smaller-size Trapezia species, which were previously thought to be ineffective guards, play important defensive roles against small corallivores. We also measured the benefits of this mutualism to corals in the midst of an Acanthaster outbreak that reduced the live coral cover on the fore reef to less than 4%. The mutualism may positively affect the reef coral demography and potential for recovery during adverse predation events through shelter of multiple species of small corals near the host coral. Our results show that while functional diversity is supported within the genus, some Trapezia species may be functionally equivalent within the same size class, decreasing the threat of gaps in coral protection caused by absence or replacement of any single Trapezia species.
format: application/pdf
format: text/html
creator: C. Seabird McKeon
creator: Jenna M. Moore
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.574
publisher: PeerJ Inc.
rights: © 2014 McKeon and Moore
abstract: Coral guard-crabs in the genus Trapezia are well-documented defenders of their pocilloporid coral hosts against coral predators such as the Crown-of-Thorns seastar (Acanthaster planci complex). The objectives of this study were to examine the protective services of six species of Trapezia against corallivory, and the extent of functional diversity among these Trapezia species. Studies conducted in Mo’orea, French Polynesia showed the Trapezia—coral mutualism protected the host corals from multiple predators through functional diversity in the assemblage of crab symbionts. Species differed in their defensive efficacy, but species within similar size classes shared similar abilities. Smaller-size Trapezia species, which were previously thought to be ineffective guards, play important defensive roles against small corallivores. We also measured the benefits of this mutualism to corals in the midst of an Acanthaster outbreak that reduced the live coral cover on the fore reef to less than 4%. The mutualism may positively affect the reef coral demography and potential for recovery during adverse predation events through shelter of multiple species of small corals near the host coral. Our results show that while functional diversity is supported within the genus, some Trapezia species may be functionally equivalent within the same size class, decreasing the threat of gaps in coral protection caused by absence or replacement of any single Trapezia species.
bibliographic citation: McKeon et al. (2014) Species and size diversity in protective services offered by coral guard-crabs. PeerJ 2:e574 https://doi.org/10.7717/peerj.574
date submitted: 2014-02-20
date accepted: 2014-08-22
issued: 2014-09-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: McKeon
  given name: C. Seabird
author list: Agent
  family name: Moore
  given name: Jenna M.
doi: 10.7717/peerj.574
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-30
copyright: © 2014 McKeon and Moore
attribution name: McKeon and Moore

Revision of the Late Jurassic crocodyliform Alligatorellus, and evidence for allopatric speciation driving high diversity in western European atoposaurids
type: item
type: AcademicArticle
description: Atoposaurid crocodyliforms represent an important faunal component of Late Jurassic to Early Cretaceous Laurasian semi-aquatic to terrestrial ecosystems, with numerous spatiotemporally contemporaneous atoposaurids known from western Europe. In particular, the Late Jurassic of France and Germany records evidence for high diversity and possible sympatric atoposaurid species belonging to Alligatorellus, Alligatorium and Atoposaurus. However, atoposaurid taxonomy has received little attention, and many species are in need of revision. As such, this potentially high European diversity within a narrow spatiotemporal range might be a taxonomic artefact. Here we provide a taxonomic and anatomical revision of the Late Jurassic atoposaurid Alligatorellus. Initially described as A. beaumonti from the Kimmeridgian of Cerin, eastern France, additional material from the Tithonian of Solnhofen, south-eastern Germany, was subsequently referred to this species, with the two occurrences differentiated as A. beaumonti beaumonti and A. beaumonti bavaricus, respectively. We provide a revised diagnosis for the genus Alligatorellus, and note a number of anatomical differences between the French and German specimens, including osteoderm morphology and the configuration and pattern of sculpting of cranial elements. Consequently, we restrict the name Alligatorellus beaumonti to include only the French remains, and raise the rank of the German material to a distinct species: Alligatorellus bavaricus. A new diagnosis is provided for both species, and we suggest that a recently referred specimen from a coeval German locality cannot be conclusively referred to Alligatorellus. Although it has previously been suggested that Alligatorellus, Alligatorium and Atoposaurus might represent a single growth series of one species, we find no conclusive evidence to support this proposal, and provide a number of morphological differences to distinguish these three taxa that appear to be independent of ontoge…
format: application/pdf
format: text/html
creator: Jonathan P. Tennant
creator: Philip D. Mannion
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.599
publisher: PeerJ Inc.
rights: © 2014 Tennant and Mannion
abstract: Atoposaurid crocodyliforms represent an important faunal component of Late Jurassic to Early Cretaceous Laurasian semi-aquatic to terrestrial ecosystems, with numerous spatiotemporally contemporaneous atoposaurids known from western Europe. In particular, the Late Jurassic of France and Germany records evidence for high diversity and possible sympatric atoposaurid species belonging to Alligatorellus, Alligatorium and Atoposaurus. However, atoposaurid taxonomy has received little attention, and many species are in need of revision. As such, this potentially high European diversity within a narrow spatiotemporal range might be a taxonomic artefact. Here we provide a taxonomic and anatomical revision of the Late Jurassic atoposaurid Alligatorellus. Initially described as A. beaumonti from the Kimmeridgian of Cerin, eastern France, additional material from the Tithonian of Solnhofen, south-eastern Germany, was subsequently referred to this species, with the two occurrences differentiated as A. beaumonti beaumonti and A. beaumonti bavaricus, respectively. We provide a revised diagnosis for the genus Alligatorellus, and note a number of anatomical differences between the French and German specimens, including osteoderm morphology and the configuration and pattern of sculpting of cranial elements. Consequently, we restrict the name Alligatorellus beaumonti to include only the French remains, and raise the rank of the German material to a distinct species: Alligatorellus bavaricus. A new diagnosis is provided for both species, and we suggest that a recently referred specimen from a coeval German locality cannot be conclusively referred to Alligatorellus. Although it has previously been suggested that Alligatorellus, Alligatorium and Atoposaurus might represent a single growth series of one species, we find no conclusive evidence to support this proposal, and provide a number of morphological differences to distinguish these three taxa that appear to be independent of ontoge…
bibliographic citation: Tennant et al. (2014) Revision of the Late Jurassic crocodyliform Alligatorellus, and evidence for allopatric speciation driving high diversity in western European atoposaurids. PeerJ 2:e599 https://doi.org/10.7717/peerj.599
date submitted: 2014-07-03
date accepted: 2014-09-08
issued: 2014-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tennant
  given name: Jonathan P.
author list: Agent
  family name: Mannion
  given name: Philip D.
doi: 10.7717/peerj.599
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-25
copyright: © 2014 Tennant and Mannion
attribution name: Tennant and Mannion

The self prefers itself? Self-referential versus parental standards in face attractiveness
type: item
type: AcademicArticle
description: Preference for phenotypic similarity in assortative mating may be influenced by either a preference for self-similarity or parent-similarity. The aim of the current study was to assess whether people’s preference in face attractiveness is influenced by resemblance to the opposite sex parent’s face (parental phenotype) or their own face (self-based phenotype or “self-imprinting”). We used computerized image manipulations of facial photographs of participants, their mothers and fathers. The original photographs were combined with 78% of the participants’ opposite sex prototype face (i.e., male and female prototypes made from equal contributions of a hundred faces), creating morphs where the contribution from the familiar faces went unnoticed. Female and male participants ranked these images together with the opposite-sex prototype different familiar morphs. Each participant did the same for the morphs generated with other same-sex participants’ faces and of their parents. We found that the female participants preferred the self-based morphs to the prototype faces. Male participants showed a general tendency towards self-referential standard. Parental face morphs were ranked low in attractiveness, which may be accounted for by the age difference of the faces blended into the self-based versus parental face morphs, since we used present-time photographs of both the participants and their parents.
format: application/pdf
format: text/html
creator: Unni Sulutvedt
creator: Bruno Laeng
subject: Ecology
subject: Evolutionary Studies
description: doi:10.7717/peerj.595
publisher: PeerJ Inc.
rights: © 2014 Sulutvedt and Laeng
abstract: Preference for phenotypic similarity in assortative mating may be influenced by either a preference for self-similarity or parent-similarity. The aim of the current study was to assess whether people’s preference in face attractiveness is influenced by resemblance to the opposite sex parent’s face (parental phenotype) or their own face (self-based phenotype or “self-imprinting”). We used computerized image manipulations of facial photographs of participants, their mothers and fathers. The original photographs were combined with 78% of the participants’ opposite sex prototype face (i.e., male and female prototypes made from equal contributions of a hundred faces), creating morphs where the contribution from the familiar faces went unnoticed. Female and male participants ranked these images together with the opposite-sex prototype different familiar morphs. Each participant did the same for the morphs generated with other same-sex participants’ faces and of their parents. We found that the female participants preferred the self-based morphs to the prototype faces. Male participants showed a general tendency towards self-referential standard. Parental face morphs were ranked low in attractiveness, which may be accounted for by the age difference of the faces blended into the self-based versus parental face morphs, since we used present-time photographs of both the participants and their parents.
bibliographic citation: Sulutvedt et al. (2014) The self prefers itself? Self-referential versus parental standards in face attractiveness. PeerJ 2:e595 https://doi.org/10.7717/peerj.595
date submitted: 2014-04-24
date accepted: 2014-09-04
issued: 2014-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sulutvedt
  given name: Unni
author list: Agent
  family name: Laeng
  given name: Bruno
doi: 10.7717/peerj.595
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-25
copyright: © 2014 Sulutvedt and Laeng
attribution name: Sulutvedt and Laeng

Chronic playback of boat noise does not impact hatching success or post-hatching larval growth and survival in a cichlid fish
type: item
type: AcademicArticle
description: Anthropogenic (man-made) noise has been shown to have a negative impact on the behaviour and physiology of a range of terrestrial and aquatic animals. However, direct assessments of fitness consequences are rare. Here we examine the effect of additional noise on early life stages in the model cichlid fish, Neolamprologus pulcher. Many fishes use and produce sounds, they are crucial elements of aquatic ecosystems, and there is mounting evidence that they are vulnerable to anthropogenic noise; adult N. pulcher have recently been shown to change key behaviours during playback of motor boat noise. Using a split-brood design to eliminate potential genetic effects, we exposed half of the eggs and fry from each clutch to four weeks of playbacks of noise originally recorded from small motor boats with the other half acting as a control (receiving no noise playback). There was no significant effect of additional noise on hatching success or fry survival, length or weight at the end of the exposure period. Although care should be taken not to generalize these findings on a single species from a laboratory study, our data suggest that moderate noise increases do not necessarily have direct negative impacts on early-life survival and growth. Further studies on a range of species in natural conditions are urgently needed to inform conservation efforts and policy decisions about the consequences of anthropogenic noise.
format: application/pdf
format: text/html
creator: Rick Bruintjes
creator: Andrew N. Radford
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.594
publisher: PeerJ Inc.
rights: © 2014 Bruintjes and Radford
abstract: Anthropogenic (man-made) noise has been shown to have a negative impact on the behaviour and physiology of a range of terrestrial and aquatic animals. However, direct assessments of fitness consequences are rare. Here we examine the effect of additional noise on early life stages in the model cichlid fish, Neolamprologus pulcher. Many fishes use and produce sounds, they are crucial elements of aquatic ecosystems, and there is mounting evidence that they are vulnerable to anthropogenic noise; adult N. pulcher have recently been shown to change key behaviours during playback of motor boat noise. Using a split-brood design to eliminate potential genetic effects, we exposed half of the eggs and fry from each clutch to four weeks of playbacks of noise originally recorded from small motor boats with the other half acting as a control (receiving no noise playback). There was no significant effect of additional noise on hatching success or fry survival, length or weight at the end of the exposure period. Although care should be taken not to generalize these findings on a single species from a laboratory study, our data suggest that moderate noise increases do not necessarily have direct negative impacts on early-life survival and growth. Further studies on a range of species in natural conditions are urgently needed to inform conservation efforts and policy decisions about the consequences of anthropogenic noise.
bibliographic citation: Bruintjes et al. (2014) Chronic playback of boat noise does not impact hatching success or post-hatching larval growth and survival in a cichlid fish. PeerJ 2:e594 https://doi.org/10.7717/peerj.594
date submitted: 2014-07-03
date accepted: 2014-09-03
issued: 2014-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bruintjes
  given name: Rick
author list: Agent
  family name: Radford
  given name: Andrew N.
doi: 10.7717/peerj.594
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-25
copyright: © 2014 Bruintjes and Radford
attribution name: Bruintjes and Radford

Swarm: robust and fast clustering method for amplicon-based studies
type: item
type: AcademicArticle
description: Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.
format: application/pdf
format: text/html
creator: Frédéric Mahé
creator: Torbjørn Rognes
creator: Christopher Quince
creator: Colomban de Vargas
creator: Micah Dunthorn
subject: Biodiversity
subject: Bioinformatics
subject: Ecology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.593
publisher: PeerJ Inc.
rights: © 2014 Mahé et al.
abstract: Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters’ internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.
bibliographic citation: Mahé et al. (2014) Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2:e593 https://doi.org/10.7717/peerj.593
date submitted: 2014-05-13
date accepted: 2014-09-03
issued: 2014-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mahé
  given name: Frédéric
author list: Agent
  family name: Rognes
  given name: Torbjørn
author list: Agent
  family name: Quince
  given name: Christopher
author list: Agent
  family name: de Vargas
  given name: Colomban
author list: Agent
  family name: Dunthorn
  given name: Micah
doi: 10.7717/peerj.593
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-25
copyright: © 2014 Mahé et al.
attribution name: Mahé et al.

Habitat creation and biodiversity maintenance in mangrove forests: teredinid bivalves as ecosystem engineers
type: item
type: AcademicArticle
description: Substantial amounts of dead wood in the intertidal zone of mature mangrove forests are tunnelled by teredinid bivalves. When the tunnels are exposed, animals are able to use tunnels as refuges. In this study, the effect of teredinid tunnelling upon mangrove forest faunal diversity was investigated. Mangrove forests exposed to long emersion times had fewer teredinid tunnels in wood and wood not containing teredinid tunnels had very few species and abundance of animals. However, with a greater cross-sectional percentage surface area of teredinid tunnels, the numbers of species and abundance of animals was significantly higher. Temperatures within teredinid-attacked wood were significantly cooler compared with air temperatures, and animal abundance was greater in wood with cooler temperatures. Animals inside the tunnels within the wood may avoid desiccation by escaping the higher temperatures. Animals co-existing in teredinid tunnelled wood ranged from animals found in terrestrial ecosystems including centipedes, crickets and spiders, and animals found in subtidal marine ecosystems such as fish, octopods and polychaetes. There was also evidence of breeding within teredinid-attacked wood, as many juvenile individuals were found, and they may also benefit from the cooler wood temperatures. Teredinid tunnelled wood is a key low-tide refuge for cryptic animals, which would otherwise be exposed to fishes and birds, and higher external temperatures. This study provides evidence that teredinids are ecosystem engineers and also provides an example of a mechanism whereby mangrove forests support intertidal biodiversity and nurseries through the wood-boring activity of teredinids.
format: application/pdf
format: text/html
creator: Ian W. Hendy
creator: Laura Michie
creator: Ben W. Taylor
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
description: doi:10.7717/peerj.591
publisher: PeerJ Inc.
rights: © 2014 Hendy et al.
abstract: Substantial amounts of dead wood in the intertidal zone of mature mangrove forests are tunnelled by teredinid bivalves. When the tunnels are exposed, animals are able to use tunnels as refuges. In this study, the effect of teredinid tunnelling upon mangrove forest faunal diversity was investigated. Mangrove forests exposed to long emersion times had fewer teredinid tunnels in wood and wood not containing teredinid tunnels had very few species and abundance of animals. However, with a greater cross-sectional percentage surface area of teredinid tunnels, the numbers of species and abundance of animals was significantly higher. Temperatures within teredinid-attacked wood were significantly cooler compared with air temperatures, and animal abundance was greater in wood with cooler temperatures. Animals inside the tunnels within the wood may avoid desiccation by escaping the higher temperatures. Animals co-existing in teredinid tunnelled wood ranged from animals found in terrestrial ecosystems including centipedes, crickets and spiders, and animals found in subtidal marine ecosystems such as fish, octopods and polychaetes. There was also evidence of breeding within teredinid-attacked wood, as many juvenile individuals were found, and they may also benefit from the cooler wood temperatures. Teredinid tunnelled wood is a key low-tide refuge for cryptic animals, which would otherwise be exposed to fishes and birds, and higher external temperatures. This study provides evidence that teredinids are ecosystem engineers and also provides an example of a mechanism whereby mangrove forests support intertidal biodiversity and nurseries through the wood-boring activity of teredinids.
bibliographic citation: Hendy et al. (2014) Habitat creation and biodiversity maintenance in mangrove forests: teredinid bivalves as ecosystem engineers. PeerJ 2:e591 https://doi.org/10.7717/peerj.591
date submitted: 2014-08-11
date accepted: 2014-09-03
issued: 2014-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hendy
  given name: Ian W.
author list: Agent
  family name: Michie
  given name: Laura
author list: Agent
  family name: Taylor
  given name: Ben W.
doi: 10.7717/peerj.591
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-25
copyright: © 2014 Hendy et al.
attribution name: Hendy et al.

Synergy as a rationale for phage therapy using phage cocktails
type: item
type: AcademicArticle
description: Where phages are used to treat bacterial contaminations and infections, multiple phages are typically applied at once as a cocktail. When two or more phages in the cocktail attack the same bacterium, the combination may produce better killing than any single phage (synergy) or the combination may be worse than the best single phage (interference). Synergy is of obvious utility, especially if it can be predicted a priori, but it remains poorly documented with few examples known. This study addresses synergy in which one phage improves adsorption by a second phage. It first presents evidence of synergy from an experimental system of two phages and a mucoid E. coli host. The synergy likely stems from a tailspike enzyme produced by one of the phages. We then offer mathematical models and simulations to understand the dynamics of synergy and the enhanced magnitude of bacterial control possible. The models and observations complement each other and suggest that synergy may be of widespread utility and may be predictable from easily observed phenotypes.
format: application/pdf
format: text/html
creator: Matthew Schmerer
creator: Ian J. Molineux
creator: James J. Bull
subject: Genomics
subject: Mathematical Biology
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.590
publisher: PeerJ Inc.
rights: © 2014 Schmerer et al.
abstract: Where phages are used to treat bacterial contaminations and infections, multiple phages are typically applied at once as a cocktail. When two or more phages in the cocktail attack the same bacterium, the combination may produce better killing than any single phage (synergy) or the combination may be worse than the best single phage (interference). Synergy is of obvious utility, especially if it can be predicted a priori, but it remains poorly documented with few examples known. This study addresses synergy in which one phage improves adsorption by a second phage. It first presents evidence of synergy from an experimental system of two phages and a mucoid E. coli host. The synergy likely stems from a tailspike enzyme produced by one of the phages. We then offer mathematical models and simulations to understand the dynamics of synergy and the enhanced magnitude of bacterial control possible. The models and observations complement each other and suggest that synergy may be of widespread utility and may be predictable from easily observed phenotypes.
bibliographic citation: Schmerer et al. (2014) Synergy as a rationale for phage therapy using phage cocktails. PeerJ 2:e590 https://doi.org/10.7717/peerj.590
date submitted: 2014-08-03
date accepted: 2014-09-02
issued: 2014-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schmerer
  given name: Matthew
author list: Agent
  family name: Molineux
  given name: Ian J.
author list: Agent
  family name: Bull
  given name: James J.
doi: 10.7717/peerj.590
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-25
copyright: © 2014 Schmerer et al.
attribution name: Schmerer et al.

Fast and accurate estimation of the covariance between pairwise maximum likelihood distances
type: item
type: AcademicArticle
description: Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.
format: application/pdf
format: text/html
creator: Manuel Gil
subject: Computational Biology
subject: Mathematical Biology
subject: Molecular Biology
subject: Statistics
subject: Computational Science
description: doi:10.7717/peerj.583
publisher: PeerJ Inc.
rights: © 2014 Gil
abstract: Pairwise evolutionary distances are a model-based summary statistic for a set of molecular sequences. They represent the leaf-to-leaf path lengths of the underlying phylogenetic tree. Estimates of pairwise distances with overlapping paths covary because of shared mutation events. It is desirable to take these covariance structure into account to increase precision in any process that compares or combines distances. This paper introduces a fast estimator for the covariance of two pairwise maximum likelihood distances, estimated under general Markov models. The estimator is based on a conjecture (going back to Nei & Jin, 1989) which links the covariance to path lengths. It is proven here under a simple symmetric substitution model. A simulation shows that the estimator outperforms previously published ones in terms of the mean squared error.
bibliographic citation: Gil (2014) Fast and accurate estimation of the covariance between pairwise maximum likelihood distances. PeerJ 2:e583 https://doi.org/10.7717/peerj.583
date submitted: 2014-05-16
date accepted: 2014-08-28
issued: 2014-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gil
  given name: Manuel
doi: 10.7717/peerj.583
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-25
copyright: © 2014 Gil
attribution name: Gil

Shared phylogeographic patterns between the ectocommensal flatworm Temnosewellia albata and its host, the endangered freshwater crayfish Euastacus robertsi
type: item
type: AcademicArticle
description: Comparative phylogeography of commensal species may show congruent patterns where the species involved share a common history. Temnosewellia is a genus of flatworms, members of which live in commensal relationships with host freshwater crustaceans. By constructing phylogenetic trees based on mitochondrial COI and 28S nuclear ribosomal gene sequences, this study investigated how evolutionary history has shaped patterns of intraspecific molecular variation in two such freshwater commensals. This study concentrates on the flatworm Temnosewellia albata and its critically endangered crayfish host Euastacus robertsi, which have a narrow climatically-restricted distribution on three mountaintops. The genetic data expands upon previous studies of Euastacus that suggested several vicariance events have led to the population subdivision of Euastacus robertsi. Further, our study compared historical phylogeographic patterning of these species. Our results showed that phylogeographic patterns shared among these commensals were largely congruent, featuring a shared history of limited dispersal between the mountaintops. Several hypotheses were proposed to explain the phylogeographic points of differences between the species. This study contributes significantly to understanding evolutionary relationships of commensal freshwater taxa.
format: application/pdf
format: text/html
creator: Charlotte R. Hurry
creator: Daniel J. Schmidt
creator: Mark Ponniah
creator: Giovannella Carini
creator: David Blair
creator: Jane M. Hughes
subject: Conservation Biology
subject: Freshwater Biology
subject: Genetics
description: doi:10.7717/peerj.552
publisher: PeerJ Inc.
rights: © 2014 Hurry et al.
abstract: Comparative phylogeography of commensal species may show congruent patterns where the species involved share a common history. Temnosewellia is a genus of flatworms, members of which live in commensal relationships with host freshwater crustaceans. By constructing phylogenetic trees based on mitochondrial COI and 28S nuclear ribosomal gene sequences, this study investigated how evolutionary history has shaped patterns of intraspecific molecular variation in two such freshwater commensals. This study concentrates on the flatworm Temnosewellia albata and its critically endangered crayfish host Euastacus robertsi, which have a narrow climatically-restricted distribution on three mountaintops. The genetic data expands upon previous studies of Euastacus that suggested several vicariance events have led to the population subdivision of Euastacus robertsi. Further, our study compared historical phylogeographic patterning of these species. Our results showed that phylogeographic patterns shared among these commensals were largely congruent, featuring a shared history of limited dispersal between the mountaintops. Several hypotheses were proposed to explain the phylogeographic points of differences between the species. This study contributes significantly to understanding evolutionary relationships of commensal freshwater taxa.
bibliographic citation: Hurry et al. (2014) Shared phylogeographic patterns between the ectocommensal flatworm Temnosewellia albata and its host, the endangered freshwater crayfish Euastacus robertsi. PeerJ 2:e552 https://doi.org/10.7717/peerj.552
date submitted: 2014-05-20
date accepted: 2014-08-10
issued: 2014-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hurry
  given name: Charlotte R.
author list: Agent
  family name: Schmidt
  given name: Daniel J.
author list: Agent
  family name: Ponniah
  given name: Mark
author list: Agent
  family name: Carini
  given name: Giovannella
author list: Agent
  family name: Blair
  given name: David
author list: Agent
  family name: Hughes
  given name: Jane M.
doi: 10.7717/peerj.552
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-25
copyright: © 2014 Hurry et al.
attribution name: Hurry et al.

Bio-inspired design of ice-retardant devices based on benthic marine invertebrates: the effect of surface texture
type: item
type: AcademicArticle
description: Growth of ice on surfaces poses a challenge for both organisms and for devices that come into contact with liquids below the freezing point. Resistance of some organisms to ice formation and growth, either in subtidal environments (e.g., Antarctic anchor ice), or in environments with moisture and cold air (e.g., plants, intertidal) begs examination of how this is accomplished. Several factors may be important in promoting or mitigating ice formation. As a start, here we examine the effect of surface texture alone. We tested four candidate surfaces, inspired by hard-shelled marine invertebrates and constructed using a three-dimensional printing process. We examined sub-polar marine organisms to develop sample textures and screened them for ice formation and accretion in submerged conditions using previous methods for comparison to data for Antarctic organisms. The sub-polar organisms tested were all found to form ice readily. We also screened artificial 3-D printed samples using the same previous methods, and developed a new test to examine ice formation from surface droplets as might be encountered in environments with moist, cold air. Despite limitations inherent to our techniques, it appears surface texture plays only a small role in delaying the onset of ice formation: a stripe feature (corresponding to patterning found on valves of blue mussels, Mytilus edulis, or on the spines of the Antarctic sea urchin Sterechinus neumayeri) slowed ice formation an average of 25% compared to a grid feature (corresponding to patterning found on sub-polar butterclams, Saxidomas nuttalli). The geometric dimensions of the features have only a small (∼6%) effect on ice formation. Surface texture affects ice formation, but does not explain by itself the large variation in ice formation and species-specific ice resistance observed in other work. This suggests future examination of other factors, such as material elastic properties and surface coatings, and their interaction with sur…
format: application/pdf
format: text/html
creator: Homayun Mehrabani
creator: Neil Ray
creator: Kyle Tse
creator: Dennis Evangelista
subject: Bioengineering
subject: Biophysics
subject: Ecosystem Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.588
publisher: PeerJ Inc.
rights: © 2014 Mehrabani et al.
abstract: Growth of ice on surfaces poses a challenge for both organisms and for devices that come into contact with liquids below the freezing point. Resistance of some organisms to ice formation and growth, either in subtidal environments (e.g., Antarctic anchor ice), or in environments with moisture and cold air (e.g., plants, intertidal) begs examination of how this is accomplished. Several factors may be important in promoting or mitigating ice formation. As a start, here we examine the effect of surface texture alone. We tested four candidate surfaces, inspired by hard-shelled marine invertebrates and constructed using a three-dimensional printing process. We examined sub-polar marine organisms to develop sample textures and screened them for ice formation and accretion in submerged conditions using previous methods for comparison to data for Antarctic organisms. The sub-polar organisms tested were all found to form ice readily. We also screened artificial 3-D printed samples using the same previous methods, and developed a new test to examine ice formation from surface droplets as might be encountered in environments with moist, cold air. Despite limitations inherent to our techniques, it appears surface texture plays only a small role in delaying the onset of ice formation: a stripe feature (corresponding to patterning found on valves of blue mussels, Mytilus edulis, or on the spines of the Antarctic sea urchin Sterechinus neumayeri) slowed ice formation an average of 25% compared to a grid feature (corresponding to patterning found on sub-polar butterclams, Saxidomas nuttalli). The geometric dimensions of the features have only a small (∼6%) effect on ice formation. Surface texture affects ice formation, but does not explain by itself the large variation in ice formation and species-specific ice resistance observed in other work. This suggests future examination of other factors, such as material elastic properties and surface coatings, and their interaction with sur…
bibliographic citation: Mehrabani et al. (2014) Bio-inspired design of ice-retardant devices based on benthic marine invertebrates: the effect of surface texture. PeerJ 2:e588 https://doi.org/10.7717/peerj.588
date submitted: 2014-06-27
date accepted: 2014-08-31
issued: 2014-09-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mehrabani
  given name: Homayun
author list: Agent
  family name: Ray
  given name: Neil
author list: Agent
  family name: Tse
  given name: Kyle
author list: Agent
  family name: Evangelista
  given name: Dennis
doi: 10.7717/peerj.588
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-23
copyright: © 2014 Mehrabani et al.
attribution name: Mehrabani et al.

Differences in healthcare expenditures for inflammatory bowel disease by insurance status, income, and clinical care setting
type: item
type: AcademicArticle
description: Background. Socioeconomic factors and insurance status have not been correlated with differential use of healthcare services in inflammatory bowel disease (IBD). Aim. To describe IBD-related expenditures based on insurance and household income with the use of inpatient, outpatient, emergency, and office-based services, and prescribed medications in the United States (US). Methods. We evaluated the Medical Expenditure Panel Survey from 1996 to 2011 of individuals with Crohn’s disease (CD) or ulcerative colitis (UC). Nationally weighted means, proportions, and multivariate regression models examined the relationships between income and insurance status with expenditures. Results. Annual per capita mean expenditures for CD, UC, and all IBD were $10,364 (N = 238), $7,827 (N = 95), and $9,528, respectively, significantly higher than non-IBD ($4,314, N = 276, 372, p < 0.05). Publicly insured patients incurred the highest costs ($18,067) over privately insured ($8,014, p < 0.05) or uninsured patients ($5,129, p < 0.05). Among all IBD patients, inpatient care composed the highest proportion of costs ($3,392, p < 0.05). Inpatient costs were disproportionately higher for publicly insured patients. Public insurance had higher odds of total costs than private (OR 2.13, CI [1.08–4.19]) or no insurance (OR 4.94, CI [1.26–19.47]), with increased odds for inpatient and emergency care. Private insurance had higher costs associated with outpatient care, office-based care, and prescribed medicines. Low-income patients had lower costs associated with outpatient (OR 0.38, CI [0.15–0.95]) and office-based care (OR 0.21, CI [0.07–0.62]). Conclusions. In the US, high inpatient utilization among publicly insured patients is a previously unrecognized driver of high IBD costs. Bridging this health services gap between SES strata for acute care services may curtail direct IBD-related costs.
format: application/pdf
format: text/html
creator: Michelle D. Park
creator: Jay Bhattacharya
creator: KT Park
subject: Gastroenterology and Hepatology
subject: Health Policy
description: doi:10.7717/peerj.587
publisher: PeerJ Inc.
rights: © 2014 Park et al.
abstract: Background. Socioeconomic factors and insurance status have not been correlated with differential use of healthcare services in inflammatory bowel disease (IBD). Aim. To describe IBD-related expenditures based on insurance and household income with the use of inpatient, outpatient, emergency, and office-based services, and prescribed medications in the United States (US). Methods. We evaluated the Medical Expenditure Panel Survey from 1996 to 2011 of individuals with Crohn’s disease (CD) or ulcerative colitis (UC). Nationally weighted means, proportions, and multivariate regression models examined the relationships between income and insurance status with expenditures. Results. Annual per capita mean expenditures for CD, UC, and all IBD were $10,364 (N = 238), $7,827 (N = 95), and $9,528, respectively, significantly higher than non-IBD ($4,314, N = 276, 372, p < 0.05). Publicly insured patients incurred the highest costs ($18,067) over privately insured ($8,014, p < 0.05) or uninsured patients ($5,129, p < 0.05). Among all IBD patients, inpatient care composed the highest proportion of costs ($3,392, p < 0.05). Inpatient costs were disproportionately higher for publicly insured patients. Public insurance had higher odds of total costs than private (OR 2.13, CI [1.08–4.19]) or no insurance (OR 4.94, CI [1.26–19.47]), with increased odds for inpatient and emergency care. Private insurance had higher costs associated with outpatient care, office-based care, and prescribed medicines. Low-income patients had lower costs associated with outpatient (OR 0.38, CI [0.15–0.95]) and office-based care (OR 0.21, CI [0.07–0.62]). Conclusions. In the US, high inpatient utilization among publicly insured patients is a previously unrecognized driver of high IBD costs. Bridging this health services gap between SES strata for acute care services may curtail direct IBD-related costs.
bibliographic citation: Park et al. (2014) Differences in healthcare expenditures for inflammatory bowel disease by insurance status, income, and clinical care setting. PeerJ 2:e587 https://doi.org/10.7717/peerj.587
date submitted: 2014-07-20
date accepted: 2014-08-29
issued: 2014-09-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Park
  given name: Michelle D.
author list: Agent
  family name: Bhattacharya
  given name: Jay
author list: Agent
  family name: Park
  given name: KT
doi: 10.7717/peerj.587
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-23
copyright: © 2014 Park et al.
attribution name: Park et al.

A simple non-invasive method for measuring gross brain size in small live fish with semi-transparent heads
type: item
type: AcademicArticle
description: This paper describes a non-invasive method for estimating gross brain size in small fish with semi-transparent heads, using system camera equipment. Macro-photographs were taken from above on backlit free-swimming fish undergoing light anaesthesia. From the photographs, the width of the optic tectum was measured. This measure (TeO-measure) correlates well with the width of the optic tectum as measured from out-dissected brains in both brown trout fry and zebrafish (Pearson r > 0.90). The TeO-measure also correlates well with overall brain wet weight in brown trout fry (r = 0.90), but less well for zebrafish (r = 0.79). A non-invasive measure makes it possible to quickly assess brain size from a large number of individuals, as well as repeatedly measuring brain size of live individuals allowing calculation of brain growth.
format: application/pdf
format: text/html
creator: Joacim Näslund
subject: Aquaculture, Fisheries and Fish Science
subject: Zoology
description: doi:10.7717/peerj.586
publisher: PeerJ Inc.
rights: © 2014 Näslund
abstract: This paper describes a non-invasive method for estimating gross brain size in small fish with semi-transparent heads, using system camera equipment. Macro-photographs were taken from above on backlit free-swimming fish undergoing light anaesthesia. From the photographs, the width of the optic tectum was measured. This measure (TeO-measure) correlates well with the width of the optic tectum as measured from out-dissected brains in both brown trout fry and zebrafish (Pearson r > 0.90). The TeO-measure also correlates well with overall brain wet weight in brown trout fry (r = 0.90), but less well for zebrafish (r = 0.79). A non-invasive measure makes it possible to quickly assess brain size from a large number of individuals, as well as repeatedly measuring brain size of live individuals allowing calculation of brain growth.
bibliographic citation: Näslund (2014) A simple non-invasive method for measuring gross brain size in small live fish with semi-transparent heads. PeerJ 2:e586 https://doi.org/10.7717/peerj.586
date submitted: 2014-05-31
date accepted: 2014-08-29
issued: 2014-09-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Näslund
  given name: Joacim
doi: 10.7717/peerj.586
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-23
copyright: © 2014 Näslund
attribution name: Näslund

Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer
type: item
type: AcademicArticle
description: Tuberculosis remains a major global health problem. Laboratory diagnostic methods that allow effective, early detection of cases are central to management of tuberculosis in the individual patient and in the community. Since the 1880s, laboratory diagnosis of tuberculosis has relied primarily on microscopy and culture. However, microscopy fails to provide species- or lineage-level identification and culture-based workflows for diagnosis of tuberculosis remain complex, expensive, slow, technically demanding and poorly able to handle mixed infections. We therefore explored the potential of shotgun metagenomics, sequencing of DNA from samples without culture or target-specific amplification or capture, to detect and characterise strains from the Mycobacterium tuberculosis complex in smear-positive sputum samples obtained from The Gambia in West Africa. Eight smear- and culture-positive sputum samples were investigated using a differential-lysis protocol followed by a kit-based DNA extraction method, with sequencing performed on a benchtop sequencing instrument, the Illumina MiSeq. The number of sequence reads in each sputum-derived metagenome ranged from 989,442 to 2,818,238. The proportion of reads in each metagenome mapping against the human genome ranged from 20% to 99%. We were able to detect sequences from the M. tuberculosis complex in all eight samples, with coverage of the H37Rv reference genome ranging from 0.002X to 0.7X. By analysing the distribution of large sequence polymorphisms (deletions and the locations of the insertion element IS6110) and single nucleotide polymorphisms (SNPs), we were able to assign seven of eight metagenome-derived genomes to a species and lineage within the M. tuberculosis complex. Two metagenome-derived mycobacterial genomes were assigned to M. africanum, a species largely confined to West Africa; the others that could be assigned belonged to lineages T, H or LAM within the clade of “modern” M. tuberculosis strains. We have provi…
format: application/pdf
format: text/html
creator: Emma L. Doughty
creator: Martin J. Sergeant
creator: Ifedayo Adetifa
creator: Martin Antonio
creator: Mark J. Pallen
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Infectious Diseases
subject: Respiratory Medicine
description: doi:10.7717/peerj.585
publisher: PeerJ Inc.
rights: © 2014 Doughty et al.
abstract: Tuberculosis remains a major global health problem. Laboratory diagnostic methods that allow effective, early detection of cases are central to management of tuberculosis in the individual patient and in the community. Since the 1880s, laboratory diagnosis of tuberculosis has relied primarily on microscopy and culture. However, microscopy fails to provide species- or lineage-level identification and culture-based workflows for diagnosis of tuberculosis remain complex, expensive, slow, technically demanding and poorly able to handle mixed infections. We therefore explored the potential of shotgun metagenomics, sequencing of DNA from samples without culture or target-specific amplification or capture, to detect and characterise strains from the Mycobacterium tuberculosis complex in smear-positive sputum samples obtained from The Gambia in West Africa. Eight smear- and culture-positive sputum samples were investigated using a differential-lysis protocol followed by a kit-based DNA extraction method, with sequencing performed on a benchtop sequencing instrument, the Illumina MiSeq. The number of sequence reads in each sputum-derived metagenome ranged from 989,442 to 2,818,238. The proportion of reads in each metagenome mapping against the human genome ranged from 20% to 99%. We were able to detect sequences from the M. tuberculosis complex in all eight samples, with coverage of the H37Rv reference genome ranging from 0.002X to 0.7X. By analysing the distribution of large sequence polymorphisms (deletions and the locations of the insertion element IS6110) and single nucleotide polymorphisms (SNPs), we were able to assign seven of eight metagenome-derived genomes to a species and lineage within the M. tuberculosis complex. Two metagenome-derived mycobacterial genomes were assigned to M. africanum, a species largely confined to West Africa; the others that could be assigned belonged to lineages T, H or LAM within the clade of “modern” M. tuberculosis strains. We have provi…
bibliographic citation: Doughty et al. (2014) Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ 2:e585 https://doi.org/10.7717/peerj.585
date submitted: 2014-08-14
date accepted: 2014-08-28
issued: 2014-09-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Doughty
  given name: Emma L.
author list: Agent
  family name: Sergeant
  given name: Martin J.
author list: Agent
  family name: Adetifa
  given name: Ifedayo
author list: Agent
  family name: Antonio
  given name: Martin
author list: Agent
  family name: Pallen
  given name: Mark J.
doi: 10.7717/peerj.585
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-23
copyright: © 2014 Doughty et al.
attribution name: Doughty et al.

The impact of atypical early histories on pet or performer chimpanzees
type: item
type: AcademicArticle
description: It is widely accepted that an animal’s early history, including but not limited to its rearing history, can have a profound impact on later behavior. In the case of captive animals, many studies have used categorical measures such as mother reared or human reared that do not account for both the influence of human and conspecific interaction. In order to account for the influence of both human and conspecific early exposure to later behavior, we collected 1385 h of data on 60 chimpanzees, of which 36 were former pets or performers, currently housed at accredited zoos or sanctuaries. We developed a unique metric, the Chimpanzee-Human Interaction (CHI) Index that represented a continuous measure of the proportion of human and chimpanzee exposure subjects experienced and here focused on their exposure during the first four years of life. We found that chimpanzees who experienced less exposure to other chimpanzees as infants showed a lower frequency of grooming and sexual behaviors later in life which can influence social dynamics within groups. We also found chimpanzees who experienced more exposure to other chimpanzees as infants showed a higher frequency of coprophagy, suggesting coprophagy could be a socially-learned behavior. These results help characterize some of the long-term effects borne by chimpanzees maintained as pets and performers and may help inform managers seeking to integrate these types of chimpanzees into larger social groups, as in zoos and sanctuaries. In addition, these results highlight the necessity of taking into account the time-weighted influence of human and conspecific interactions when assessing the impact that humans can have on animals living in captivity.
format: application/pdf
format: text/html
creator: Hani D. Freeman
creator: Stephen R. Ross
subject: Animal Behavior
subject: Anthropology
subject: Ethical Issues
description: doi:10.7717/peerj.579
publisher: PeerJ Inc.
rights: © 2014 Freeman and Ross
abstract: It is widely accepted that an animal’s early history, including but not limited to its rearing history, can have a profound impact on later behavior. In the case of captive animals, many studies have used categorical measures such as mother reared or human reared that do not account for both the influence of human and conspecific interaction. In order to account for the influence of both human and conspecific early exposure to later behavior, we collected 1385 h of data on 60 chimpanzees, of which 36 were former pets or performers, currently housed at accredited zoos or sanctuaries. We developed a unique metric, the Chimpanzee-Human Interaction (CHI) Index that represented a continuous measure of the proportion of human and chimpanzee exposure subjects experienced and here focused on their exposure during the first four years of life. We found that chimpanzees who experienced less exposure to other chimpanzees as infants showed a lower frequency of grooming and sexual behaviors later in life which can influence social dynamics within groups. We also found chimpanzees who experienced more exposure to other chimpanzees as infants showed a higher frequency of coprophagy, suggesting coprophagy could be a socially-learned behavior. These results help characterize some of the long-term effects borne by chimpanzees maintained as pets and performers and may help inform managers seeking to integrate these types of chimpanzees into larger social groups, as in zoos and sanctuaries. In addition, these results highlight the necessity of taking into account the time-weighted influence of human and conspecific interactions when assessing the impact that humans can have on animals living in captivity.
bibliographic citation: Freeman et al. (2014) The impact of atypical early histories on pet or performer chimpanzees. PeerJ 2:e579 https://doi.org/10.7717/peerj.579
date submitted: 2014-03-19
date accepted: 2014-08-26
issued: 2014-09-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Freeman
  given name: Hani D.
author list: Agent
  family name: Ross
  given name: Stephen R.
doi: 10.7717/peerj.579
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-23
copyright: © 2014 Freeman and Ross
attribution name: Freeman and Ross

Error estimates for the analysis of differential expression from RNA-seq count data
type: item
type: AcademicArticle
description: Background. A number of algorithms exist for analysing RNA-sequencing data to infer profiles of differential gene expression. Problems inherent in building algorithms around statistical models of over dispersed count data are formidable and frequently lead to non-uniform p-value distributions for null-hypothesis data and to inaccurate estimates of false discovery rates (FDRs). This can lead to an inaccurate measure of significance and loss of power to detect differential expression. Results. We use synthetic and real biological data to assess the ability of several available R packages to accurately estimate FDRs. The packages surveyed are based on statistical models of overdispersed Poisson data and include edgeR, DESeq, DESeq2, PoissonSeq and QuasiSeq. Also tested is an add-on package to edgeR and DESeq which we introduce called Polyfit. Polyfit aims to address the problem of a non-uniform null p-value distribution for two-class datasets by adapting the Storey–Tibshirani procedure. Conclusions. We find the best performing package in the sense that it achieves a low FDR which is accurately estimated over the full range of p-values, albeit with a very slow run time, is the QLSpline implementation of QuasiSeq. This finding holds provided the number of biological replicates in each condition is at least 4. The next best performing packages are edgeR and DESeq2. When the number of biological replicates is sufficiently high, and within a range accessible to multiplexed experimental designs, the Polyfit extension improves the performance DESeq (for approximately 6 or more replicates per condition), making its performance comparable with that of edgeR and DESeq2 in our tests with synthetic data.
format: application/pdf
format: text/html
creator: Conrad J. Burden
creator: Sumaira E. Qureshi
creator: Susan R. Wilson
subject: Bioinformatics
subject: Statistics
description: doi:10.7717/peerj.576
publisher: PeerJ Inc.
rights: © 2014 Burden et al.
abstract: Background. A number of algorithms exist for analysing RNA-sequencing data to infer profiles of differential gene expression. Problems inherent in building algorithms around statistical models of over dispersed count data are formidable and frequently lead to non-uniform p-value distributions for null-hypothesis data and to inaccurate estimates of false discovery rates (FDRs). This can lead to an inaccurate measure of significance and loss of power to detect differential expression. Results. We use synthetic and real biological data to assess the ability of several available R packages to accurately estimate FDRs. The packages surveyed are based on statistical models of overdispersed Poisson data and include edgeR, DESeq, DESeq2, PoissonSeq and QuasiSeq. Also tested is an add-on package to edgeR and DESeq which we introduce called Polyfit. Polyfit aims to address the problem of a non-uniform null p-value distribution for two-class datasets by adapting the Storey–Tibshirani procedure. Conclusions. We find the best performing package in the sense that it achieves a low FDR which is accurately estimated over the full range of p-values, albeit with a very slow run time, is the QLSpline implementation of QuasiSeq. This finding holds provided the number of biological replicates in each condition is at least 4. The next best performing packages are edgeR and DESeq2. When the number of biological replicates is sufficiently high, and within a range accessible to multiplexed experimental designs, the Polyfit extension improves the performance DESeq (for approximately 6 or more replicates per condition), making its performance comparable with that of edgeR and DESeq2 in our tests with synthetic data.
bibliographic citation: Burden et al. (2014) Error estimates for the analysis of differential expression from RNA-seq count data. PeerJ 2:e576 https://doi.org/10.7717/peerj.576
date submitted: 2014-05-22
date accepted: 2014-08-25
issued: 2014-09-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Burden
  given name: Conrad J.
author list: Agent
  family name: Qureshi
  given name: Sumaira E.
author list: Agent
  family name: Wilson
  given name: Susan R.
doi: 10.7717/peerj.576
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-23
copyright: © 2014 Burden et al.
attribution name: Burden et al.

Livestock as a potential biological control agent for an invasive wetland plant
type: item
type: AcademicArticle
description: Invasive species threaten biodiversity and incur costs exceeding billions of US$. Eradication efforts, however, are nearly always unsuccessful. Throughout much of North America, land managers have used expensive, and ultimately ineffective, techniques to combat invasive Phragmites australis in marshes. Here, we reveal that Phragmites may potentially be controlled by employing an affordable measure from its native European range: livestock grazing. Experimental field tests demonstrate that rotational goat grazing (where goats have no choice but to graze Phragmites) can reduce Phragmites cover from 100 to 20% and that cows and horses also readily consume this plant. These results, combined with the fact that Europeans have suppressed Phragmites through seasonal livestock grazing for 6,000 years, suggest Phragmites management can shift to include more economical and effective top-down control strategies. More generally, these findings support an emerging paradigm shift in conservation from high-cost eradication to economically sustainable control of dominant invasive species.
format: application/pdf
format: text/html
creator: Brian R. Silliman
creator: Thomas Mozdzer
creator: Christine Angelini
creator: Jennifer E. Brundage
creator: Peter Esselink
creator: Jan P. Bakker
creator: Keryn B. Gedan
creator: Johan van de Koppel
creator: Andrew H. Baldwin
subject: Ecology
subject: Natural Resource Management
description: doi:10.7717/peerj.567
publisher: PeerJ Inc.
rights: © 2014 Silliman et al.
abstract: Invasive species threaten biodiversity and incur costs exceeding billions of US$. Eradication efforts, however, are nearly always unsuccessful. Throughout much of North America, land managers have used expensive, and ultimately ineffective, techniques to combat invasive Phragmites australis in marshes. Here, we reveal that Phragmites may potentially be controlled by employing an affordable measure from its native European range: livestock grazing. Experimental field tests demonstrate that rotational goat grazing (where goats have no choice but to graze Phragmites) can reduce Phragmites cover from 100 to 20% and that cows and horses also readily consume this plant. These results, combined with the fact that Europeans have suppressed Phragmites through seasonal livestock grazing for 6,000 years, suggest Phragmites management can shift to include more economical and effective top-down control strategies. More generally, these findings support an emerging paradigm shift in conservation from high-cost eradication to economically sustainable control of dominant invasive species.
bibliographic citation: Silliman et al. (2014) Livestock as a potential biological control agent for an invasive wetland plant. PeerJ 2:e567 https://doi.org/10.7717/peerj.567
date submitted: 2014-04-20
date accepted: 2014-08-18
issued: 2014-09-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silliman
  given name: Brian R.
author list: Agent
  family name: Mozdzer
  given name: Thomas
author list: Agent
  family name: Angelini
  given name: Christine
author list: Agent
  family name: Brundage
  given name: Jennifer E.
author list: Agent
  family name: Esselink
  given name: Peter
author list: Agent
  family name: Bakker
  given name: Jan P.
author list: Agent
  family name: Gedan
  given name: Keryn B.
author list: Agent
  family name: van de Koppel
  given name: Johan
author list: Agent
  family name: Baldwin
  given name: Andrew H.
doi: 10.7717/peerj.567
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-23
copyright: © 2014 Silliman et al.
attribution name: Silliman et al.

Removing batch effects for prediction problems with frozen surrogate variable analysis
type: item
type: AcademicArticle
description: Batch effects are responsible for the failure of promising genomic prognostic signatures, major ambiguities in published genomic results, and retractions of widely-publicized findings. Batch effect corrections have been developed to remove these artifacts, but they are designed to be used in population studies. But genomic technologies are beginning to be used in clinical applications where samples are analyzed one at a time for diagnostic, prognostic, and predictive applications. There are currently no batch correction methods that have been developed specifically for prediction. In this paper, we propose an new method called frozen surrogate variable analysis (fSVA) that borrows strength from a training set for individual sample batch correction. We show that fSVA improves prediction accuracy in simulations and in public genomic studies. fSVA is available as part of the sva Bioconductor package.
format: application/pdf
format: text/html
creator: Hilary S. Parker
creator: Héctor Corrada Bravo
creator: Jeffrey T. Leek
subject: Bioinformatics
subject: Computational Biology
subject: Statistics
subject: Computational Science
description: doi:10.7717/peerj.561
publisher: PeerJ Inc.
rights: © 2014 Parker et al.
abstract: Batch effects are responsible for the failure of promising genomic prognostic signatures, major ambiguities in published genomic results, and retractions of widely-publicized findings. Batch effect corrections have been developed to remove these artifacts, but they are designed to be used in population studies. But genomic technologies are beginning to be used in clinical applications where samples are analyzed one at a time for diagnostic, prognostic, and predictive applications. There are currently no batch correction methods that have been developed specifically for prediction. In this paper, we propose an new method called frozen surrogate variable analysis (fSVA) that borrows strength from a training set for individual sample batch correction. We show that fSVA improves prediction accuracy in simulations and in public genomic studies. fSVA is available as part of the sva Bioconductor package.
bibliographic citation: Parker et al. (2014) Removing batch effects for prediction problems with frozen surrogate variable analysis. PeerJ 2:e561 https://doi.org/10.7717/peerj.561
date submitted: 2014-06-20
date accepted: 2014-08-15
issued: 2014-09-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Parker
  given name: Hilary S.
author list: Agent
  family name: Corrada Bravo
  given name: Héctor
author list: Agent
  family name: Leek
  given name: Jeffrey T.
doi: 10.7717/peerj.561
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-23
copyright: © 2014 Parker et al.
attribution name: Parker et al.

Anopheles gambiae densovirus (AgDNV) has negligible effects on adult survival and transcriptome of its mosquito host
type: item
type: AcademicArticle
description: Mosquito densoviruses (DNVs) are candidate agents for paratransgenic control of malaria and other vector-borne diseases. Unlike other mosquito DNVs, the Anopheles gambiae DNV (AgDNV) is non-pathogenic to larval mosquitoes. However, the cost of infection upon adults and the molecular mechanisms underpinning infection in the mosquito host are unknown. Using life table analysis, we show that AgDNV infection has minimal effects on An. gambiae survival (no significant effect in 2 replicates and a slight 2 day survival decrease in the third replicate). Using microarrays, we show that AgDNV has very minimal effect on the adult mosquito transcriptome, with only 4–15 genes differentially regulated depending on the statistical criteria imposed. The minimal impact upon global transcription provides some mechanistic understanding of lack of virus pathogenicity, suggesting a long co-evolutionary history that has shifted towards avirulence. From an applied standpoint, lack of strong induced fitness costs makes AgDNV an attractive agent for paratransgenic malaria control.
format: application/pdf
format: text/html
creator: Xiaoxia Ren
creator: Grant L. Hughes
creator: Guodong Niu
creator: Yasutsugu Suzuki
creator: Jason L. Rasgon
subject: Entomology
subject: Microbiology
subject: Virology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.584
publisher: PeerJ Inc.
rights: © 2014 Ren et al.
abstract: Mosquito densoviruses (DNVs) are candidate agents for paratransgenic control of malaria and other vector-borne diseases. Unlike other mosquito DNVs, the Anopheles gambiae DNV (AgDNV) is non-pathogenic to larval mosquitoes. However, the cost of infection upon adults and the molecular mechanisms underpinning infection in the mosquito host are unknown. Using life table analysis, we show that AgDNV infection has minimal effects on An. gambiae survival (no significant effect in 2 replicates and a slight 2 day survival decrease in the third replicate). Using microarrays, we show that AgDNV has very minimal effect on the adult mosquito transcriptome, with only 4–15 genes differentially regulated depending on the statistical criteria imposed. The minimal impact upon global transcription provides some mechanistic understanding of lack of virus pathogenicity, suggesting a long co-evolutionary history that has shifted towards avirulence. From an applied standpoint, lack of strong induced fitness costs makes AgDNV an attractive agent for paratransgenic malaria control.
bibliographic citation: Ren et al. (2014) Anopheles gambiae densovirus (AgDNV) has negligible effects on adult survival and transcriptome of its mosquito host. PeerJ 2:e584 https://doi.org/10.7717/peerj.584
date submitted: 2014-08-07
date accepted: 2014-08-28
issued: 2014-09-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Xiaoxia
author list: Agent
  family name: Hughes
  given name: Grant L.
author list: Agent
  family name: Niu
  given name: Guodong
author list: Agent
  family name: Suzuki
  given name: Yasutsugu
author list: Agent
  family name: Rasgon
  given name: Jason L.
doi: 10.7717/peerj.584
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-18
copyright: © 2014 Ren et al.
attribution name: Ren et al.

MicroRNAs expression profile in CCR6+ regulatory T cells
type: item
type: AcademicArticle
description: Backgroud. CCR6+ CD4+ regulatory T cells (CCR6+ Tregs), a distinct Tregs subset, played an important role in various immune diseases. Recent evidence showed that microRNAs (miRNAs) are vital regulators in the function of immune cells. However, the potential role of miRNAs in the function of CCR6+ Tregs remains largely unknown. In this study, we detected the expression profile of miRNAs in CCR6+ Tregs. Materials and Methods. The expression profile of miRNAs as well as genes in CCR6+ Tregs or CCR6- Tregs from Balb/c mice were detected by microarray. The signaling pathways were analyzed using the Keggs pathway library. Results. We found that there were 58 miRNAs significantly upregulated and 62 downregulated up to 2 fold in CCR6+ Tregs compared with CCR6- Tregs. Moreover, 1,391 genes were observed with 3 fold change and 20 signaling pathways were enriched using the Keggs pathway library. Conclusion. The present data showed CCR6+ Tregs expressed specific miRNAs pattern, which provides insight into the role of miRNAs in the biological function of distinct Tregs subsets.
format: application/pdf
format: text/html
creator: Juanjuan Zhao
creator: Yongju Li
creator: Yan Hu
creator: Chao Chen
creator: Ya Zhou
creator: Yijin Tao
creator: Mengmeng Guo
creator: Nalin Qin
creator: Lin Xu
subject: Biotechnology
subject: Cell Biology
subject: Allergy and Clinical Immunology
subject: Hematology
subject: Immunology
description: doi:10.7717/peerj.575
publisher: PeerJ Inc.
rights: © 2014 Zhao et al.
abstract: Backgroud. CCR6+ CD4+ regulatory T cells (CCR6+ Tregs), a distinct Tregs subset, played an important role in various immune diseases. Recent evidence showed that microRNAs (miRNAs) are vital regulators in the function of immune cells. However, the potential role of miRNAs in the function of CCR6+ Tregs remains largely unknown. In this study, we detected the expression profile of miRNAs in CCR6+ Tregs. Materials and Methods. The expression profile of miRNAs as well as genes in CCR6+ Tregs or CCR6- Tregs from Balb/c mice were detected by microarray. The signaling pathways were analyzed using the Keggs pathway library. Results. We found that there were 58 miRNAs significantly upregulated and 62 downregulated up to 2 fold in CCR6+ Tregs compared with CCR6- Tregs. Moreover, 1,391 genes were observed with 3 fold change and 20 signaling pathways were enriched using the Keggs pathway library. Conclusion. The present data showed CCR6+ Tregs expressed specific miRNAs pattern, which provides insight into the role of miRNAs in the biological function of distinct Tregs subsets.
bibliographic citation: Zhao et al. (2014) MicroRNAs expression profile in CCR6+ regulatory T cells. PeerJ 2:e575 https://doi.org/10.7717/peerj.575
date submitted: 2014-07-17
date accepted: 2014-08-22
issued: 2014-09-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Juanjuan
author list: Agent
  family name: Li
  given name: Yongju
author list: Agent
  family name: Hu
  given name: Yan
author list: Agent
  family name: Chen
  given name: Chao
author list: Agent
  family name: Zhou
  given name: Ya
author list: Agent
  family name: Tao
  given name: Yijin
author list: Agent
  family name: Guo
  given name: Mengmeng
author list: Agent
  family name: Qin
  given name: Nalin
author list: Agent
  family name: Xu
  given name: Lin
doi: 10.7717/peerj.575
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-18
copyright: © 2014 Zhao et al.
attribution name: Zhao et al.

Students distracted by electronic devices perform at the same level as those who are focused on the lecture
type: item
type: AcademicArticle
description: Background. Little is known about the characteristics of internet distractions that students may engage in during lecture. The objective of this pilot study is to identify some of the internet-based distractions students engage in during in-person lectures. The findings will help identify what activities most commonly cause students to be distracted from the lecture and if these activities impact student learning. Methods. This study is a quasi-experimental pilot study of 26 students from a single institution. In the current study, one class of third-year students were surveyed after a lecture on special needs dentistry. The survey identified self-reported utilization patterns of “smart” devices during the lecture. Additionally, twelve quiz-type questions were given to assess the students’ recall of important points in the lecture material that had just been covered. Results. The sample was comprised of 26 students. Of these, 17 were distracted in some form (either checking email, sending email, checking Facebook, or sending texts). The overall mean score on the test was 9.85 (9.53 for distracted students and 10.44 for non-distracted students). There were no significant differences in test scores between distracted and non-distracted students (p = 0.652). Gender and types of distractions were not significantly associated with test scores (p > 0.05). All students believed that they understood all the important points from the lecture. Conclusions. Every class member felt that they acquired the important learning points during the lecture. Those who were distracted by electronic devices during the lecture performed similarly to those who were not. However, results should be interpreted with caution as this study was a small quasi-experimental design and further research should examine the influence of different types of distraction on different types of learning.
format: application/pdf
format: text/html
creator: Romesh P. Nalliah
creator: Veerasathpurush Allareddy
subject: Human-Computer Interaction
subject: Science and Medical Education
description: doi:10.7717/peerj.572
publisher: PeerJ Inc.
rights: © 2014 Nalliah and Allareddy
abstract: Background. Little is known about the characteristics of internet distractions that students may engage in during lecture. The objective of this pilot study is to identify some of the internet-based distractions students engage in during in-person lectures. The findings will help identify what activities most commonly cause students to be distracted from the lecture and if these activities impact student learning. Methods. This study is a quasi-experimental pilot study of 26 students from a single institution. In the current study, one class of third-year students were surveyed after a lecture on special needs dentistry. The survey identified self-reported utilization patterns of “smart” devices during the lecture. Additionally, twelve quiz-type questions were given to assess the students’ recall of important points in the lecture material that had just been covered. Results. The sample was comprised of 26 students. Of these, 17 were distracted in some form (either checking email, sending email, checking Facebook, or sending texts). The overall mean score on the test was 9.85 (9.53 for distracted students and 10.44 for non-distracted students). There were no significant differences in test scores between distracted and non-distracted students (p = 0.652). Gender and types of distractions were not significantly associated with test scores (p > 0.05). All students believed that they understood all the important points from the lecture. Conclusions. Every class member felt that they acquired the important learning points during the lecture. Those who were distracted by electronic devices during the lecture performed similarly to those who were not. However, results should be interpreted with caution as this study was a small quasi-experimental design and further research should examine the influence of different types of distraction on different types of learning.
bibliographic citation: Nalliah et al. (2014) Students distracted by electronic devices perform at the same level as those who are focused on the lecture. PeerJ 2:e572 https://doi.org/10.7717/peerj.572
date submitted: 2014-02-20
date accepted: 2014-08-19
issued: 2014-09-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nalliah
  given name: Romesh P.
author list: Agent
  family name: Allareddy
  given name: Veerasathpurush
doi: 10.7717/peerj.572
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-16
copyright: © 2014 Nalliah and Allareddy
attribution name: Nalliah and Allareddy

Turf algae-mediated coral damage in coastal reefs of Belize, Central America
type: item
type: AcademicArticle
description: Many coral reefs in the Caribbean experienced substantial changes in their benthic community composition during the last decades. This often resulted in phase shifts from scleractinian coral dominance to that by other benthic invertebrate or algae. However, knowledge about how the related role of coral-algae contacts may negatively affect corals is scarce. Therefore, benthic community composition, abundance of algae grazers, and the abundance and character of coral-algae contacts were assessed in situ at 13 Belizean reef sites distributed along a distance gradient to the Belizean mainland (12–70 km): Mesoamerican Barrier Reef (inshore), Turneffe Atoll (inner and outer midshore), and Lighthouse Reef (offshore). In situ surveys revealed significantly higher benthic cover by scleractinian corals at the remote Lighthouse Reef (26–29%) when compared to the other sites (4–19%). The abundance of herbivorous fish and the sea urchin Diadema antillarum significantly increased towards the offshore reef sites, while the occurrence of direct coral-algae contacts consequently increased significantly with decreasing distance to shore. About 60% of these algae contacts were harmful (exhibiting coral tissue damage, pigmentation change, or overgrowth) for corals (mainly genera Orbicella and Agaricia), particularly when filamentous turf algae were involved. These findings provide support to the hypothesis that (turf) algae-mediated coral damage occurs in Belizean coastal, near-shore coral reefs.
format: application/pdf
format: text/html
creator: Christian Wild
creator: Carin Jantzen
creator: Stephan Georg Kremb
subject: Ecosystem Science
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.571
publisher: PeerJ Inc.
rights: © 2014 Wild et al.
abstract: Many coral reefs in the Caribbean experienced substantial changes in their benthic community composition during the last decades. This often resulted in phase shifts from scleractinian coral dominance to that by other benthic invertebrate or algae. However, knowledge about how the related role of coral-algae contacts may negatively affect corals is scarce. Therefore, benthic community composition, abundance of algae grazers, and the abundance and character of coral-algae contacts were assessed in situ at 13 Belizean reef sites distributed along a distance gradient to the Belizean mainland (12–70 km): Mesoamerican Barrier Reef (inshore), Turneffe Atoll (inner and outer midshore), and Lighthouse Reef (offshore). In situ surveys revealed significantly higher benthic cover by scleractinian corals at the remote Lighthouse Reef (26–29%) when compared to the other sites (4–19%). The abundance of herbivorous fish and the sea urchin Diadema antillarum significantly increased towards the offshore reef sites, while the occurrence of direct coral-algae contacts consequently increased significantly with decreasing distance to shore. About 60% of these algae contacts were harmful (exhibiting coral tissue damage, pigmentation change, or overgrowth) for corals (mainly genera Orbicella and Agaricia), particularly when filamentous turf algae were involved. These findings provide support to the hypothesis that (turf) algae-mediated coral damage occurs in Belizean coastal, near-shore coral reefs.
bibliographic citation: Wild et al. (2014) Turf algae-mediated coral damage in coastal reefs of Belize, Central America. PeerJ 2:e571 https://doi.org/10.7717/peerj.571
date submitted: 2014-05-15
date accepted: 2014-08-20
issued: 2014-09-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wild
  given name: Christian
author list: Agent
  family name: Jantzen
  given name: Carin
author list: Agent
  family name: Kremb
  given name: Stephan Georg
doi: 10.7717/peerj.571
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-16
copyright: © 2014 Wild et al.
attribution name: Wild et al.

What’s for dinner? Undescribed species of porcini in a commercial packet
type: item
type: AcademicArticle
description: Accurate diagnosis of the components of our food and a standard lexicon for clear communication is essential for regulating global food trade and identifying food frauds. Reliable identification of wild collected foods can be particularly difficult, especially when they originate in under-documented regions or belong to poorly known groups such as Fungi. Porcini, one of the most widely traded wild edible mushrooms in the world, are large and conspicuous and they are used as a food both on their own and in processed food products. China is a major exporter of porcini, most of it ending up in Europe. We used DNA-sequencing to identify three species of mushroom contained within a commercial packet of dried Chinese porcini purchased in London. Surprisingly, all three have never been formally described by science and required new scientific names. This demonstrates the ubiquity of unknown fungal diversity even in widely traded commercial food products from one of the most charismatic and least overlooked groups of mushrooms. Our rapid analysis and description makes it possible to reliably identify these species, allowing their harvest to be monitored and their presence tracked in the food chain.
format: application/pdf
format: text/html
creator: Bryn T.M. Dentinger
creator: Laura M. Suz
subject: Conservation Biology
subject: Evolutionary Studies
subject: Food Science and Technology
subject: Mycology
subject: Taxonomy
description: doi:10.7717/peerj.570
publisher: PeerJ Inc.
rights: © 2014 Dentinger and Suz
abstract: Accurate diagnosis of the components of our food and a standard lexicon for clear communication is essential for regulating global food trade and identifying food frauds. Reliable identification of wild collected foods can be particularly difficult, especially when they originate in under-documented regions or belong to poorly known groups such as Fungi. Porcini, one of the most widely traded wild edible mushrooms in the world, are large and conspicuous and they are used as a food both on their own and in processed food products. China is a major exporter of porcini, most of it ending up in Europe. We used DNA-sequencing to identify three species of mushroom contained within a commercial packet of dried Chinese porcini purchased in London. Surprisingly, all three have never been formally described by science and required new scientific names. This demonstrates the ubiquity of unknown fungal diversity even in widely traded commercial food products from one of the most charismatic and least overlooked groups of mushrooms. Our rapid analysis and description makes it possible to reliably identify these species, allowing their harvest to be monitored and their presence tracked in the food chain.
bibliographic citation: Dentinger et al. (2014) What’s for dinner? Undescribed species of porcini in a commercial packet. PeerJ 2:e570 https://doi.org/10.7717/peerj.570
date submitted: 2014-05-23
date accepted: 2014-08-20
issued: 2014-09-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dentinger
  given name: Bryn T.M.
author list: Agent
  family name: Suz
  given name: Laura M.
doi: 10.7717/peerj.570
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-16
copyright: © 2014 Dentinger and Suz
attribution name: Dentinger and Suz

Role of enzymatic activity in muscle damage and cytotoxicity induced by Bothrops asper Asp49 phospholipase A2 myotoxins: are there additional effector mechanisms involved?
type: item
type: AcademicArticle
description: Viperid venoms often contain mixtures of Asp49 and Lys49 PLA2 myotoxin isoforms, relevant to development of myonecrosis. Given their difference in catalytic activity, mechanistic studies on each type require highly purified samples. Studies on Asp49 PLA2s have shown that enzyme inactivation using p-bromophenacyl bromide (p-BPB) drastically affects toxicity. However, based on the variable levels of residual toxicity observed in some studies, it has been suggested that effector mechanisms independent of catalysis may additionally be involved in the toxicity of these enzymes, possibly resembling those of the enzymatically inactive Lys49 myotoxins. A possibility that Lys49 isoforms could be present in Asp49 PLA2 preparations exists and, if undetected in previous studies, could explain the variable residual toxicity. This question is here addressed by using an enzyme preparation ascertained to be free of Lys49 myotoxins. In agreement with previous reports, inactivation of the catalytic activity of an Asp49 myotoxin preparation led to major inhibition of toxic effects in vitro and in vivo. The very low residual levels of myotoxicity (7%) and cytotoxicity (4%) observed can be attributed to the low, although detectable, enzyme remaining active after p-BPB treatment (2.7%), and would be difficult to reconcile with the proposed existence of additional catalytic-independent toxic mechanisms. These findings favor the concept that the effector mechanism of toxicity of Asp49 PLA2 myotoxins from viperids fundamentally relies on their ability to hydrolyze phospholipids, arguing against the proposal that membrane disruption may also be caused by additional mechanisms that are independent of catalysis.
format: application/pdf
format: text/html
creator: Diana Mora-Obando
creator: Cecilia Díaz
creator: Yamileth Angulo
creator: José María Gutiérrez
creator: Bruno Lomonte
subject: Biochemistry
subject: Toxicology
subject: Pharmacology
description: doi:10.7717/peerj.569
publisher: PeerJ Inc.
rights: © 2014 Mora-Obando et al.
abstract: Viperid venoms often contain mixtures of Asp49 and Lys49 PLA2 myotoxin isoforms, relevant to development of myonecrosis. Given their difference in catalytic activity, mechanistic studies on each type require highly purified samples. Studies on Asp49 PLA2s have shown that enzyme inactivation using p-bromophenacyl bromide (p-BPB) drastically affects toxicity. However, based on the variable levels of residual toxicity observed in some studies, it has been suggested that effector mechanisms independent of catalysis may additionally be involved in the toxicity of these enzymes, possibly resembling those of the enzymatically inactive Lys49 myotoxins. A possibility that Lys49 isoforms could be present in Asp49 PLA2 preparations exists and, if undetected in previous studies, could explain the variable residual toxicity. This question is here addressed by using an enzyme preparation ascertained to be free of Lys49 myotoxins. In agreement with previous reports, inactivation of the catalytic activity of an Asp49 myotoxin preparation led to major inhibition of toxic effects in vitro and in vivo. The very low residual levels of myotoxicity (7%) and cytotoxicity (4%) observed can be attributed to the low, although detectable, enzyme remaining active after p-BPB treatment (2.7%), and would be difficult to reconcile with the proposed existence of additional catalytic-independent toxic mechanisms. These findings favor the concept that the effector mechanism of toxicity of Asp49 PLA2 myotoxins from viperids fundamentally relies on their ability to hydrolyze phospholipids, arguing against the proposal that membrane disruption may also be caused by additional mechanisms that are independent of catalysis.
bibliographic citation: Mora-Obando et al. (2014) Role of enzymatic activity in muscle damage and cytotoxicity induced by Bothrops asper Asp49 phospholipase A2 myotoxins: are there additional effector mechanisms involved?. PeerJ 2:e569 https://doi.org/10.7717/peerj.569
date submitted: 2014-07-02
date accepted: 2014-08-20
issued: 2014-09-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mora-Obando
  given name: Diana
author list: Agent
  family name: Díaz
  given name: Cecilia
author list: Agent
  family name: Angulo
  given name: Yamileth
author list: Agent
  family name: Gutiérrez
  given name: José María
author list: Agent
  family name: Lomonte
  given name: Bruno
doi: 10.7717/peerj.569
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-16
copyright: © 2014 Mora-Obando et al.
attribution name: Mora-Obando et al.

Nestling activity levels during begging behaviour predicts activity level and body mass in adulthood
type: item
type: AcademicArticle
description: Across a range of species including humans, personality traits, or differences in behaviour between individuals that are consistent over time, have been demonstrated. However, few studies have measured whether these consistent differences are evident in very young animals, and whether they persist over an individual’s entire lifespan. Here we investigated the begging behaviour of very young cross-fostered zebra finch nestlings and the relationship between that and adult activity levels. We found a link between the nestling activity behaviour head movements during begging, measured at just five and seven days after hatching, and adult activity levels, measured when individuals were between three and three and a half years old. Moreover, body mass was found to be negatively correlated with both nestling and adult activity levels, suggesting that individuals which carry less body fat as adults are less active both as adults and during begging as nestlings. Our work suggests that the personality traits identified here in both very young nestlings and adults may be linked to physiological factors such as metabolism or environmental sources of variation. Moreover, our work suggests it may be possible to predict an individual’s future adult personality at a very young age, opening up new avenues for future work to explore the relationship between personality and a number of aspects of individual life history and survival.
format: application/pdf
format: text/html
creator: Luke S.C. McCowan
creator: Simon C. Griffith
subject: Animal Behavior
subject: Developmental Biology
description: doi:10.7717/peerj.566
publisher: PeerJ Inc.
rights: © 2014 McCowan and Griffith
abstract: Across a range of species including humans, personality traits, or differences in behaviour between individuals that are consistent over time, have been demonstrated. However, few studies have measured whether these consistent differences are evident in very young animals, and whether they persist over an individual’s entire lifespan. Here we investigated the begging behaviour of very young cross-fostered zebra finch nestlings and the relationship between that and adult activity levels. We found a link between the nestling activity behaviour head movements during begging, measured at just five and seven days after hatching, and adult activity levels, measured when individuals were between three and three and a half years old. Moreover, body mass was found to be negatively correlated with both nestling and adult activity levels, suggesting that individuals which carry less body fat as adults are less active both as adults and during begging as nestlings. Our work suggests that the personality traits identified here in both very young nestlings and adults may be linked to physiological factors such as metabolism or environmental sources of variation. Moreover, our work suggests it may be possible to predict an individual’s future adult personality at a very young age, opening up new avenues for future work to explore the relationship between personality and a number of aspects of individual life history and survival.
bibliographic citation: McCowan et al. (2014) Nestling activity levels during begging behaviour predicts activity level and body mass in adulthood. PeerJ 2:e566 https://doi.org/10.7717/peerj.566
date submitted: 2014-04-02
date accepted: 2014-08-18
issued: 2014-09-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McCowan
  given name: Luke S.C.
author list: Agent
  family name: Griffith
  given name: Simon C.
doi: 10.7717/peerj.566
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-16
copyright: © 2014 McCowan and Griffith
attribution name: McCowan and Griffith

Translation, adaptation, validation and performance of the American Weight Efficacy Lifestyle Questionnaire Short Form (WEL-SF) to a Norwegian version: a cross-sectional study
type: item
type: AcademicArticle
description: Background. Researchers have emphasized a need to identify predictors that can explain the variability in weight management after bariatric surgery. Eating self-efficacy has demonstrated predictive impact on patients’ adherence to recommended eating habits following multidisciplinary treatment programs, but has to a limited extent been subject for research after bariatric surgery. Recently an American short form version (WEL-SF) of the commonly used Weight Efficacy Lifestyle Questionnaire (WEL) was available for research and clinical purposes. Objectives. We intended to translate and culturally adapt the WEL-SF to Norwegian conditions, and to evaluate the new versions’ psychometrical properties in a Norwegian population of morbidly obese patients eligible for bariatric surgery. Design. Cross-sectional Methods. A total of 225 outpatients selected for Laparoscopic sleeve gastrectomy (LSG) were recruited; 114 non-operated and 111 operated patients, respectively. The questionnaire was translated through forward and backward procedures. Structural properties were assessed performing principal component analysis (PCA), correlation and regression analysis were conducted to evaluate convergent validity and sensitivity, respectively. Data was assessed by mean, median, item response, missing values, floor- and ceiling effect, Cronbach’s alpha and alpha if item deleted. Results. The PCA resulted in one factor with eigenvalue > 1, explaining 63.0% of the variability. The WEL-SF sum scores were positively correlated with the Self-efficacy and quality of life instruments (p < 0.001). The WEL-SF was associated with body mass index (BMI) (p < 0.001) and changes in BMI (p = 0.026). A very high item response was obtained with only one missing value (0.4%). The ceiling effect was in average 0.9 and 17.1% in the non-operated and operated sample, respectively. Strong internal consistency (r = 0.92) was obtained, and Cronbach’s alpha remained high (0.86–0.92) if single items were deleted…
format: application/pdf
format: text/html
creator: Tone N. Flølo
creator: John R. Andersen
creator: Hans J. Nielsen
creator: Gerd K. Natvig
subject: Nursing
subject: Nutrition
subject: Psychiatry and Psychology
subject: Public Health
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.565
publisher: PeerJ Inc.
rights: © 2014 Flølo et al.
abstract: Background. Researchers have emphasized a need to identify predictors that can explain the variability in weight management after bariatric surgery. Eating self-efficacy has demonstrated predictive impact on patients’ adherence to recommended eating habits following multidisciplinary treatment programs, but has to a limited extent been subject for research after bariatric surgery. Recently an American short form version (WEL-SF) of the commonly used Weight Efficacy Lifestyle Questionnaire (WEL) was available for research and clinical purposes. Objectives. We intended to translate and culturally adapt the WEL-SF to Norwegian conditions, and to evaluate the new versions’ psychometrical properties in a Norwegian population of morbidly obese patients eligible for bariatric surgery. Design. Cross-sectional Methods. A total of 225 outpatients selected for Laparoscopic sleeve gastrectomy (LSG) were recruited; 114 non-operated and 111 operated patients, respectively. The questionnaire was translated through forward and backward procedures. Structural properties were assessed performing principal component analysis (PCA), correlation and regression analysis were conducted to evaluate convergent validity and sensitivity, respectively. Data was assessed by mean, median, item response, missing values, floor- and ceiling effect, Cronbach’s alpha and alpha if item deleted. Results. The PCA resulted in one factor with eigenvalue > 1, explaining 63.0% of the variability. The WEL-SF sum scores were positively correlated with the Self-efficacy and quality of life instruments (p < 0.001). The WEL-SF was associated with body mass index (BMI) (p < 0.001) and changes in BMI (p = 0.026). A very high item response was obtained with only one missing value (0.4%). The ceiling effect was in average 0.9 and 17.1% in the non-operated and operated sample, respectively. Strong internal consistency (r = 0.92) was obtained, and Cronbach’s alpha remained high (0.86–0.92) if single items were deleted…
bibliographic citation: Flølo et al. (2014) Translation, adaptation, validation and performance of the American Weight Efficacy Lifestyle Questionnaire Short Form (WEL-SF) to a Norwegian version: a cross-sectional study. PeerJ 2:e565 https://doi.org/10.7717/peerj.565
date submitted: 2014-06-26
date accepted: 2014-08-18
issued: 2014-09-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Flølo
  given name: Tone N.
author list: Agent
  family name: Andersen
  given name: John R.
author list: Agent
  family name: Nielsen
  given name: Hans J.
author list: Agent
  family name: Natvig
  given name: Gerd K.
doi: 10.7717/peerj.565
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-16
copyright: © 2014 Flølo et al.
attribution name: Flølo et al.

Population structure and residency patterns of whale sharks, Rhincodon typus, at a provisioning site in Cebu, Philippines
type: item
type: AcademicArticle
description: This study represents the first description of whale sharks, Rhincodon typus, occurring at a provisioning site in Oslob, Cebu, Philippines. Frequent observations of sharks are often difficult, even at tourism sites, giving rise to provisioning activities to attract them. The present study provides repeated longitudinal data at a site where daily provisioning activities took place, and whale sharks were present every day. A total of 158 individual whale sharks were photographically identified between Mar 2012 and Dec 2013, with 129 males (82%), 19 females (12%) and 10 (6%) of undetermined sex. Mean estimated total length was 5.5 m (±1.3 m S.D.). Twenty individuals were measured with laser photogrammetry to validate researchers’ estimated sizes, yielding a good correlation (r2 = 0.83). Fifty-four (34%) individuals were observed being hand-fed by local fishermen (provisioned), through in-water behavioural observations. Maximum likelihood methods were used to model mean residency time of 44.9 days (±20.6 days S.E.) for provisioned R. typus contrasting with 22.4 days (±8.9 days S.E.) for non-provisioned individuals. Propeller scars were observed in 47% of the animals. A mean of 12.7 (±4.3 S.D.) R. typus were present in the survey area daily, with a maximum of 26 individuals (Aug 10 2013) and a minimum of 2 (Dec 6 2012). Twelve (8%) individuals were seen on at least 50% of survey days (n = 621), with a maximum residency of 572 days for one individual (P-396). Twenty four individuals were photographically identified across regional hotsposts, highlighting the species’ migratory nature and distribution. Extended residency and differences in lagged identification rates suggest behavioural modification on provisioned individuals, underlying the necessity for proper management of this tourism activity.
format: application/pdf
format: text/html
creator: Gonzalo Araujo
creator: Anna Lucey
creator: Jessica Labaja
creator: Catherine Lee So
creator: Sally Snow
creator: Alessandro Ponzo
subject: Animal Behavior
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.543
publisher: PeerJ Inc.
rights: © 2014 Araujo et al.
abstract: This study represents the first description of whale sharks, Rhincodon typus, occurring at a provisioning site in Oslob, Cebu, Philippines. Frequent observations of sharks are often difficult, even at tourism sites, giving rise to provisioning activities to attract them. The present study provides repeated longitudinal data at a site where daily provisioning activities took place, and whale sharks were present every day. A total of 158 individual whale sharks were photographically identified between Mar 2012 and Dec 2013, with 129 males (82%), 19 females (12%) and 10 (6%) of undetermined sex. Mean estimated total length was 5.5 m (±1.3 m S.D.). Twenty individuals were measured with laser photogrammetry to validate researchers’ estimated sizes, yielding a good correlation (r2 = 0.83). Fifty-four (34%) individuals were observed being hand-fed by local fishermen (provisioned), through in-water behavioural observations. Maximum likelihood methods were used to model mean residency time of 44.9 days (±20.6 days S.E.) for provisioned R. typus contrasting with 22.4 days (±8.9 days S.E.) for non-provisioned individuals. Propeller scars were observed in 47% of the animals. A mean of 12.7 (±4.3 S.D.) R. typus were present in the survey area daily, with a maximum of 26 individuals (Aug 10 2013) and a minimum of 2 (Dec 6 2012). Twelve (8%) individuals were seen on at least 50% of survey days (n = 621), with a maximum residency of 572 days for one individual (P-396). Twenty four individuals were photographically identified across regional hotsposts, highlighting the species’ migratory nature and distribution. Extended residency and differences in lagged identification rates suggest behavioural modification on provisioned individuals, underlying the necessity for proper management of this tourism activity.
bibliographic citation: Araujo et al. (2014) Population structure and residency patterns of whale sharks, Rhincodon typus, at a provisioning site in Cebu, Philippines. PeerJ 2:e543 https://doi.org/10.7717/peerj.543
date submitted: 2014-04-03
date accepted: 2014-08-06
issued: 2014-09-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Araujo
  given name: Gonzalo
author list: Agent
  family name: Lucey
  given name: Anna
author list: Agent
  family name: Labaja
  given name: Jessica
author list: Agent
  family name: So
  given name: Catherine Lee
author list: Agent
  family name: Snow
  given name: Sally
author list: Agent
  family name: Ponzo
  given name: Alessandro
doi: 10.7717/peerj.543
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-16
copyright: © 2014 Araujo et al.
attribution name: Araujo et al.

Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity
type: item
type: AcademicArticle
description: The role of species’ interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran’s eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners’ genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence …
format: application/pdf
format: text/html
creator: Hannah L. Buckley
creator: Arash Rafat
creator: Johnathon D. Ridden
creator: Robert H. Cruickshank
creator: Hayley J. Ridgway
creator: Adrian M. Paterson
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
description: doi:10.7717/peerj.573
publisher: PeerJ Inc.
rights: © 2014 Buckley et al.
abstract: The role of species’ interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran’s eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners’ genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence …
bibliographic citation: Buckley et al. (2014) Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity. PeerJ 2:e573 https://doi.org/10.7717/peerj.573
date submitted: 2014-05-25
date accepted: 2014-08-20
issued: 2014-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buckley
  given name: Hannah L.
author list: Agent
  family name: Rafat
  given name: Arash
author list: Agent
  family name: Ridden
  given name: Johnathon D.
author list: Agent
  family name: Cruickshank
  given name: Robert H.
author list: Agent
  family name: Ridgway
  given name: Hayley J.
author list: Agent
  family name: Paterson
  given name: Adrian M.
doi: 10.7717/peerj.573
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-11
copyright: © 2014 Buckley et al.
attribution name: Buckley et al.

Tracheostomy in children with congenital heart disease: a national analysis of the Kids’ Inpatient Database
type: item
type: AcademicArticle
description: Background. While single-institution studies reported the indications and outcomes of tracheostomy in children with congenital heart disease (CHD), no national analyses have been performed. We sought to examine the indications, performance, outcomes, and resource utilization of tracheostomy in children with CHD using a nationally representative database. Methods. We identified all children undergoing tracheostomy in the Kids’ Inpatient Database 1997 through 2009, and we compared children with CHD to children without CHD. Within the CHD group, we compared children whose tracheostomy occurred in the same hospital admission as a cardiac operation to those whose tracheostomy occurred without a cardiac operation in the same admission. Results. Tracheostomy was performed in n = 2,495 children with CHD, which represents 9.6% of all tracheostomies performed in children (n = 25,928), and 3.5% of all admissions for children with CHD (n = 355,460). Over the study period, there was an increasing trend in the proportion of all tracheostomies that were done in children with CHD (p < 0.0001) and an increasing trend in the proportion of admissions for children with CHD that involved a tracheostomy (p < 0.0001). The population of children with CHD undergoing tracheostomy differed markedly in baseline characteristics, outcomes, and resource utilization. Similarly, the subgroup of children whose tracheostomy was performed in the same admission as a cardiac operation differed significantly from those whose tracheostomy was not. Conclusions. Tracheostomy is an increasingly common procedure in children with CHD despite being associated with significantly greater resource utilization and in-hospital mortality. The population of children with CHD who undergo tracheostomy differs markedly from that of children without CHD who undergo tracheostomy, and important differences are observed between children who undergo tracheostomy in the same admission as a cardiac surgical procedure and those …
format: application/pdf
format: text/html
creator: Bryan G. Maxwell
creator: Kristen Nelson McMillan
subject: Anesthesiology and Pain Management
subject: Cardiology
subject: Epidemiology
subject: Pediatrics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.568
publisher: PeerJ Inc.
rights: © 2014 Maxwell and McMillan
abstract: Background. While single-institution studies reported the indications and outcomes of tracheostomy in children with congenital heart disease (CHD), no national analyses have been performed. We sought to examine the indications, performance, outcomes, and resource utilization of tracheostomy in children with CHD using a nationally representative database. Methods. We identified all children undergoing tracheostomy in the Kids’ Inpatient Database 1997 through 2009, and we compared children with CHD to children without CHD. Within the CHD group, we compared children whose tracheostomy occurred in the same hospital admission as a cardiac operation to those whose tracheostomy occurred without a cardiac operation in the same admission. Results. Tracheostomy was performed in n = 2,495 children with CHD, which represents 9.6% of all tracheostomies performed in children (n = 25,928), and 3.5% of all admissions for children with CHD (n = 355,460). Over the study period, there was an increasing trend in the proportion of all tracheostomies that were done in children with CHD (p < 0.0001) and an increasing trend in the proportion of admissions for children with CHD that involved a tracheostomy (p < 0.0001). The population of children with CHD undergoing tracheostomy differed markedly in baseline characteristics, outcomes, and resource utilization. Similarly, the subgroup of children whose tracheostomy was performed in the same admission as a cardiac operation differed significantly from those whose tracheostomy was not. Conclusions. Tracheostomy is an increasingly common procedure in children with CHD despite being associated with significantly greater resource utilization and in-hospital mortality. The population of children with CHD who undergo tracheostomy differs markedly from that of children without CHD who undergo tracheostomy, and important differences are observed between children who undergo tracheostomy in the same admission as a cardiac surgical procedure and those …
bibliographic citation: Maxwell et al. (2014) Tracheostomy in children with congenital heart disease: a national analysis of the Kids’ Inpatient Database. PeerJ 2:e568 https://doi.org/10.7717/peerj.568
date submitted: 2014-06-20
date accepted: 2014-08-19
issued: 2014-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maxwell
  given name: Bryan G.
author list: Agent
  family name: McMillan
  given name: Kristen Nelson
doi: 10.7717/peerj.568
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-11
copyright: © 2014 Maxwell and McMillan
attribution name: Maxwell and McMillan

Identification of a truncated splice variant of IL-18 receptor alpha in the human and rat, with evidence of wider evolutionary conservation
type: item
type: AcademicArticle
description: Interleukin-18 (IL-18) is a pro-inflammatory cytokine which stimulates activation of the nuclear factor kappa beta (NF-κB) pathway via interaction with the IL-18 receptor. The receptor itself is formed from a dimer of two subunits, with the ligand-binding IL-18Rα subunit being encoded by the IL18R1 gene. A splice variant of murine IL18r1, which has been previously described, is formed by transcription of an unspliced intron (forming a ‘type II’ IL18r1 transcript) and is predicted to encode a receptor with a truncated intracellular domain lacking the capacity to generate downstream signalling. In order to examine the relevance of this finding to human IL-18 function, we assessed the presence of a homologous transcript by reverse transcription-polymerase chain reaction (RT-PCR) in the human and rat as another common laboratory animal. We present evidence for type II IL18R1 transcripts in both species. While the mouse and rat transcripts are predicted to encode a truncated receptor with a novel 5 amino acid C-terminal domain, the human sequence is predicted to encode a truncated protein with a novel 22 amino acid sequence bearing resemblance to the ‘Box 1’ motif of the Toll/interleukin-1 receptor (TIR) domain, in a similar fashion to the inhibitory interleukin-1 receptor 2. Given that transcripts from these three species are all formed by inclusion of homologous unspliced intronic regions, an analysis of homologous introns across a wider array of 33 species with available IL18R1 gene records was performed, which suggests similar transcripts may encode truncated type II IL-18Rα subunits in other species. This splice variant may represent a conserved evolutionary mechanism for regulating IL-18 activity.
format: application/pdf
format: text/html
creator: Chris S. Booker
creator: David R. Grattan
subject: Evolutionary Studies
subject: Genetics
subject: Molecular Biology
subject: Immunology
description: doi:10.7717/peerj.560
publisher: PeerJ Inc.
rights: © 2014 Booker and Grattan
abstract: Interleukin-18 (IL-18) is a pro-inflammatory cytokine which stimulates activation of the nuclear factor kappa beta (NF-κB) pathway via interaction with the IL-18 receptor. The receptor itself is formed from a dimer of two subunits, with the ligand-binding IL-18Rα subunit being encoded by the IL18R1 gene. A splice variant of murine IL18r1, which has been previously described, is formed by transcription of an unspliced intron (forming a ‘type II’ IL18r1 transcript) and is predicted to encode a receptor with a truncated intracellular domain lacking the capacity to generate downstream signalling. In order to examine the relevance of this finding to human IL-18 function, we assessed the presence of a homologous transcript by reverse transcription-polymerase chain reaction (RT-PCR) in the human and rat as another common laboratory animal. We present evidence for type II IL18R1 transcripts in both species. While the mouse and rat transcripts are predicted to encode a truncated receptor with a novel 5 amino acid C-terminal domain, the human sequence is predicted to encode a truncated protein with a novel 22 amino acid sequence bearing resemblance to the ‘Box 1’ motif of the Toll/interleukin-1 receptor (TIR) domain, in a similar fashion to the inhibitory interleukin-1 receptor 2. Given that transcripts from these three species are all formed by inclusion of homologous unspliced intronic regions, an analysis of homologous introns across a wider array of 33 species with available IL18R1 gene records was performed, which suggests similar transcripts may encode truncated type II IL-18Rα subunits in other species. This splice variant may represent a conserved evolutionary mechanism for regulating IL-18 activity.
bibliographic citation: Booker et al. (2014) Identification of a truncated splice variant of IL-18 receptor alpha in the human and rat, with evidence of wider evolutionary conservation. PeerJ 2:e560 https://doi.org/10.7717/peerj.560
date submitted: 2014-05-31
date accepted: 2014-08-15
issued: 2014-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Booker
  given name: Chris S.
author list: Agent
  family name: Grattan
  given name: David R.
doi: 10.7717/peerj.560
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-11
copyright: © 2014 Booker and Grattan
attribution name: Booker and Grattan

Modelling foraging movements of diving predators: a theoretical study exploring the effect of heterogeneous landscapes on foraging efficiency
type: item
type: AcademicArticle
description: Foraging in the marine environment presents particular challenges for air-breathing predators. Information about prey capture rates, the strategies that diving predators use to maximise prey encounter rates and foraging success are still largely unknown and difficult to observe. As well, with the growing awareness of potential climate change impacts and the increasing interest in the development of renewable sources it is unknown how the foraging activity of diving predators such as seabirds will respond to both the presence of underwater structures and the potential corresponding changes in prey distributions. Motivated by this issue we developed a theoretical model to gain general understanding of how the foraging efficiency of diving predators may vary according to landscape structure and foraging strategy. Our theoretical model highlights that animal movements, intervals between prey capture and foraging efficiency are likely to critically depend on the distribution of the prey resource and the size and distribution of introduced underwater structures. For multiple prey loaders, changes in prey distribution affected the searching time necessary to catch a set amount of prey which in turn affected the foraging efficiency. The spatial aggregation of prey around small devices (∼ 9 × 9 m) created a valuable habitat for a successful foraging activity resulting in shorter intervals between prey captures and higher foraging efficiency. The presence of large devices (∼ 24 × 24 m) however represented an obstacle for predator movement, thus increasing the intervals between prey captures. In contrast, for single prey loaders the introduction of spatial aggregation of the resources did not represent an advantage suggesting that their foraging efficiency is more strongly affected by other factors such as the timing to find the first prey item which was found to occur faster in the presence of large devices. The development of this theoretical model represents a useful starti…
format: application/pdf
format: text/html
creator: Marianna Chimienti
creator: Kamil A. Bartoń
creator: Beth E. Scott
creator: Justin M.J. Travis
subject: Animal Behavior
subject: Computational Biology
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.544
publisher: PeerJ Inc.
rights: © 2014 Chimienti et al.
abstract: Foraging in the marine environment presents particular challenges for air-breathing predators. Information about prey capture rates, the strategies that diving predators use to maximise prey encounter rates and foraging success are still largely unknown and difficult to observe. As well, with the growing awareness of potential climate change impacts and the increasing interest in the development of renewable sources it is unknown how the foraging activity of diving predators such as seabirds will respond to both the presence of underwater structures and the potential corresponding changes in prey distributions. Motivated by this issue we developed a theoretical model to gain general understanding of how the foraging efficiency of diving predators may vary according to landscape structure and foraging strategy. Our theoretical model highlights that animal movements, intervals between prey capture and foraging efficiency are likely to critically depend on the distribution of the prey resource and the size and distribution of introduced underwater structures. For multiple prey loaders, changes in prey distribution affected the searching time necessary to catch a set amount of prey which in turn affected the foraging efficiency. The spatial aggregation of prey around small devices (∼ 9 × 9 m) created a valuable habitat for a successful foraging activity resulting in shorter intervals between prey captures and higher foraging efficiency. The presence of large devices (∼ 24 × 24 m) however represented an obstacle for predator movement, thus increasing the intervals between prey captures. In contrast, for single prey loaders the introduction of spatial aggregation of the resources did not represent an advantage suggesting that their foraging efficiency is more strongly affected by other factors such as the timing to find the first prey item which was found to occur faster in the presence of large devices. The development of this theoretical model represents a useful starti…
bibliographic citation: Chimienti et al. (2014) Modelling foraging movements of diving predators: a theoretical study exploring the effect of heterogeneous landscapes on foraging efficiency. PeerJ 2:e544 https://doi.org/10.7717/peerj.544
date submitted: 2014-05-12
date accepted: 2014-08-06
issued: 2014-09-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chimienti
  given name: Marianna
author list: Agent
  family name: Bartoń
  given name: Kamil A.
author list: Agent
  family name: Scott
  given name: Beth E.
author list: Agent
  family name: Travis
  given name: Justin M.J.
doi: 10.7717/peerj.544
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-11
copyright: © 2014 Chimienti et al.
attribution name: Chimienti et al.

Mitochondrial cytochrome b sequence data are not an improvement for species identification in scleractinian corals
type: item
type: AcademicArticle
description: There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promising gene regions for species delineation. I assembled the whole mitochondrial genome for Agaricia fragilis from Illumina single-end 250 bp reads and compared this sequence to that of the congener A. humilis. Although these data suggest that the cytochrome b (CYB) gene region is more promising, comparison of available CYB sequence data from scleractinian and other reef-building corals indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.
format: application/pdf
format: text/html
creator: John P. Wares
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.564
publisher: PeerJ Inc.
rights: © 2014 Wares
abstract: There are well-known difficulties in using the cytochrome oxidase I (COI) mitochondrial gene region for population genetics and DNA barcoding in corals. A recent study of species divergence in the endemic Caribbean genus Agaricia reinforced such knowledge. However, the growing availability of whole mitochondrial genomes may help indicate more promising gene regions for species delineation. I assembled the whole mitochondrial genome for Agaricia fragilis from Illumina single-end 250 bp reads and compared this sequence to that of the congener A. humilis. Although these data suggest that the cytochrome b (CYB) gene region is more promising, comparison of available CYB sequence data from scleractinian and other reef-building corals indicates that multilocus approaches are still probably necessary for phylogenetic and population genetic analysis of recently-diverged coral taxa.
bibliographic citation: Wares (2014) Mitochondrial cytochrome b sequence data are not an improvement for species identification in scleractinian corals. PeerJ 2:e564 https://doi.org/10.7717/peerj.564
date submitted: 2014-07-11
date accepted: 2014-08-16
issued: 2014-09-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wares
  given name: John P.
doi: 10.7717/peerj.564
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-09
copyright: © 2014 Wares
attribution name: Wares

Estimating the prevalence of researcher misconduct: a study of UK academics within biological sciences
type: item
type: AcademicArticle
description: Misconduct in academic research is undoubtedly increasing, but studies estimating the prevalence of such behaviour suffer from biases inherent in researching sensitive topics. We compared the unmatched-count technique (UCT) and the crosswise-model (CM), two methods specifically designed to increase honest reporting to sensitive questions, with direct questioning (DQ) for five types of misconduct in the biological sciences. UCT performed better than CM and either outperformed or produced similar estimates to DQ depending on the question. Estimates of academic misconduct increased with decreasing seriousness of the behaviour, from c. 0% for data fabrication to >68% for inappropriate co-authorship. Results show that research into even minor issues of misconduct, is sensitive, suggesting that future studies should consider using specialised questioning techniques as they are more likely to yield accurate figures.
format: application/pdf
format: text/html
creator: David L. Roberts
creator: Freya A.V. St. John
subject: Ethical Issues
subject: Science and Medical Education
subject: Science Policy
description: doi:10.7717/peerj.562
publisher: PeerJ Inc.
rights: © 2014 Roberts and St. John
abstract: Misconduct in academic research is undoubtedly increasing, but studies estimating the prevalence of such behaviour suffer from biases inherent in researching sensitive topics. We compared the unmatched-count technique (UCT) and the crosswise-model (CM), two methods specifically designed to increase honest reporting to sensitive questions, with direct questioning (DQ) for five types of misconduct in the biological sciences. UCT performed better than CM and either outperformed or produced similar estimates to DQ depending on the question. Estimates of academic misconduct increased with decreasing seriousness of the behaviour, from c. 0% for data fabrication to >68% for inappropriate co-authorship. Results show that research into even minor issues of misconduct, is sensitive, suggesting that future studies should consider using specialised questioning techniques as they are more likely to yield accurate figures.
bibliographic citation: Roberts et al. (2014) Estimating the prevalence of researcher misconduct: a study of UK academics within biological sciences. PeerJ 2:e562 https://doi.org/10.7717/peerj.562
date submitted: 2014-07-03
date accepted: 2014-08-15
issued: 2014-09-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roberts
  given name: David L.
author list: Agent
  family name: St. John
  given name: Freya A.V.
doi: 10.7717/peerj.562
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-09
copyright: © 2014 Roberts and St. John
attribution name: Roberts and St. John

Psoralidin induces autophagy through ROS generation which inhibits the proliferation of human lung cancer A549 cells
type: item
type: AcademicArticle
description: Psoralidin (PSO), a natural furanocoumarin, is isolated from Psoralea corylifolia L. possessing anti-cancer properties. However, the mechanisms of its effects remain unclear. Herein, we investigated its anti-proliferative effect and potential approaches of action on human lung cancer A549 cells. Cell proliferation and death were measured by MTT and LDH assay respectively. Apoptosis was detected with Hoechst 33342 staining by fluorescence microscopy, Annexin V-FITC by flow cytometry and Western blot analysis for apoptosis-related proteins. The autophagy was evaluated using MDC staining, immunofluorescence assay and Western blot analyses for LC3-I and LC3-II. In addition, the reactive oxygen species (ROS) generation was measured by DCFH2-DA with flow cytometry. PSO dramatically decreased the cell viabilities in dose- and time-dependent manner. However, no significant change was observed between the control group and the PSO-treated groups in Hoechst 33342 and Annexin V-FITC staining. The expression of apoptosis-related proteins was not altered significantly either. While the MDC-fluorescence intensity and the expression ratio of LC3-II/LC3-I was remarkably increased after PSO treatment. Autophagy inhibitor 3-MA blocked the production of LC3-II and reduced the cytotoxicity in response to PSO. Furthermore, PSO increased intracellular ROS level which was correlated to the elevation of LC3-II. ROS scavenger N-acetyl cysteine pretreatment not only decreased the ROS level, reduced the expression of LC3-II but also reversed PSO induced cytotoxicity. PSO inhibited the proliferation of A549 cells through autophagy but not apoptosis, which was mediated by inducing ROS production.
format: application/pdf
format: text/html
creator: Wenhui Hao
creator: Xuenong Zhang
creator: Wenwen Zhao
creator: Xiuping Chen
subject: Cell Biology
subject: Oncology
subject: Pharmacology
subject: Translational Medicine
description: doi:10.7717/peerj.555
publisher: PeerJ Inc.
rights: © 2014 Hao et al.
abstract: Psoralidin (PSO), a natural furanocoumarin, is isolated from Psoralea corylifolia L. possessing anti-cancer properties. However, the mechanisms of its effects remain unclear. Herein, we investigated its anti-proliferative effect and potential approaches of action on human lung cancer A549 cells. Cell proliferation and death were measured by MTT and LDH assay respectively. Apoptosis was detected with Hoechst 33342 staining by fluorescence microscopy, Annexin V-FITC by flow cytometry and Western blot analysis for apoptosis-related proteins. The autophagy was evaluated using MDC staining, immunofluorescence assay and Western blot analyses for LC3-I and LC3-II. In addition, the reactive oxygen species (ROS) generation was measured by DCFH2-DA with flow cytometry. PSO dramatically decreased the cell viabilities in dose- and time-dependent manner. However, no significant change was observed between the control group and the PSO-treated groups in Hoechst 33342 and Annexin V-FITC staining. The expression of apoptosis-related proteins was not altered significantly either. While the MDC-fluorescence intensity and the expression ratio of LC3-II/LC3-I was remarkably increased after PSO treatment. Autophagy inhibitor 3-MA blocked the production of LC3-II and reduced the cytotoxicity in response to PSO. Furthermore, PSO increased intracellular ROS level which was correlated to the elevation of LC3-II. ROS scavenger N-acetyl cysteine pretreatment not only decreased the ROS level, reduced the expression of LC3-II but also reversed PSO induced cytotoxicity. PSO inhibited the proliferation of A549 cells through autophagy but not apoptosis, which was mediated by inducing ROS production.
bibliographic citation: Hao et al. (2014) Psoralidin induces autophagy through ROS generation which inhibits the proliferation of human lung cancer A549 cells. PeerJ 2:e555 https://doi.org/10.7717/peerj.555
date submitted: 2014-05-26
date accepted: 2014-08-12
issued: 2014-09-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Wenhui
author list: Agent
  family name: Zhang
  given name: Xuenong
author list: Agent
  family name: Zhao
  given name: Wenwen
author list: Agent
  family name: Chen
  given name: Xiuping
doi: 10.7717/peerj.555
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-09
copyright: © 2014 Hao et al.
attribution name: Hao et al.

Digging the pupfish out of its hole: risk analyses to guide harvest of Devils Hole pupfish for captive breeding
type: item
type: AcademicArticle
description: The Devils Hole pupfish is restricted to one wild population in a single aquifer-fed thermal pool in the Desert National Wildlife Refuge Complex. Since 1995 the pupfish has been in a nearly steady decline, where it was perched on the brink of extinction at 35–68 fish in 2013. A major strategy for conserving the pupfish has been the establishment of additional captive or “refuge” populations, but all ended in failure. In 2013 a new captive propagation facility designed specifically to breed pupfish was opened. I examine how a captive population can be initiated by removing fish from the wild without unduly accelerating extinction risk for the pupfish in Devils Hole. I construct a count-based PVA model, parameterized from estimates of the intrinsic rate of increase and its variance using counts in spring and fall from 1995–2013, to produce the first risk assessment for the pupfish. Median time to extinction was 26 and 27 years from spring and fall counts, respectively, and the probability of extinction in 20 years was 26–33%. Removing individuals in the fall had less risk to the wild population than harvest in spring. For both spring and fall harvest, risk increased rapidly when levels exceeded six adult pupfish per year for three years. Extinction risk was unaffected by the apportionment of total harvest among years. A demographic model was used to examine how removal of different stage classes affects the dynamics of the wild population based on reproductive value (RV) and elasticity. Removing eggs had the least impact on the pupfish in Devils Hole; RV of an adult was roughly 25 times that of an egg. To evaluate when it might be prudent to remove all pupfish from Devils Hole for captive breeding, I used the count-based model to examine how extinction risk related to pupfish population size. Risk accelerated when initial populations were less than 30 individuals. Results are discussed in relation to the challenges facing pupfish recovery compared to management of oth…
format: application/pdf
format: text/html
creator: Steven R. Beissinger
subject: Conservation Biology
subject: Ecology
subject: Statistics
description: doi:10.7717/peerj.549
publisher: PeerJ Inc.
rights: © 2014 Beissinger
abstract: The Devils Hole pupfish is restricted to one wild population in a single aquifer-fed thermal pool in the Desert National Wildlife Refuge Complex. Since 1995 the pupfish has been in a nearly steady decline, where it was perched on the brink of extinction at 35–68 fish in 2013. A major strategy for conserving the pupfish has been the establishment of additional captive or “refuge” populations, but all ended in failure. In 2013 a new captive propagation facility designed specifically to breed pupfish was opened. I examine how a captive population can be initiated by removing fish from the wild without unduly accelerating extinction risk for the pupfish in Devils Hole. I construct a count-based PVA model, parameterized from estimates of the intrinsic rate of increase and its variance using counts in spring and fall from 1995–2013, to produce the first risk assessment for the pupfish. Median time to extinction was 26 and 27 years from spring and fall counts, respectively, and the probability of extinction in 20 years was 26–33%. Removing individuals in the fall had less risk to the wild population than harvest in spring. For both spring and fall harvest, risk increased rapidly when levels exceeded six adult pupfish per year for three years. Extinction risk was unaffected by the apportionment of total harvest among years. A demographic model was used to examine how removal of different stage classes affects the dynamics of the wild population based on reproductive value (RV) and elasticity. Removing eggs had the least impact on the pupfish in Devils Hole; RV of an adult was roughly 25 times that of an egg. To evaluate when it might be prudent to remove all pupfish from Devils Hole for captive breeding, I used the count-based model to examine how extinction risk related to pupfish population size. Risk accelerated when initial populations were less than 30 individuals. Results are discussed in relation to the challenges facing pupfish recovery compared to management of oth…
bibliographic citation: Beissinger (2014) Digging the pupfish out of its hole: risk analyses to guide harvest of Devils Hole pupfish for captive breeding. PeerJ 2:e549 https://doi.org/10.7717/peerj.549
date submitted: 2014-06-16
date accepted: 2014-08-07
issued: 2014-09-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beissinger
  given name: Steven R.
doi: 10.7717/peerj.549
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-09
copyright: © 2014 Beissinger
attribution name: Beissinger

Trace element profiles of the sea anemone Anemonia viridis living nearby a natural CO2 vent
type: item
type: AcademicArticle
description: Ocean acidification (OA) is not an isolated threat, but acts in concert with other impacts on ecosystems and species. Coastal marine invertebrates will have to face the synergistic interactions of OA with other global and local stressors. One local factor, common in coastal environments, is trace element contamination. CO2 vent sites are extensively studied in the context of OA and are often considered analogous to the oceans in the next few decades. The CO2 vent found at Levante Bay (Vulcano, NE Sicily, Italy) also releases high concentrations of trace elements to its surrounding seawater, and is therefore a unique site to examine the effects of long-term exposure of nearby organisms to high pCO2 and trace element enrichment in situ. The sea anemone Anemonia viridis is prevalent next to the Vulcano vent and does not show signs of trace element poisoning/stress. The aim of our study was to compare A. viridis trace element profiles and compartmentalization between high pCO2 and control environments. Rather than examining whole anemone tissue, we analyzed two different body compartments—the pedal disc and the tentacles, and also examined the distribution of trace elements in the tentacles between the animal and the symbiotic algae. We found dramatic changes in trace element tissue concentrations between the high pCO2/high trace element and control sites, with strong accumulation of iron, lead, copper and cobalt, but decreased concentrations of cadmium, zinc and arsenic proximate to the vent. The pedal disc contained substantially more trace elements than the anemone’s tentacles, suggesting the pedal disc may serve as a detoxification/storage site for excess trace elements. Within the tentacles, the various trace elements displayed different partitioning patterns between animal tissue and algal symbionts. At both sites iron was found primarily in the algae, whereas cadmium, zinc and arsenic were primarily found in the animal tissue. Our data suggests that A. viridis re…
format: application/pdf
format: text/html
creator: Rael Horwitz
creator: Esther M. Borell
creator: Maoz Fine
creator: Yeala Shaked
subject: Aquatic and Marine Chemistry
subject: Biological Oceanography
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.538
publisher: PeerJ Inc.
rights: © 2014 Horwitz et al.
abstract: Ocean acidification (OA) is not an isolated threat, but acts in concert with other impacts on ecosystems and species. Coastal marine invertebrates will have to face the synergistic interactions of OA with other global and local stressors. One local factor, common in coastal environments, is trace element contamination. CO2 vent sites are extensively studied in the context of OA and are often considered analogous to the oceans in the next few decades. The CO2 vent found at Levante Bay (Vulcano, NE Sicily, Italy) also releases high concentrations of trace elements to its surrounding seawater, and is therefore a unique site to examine the effects of long-term exposure of nearby organisms to high pCO2 and trace element enrichment in situ. The sea anemone Anemonia viridis is prevalent next to the Vulcano vent and does not show signs of trace element poisoning/stress. The aim of our study was to compare A. viridis trace element profiles and compartmentalization between high pCO2 and control environments. Rather than examining whole anemone tissue, we analyzed two different body compartments—the pedal disc and the tentacles, and also examined the distribution of trace elements in the tentacles between the animal and the symbiotic algae. We found dramatic changes in trace element tissue concentrations between the high pCO2/high trace element and control sites, with strong accumulation of iron, lead, copper and cobalt, but decreased concentrations of cadmium, zinc and arsenic proximate to the vent. The pedal disc contained substantially more trace elements than the anemone’s tentacles, suggesting the pedal disc may serve as a detoxification/storage site for excess trace elements. Within the tentacles, the various trace elements displayed different partitioning patterns between animal tissue and algal symbionts. At both sites iron was found primarily in the algae, whereas cadmium, zinc and arsenic were primarily found in the animal tissue. Our data suggests that A. viridis re…
bibliographic citation: Horwitz et al. (2014) Trace element profiles of the sea anemone Anemonia viridis living nearby a natural CO2 vent. PeerJ 2:e538 https://doi.org/10.7717/peerj.538
date submitted: 2014-04-29
date accepted: 2014-08-04
issued: 2014-09-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Horwitz
  given name: Rael
author list: Agent
  family name: Borell
  given name: Esther M.
author list: Agent
  family name: Fine
  given name: Maoz
author list: Agent
  family name: Shaked
  given name: Yeala
doi: 10.7717/peerj.538
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-09
copyright: © 2014 Horwitz et al.
attribution name: Horwitz et al.

Alterations in fiber pathways reveal brain tumor typology: a diffusion tractography study
type: item
type: AcademicArticle
description: Conventional structural Magnetic Resonance (MR) techniques can accurately identify brain tumors but do not provide exhaustive information about the integrity of the surrounding/embedded white matter (WM). In this study, we used Diffusion-Weighted (DW) MRI tractography to explore tumor-induced alterations of WM architecture without any a priori knowledge about the fiber paths under consideration. We used deterministic multi-fiber tractography to analyze 16 cases of histologically classified brain tumors (meningioma, low-grade glioma, high-grade glioma) to evaluate the integrity of WM bundles in the tumoral region, in relation to the contralateral unaffected hemisphere. Our new tractographic approach yielded measures of WM involvement which were strongly correlated with the histopathological features of the tumor (r = 0.83, p = 0.0001). In particular, the number of affected fiber tracts were significantly (p = 0.0006) different among tumor types. Our method proposes a new application of diffusion tractography for the detection of tumor aggressiveness in those cases in which the lesion does not involve any major/known WM paths and when a priori information about the local fiber anatomy is lacking.
format: application/pdf
format: text/html
creator: Martina Campanella
creator: Tamara Ius
creator: Miran Skrap
creator: Luciano Fadiga
subject: Neuroscience
description: doi:10.7717/peerj.497
publisher: PeerJ Inc.
rights: © 2014 Campanella et al.
abstract: Conventional structural Magnetic Resonance (MR) techniques can accurately identify brain tumors but do not provide exhaustive information about the integrity of the surrounding/embedded white matter (WM). In this study, we used Diffusion-Weighted (DW) MRI tractography to explore tumor-induced alterations of WM architecture without any a priori knowledge about the fiber paths under consideration. We used deterministic multi-fiber tractography to analyze 16 cases of histologically classified brain tumors (meningioma, low-grade glioma, high-grade glioma) to evaluate the integrity of WM bundles in the tumoral region, in relation to the contralateral unaffected hemisphere. Our new tractographic approach yielded measures of WM involvement which were strongly correlated with the histopathological features of the tumor (r = 0.83, p = 0.0001). In particular, the number of affected fiber tracts were significantly (p = 0.0006) different among tumor types. Our method proposes a new application of diffusion tractography for the detection of tumor aggressiveness in those cases in which the lesion does not involve any major/known WM paths and when a priori information about the local fiber anatomy is lacking.
bibliographic citation: Campanella et al. (2014) Alterations in fiber pathways reveal brain tumor typology: a diffusion tractography study. PeerJ 2:e497 https://doi.org/10.7717/peerj.497
date submitted: 2013-12-27
date accepted: 2014-07-06
issued: 2014-09-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Campanella
  given name: Martina
author list: Agent
  family name: Ius
  given name: Tamara
author list: Agent
  family name: Skrap
  given name: Miran
author list: Agent
  family name: Fadiga
  given name: Luciano
doi: 10.7717/peerj.497
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-09
copyright: © 2014 Campanella et al.
attribution name: Campanella et al.

Metagenome fragment classification based on multiple motif-occurrence profiles
type: item
type: AcademicArticle
description: A vast amount of metagenomic data has been obtained by extracting multiple genomes simultaneously from microbial communities, including genomes from uncultivable microbes. By analyzing these metagenomic data, novel microbes are discovered and new microbial functions are elucidated. The first step in analyzing these data is sequenced-read classification into reference genomes from which each read can be derived. The Naïve Bayes Classifier is a method for this classification. To identify the derivation of the reads, this method calculates a score based on the occurrence of a DNA sequence motif in each reference genome. However, large differences in the sizes of the reference genomes can bias the scoring of the reads. This bias might cause erroneous classification and decrease the classification accuracy. To address this issue, we have updated the Naïve Bayes Classifier method using multiple sets of occurrence profiles for each reference genome by normalizing the genome sizes, dividing each genome sequence into a set of subsequences of similar length and generating profiles for each subsequence. This multiple profile strategy improves the accuracy of the results generated by the Naïve Bayes Classifier method for simulated and Sargasso Sea datasets.
format: application/pdf
format: text/html
creator: Naoki Matsushita
creator: Shigeto Seno
creator: Yoichi Takenaka
creator: Hideo Matsuda
subject: Bioinformatics
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.559
publisher: PeerJ Inc.
rights: © 2014 Matsushita et al.
abstract: A vast amount of metagenomic data has been obtained by extracting multiple genomes simultaneously from microbial communities, including genomes from uncultivable microbes. By analyzing these metagenomic data, novel microbes are discovered and new microbial functions are elucidated. The first step in analyzing these data is sequenced-read classification into reference genomes from which each read can be derived. The Naïve Bayes Classifier is a method for this classification. To identify the derivation of the reads, this method calculates a score based on the occurrence of a DNA sequence motif in each reference genome. However, large differences in the sizes of the reference genomes can bias the scoring of the reads. This bias might cause erroneous classification and decrease the classification accuracy. To address this issue, we have updated the Naïve Bayes Classifier method using multiple sets of occurrence profiles for each reference genome by normalizing the genome sizes, dividing each genome sequence into a set of subsequences of similar length and generating profiles for each subsequence. This multiple profile strategy improves the accuracy of the results generated by the Naïve Bayes Classifier method for simulated and Sargasso Sea datasets.
bibliographic citation: Matsushita et al. (2014) Metagenome fragment classification based on multiple motif-occurrence profiles. PeerJ 2:e559 https://doi.org/10.7717/peerj.559
date submitted: 2014-05-21
date accepted: 2014-08-15
issued: 2014-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matsushita
  given name: Naoki
author list: Agent
  family name: Seno
  given name: Shigeto
author list: Agent
  family name: Takenaka
  given name: Yoichi
author list: Agent
  family name: Matsuda
  given name: Hideo
doi: 10.7717/peerj.559
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-04
copyright: © 2014 Matsushita et al.
attribution name: Matsushita et al.

Protein kinase C in the wood frog, Rana sylvatica: reassessing the tissue-specific regulation of PKC isozymes during freezing
type: item
type: AcademicArticle
description: The wood frog, Rana sylvatica, survives whole-body freezing and thawing each winter. The extensive adaptations required at the biochemical level are facilitated by alterations to signaling pathways, including the insulin/Akt and AMPK pathways. Past studies investigating changing tissue-specific patterns of the second messenger IP3 in adapted frogs have suggested important roles for protein kinase C (PKC) in response to stress. In addition to their dependence on second messengers, phosphorylation of three PKC sites by upstream kinases (most notably PDK1) is needed for full PKC activation, according to widely-accepted models. The present study uses phospho-specific immunoblotting to investigate phosphorylation states of PKC—as they relate to distinct tissues, PKC isozymes, and phosphorylation sites—in control and frozen frogs. In contrast to past studies where second messengers of PKC increased during the freezing process, phosphorylation of PKC tended to generally decline in most tissues of frozen frogs. All PKC isozymes and specific phosphorylation sites detected by immunoblotting decreased in phosphorylation levels in hind leg skeletal muscle and hearts of frozen frogs. Most PKC isozymes and specific phosphorylation sites detected in livers and kidneys also declined; the only exceptions were the levels of isozymes/phosphorylation sites detected by the phospho-PKCα/βII (Thr638/641) antibody, which remained unchanged from control to frozen frogs. Changes in brains of frozen frogs were unique; no decreases were observed in the phosphorylation levels of any of the PKC isozymes and/or specific phosphorylation sites detected by immunoblotting. Rather, increases were observed for the levels of isozymes/phosphorylation sites detected by the phospho-PKCα/βII (Thr638/641), phospho-PKCδ (Thr505), and phospho-PKCθ (Thr538) antibodies; all other isozymes/phosphorylation sites detected in brain remained unchanged from control to frozen frogs. The results of this study indicate a…
format: application/pdf
format: text/html
creator: Christopher A. Dieni
creator: Kenneth B. Storey
subject: Biochemistry
subject: Zoology
description: doi:10.7717/peerj.558
publisher: PeerJ Inc.
rights: © 2014 Dieni and Storey
abstract: The wood frog, Rana sylvatica, survives whole-body freezing and thawing each winter. The extensive adaptations required at the biochemical level are facilitated by alterations to signaling pathways, including the insulin/Akt and AMPK pathways. Past studies investigating changing tissue-specific patterns of the second messenger IP3 in adapted frogs have suggested important roles for protein kinase C (PKC) in response to stress. In addition to their dependence on second messengers, phosphorylation of three PKC sites by upstream kinases (most notably PDK1) is needed for full PKC activation, according to widely-accepted models. The present study uses phospho-specific immunoblotting to investigate phosphorylation states of PKC—as they relate to distinct tissues, PKC isozymes, and phosphorylation sites—in control and frozen frogs. In contrast to past studies where second messengers of PKC increased during the freezing process, phosphorylation of PKC tended to generally decline in most tissues of frozen frogs. All PKC isozymes and specific phosphorylation sites detected by immunoblotting decreased in phosphorylation levels in hind leg skeletal muscle and hearts of frozen frogs. Most PKC isozymes and specific phosphorylation sites detected in livers and kidneys also declined; the only exceptions were the levels of isozymes/phosphorylation sites detected by the phospho-PKCα/βII (Thr638/641) antibody, which remained unchanged from control to frozen frogs. Changes in brains of frozen frogs were unique; no decreases were observed in the phosphorylation levels of any of the PKC isozymes and/or specific phosphorylation sites detected by immunoblotting. Rather, increases were observed for the levels of isozymes/phosphorylation sites detected by the phospho-PKCα/βII (Thr638/641), phospho-PKCδ (Thr505), and phospho-PKCθ (Thr538) antibodies; all other isozymes/phosphorylation sites detected in brain remained unchanged from control to frozen frogs. The results of this study indicate a…
bibliographic citation: Dieni et al. (2014) Protein kinase C in the wood frog, Rana sylvatica: reassessing the tissue-specific regulation of PKC isozymes during freezing. PeerJ 2:e558 https://doi.org/10.7717/peerj.558
date submitted: 2014-05-19
date accepted: 2014-08-14
issued: 2014-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dieni
  given name: Christopher A.
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.558
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-04
copyright: © 2014 Dieni and Storey
attribution name: Dieni and Storey

Effects of low and high dose intraarticular tiludronate on synovial fluid and clinical variables in healthy horses—a preliminary investigation
type: item
type: AcademicArticle
description: To determine effects of intraarticularly administered tiludronate on articular cartilage in vivo, eight healthy horses were injected once with tiludronate (low dose tiludronate [LDT] 0.017 mg, n = 4; high dose tiludronate [HDT] 50 mg, n = 4) into one middle carpal joint and with saline into the contralateral joint. Arthrocentesis of both middle carpal joints was performed pre-treatment, and 10 min, 24 h, 48 h, 7 and 14 days after treatment. Synovial nucleated cell counts and total solids, tiludronate, sulfated glycosaminoglycan (sGAG), chondroitin sulfate 846 epitope (CS-846, a measure of aggrecan synthesis), and collagen type II cleavage neoepitope (C2C) concentrations were determined. Histologic analysis of joint tissues and sGAG quantitation in cartilage was performed at 14 days in HDT horses. Data were analyzed by repeated measures non-parametric ANOVA and Wilcoxon signed-rank test. High dose tiludronate administration produced synovial fluid tiludronate concentrations of 2,677,500 ng/mL, exceeding concentrations that were safe for cartilage in vitro, and LDT administration produced synovial fluid concentrations of 1,353 ng/mL, remaining below concentrations considered potentially detrimental to cartilage. With HDT, synovial fluid total solids concentration was higher at 24 h and 7 days and sGAG concentration was higher at 48 h, compared to control joints. Synovial fluid CS-846 concentration was increased over pre-treatment values in HDT control but not in HDT treated joints at 24 and 48 h. All joints (HDT and LDT control and treated) showed a temporary decrease in synovial fluid C2C concentration, compared to pre-treatment values. Histologic features of articular cartilage and synovial membrane did not differ between HDT treated and control joints. High dose tiludronate treatment caused a transient increase in synovial total solids and temporarily increased proteoglycan degradation in cartilage. Although clinical significance of these changes are questionable, …
format: application/pdf
format: text/html
creator: Katja F. Duesterdieck-Zellmer
creator: Lindsey Moneta
creator: Jesse F. Ott
creator: Maureen K. Larson
creator: Elena M. Gorman
creator: Barbara Hunter
creator: Christiane V. Löhr
creator: Mark E. Payton
creator: Jeffrey T. Morré
creator: Claudia S. Maier
subject: Veterinary Medicine
subject: Drugs and Devices
subject: Rheumatology
description: doi:10.7717/peerj.534
publisher: PeerJ Inc.
rights: © 2014 Duesterdieck-Zellmer et al.
abstract: To determine effects of intraarticularly administered tiludronate on articular cartilage in vivo, eight healthy horses were injected once with tiludronate (low dose tiludronate [LDT] 0.017 mg, n = 4; high dose tiludronate [HDT] 50 mg, n = 4) into one middle carpal joint and with saline into the contralateral joint. Arthrocentesis of both middle carpal joints was performed pre-treatment, and 10 min, 24 h, 48 h, 7 and 14 days after treatment. Synovial nucleated cell counts and total solids, tiludronate, sulfated glycosaminoglycan (sGAG), chondroitin sulfate 846 epitope (CS-846, a measure of aggrecan synthesis), and collagen type II cleavage neoepitope (C2C) concentrations were determined. Histologic analysis of joint tissues and sGAG quantitation in cartilage was performed at 14 days in HDT horses. Data were analyzed by repeated measures non-parametric ANOVA and Wilcoxon signed-rank test. High dose tiludronate administration produced synovial fluid tiludronate concentrations of 2,677,500 ng/mL, exceeding concentrations that were safe for cartilage in vitro, and LDT administration produced synovial fluid concentrations of 1,353 ng/mL, remaining below concentrations considered potentially detrimental to cartilage. With HDT, synovial fluid total solids concentration was higher at 24 h and 7 days and sGAG concentration was higher at 48 h, compared to control joints. Synovial fluid CS-846 concentration was increased over pre-treatment values in HDT control but not in HDT treated joints at 24 and 48 h. All joints (HDT and LDT control and treated) showed a temporary decrease in synovial fluid C2C concentration, compared to pre-treatment values. Histologic features of articular cartilage and synovial membrane did not differ between HDT treated and control joints. High dose tiludronate treatment caused a transient increase in synovial total solids and temporarily increased proteoglycan degradation in cartilage. Although clinical significance of these changes are questionable, …
bibliographic citation: Duesterdieck-Zellmer et al. (2014) Effects of low and high dose intraarticular tiludronate on synovial fluid and clinical variables in healthy horses—a preliminary investigation. PeerJ 2:e534 https://doi.org/10.7717/peerj.534
date submitted: 2014-03-30
date accepted: 2014-08-02
issued: 2014-09-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duesterdieck-Zellmer
  given name: Katja F.
author list: Agent
  family name: Moneta
  given name: Lindsey
author list: Agent
  family name: Ott
  given name: Jesse F.
author list: Agent
  family name: Larson
  given name: Maureen K.
author list: Agent
  family name: Gorman
  given name: Elena M.
author list: Agent
  family name: Hunter
  given name: Barbara
author list: Agent
  family name: Löhr
  given name: Christiane V.
author list: Agent
  family name: Payton
  given name: Mark E.
author list: Agent
  family name: Morré
  given name: Jeffrey T.
author list: Agent
  family name: Maier
  given name: Claudia S.
doi: 10.7717/peerj.534
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-04
copyright: © 2014 Duesterdieck-Zellmer et al.
attribution name: Duesterdieck-Zellmer et al.

Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene
type: item
type: AcademicArticle
description: An understanding of the timescale of evolution is critical for comparative virology but remains elusive for many RNA viruses. Age estimates based on mutation rates can severely underestimate divergences for ancient viral genes that are evolving under strong purifying selection. Paleoviral dating, however, can provide minimum age estimates for ancient divergence, but few orthologous paleoviruses are known within clades of extant viruses. For example, ebolaviruses and marburgviruses are well-studied mammalian pathogens, but their comparative biology is difficult to interpret because the existing estimates of divergence are controversial. Here we provide evidence that paleoviral elements of two genes (ebolavirus-like VP35 and NP) in cricetid rodent genomes originated after the divergence of ebolaviruses and cuevaviruses from marburgviruses. We provide evidence of orthology by identifying common paleoviral insertion sites among the rodent genomes. Our findings indicate that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the early Miocene.
format: application/pdf
format: text/html
creator: Derek J. Taylor
creator: Matthew J. Ballinger
creator: Jack J. Zhan
creator: Laura E. Hanzly
creator: Jeremy A. Bruenn
subject: Evolutionary Studies
subject: Genomics
subject: Virology
description: doi:10.7717/peerj.556
publisher: PeerJ Inc.
rights: © 2014 Taylor et al.
abstract: An understanding of the timescale of evolution is critical for comparative virology but remains elusive for many RNA viruses. Age estimates based on mutation rates can severely underestimate divergences for ancient viral genes that are evolving under strong purifying selection. Paleoviral dating, however, can provide minimum age estimates for ancient divergence, but few orthologous paleoviruses are known within clades of extant viruses. For example, ebolaviruses and marburgviruses are well-studied mammalian pathogens, but their comparative biology is difficult to interpret because the existing estimates of divergence are controversial. Here we provide evidence that paleoviral elements of two genes (ebolavirus-like VP35 and NP) in cricetid rodent genomes originated after the divergence of ebolaviruses and cuevaviruses from marburgviruses. We provide evidence of orthology by identifying common paleoviral insertion sites among the rodent genomes. Our findings indicate that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the early Miocene.
bibliographic citation: Taylor et al. (2014) Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene. PeerJ 2:e556 https://doi.org/10.7717/peerj.556
date submitted: 2014-07-16
date accepted: 2014-08-12
issued: 2014-09-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Taylor
  given name: Derek J.
author list: Agent
  family name: Ballinger
  given name: Matthew J.
author list: Agent
  family name: Zhan
  given name: Jack J.
author list: Agent
  family name: Hanzly
  given name: Laura E.
author list: Agent
  family name: Bruenn
  given name: Jeremy A.
doi: 10.7717/peerj.556
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-02
copyright: © 2014 Taylor et al.
attribution name: Taylor et al.

Benthic primary production in an upwelling-influenced coral reef, Colombian Caribbean
type: item
type: AcademicArticle
description: In Tayrona National Natural Park (Colombian Caribbean), abiotic factors such as light intensity, water temperature, and nutrient availability are subjected to high temporal variability due to seasonal coastal upwelling. These factors are the major drivers controlling coral reef primary production as one of the key ecosystem services. This offers the opportunity to assess the effects of abiotic factors on reef productivity. We therefore quantified primary net (Pn) and gross production (Pg) of the dominant local primary producers (scleractinian corals, macroalgae, algal turfs, crustose coralline algae, and microphytobenthos) at a water current/wave-exposed and-sheltered site in an exemplary bay of Tayrona National Natural Park. A series of short-term incubations was conducted to quantify O2 fluxes of the different primary producers during non-upwelling and the upwelling event 2011/2012, and generalized linear models were used to analyze group-specific O2 production, their contribution to benthic O2 fluxes, and total daily benthic O2 production. At the organism level, scleractinian corals showed highest Pn and Pg rates during non-upwelling (16 and 19 mmol O2 m−2 specimen area h−1), and corals and algal turfs dominated the primary production during upwelling (12 and 19 mmol O2 m−2 specimen area h−1, respectively). At the ecosystem level, corals contributed most to total Pn and Pg during non-upwelling, while during upwelling, corals contributed most to Pn and Pg only at the exposed site and macroalgae at the sheltered site, respectively. Despite the significant spatial and temporal differences in individual productivity of the investigated groups and their different contribution to reef productivity, differences for daily ecosystem productivity were only present for Pg at exposed with higher O2 fluxes during non-upwelling compared to upwelling. Our findings therefore indicate that total benthic primary productivity of local autotrophic reef communities is relatively stab…
format: application/pdf
format: text/html
creator: Corvin Eidens
creator: Elisa Bayraktarov
creator: Torsten Hauffe
creator: Valeria Pizarro
creator: Thomas Wilke
creator: Christian Wild
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.554
publisher: PeerJ Inc.
rights: © 2014 Eidens et al.
abstract: In Tayrona National Natural Park (Colombian Caribbean), abiotic factors such as light intensity, water temperature, and nutrient availability are subjected to high temporal variability due to seasonal coastal upwelling. These factors are the major drivers controlling coral reef primary production as one of the key ecosystem services. This offers the opportunity to assess the effects of abiotic factors on reef productivity. We therefore quantified primary net (Pn) and gross production (Pg) of the dominant local primary producers (scleractinian corals, macroalgae, algal turfs, crustose coralline algae, and microphytobenthos) at a water current/wave-exposed and-sheltered site in an exemplary bay of Tayrona National Natural Park. A series of short-term incubations was conducted to quantify O2 fluxes of the different primary producers during non-upwelling and the upwelling event 2011/2012, and generalized linear models were used to analyze group-specific O2 production, their contribution to benthic O2 fluxes, and total daily benthic O2 production. At the organism level, scleractinian corals showed highest Pn and Pg rates during non-upwelling (16 and 19 mmol O2 m−2 specimen area h−1), and corals and algal turfs dominated the primary production during upwelling (12 and 19 mmol O2 m−2 specimen area h−1, respectively). At the ecosystem level, corals contributed most to total Pn and Pg during non-upwelling, while during upwelling, corals contributed most to Pn and Pg only at the exposed site and macroalgae at the sheltered site, respectively. Despite the significant spatial and temporal differences in individual productivity of the investigated groups and their different contribution to reef productivity, differences for daily ecosystem productivity were only present for Pg at exposed with higher O2 fluxes during non-upwelling compared to upwelling. Our findings therefore indicate that total benthic primary productivity of local autotrophic reef communities is relatively stab…
bibliographic citation: Eidens et al. (2014) Benthic primary production in an upwelling-influenced coral reef, Colombian Caribbean. PeerJ 2:e554 https://doi.org/10.7717/peerj.554
date submitted: 2014-02-26
date accepted: 2014-08-12
issued: 2014-09-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eidens
  given name: Corvin
author list: Agent
  family name: Bayraktarov
  given name: Elisa
author list: Agent
  family name: Hauffe
  given name: Torsten
author list: Agent
  family name: Pizarro
  given name: Valeria
author list: Agent
  family name: Wilke
  given name: Thomas
author list: Agent
  family name: Wild
  given name: Christian
doi: 10.7717/peerj.554
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-02
copyright: © 2014 Eidens et al.
attribution name: Eidens et al.

Effects of deuterium oxide on cell growth and vesicle speed in RBL-2H3 cells
type: item
type: AcademicArticle
description: For the first time we show the effects of deuterium oxide on cell growth and vesicle transport in rat basophilic leukemia (RBL-2H3) cells. RBL-2H3 cells cultured with 15 moles/L deuterium showed decreased cell growth which was attributed to cells not doubling their DNA content. Experimental observations also showed an increase in vesicle speed for cells cultured in deuterium oxide. This increase in vesicle speed was not observed in deuterium oxide cultures treated with a microtubule-destabilizing drug, suggesting that deuterium oxide affects microtubule-dependent vesicle transport.
format: application/pdf
format: text/html
creator: Roshni S. Kalkur
creator: Andrew C. Ballast
creator: Ashley R. Triplett
creator: Kathrin Spendier
subject: Biophysics
subject: Biotechnology
subject: Cell Biology
description: doi:10.7717/peerj.553
publisher: PeerJ Inc.
rights: © 2014 Kalkur et al.
abstract: For the first time we show the effects of deuterium oxide on cell growth and vesicle transport in rat basophilic leukemia (RBL-2H3) cells. RBL-2H3 cells cultured with 15 moles/L deuterium showed decreased cell growth which was attributed to cells not doubling their DNA content. Experimental observations also showed an increase in vesicle speed for cells cultured in deuterium oxide. This increase in vesicle speed was not observed in deuterium oxide cultures treated with a microtubule-destabilizing drug, suggesting that deuterium oxide affects microtubule-dependent vesicle transport.
bibliographic citation: Kalkur et al. (2014) Effects of deuterium oxide on cell growth and vesicle speed in RBL-2H3 cells. PeerJ 2:e553 https://doi.org/10.7717/peerj.553
date submitted: 2014-06-18
date accepted: 2014-08-10
issued: 2014-09-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kalkur
  given name: Roshni S.
author list: Agent
  family name: Ballast
  given name: Andrew C.
author list: Agent
  family name: Triplett
  given name: Ashley R.
author list: Agent
  family name: Spendier
  given name: Kathrin
doi: 10.7717/peerj.553
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-02
copyright: © 2014 Kalkur et al.
attribution name: Kalkur et al.

With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase
type: item
type: AcademicArticle
description: The addition of two electrons and two protons to the C17=C18 bond in protochlorophyllide is catalyzed by a light-dependent enzyme relying on NADPH as electron donor, and by a light-independent enzyme bearing a (Cys)3Asp-ligated [4Fe–4S] cluster which is reduced by cytoplasmic electron donors in an ATP-dependent manner and then functions as electron donor to protochlorophyllide. The precise sequence of events occurring at the C17=C18 bond has not, however, been determined experimentally in the dark-operating enzyme. In this paper, we present the computational investigation of the reaction mechanism of this enzyme at the B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) level of theory. The reaction mechanism begins with single-electron reduction of the substrate by the (Cys)3Asp-ligated [4Fe–4S], yielding a negatively-charged intermediate. Depending on the rate of Fe–S cluster re-reduction, the reaction either proceeds through double protonation of the single-electron-reduced substrate, or by alternating proton/electron transfer. The computed reaction barriers suggest that Fe–S cluster re-reduction should be the rate-limiting stage of the process. Poisson–Boltzmann computations on the full enzyme–substrate complex, followed by Monte Carlo simulations of redox and protonation titrations revealed a hitherto unsuspected pH-dependence of the reaction potential of the Fe–S cluster. Furthermore, the computed distributions of protonation states of the His, Asp and Glu residues were used in conjuntion with single-point ONIOM computations to obtain, for the first time, the influence of all protonation states of an enzyme on the reaction it catalyzes. Despite exaggerating the ease of reduction of the substrate, these computations confirmed the broad features of the reaction mechanism obtained with the medium-sized models, and afforded valuable insights on the influence of the titratable amino acids on each reaction step. Additional comparisons of the energetic features of the reaction interm…
format: application/pdf
format: text/html
creator: Pedro J. Silva
subject: Biochemistry
subject: Biophysics
subject: Computational Biology
subject: Computational Science
description: doi:10.7717/peerj.551
publisher: PeerJ Inc.
rights: © 2014 Silva
abstract: The addition of two electrons and two protons to the C17=C18 bond in protochlorophyllide is catalyzed by a light-dependent enzyme relying on NADPH as electron donor, and by a light-independent enzyme bearing a (Cys)3Asp-ligated [4Fe–4S] cluster which is reduced by cytoplasmic electron donors in an ATP-dependent manner and then functions as electron donor to protochlorophyllide. The precise sequence of events occurring at the C17=C18 bond has not, however, been determined experimentally in the dark-operating enzyme. In this paper, we present the computational investigation of the reaction mechanism of this enzyme at the B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) level of theory. The reaction mechanism begins with single-electron reduction of the substrate by the (Cys)3Asp-ligated [4Fe–4S], yielding a negatively-charged intermediate. Depending on the rate of Fe–S cluster re-reduction, the reaction either proceeds through double protonation of the single-electron-reduced substrate, or by alternating proton/electron transfer. The computed reaction barriers suggest that Fe–S cluster re-reduction should be the rate-limiting stage of the process. Poisson–Boltzmann computations on the full enzyme–substrate complex, followed by Monte Carlo simulations of redox and protonation titrations revealed a hitherto unsuspected pH-dependence of the reaction potential of the Fe–S cluster. Furthermore, the computed distributions of protonation states of the His, Asp and Glu residues were used in conjuntion with single-point ONIOM computations to obtain, for the first time, the influence of all protonation states of an enzyme on the reaction it catalyzes. Despite exaggerating the ease of reduction of the substrate, these computations confirmed the broad features of the reaction mechanism obtained with the medium-sized models, and afforded valuable insights on the influence of the titratable amino acids on each reaction step. Additional comparisons of the energetic features of the reaction interm…
bibliographic citation: Silva (2014) With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase. PeerJ 2:e551 https://doi.org/10.7717/peerj.551
date submitted: 2014-03-24
date accepted: 2014-08-09
issued: 2014-09-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Pedro J.
doi: 10.7717/peerj.551
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-02
copyright: © 2014 Silva
attribution name: Silva

The effect of cigarette smoking habits on the outcome of dental implant treatment
type: item
type: AcademicArticle
description: The aim of this study was to analyze the influence of smoking habits and other possibly relevant factors on dental implant survival. The study population included all patients who underwent dental implants between the years 1999 and 2008 at a large military dental clinic and were examined in the periodic medical examination center. Correlation between implant characteristics and patients’ smoking habits, as mentioned in the questionnaire answered by patients in the periodic examination, was performed. Besides standard statistical methods, multiple linear regression models were constructed for estimation of the relative influence of some factors on implant survival rate. The long-term results of the implant treatment were good. The study refers to 7,680 implants. 7,359 (95.8%) survived and 321 (4.2%) did not survive. Concerning smoking habits, in a uni-variable analysis, factors found to have an association with implant survival were the smoking status of the patients (smoking/no smoking), the amount of smoking, passive smoking, and the time elapsed in ex-smokers from the time they ceased smoking to the time of implantation. In a multi-variable analysis, factors found to have an association with implant survival were smoking status (smoking/no smoking) and amounts of smoking as expressed in pack years.
format: application/pdf
format: text/html
creator: Dror Twito
creator: Paul Sade
subject: Dentistry
description: doi:10.7717/peerj.546
publisher: PeerJ Inc.
rights: © 2014 Twito and Sade
abstract: The aim of this study was to analyze the influence of smoking habits and other possibly relevant factors on dental implant survival. The study population included all patients who underwent dental implants between the years 1999 and 2008 at a large military dental clinic and were examined in the periodic medical examination center. Correlation between implant characteristics and patients’ smoking habits, as mentioned in the questionnaire answered by patients in the periodic examination, was performed. Besides standard statistical methods, multiple linear regression models were constructed for estimation of the relative influence of some factors on implant survival rate. The long-term results of the implant treatment were good. The study refers to 7,680 implants. 7,359 (95.8%) survived and 321 (4.2%) did not survive. Concerning smoking habits, in a uni-variable analysis, factors found to have an association with implant survival were the smoking status of the patients (smoking/no smoking), the amount of smoking, passive smoking, and the time elapsed in ex-smokers from the time they ceased smoking to the time of implantation. In a multi-variable analysis, factors found to have an association with implant survival were smoking status (smoking/no smoking) and amounts of smoking as expressed in pack years.
bibliographic citation: Twito et al. (2014) The effect of cigarette smoking habits on the outcome of dental implant treatment. PeerJ 2:e546 https://doi.org/10.7717/peerj.546
date submitted: 2014-01-28
date accepted: 2014-08-07
issued: 2014-09-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Twito
  given name: Dror
author list: Agent
  family name: Sade
  given name: Paul
doi: 10.7717/peerj.546
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-02
copyright: © 2014 Twito and Sade
attribution name: Twito and Sade

Too big to be noticed: cryptic invasion of Asian camel crickets in North American houses
type: item
type: AcademicArticle
description: Despite the rapid expansion of the built environment, we know little about the biology of species living in human-constructed habitats. Camel crickets (Rhaphidophoridae) are commonly observed in North American houses and include a range of native taxa as well as the Asian Diestrammena asynamora (Adelung), a species occasionally reported from houses though considered to be established only in greenhouses. We launched a continental-scale citizen science campaign to better understand the relative distributions and frequency of native and nonnative camel crickets in human homes across North America. Participants contributed survey data about the presence or absence of camel crickets in homes, as well as photographs and specimens of camel crickets allowing us to identify the major genera and/or species in and around houses. Together, these data offer insight into the geographical distribution of camel crickets as a presence in homes, as well as the relative frequency and distribution of native and nonnative camel crickets encountered in houses. In so doing, we show that the exotic Diestrammena asynamora not only has become a common presence in eastern houses, but is found in these environments far more frequently than native camel crickets. Supplemental pitfall trapping along transects in 10 urban yards in Raleigh, NC revealed that D. asynamora can be extremely abundant locally around some homes, with as many as 52 individuals collected from pitfalls in a single yard over two days of sampling. The number of D. asynamora individuals present in a trap was negatively correlated with the trap’s distance from a house, suggesting that these insects may be preferentially associated with houses but also are present outside. In addition, we report the establishment in the northeastern United States of a second exotic species, putatively Diestrammena japanica Blatchley, which was previously undocumented in the literature. Our results offer new insight into the relative frequency a…
format: application/pdf
format: text/html
creator: Mary Jane Epps
creator: Holly L. Menninger
creator: Nathan LaSala
creator: Robert R. Dunn
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.523
publisher: PeerJ Inc.
rights: © 2014 Epps et al.
abstract: Despite the rapid expansion of the built environment, we know little about the biology of species living in human-constructed habitats. Camel crickets (Rhaphidophoridae) are commonly observed in North American houses and include a range of native taxa as well as the Asian Diestrammena asynamora (Adelung), a species occasionally reported from houses though considered to be established only in greenhouses. We launched a continental-scale citizen science campaign to better understand the relative distributions and frequency of native and nonnative camel crickets in human homes across North America. Participants contributed survey data about the presence or absence of camel crickets in homes, as well as photographs and specimens of camel crickets allowing us to identify the major genera and/or species in and around houses. Together, these data offer insight into the geographical distribution of camel crickets as a presence in homes, as well as the relative frequency and distribution of native and nonnative camel crickets encountered in houses. In so doing, we show that the exotic Diestrammena asynamora not only has become a common presence in eastern houses, but is found in these environments far more frequently than native camel crickets. Supplemental pitfall trapping along transects in 10 urban yards in Raleigh, NC revealed that D. asynamora can be extremely abundant locally around some homes, with as many as 52 individuals collected from pitfalls in a single yard over two days of sampling. The number of D. asynamora individuals present in a trap was negatively correlated with the trap’s distance from a house, suggesting that these insects may be preferentially associated with houses but also are present outside. In addition, we report the establishment in the northeastern United States of a second exotic species, putatively Diestrammena japanica Blatchley, which was previously undocumented in the literature. Our results offer new insight into the relative frequency a…
bibliographic citation: Epps et al. (2014) Too big to be noticed: cryptic invasion of Asian camel crickets in North American houses. PeerJ 2:e523 https://doi.org/10.7717/peerj.523
date submitted: 2014-05-28
date accepted: 2014-07-25
issued: 2014-09-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Epps
  given name: Mary Jane
author list: Agent
  family name: Menninger
  given name: Holly L.
author list: Agent
  family name: LaSala
  given name: Nathan
author list: Agent
  family name: Dunn
  given name: Robert R.
doi: 10.7717/peerj.523
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-02
copyright: © 2014 Epps et al.
attribution name: Epps et al.

Hand infections: a retrospective analysis
type: item
type: AcademicArticle
description: Purpose. Hand infections are common, usually resulting from an untreated injury. In this retrospective study, we report on hand infection cases needing surgical drainage in order to assess patient demographics, causation of infection, clinical course, and clinical management. Methods. Medical records of patients presenting with hand infections, excluding post-surgical infections, treated with incision and debridement over a one-year period were reviewed. Patient demographics; past medical history; infection site(s) and causation; intervals between onset of infection, hospital admission, surgical intervention and days of hospitalization; gram stains and cultures; choice of antibiotics; complications; and outcomes were reviewed. Results. Most infections were caused by laceration and the most common site of infection was the palm or dorsum of the hand. Mean length of hospitalization was 6 days. Methicillin-resistant Staphylococcus aureus, beta-hemolytic Streptococcus and methicillin-susceptible Staphylococcus aureus were the most commonly cultured microorganisms. Cephalosporins, clindamycin, amoxicillin/clavulanate, penicillin, vancomycin, and trimethoprim/sulfamethoxazole were major antibiotic choices. Amputations and contracture were the primary complications. Conclusions. Surgery along with medical management were key to treatment and most soft tissue infections resolved without further complications. With prompt and appropriate care, most hand infection patients can achieve full resolution of their infection.
format: application/pdf
format: text/html
creator: Tolga Türker
creator: Nicole Capdarest-Arest
creator: Spencer T. Bertoch
creator: Erik C. Bakken
creator: Susan E. Hoover
creator: Jiyao Zou
subject: Infectious Diseases
subject: Orthopedics
description: doi:10.7717/peerj.513
publisher: PeerJ Inc.
rights: © 2014 Türker et al.
abstract: Purpose. Hand infections are common, usually resulting from an untreated injury. In this retrospective study, we report on hand infection cases needing surgical drainage in order to assess patient demographics, causation of infection, clinical course, and clinical management. Methods. Medical records of patients presenting with hand infections, excluding post-surgical infections, treated with incision and debridement over a one-year period were reviewed. Patient demographics; past medical history; infection site(s) and causation; intervals between onset of infection, hospital admission, surgical intervention and days of hospitalization; gram stains and cultures; choice of antibiotics; complications; and outcomes were reviewed. Results. Most infections were caused by laceration and the most common site of infection was the palm or dorsum of the hand. Mean length of hospitalization was 6 days. Methicillin-resistant Staphylococcus aureus, beta-hemolytic Streptococcus and methicillin-susceptible Staphylococcus aureus were the most commonly cultured microorganisms. Cephalosporins, clindamycin, amoxicillin/clavulanate, penicillin, vancomycin, and trimethoprim/sulfamethoxazole were major antibiotic choices. Amputations and contracture were the primary complications. Conclusions. Surgery along with medical management were key to treatment and most soft tissue infections resolved without further complications. With prompt and appropriate care, most hand infection patients can achieve full resolution of their infection.
bibliographic citation: Türker et al. (2014) Hand infections: a retrospective analysis. PeerJ 2:e513 https://doi.org/10.7717/peerj.513
date submitted: 2014-04-07
date accepted: 2014-07-22
issued: 2014-09-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Türker
  given name: Tolga
author list: Agent
  family name: Capdarest-Arest
  given name: Nicole
author list: Agent
  family name: Bertoch
  given name: Spencer T.
author list: Agent
  family name: Bakken
  given name: Erik C.
author list: Agent
  family name: Hoover
  given name: Susan E.
author list: Agent
  family name: Zou
  given name: Jiyao
doi: 10.7717/peerj.513
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-02
copyright: © 2014 Türker et al.
attribution name: Türker et al.

Exceptionally preserved insect fossils in the Late Jurassic lagoon of Orbagnoux (Rhône Valley, France)
type: item
type: AcademicArticle
description: The Late Kimmeridgian marine limestones of the area around Orbagnoux (Rhône, France) are well known for their fish fauna and terrestrial flora. Here we record the first insects and their activities (mines on leaves and trails in sediments) from these layers, including the oldest record of the gerromorphan bugs, as a new genus and species Gallomesovelia grioti, attributed to the most basal family Mesoveliidae and subfamily Madeoveliinae. These new fossils suggest the presence of a complex terrestrial palaeoecosystem on emerged lands near the lagoon where the limestones were deposited. The exquisite state of preservation of these fossils also suggests that these outcrops can potentially become an important Konservat-Lagerstätte for the Late Jurassic of Western Europe.
format: application/pdf
format: text/html
creator: André Nel
creator: Patricia Nel
creator: Régis Krieg-Jacquier
creator: Jean-Marc Pouillon
creator: Romain Garrouste
subject: Entomology
subject: Paleontology
description: doi:10.7717/peerj.510
publisher: PeerJ Inc.
rights: © 2014 Nel et al.
abstract: The Late Kimmeridgian marine limestones of the area around Orbagnoux (Rhône, France) are well known for their fish fauna and terrestrial flora. Here we record the first insects and their activities (mines on leaves and trails in sediments) from these layers, including the oldest record of the gerromorphan bugs, as a new genus and species Gallomesovelia grioti, attributed to the most basal family Mesoveliidae and subfamily Madeoveliinae. These new fossils suggest the presence of a complex terrestrial palaeoecosystem on emerged lands near the lagoon where the limestones were deposited. The exquisite state of preservation of these fossils also suggests that these outcrops can potentially become an important Konservat-Lagerstätte for the Late Jurassic of Western Europe.
bibliographic citation: Nel et al. (2014) Exceptionally preserved insect fossils in the Late Jurassic lagoon of Orbagnoux (Rhône Valley, France). PeerJ 2:e510 https://doi.org/10.7717/peerj.510
date submitted: 2014-06-15
date accepted: 2014-07-21
issued: 2014-09-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nel
  given name: André
author list: Agent
  family name: Nel
  given name: Patricia
author list: Agent
  family name: Krieg-Jacquier
  given name: Régis
author list: Agent
  family name: Pouillon
  given name: Jean-Marc
author list: Agent
  family name: Garrouste
  given name: Romain
doi: 10.7717/peerj.510
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-09-02
copyright: © 2014 Nel et al.
attribution name: Nel et al.

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