PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Using laser micro-dissection and qRT-PCR to analyze cell type-specific gene expression in Norway spruce phloem
items: Association between in-scanner head motion with cerebral white matter microstructure: a multiband diffusion-weighted MRI study
items: Microbial communities respond to experimental warming, but site matters
items: A survey of authors publishing in four megajournals
items: A probabilistic analysis reveals fundamental limitations with the environmental impact quotient and similar systems for rating pesticide risks
items: The perception of shape from shading in a new light
items: Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix
items: Oppositional defiant- and conduct disorder-like problems: neurodevelopmental predictors and genetic background in boys and girls, in a nationwide twin study
items: A new direction for prenatal chromosome microarray testing: software-targeting for detection of clinically significant chromosome imbalance without equivocal findings
items: The spectacular human nose: an amplifier of individual quality?
items: Culture of equine fibroblast-like synoviocytes on synthetic tissue scaffolds towards meniscal tissue engineering: a preliminary cell-seeding study
items: Can head louse repellents really work? Field studies of piperonal 2% spray
items: The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica
items: Diet and kwashiorkor: a prospective study from rural DR Congo
items: Re-examining the relationship between invasive lionfish and native grouper in the Caribbean
items: There and back again: putting the vectorial movement planning hypothesis to a critical test
items: Castration modulates singing patterns and electrophysiological properties of RA projection neurons in adult male zebra finches
items: TMEM65 is a mitochondrial inner-membrane protein
items: Fluvial transport potential of shed and root-bearing dinosaur teeth from the late Jurassic Morrison Formation
items: Vertebrate blood cell volume increases with temperature: implications for aerobic activity
items: Peruvians’ sleep duration: analysis of a population-based survey on adolescents and adults
items: Red deer synchronise their activity with close neighbours
items: Automated electronic medical record sepsis detection in the emergency department
items: The challenge of evaluating pain and a pre-incisional local anesthetic block
items: In situ effects of simulated overfishing and eutrophication on settlement of benthic coral reef invertebrates in the Central Red Sea
items: Evaluation of granular anaerobic ammonium oxidation process for the disposal of pre-treated swine manure
items: Comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus DNA in fluids and tissues
items: A cross-ocean comparison of responses to settlement cues in reef-building corals
items: Can resistant coral-Symbiodinium associations enable coral communities to survive climate change? A study of a site exposed to long-term hot water input
items: Bone microstructure and the evolution of growth patterns in Permo-Triassic therocephalians (Amniota, Therapsida) of South Africa
items: Honey bee sting pain index by body location
items: Sense of presence and anxiety during virtual social interactions between a human and virtual humans
items: Leishmania amazonensis promastigotes in 3D Collagen I culture: an in vitro physiological environment for the study of extracellular matrix and host cell interactions
items: Internet publicity of data problems in the bioscience literature correlates with enhanced corrective action
items: Predicting changes in language skills between 2 and 3 years in the EDEN mother–child cohort
items: The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes
items: Association between shell morphology of micro-land snails (genus Plectostoma) and their predator’s predatory behaviour
items: Tumor vascular disruption using various radiation types

Using laser micro-dissection and qRT-PCR to analyze cell type-specific gene expression in Norway spruce phloem
type: item
type: AcademicArticle
description: The tangentially oriented polyphenolic parenchyma (PP) and radially organized ray parenchyma in the phloem are central in the defense of conifer stems against insects and pathogens. Laser micro-dissection enables examination of cell-specific defense responses. To examine induced defense responses in Norway spruce stems inoculated with the necrotrophic blue-stain fungus Ceratocystis polonica, RNA extracted from laser micro-dissected phloem parenchyma and vascular cambium was analyzed using real-time RT-PCR (qRT-PCR) to profile transcript levels of selected resistance marker genes. The monitored transcripts included three pathogenesis-related proteins (class IV chitinase (CHI4), defensin (SPI1), peroxidase (PX3), two terpene synthesis related proteins (DXPS and LAS), one ethylene biosynthesis related protein (ACS), and a phenylalanine ammonia-lyase (PAL). Three days following inoculation, four genes (CHI4, PAL, PX3, SPI1) were differentially induced in individual cell and tissue types, both close to the inoculation site (5 mm above) and, to a lesser degree, further away (10 mm above). These resistance marker genes were all highly induced in ray parenchyma, supporting the important role of the rays in spruce defense propagation. CHI4 and PAL were also induced in PP cells and in conducting secondary phloem tissues. Our data suggests that different cell types in the secondary phloem of Norway spruce have overlapping but not fully redundant roles in active host defense. Furthermore, the study demonstrates the usefulness of laser micro-dissection coupled with qRT-PCR to characterize gene expression in different cell types of conifer bark.
format: application/pdf
format: text/html
creator: Nina E. Nagy
creator: Katarzyna Sikora
creator: Paal Krokene
creator: Ari M. Hietala
creator: Halvor Solheim
creator: Carl Gunnar Fossdal
subject: Plant Science
description: doi:10.7717/peerj.362
publisher: PeerJ Inc.
rights: © 2014 Nagy et al.
abstract: The tangentially oriented polyphenolic parenchyma (PP) and radially organized ray parenchyma in the phloem are central in the defense of conifer stems against insects and pathogens. Laser micro-dissection enables examination of cell-specific defense responses. To examine induced defense responses in Norway spruce stems inoculated with the necrotrophic blue-stain fungus Ceratocystis polonica, RNA extracted from laser micro-dissected phloem parenchyma and vascular cambium was analyzed using real-time RT-PCR (qRT-PCR) to profile transcript levels of selected resistance marker genes. The monitored transcripts included three pathogenesis-related proteins (class IV chitinase (CHI4), defensin (SPI1), peroxidase (PX3), two terpene synthesis related proteins (DXPS and LAS), one ethylene biosynthesis related protein (ACS), and a phenylalanine ammonia-lyase (PAL). Three days following inoculation, four genes (CHI4, PAL, PX3, SPI1) were differentially induced in individual cell and tissue types, both close to the inoculation site (5 mm above) and, to a lesser degree, further away (10 mm above). These resistance marker genes were all highly induced in ray parenchyma, supporting the important role of the rays in spruce defense propagation. CHI4 and PAL were also induced in PP cells and in conducting secondary phloem tissues. Our data suggests that different cell types in the secondary phloem of Norway spruce have overlapping but not fully redundant roles in active host defense. Furthermore, the study demonstrates the usefulness of laser micro-dissection coupled with qRT-PCR to characterize gene expression in different cell types of conifer bark.
bibliographic citation: Nagy et al. (2014) Using laser micro-dissection and qRT-PCR to analyze cell type-specific gene expression in Norway spruce phloem. PeerJ 2:e362 https://doi.org/10.7717/peerj.362
date submitted: 2013-12-04
date accepted: 2014-04-04
issued: 2014-04-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Nagy
  given name: Nina E.
author list: Agent
  family name: Sikora
  given name: Katarzyna
author list: Agent
  family name: Krokene
  given name: Paal
author list: Agent
  family name: Hietala
  given name: Ari M.
author list: Agent
  family name: Solheim
  given name: Halvor
author list: Agent
  family name: Fossdal
  given name: Carl Gunnar
doi: 10.7717/peerj.362
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-29
copyright: © 2014 Nagy et al.
attribution name: Nagy et al.

Association between in-scanner head motion with cerebral white matter microstructure: a multiband diffusion-weighted MRI study
type: item
type: AcademicArticle
description: Diffusion-weighted Magnetic Resonance Imaging (DW-MRI) has emerged as the most popular neuroimaging technique used to depict the biological microstructural properties of human brain white matter. However, like other MRI techniques, traditional DW-MRI data remains subject to head motion artifacts during scanning. For example, previous studies have indicated that, with traditional DW-MRI data, head motion artifacts significantly affect the evaluation of diffusion metrics. Actually, DW-MRI data scanned with higher sampling rate are important for accurately evaluating diffusion metrics because it allows for full-brain coverage through the acquisition of multiple slices simultaneously and more gradient directions. Here, we employed a publicly available multiband DW-MRI dataset to investigate the association between motion and diffusion metrics with the standard pipeline, tract-based spatial statistics (TBSS). The diffusion metrics used in this study included not only the commonly used metrics (i.e., FA and MD) in DW-MRI studies, but also newly proposed inter-voxel metric, local diffusion homogeneity (LDH). We found that the motion effects in FA and MD seems to be mitigated to some extent, but the effect on MD still exists. Furthermore, the effect in LDH is much more pronounced. These results indicate that researchers shall be cautious when conducting data analysis and interpretation. Finally, the motion-diffusion association is discussed.
format: application/pdf
format: text/html
creator: Xiang-zhen Kong
subject: Neurology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.366
publisher: PeerJ Inc.
rights: © 2014 Kong
abstract: Diffusion-weighted Magnetic Resonance Imaging (DW-MRI) has emerged as the most popular neuroimaging technique used to depict the biological microstructural properties of human brain white matter. However, like other MRI techniques, traditional DW-MRI data remains subject to head motion artifacts during scanning. For example, previous studies have indicated that, with traditional DW-MRI data, head motion artifacts significantly affect the evaluation of diffusion metrics. Actually, DW-MRI data scanned with higher sampling rate are important for accurately evaluating diffusion metrics because it allows for full-brain coverage through the acquisition of multiple slices simultaneously and more gradient directions. Here, we employed a publicly available multiband DW-MRI dataset to investigate the association between motion and diffusion metrics with the standard pipeline, tract-based spatial statistics (TBSS). The diffusion metrics used in this study included not only the commonly used metrics (i.e., FA and MD) in DW-MRI studies, but also newly proposed inter-voxel metric, local diffusion homogeneity (LDH). We found that the motion effects in FA and MD seems to be mitigated to some extent, but the effect on MD still exists. Furthermore, the effect in LDH is much more pronounced. These results indicate that researchers shall be cautious when conducting data analysis and interpretation. Finally, the motion-diffusion association is discussed.
bibliographic citation: Kong (2014) Association between in-scanner head motion with cerebral white matter microstructure: a multiband diffusion-weighted MRI study. PeerJ 2:e366 https://doi.org/10.7717/peerj.366
date submitted: 2014-01-24
date accepted: 2014-04-09
issued: 2014-04-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kong
  given name: Xiang-zhen
doi: 10.7717/peerj.366
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-24
copyright: © 2014 Kong
attribution name: Kong

Microbial communities respond to experimental warming, but site matters
type: item
type: AcademicArticle
description: Because microorganisms are sensitive to temperature, ongoing global warming is predicted to influence microbial community structure and function. We used large-scale warming experiments established at two sites near the northern and southern boundaries of US eastern deciduous forests to explore how microbial communities and their function respond to warming at sites with differing climatic regimes. Soil microbial community structure and function responded to warming at the southern but not the northern site. However, changes in microbial community structure and function at the southern site did not result in changes in cellulose decomposition rates. While most global change models rest on the assumption that taxa will respond similarly to warming across sites and their ranges, these results suggest that the responses of microorganisms to warming may be mediated by differences across the geographic boundaries of ecosystems.
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creator: Melissa A. Cregger
creator: Nathan J. Sanders
creator: Robert R. Dunn
creator: Aimée T. Classen
subject: Climate Change Biology
subject: Ecology
description: doi:10.7717/peerj.358
publisher: PeerJ Inc.
rights: © 2014 Cregger et al.
abstract: Because microorganisms are sensitive to temperature, ongoing global warming is predicted to influence microbial community structure and function. We used large-scale warming experiments established at two sites near the northern and southern boundaries of US eastern deciduous forests to explore how microbial communities and their function respond to warming at sites with differing climatic regimes. Soil microbial community structure and function responded to warming at the southern but not the northern site. However, changes in microbial community structure and function at the southern site did not result in changes in cellulose decomposition rates. While most global change models rest on the assumption that taxa will respond similarly to warming across sites and their ranges, these results suggest that the responses of microorganisms to warming may be mediated by differences across the geographic boundaries of ecosystems.
bibliographic citation: Cregger et al. (2014) Microbial communities respond to experimental warming, but site matters. PeerJ 2:e358 https://doi.org/10.7717/peerj.358
date submitted: 2013-12-04
date accepted: 2014-04-02
issued: 2014-04-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Cregger
  given name: Melissa A.
author list: Agent
  family name: Sanders
  given name: Nathan J.
author list: Agent
  family name: Dunn
  given name: Robert R.
author list: Agent
  family name: Classen
  given name: Aimée T.
doi: 10.7717/peerj.358
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-24
copyright: © 2014 Cregger et al.
attribution name: Cregger et al.

A survey of authors publishing in four megajournals
type: item
type: AcademicArticle
description: Aim. To determine the characteristics of megajournal authors, the nature of the manuscripts they are submitting to these journals, factors influencing their decision to publish in a megajournal, sources of funding for article processing charges (APCs) or other fees and their likelihood of submitting to a megajournal in the future. Methods. Web-based survey of 2,128 authors who recently published in BMJ Open, PeerJ, PLOS ONE or SAGE Open. Results. The response rate ranged from 26% for BMJ Open to 47% for SAGE Open. The authors were international, largely academics who had recently published in both subscription and Open Access (OA) journals. Across journals about 25% of the articles were preliminary findings and just under half were resubmissions of manuscripts rejected by other journals. Editors from other BMJ journals and perhaps to a lesser extent SAGE and PLOS journals appear to be encouraging authors to submit manuscripts that were rejected by the editor’s journals to a megajournal published by the same publisher. Quality of the journal and speed of the review process were important factors across all four journals. Impact factor was important for PLOS ONE authors but less so for BMJ Open authors, which also has an impact factor. The review criteria and the fact the journal was OA were other significant factors particularly important for PeerJ authors. The reputation of the publisher was an important factor for SAGE Open and BMJ Open. About half of PLOS ONE and around a third of BMJ Open and PeerJ authors used grant funding for publishing charges while only about 10% of SAGE Open used grant funding for publication charges. Around 60% of SAGE Open and 32% of PeerJ authors self-funded their publication fees however the fees are modest for these journals. The majority of authors from all 4 journals were pleased with their experience and indicated they were likely to submit to the same or similar journal in the future. Conclusions. Megajournals are drawing an intern…
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format: text/html
creator: David J. Solomon
subject: Science Policy
description: doi:10.7717/peerj.365
publisher: PeerJ Inc.
rights: © 2014 Solomon
abstract: Aim. To determine the characteristics of megajournal authors, the nature of the manuscripts they are submitting to these journals, factors influencing their decision to publish in a megajournal, sources of funding for article processing charges (APCs) or other fees and their likelihood of submitting to a megajournal in the future. Methods. Web-based survey of 2,128 authors who recently published in BMJ Open, PeerJ, PLOS ONE or SAGE Open. Results. The response rate ranged from 26% for BMJ Open to 47% for SAGE Open. The authors were international, largely academics who had recently published in both subscription and Open Access (OA) journals. Across journals about 25% of the articles were preliminary findings and just under half were resubmissions of manuscripts rejected by other journals. Editors from other BMJ journals and perhaps to a lesser extent SAGE and PLOS journals appear to be encouraging authors to submit manuscripts that were rejected by the editor’s journals to a megajournal published by the same publisher. Quality of the journal and speed of the review process were important factors across all four journals. Impact factor was important for PLOS ONE authors but less so for BMJ Open authors, which also has an impact factor. The review criteria and the fact the journal was OA were other significant factors particularly important for PeerJ authors. The reputation of the publisher was an important factor for SAGE Open and BMJ Open. About half of PLOS ONE and around a third of BMJ Open and PeerJ authors used grant funding for publishing charges while only about 10% of SAGE Open used grant funding for publication charges. Around 60% of SAGE Open and 32% of PeerJ authors self-funded their publication fees however the fees are modest for these journals. The majority of authors from all 4 journals were pleased with their experience and indicated they were likely to submit to the same or similar journal in the future. Conclusions. Megajournals are drawing an intern…
bibliographic citation: Solomon (2014) A survey of authors publishing in four megajournals. PeerJ 2:e365 https://doi.org/10.7717/peerj.365
date submitted: 2014-03-19
date accepted: 2014-04-07
issued: 2014-04-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Solomon
  given name: David J.
doi: 10.7717/peerj.365
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-22
copyright: © 2014 Solomon
attribution name: Solomon

A probabilistic analysis reveals fundamental limitations with the environmental impact quotient and similar systems for rating pesticide risks
type: item
type: AcademicArticle
description: Comparing risks among pesticides has substantial utility for decision makers. However, if rating schemes to compare risks are to be used, they must be conceptually and mathematically sound. We address limitations with pesticide risk rating schemes by examining in particular the Environmental Impact Quotient (EIQ) using, for the first time, a probabilistic analytic technique. To demonstrate the consequences of mapping discrete risk ratings to probabilities, adjusted EIQs were calculated for a group of 20 insecticides in four chemical classes. Using Monte Carlo simulation, adjusted EIQs were determined under different hypothetical scenarios by incorporating probability ranges. The analysis revealed that pesticides that have different EIQs, and therefore different putative environmental effects, actually may be no different when incorporating uncertainty. The EIQ equation cannot take into account uncertainty the way that it is structured and provide reliable quotients of pesticide impact. The EIQ also is inconsistent with the accepted notion of risk as a joint probability of toxicity and exposure. Therefore, our results suggest that the EIQ and other similar schemes be discontinued in favor of conceptually sound schemes to estimate risk that rely on proper integration of toxicity and exposure information.
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creator: Robert K.D. Peterson
creator: Jerome J. Schleier
subject: Agricultural Science
subject: Ecotoxicology
subject: Entomology
subject: Environmental Sciences
subject: Toxicology
description: doi:10.7717/peerj.364
publisher: PeerJ Inc.
rights: © 2014 Peterson and Schleier III
abstract: Comparing risks among pesticides has substantial utility for decision makers. However, if rating schemes to compare risks are to be used, they must be conceptually and mathematically sound. We address limitations with pesticide risk rating schemes by examining in particular the Environmental Impact Quotient (EIQ) using, for the first time, a probabilistic analytic technique. To demonstrate the consequences of mapping discrete risk ratings to probabilities, adjusted EIQs were calculated for a group of 20 insecticides in four chemical classes. Using Monte Carlo simulation, adjusted EIQs were determined under different hypothetical scenarios by incorporating probability ranges. The analysis revealed that pesticides that have different EIQs, and therefore different putative environmental effects, actually may be no different when incorporating uncertainty. The EIQ equation cannot take into account uncertainty the way that it is structured and provide reliable quotients of pesticide impact. The EIQ also is inconsistent with the accepted notion of risk as a joint probability of toxicity and exposure. Therefore, our results suggest that the EIQ and other similar schemes be discontinued in favor of conceptually sound schemes to estimate risk that rely on proper integration of toxicity and exposure information.
bibliographic citation: Peterson et al. (2014) A probabilistic analysis reveals fundamental limitations with the environmental impact quotient and similar systems for rating pesticide risks. PeerJ 2:e364 https://doi.org/10.7717/peerj.364
date submitted: 2014-01-15
date accepted: 2014-04-06
issued: 2014-04-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Peterson
  given name: Robert K.D.
author list: Agent
  family name: Schleier
  given name: Jerome J.
doi: 10.7717/peerj.364
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-22
copyright: © 2014 Peterson and Schleier III
attribution name: Peterson and Schleier III

The perception of shape from shading in a new light
type: item
type: AcademicArticle
description: How do humans see three-dimensional shape based on two-dimensional shading? Much research has assumed that a ‘light from above’ bias solves the ambiguity of shape from shading. Counter to the ‘light from above’ bias, studies of Bayesian priors have found that such a bias can be swayed by other light cues. Despite the persuasive power of the Bayesian models, many new studies and books cite the original ‘light from above’ findings. Here I present a version of the Bayesian result that can be experienced. The perception of shape-from-shading was found here to be influenced by an external light source, even when the light was obstructed and did not directly illuminate a two-dimensional stimulus. The results imply that this effect is robust and not low-level in nature. The perception of shape from shading is not necessarily based on a hard-wired internal representation of lighting direction, but rather assesses the direction of lighting in the scene adaptively. Here, for the first time, is an experiential opportunity to see what the Bayesian models have supported all along.
format: application/pdf
format: text/html
creator: Michael J. Proulx
subject: Human-Computer Interaction
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.363
publisher: PeerJ Inc.
rights: © 2014 Proulx
abstract: How do humans see three-dimensional shape based on two-dimensional shading? Much research has assumed that a ‘light from above’ bias solves the ambiguity of shape from shading. Counter to the ‘light from above’ bias, studies of Bayesian priors have found that such a bias can be swayed by other light cues. Despite the persuasive power of the Bayesian models, many new studies and books cite the original ‘light from above’ findings. Here I present a version of the Bayesian result that can be experienced. The perception of shape-from-shading was found here to be influenced by an external light source, even when the light was obstructed and did not directly illuminate a two-dimensional stimulus. The results imply that this effect is robust and not low-level in nature. The perception of shape from shading is not necessarily based on a hard-wired internal representation of lighting direction, but rather assesses the direction of lighting in the scene adaptively. Here, for the first time, is an experiential opportunity to see what the Bayesian models have supported all along.
bibliographic citation: Proulx (2014) The perception of shape from shading in a new light. PeerJ 2:e363 https://doi.org/10.7717/peerj.363
date submitted: 2013-12-17
date accepted: 2014-04-05
issued: 2014-04-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Proulx
  given name: Michael J.
doi: 10.7717/peerj.363
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-22
copyright: © 2014 Proulx
attribution name: Proulx

Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix
type: item
type: AcademicArticle
description: The resolution of rapid evolutionary radiations or “bushes” in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets that are independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. The inclusion or exclusion of mitochondrial data had a limited impact upon analyses upon analyses using either concatenated data or multispecies coalescent methods. Some of the key phylogenetic findings include support for a second major clade within the core phasianids that includes the chicken and Japanese quail and clarification of the phylogenetic relationships of turkey. Jackknifed datasets suggested that there is an advantage to sampling many independent regions across the genome rather than obtaining long sequences for a small number of loci, possibly reflecting the differences among gene trees that differ due to incomplete lineage sorting. Despite the novel insights we obtained using this increased sampling of gene regions, some nodes remain unresolved, likely due to periods of rapid diversification. Resolving these remaining groups will likely require sequencing a very large number of gene regions, but our analyses now appear to support a robust backbone for this order.
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creator: Rebecca T. Kimball
creator: Edward L. Braun
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.361
publisher: PeerJ Inc.
rights: © 2014 Kimball and Braun
abstract: The resolution of rapid evolutionary radiations or “bushes” in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets that are independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. The inclusion or exclusion of mitochondrial data had a limited impact upon analyses upon analyses using either concatenated data or multispecies coalescent methods. Some of the key phylogenetic findings include support for a second major clade within the core phasianids that includes the chicken and Japanese quail and clarification of the phylogenetic relationships of turkey. Jackknifed datasets suggested that there is an advantage to sampling many independent regions across the genome rather than obtaining long sequences for a small number of loci, possibly reflecting the differences among gene trees that differ due to incomplete lineage sorting. Despite the novel insights we obtained using this increased sampling of gene regions, some nodes remain unresolved, likely due to periods of rapid diversification. Resolving these remaining groups will likely require sequencing a very large number of gene regions, but our analyses now appear to support a robust backbone for this order.
bibliographic citation: Kimball et al. (2014) Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix. PeerJ 2:e361 https://doi.org/10.7717/peerj.361
date submitted: 2013-11-30
date accepted: 2014-04-03
issued: 2014-04-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Kimball
  given name: Rebecca T.
author list: Agent
  family name: Braun
  given name: Edward L.
doi: 10.7717/peerj.361
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-22
copyright: © 2014 Kimball and Braun
attribution name: Kimball and Braun

Oppositional defiant- and conduct disorder-like problems: neurodevelopmental predictors and genetic background in boys and girls, in a nationwide twin study
type: item
type: AcademicArticle
description: Background. Previous research has supported gender-specific aetiological factors in oppositional defiant disorder (ODD) and conduct disorder (CD). The aims of this study were to identify gender-specific associations between the behavioural problems–ODD/CD-like problems–and the neurodevelopmental disorders–attention deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD)–and to investigate underlying genetic effects. Methods. 17,220 twins aged 9 or 12 were screened using the Autism–Tics, AD/HD and other Comorbidities inventory. The main covariates of ODD- and CD-like problems were investigated, and the relative importance of unique versus shared hereditary and environmental effects was estimated using twin model fitting. Results. Social interaction problems (one of the ASD subdomains) was the strongest neurodevelopmental covariate of the behavioural problems in both genders, while ADHD-related hyperactivity/impulsiveness in boys and inattention in girls stood out as important covariates of CD-like problems. Genetic effects accounted for 50%–62% of the variance in behavioural problems, except in CD-like problems in girls (26%). Genetic and environmental effects linked to ADHD and ASD also influenced ODD-like problems in both genders and, to a lesser extent, CD-like problems in boys, but not in girls. Conclusions. The gender-specific patterns should be considered in the assessment and treatment, especially of CD.
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creator: Nóra Kerekes
creator: Sebastian Lundström
creator: Zheng Chang
creator: Armin Tajnia
creator: Patrick Jern
creator: Paul Lichtenstein
creator: Thomas Nilsson
creator: Henrik Anckarsäter
subject: Genetics
subject: Epidemiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.359
publisher: PeerJ Inc.
rights: © 2014 Kerekes et al.
abstract: Background. Previous research has supported gender-specific aetiological factors in oppositional defiant disorder (ODD) and conduct disorder (CD). The aims of this study were to identify gender-specific associations between the behavioural problems–ODD/CD-like problems–and the neurodevelopmental disorders–attention deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD)–and to investigate underlying genetic effects. Methods. 17,220 twins aged 9 or 12 were screened using the Autism–Tics, AD/HD and other Comorbidities inventory. The main covariates of ODD- and CD-like problems were investigated, and the relative importance of unique versus shared hereditary and environmental effects was estimated using twin model fitting. Results. Social interaction problems (one of the ASD subdomains) was the strongest neurodevelopmental covariate of the behavioural problems in both genders, while ADHD-related hyperactivity/impulsiveness in boys and inattention in girls stood out as important covariates of CD-like problems. Genetic effects accounted for 50%–62% of the variance in behavioural problems, except in CD-like problems in girls (26%). Genetic and environmental effects linked to ADHD and ASD also influenced ODD-like problems in both genders and, to a lesser extent, CD-like problems in boys, but not in girls. Conclusions. The gender-specific patterns should be considered in the assessment and treatment, especially of CD.
bibliographic citation: Kerekes et al. (2014) Oppositional defiant- and conduct disorder-like problems: neurodevelopmental predictors and genetic background in boys and girls, in a nationwide twin study. PeerJ 2:e359 https://doi.org/10.7717/peerj.359
date submitted: 2013-12-27
date accepted: 2014-04-03
issued: 2014-04-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Kerekes
  given name: Nóra
author list: Agent
  family name: Lundström
  given name: Sebastian
author list: Agent
  family name: Chang
  given name: Zheng
author list: Agent
  family name: Tajnia
  given name: Armin
author list: Agent
  family name: Jern
  given name: Patrick
author list: Agent
  family name: Lichtenstein
  given name: Paul
author list: Agent
  family name: Nilsson
  given name: Thomas
author list: Agent
  family name: Anckarsäter
  given name: Henrik
doi: 10.7717/peerj.359
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-22
copyright: © 2014 Kerekes et al.
attribution name: Kerekes et al.

A new direction for prenatal chromosome microarray testing: software-targeting for detection of clinically significant chromosome imbalance without equivocal findings
type: item
type: AcademicArticle
description: Purpose. To design and validate a prenatal chromosomal microarray testing strategy that moves away from size-based detection thresholds, towards a more clinically relevant analysis, providing higher resolution than G-banded chromosomes but avoiding the detection of copy number variants (CNVs) of unclear prognosis that cause parental anxiety. Methods. All prenatal samples fulfilling our criteria for karyotype analysis (n = 342) were tested by chromosomal microarray and only CNVs of established deletion/duplication syndrome regions and any other CNV >3 Mb were detected and reported. A retrospective full-resolution analysis of 249 of these samples was carried out to ascertain the performance of this testing strategy. Results. Using our prenatal analysis, 23/342 (6.7%) samples were found to be abnormal. Of the remaining samples, 249 were anonymized and reanalyzed at full-resolution; a further 46 CNVs were detected in 44 of these cases (17.7%). None of these additional CNVs were of clear clinical significance. Conclusion. This prenatal chromosomal microarray strategy detected all CNVs of clear prognostic value and did not miss any CNVs of clear clinical significance. This strategy avoided both the problems associated with interpreting CNVs of uncertain prognosis and the parental anxiety that are a result of such findings.
format: application/pdf
format: text/html
creator: Joo Wook Ahn
creator: Susan Bint
creator: Melita D. Irving
creator: Phillipa M. Kyle
creator: Ranjit Akolekar
creator: Shehla N. Mohammed
creator: Caroline Mackie Ogilvie
subject: Genetics
subject: Medical Genetics
subject: Ethical Issues
description: doi:10.7717/peerj.354
publisher: PeerJ Inc.
rights: © 2014 Ahn et al.
abstract: Purpose. To design and validate a prenatal chromosomal microarray testing strategy that moves away from size-based detection thresholds, towards a more clinically relevant analysis, providing higher resolution than G-banded chromosomes but avoiding the detection of copy number variants (CNVs) of unclear prognosis that cause parental anxiety. Methods. All prenatal samples fulfilling our criteria for karyotype analysis (n = 342) were tested by chromosomal microarray and only CNVs of established deletion/duplication syndrome regions and any other CNV >3 Mb were detected and reported. A retrospective full-resolution analysis of 249 of these samples was carried out to ascertain the performance of this testing strategy. Results. Using our prenatal analysis, 23/342 (6.7%) samples were found to be abnormal. Of the remaining samples, 249 were anonymized and reanalyzed at full-resolution; a further 46 CNVs were detected in 44 of these cases (17.7%). None of these additional CNVs were of clear clinical significance. Conclusion. This prenatal chromosomal microarray strategy detected all CNVs of clear prognostic value and did not miss any CNVs of clear clinical significance. This strategy avoided both the problems associated with interpreting CNVs of uncertain prognosis and the parental anxiety that are a result of such findings.
bibliographic citation: Ahn et al. (2014) A new direction for prenatal chromosome microarray testing: software-targeting for detection of clinically significant chromosome imbalance without equivocal findings. PeerJ 2:e354 https://doi.org/10.7717/peerj.354
date submitted: 2014-01-26
date accepted: 2014-03-31
issued: 2014-04-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahn
  given name: Joo Wook
author list: Agent
  family name: Bint
  given name: Susan
author list: Agent
  family name: Irving
  given name: Melita D.
author list: Agent
  family name: Kyle
  given name: Phillipa M.
author list: Agent
  family name: Akolekar
  given name: Ranjit
author list: Agent
  family name: Mohammed
  given name: Shehla N.
author list: Agent
  family name: Mackie Ogilvie
  given name: Caroline
doi: 10.7717/peerj.354
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-22
copyright: © 2014 Ahn et al.
attribution name: Ahn et al.

The spectacular human nose: an amplifier of individual quality?
type: item
type: AcademicArticle
description: Amplifiers are signals that improve the perception of underlying differences in quality. They are cost free and advantageous to high quality individuals, but disadvantageous to low quality individuals, as poor quality is easier perceived because of the amplifier. For an amplifier to evolve, the average fitness benefit to the high quality individuals should be higher than the average cost for the low quality individuals. The human nose is, compared to the nose of most other primates, extraordinary large, fragile and easily broken—especially in male–male interactions. May it have evolved as an amplifier among high quality individuals, allowing easy assessment of individual quality and influencing the perception of attractiveness? We tested the latter by manipulating the position of the nose tip or, as a control, the mouth in facial pictures and had the pictures rated for attractiveness. Our results show that facial attractiveness failed to be influenced by mouth manipulations. Yet, facial attractiveness increased when the nose tip was artificially centered according to other facial features. Conversely, attractiveness decreased when the nose tip was displaced away from its central position. Our results suggest that our evaluation of attractiveness is clearly sensitive to the centering of the nose tip, possibly because it affects our perception of the face’s symmetry and/or averageness. However, whether such centering is related to individual quality remains unclear.
format: application/pdf
format: text/html
creator: Åse Kristine Rognmo Mikalsen
creator: Ivar Folstad
creator: Nigel Gilles Yoccoz
creator: Bruno Laeng
subject: Animal Behavior
subject: Anthropology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.357
publisher: PeerJ Inc.
rights: © 2014 Mikalsen et al.
abstract: Amplifiers are signals that improve the perception of underlying differences in quality. They are cost free and advantageous to high quality individuals, but disadvantageous to low quality individuals, as poor quality is easier perceived because of the amplifier. For an amplifier to evolve, the average fitness benefit to the high quality individuals should be higher than the average cost for the low quality individuals. The human nose is, compared to the nose of most other primates, extraordinary large, fragile and easily broken—especially in male–male interactions. May it have evolved as an amplifier among high quality individuals, allowing easy assessment of individual quality and influencing the perception of attractiveness? We tested the latter by manipulating the position of the nose tip or, as a control, the mouth in facial pictures and had the pictures rated for attractiveness. Our results show that facial attractiveness failed to be influenced by mouth manipulations. Yet, facial attractiveness increased when the nose tip was artificially centered according to other facial features. Conversely, attractiveness decreased when the nose tip was displaced away from its central position. Our results suggest that our evaluation of attractiveness is clearly sensitive to the centering of the nose tip, possibly because it affects our perception of the face’s symmetry and/or averageness. However, whether such centering is related to individual quality remains unclear.
bibliographic citation: Mikalsen et al. (2014) The spectacular human nose: an amplifier of individual quality?. PeerJ 2:e357 https://doi.org/10.7717/peerj.357
date submitted: 2014-02-12
date accepted: 2014-04-01
issued: 2014-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Mikalsen
  given name: Åse Kristine Rognmo
author list: Agent
  family name: Folstad
  given name: Ivar
author list: Agent
  family name: Yoccoz
  given name: Nigel Gilles
author list: Agent
  family name: Laeng
  given name: Bruno
doi: 10.7717/peerj.357
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-17
copyright: © 2014 Mikalsen et al.
attribution name: Mikalsen et al.

Culture of equine fibroblast-like synoviocytes on synthetic tissue scaffolds towards meniscal tissue engineering: a preliminary cell-seeding study
type: item
type: AcademicArticle
description: Introduction. Tissue engineering is a new methodology for addressing meniscal injury or loss. Synovium may be an ideal source of cells for in vitro meniscal fibrocartilage formation, however, favorable in vitro culture conditions for synovium must be established in order to achieve this goal. The objective of this study was to determine cellularity, cell distribution, and extracellular matrix (ECM) formation of equine fibroblast-like synoviocytes (FLS) cultured on synthetic scaffolds, for potential application in synovium-based meniscal tissue engineering. Scaffolds included open-cell poly-L-lactic acid (OPLA) sponges and polyglycolic acid (PGA) scaffolds cultured in static and dynamic culture conditions, and PGA scaffolds coated in poly-L-lactic (PLLA) in dynamic culture conditions. Materials and Methods. Equine FLS were seeded on OPLA and PGA scaffolds, and cultured in a static environment or in a rotating bioreactor for 12 days. Equine FLS were also seeded on PGA scaffolds coated in 2% or 4% PLLA and cultured in a rotating bioreactor for 14 and 21 days. Three scaffolds from each group were fixed, sectioned and stained with Masson’s Trichrome, Safranin-O, and Hematoxylin and Eosin, and cell numbers and distribution were analyzed using computer image analysis. Three PGA and OPLA scaffolds from each culture condition were also analyzed for extracellular matrix (ECM) production via dimethylmethylene blue (sulfated glycosaminoglycan) assay and hydroxyproline (collagen) assay. PLLA coated PGA scaffolds were analyzed using double stranded DNA quantification as areflection of cellularity and confocal laser microscopy in a fluorescent cell viability assay. Results. The highest cellularity occurred in PGA constructs cultured in a rotating bioreactor, which also had a mean sulfated glycosaminoglycan content of 22.3 µg per scaffold. PGA constructs cultured in static conditions had the lowest cellularity. Cells had difficulty adhering to OPLA and the PLLA coating of PGA scaff…
format: application/pdf
format: text/html
creator: Jennifer J. Warnock
creator: Derek B. Fox
creator: Aaron M. Stoker
creator: Mark Beatty
creator: Mary Cockrell
creator: John C. Janicek
creator: James L. Cook
subject: Bioengineering
subject: Veterinary Medicine
subject: Orthopedics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.353
publisher: PeerJ Inc.
rights: © 2014 Warnock et al.
abstract: Introduction. Tissue engineering is a new methodology for addressing meniscal injury or loss. Synovium may be an ideal source of cells for in vitro meniscal fibrocartilage formation, however, favorable in vitro culture conditions for synovium must be established in order to achieve this goal. The objective of this study was to determine cellularity, cell distribution, and extracellular matrix (ECM) formation of equine fibroblast-like synoviocytes (FLS) cultured on synthetic scaffolds, for potential application in synovium-based meniscal tissue engineering. Scaffolds included open-cell poly-L-lactic acid (OPLA) sponges and polyglycolic acid (PGA) scaffolds cultured in static and dynamic culture conditions, and PGA scaffolds coated in poly-L-lactic (PLLA) in dynamic culture conditions. Materials and Methods. Equine FLS were seeded on OPLA and PGA scaffolds, and cultured in a static environment or in a rotating bioreactor for 12 days. Equine FLS were also seeded on PGA scaffolds coated in 2% or 4% PLLA and cultured in a rotating bioreactor for 14 and 21 days. Three scaffolds from each group were fixed, sectioned and stained with Masson’s Trichrome, Safranin-O, and Hematoxylin and Eosin, and cell numbers and distribution were analyzed using computer image analysis. Three PGA and OPLA scaffolds from each culture condition were also analyzed for extracellular matrix (ECM) production via dimethylmethylene blue (sulfated glycosaminoglycan) assay and hydroxyproline (collagen) assay. PLLA coated PGA scaffolds were analyzed using double stranded DNA quantification as areflection of cellularity and confocal laser microscopy in a fluorescent cell viability assay. Results. The highest cellularity occurred in PGA constructs cultured in a rotating bioreactor, which also had a mean sulfated glycosaminoglycan content of 22.3 µg per scaffold. PGA constructs cultured in static conditions had the lowest cellularity. Cells had difficulty adhering to OPLA and the PLLA coating of PGA scaff…
bibliographic citation: Warnock et al. (2014) Culture of equine fibroblast-like synoviocytes on synthetic tissue scaffolds towards meniscal tissue engineering: a preliminary cell-seeding study. PeerJ 2:e353 https://doi.org/10.7717/peerj.353
date submitted: 2014-02-02
date accepted: 2014-03-28
issued: 2014-04-17
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: Fox
  given name: Derek B.
author list: Agent
  family name: Stoker
  given name: Aaron M.
author list: Agent
  family name: Beatty
  given name: Mark
author list: Agent
  family name: Cockrell
  given name: Mary
author list: Agent
  family name: Janicek
  given name: John C.
author list: Agent
  family name: Cook
  given name: James L.
doi: 10.7717/peerj.353
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-17
copyright: © 2014 Warnock et al.
attribution name: Warnock et al.

Can head louse repellents really work? Field studies of piperonal 2% spray
type: item
type: AcademicArticle
description: Background. Many families find regular checking of children’s heads for head louse infestation too onerous and would prefer to be able to prevent infestation by use of a topical application that deters lice from infesting the head. Identification in the laboratory of a repellent activity for piperonal provided the basis for developing a spray product to repel lice. Methods. A proof of principle field study in Dhaka, Bangladesh, compared the effect of using 2% piperonal spray with that of a placebo in 105 children and adults from three communities with infestation levels close to 100%. All participants were treated for infestation and subsequent incidence of reinfestation monitored daily by investigators. A second randomised, controlled, double blind, study in North London, UK, evaluated the effect of the product in normal use. One hundred and sixty-three children from schools with a high level (20–25%) of infestation were treated and confirmed louse free and randomly divided between 2% piperonal, a placebo spray, and a control group for up to 22 weeks. Parents applied the spray and monitored for infestation. Regular investigator visits confirmed the parental monitoring and replenished supplies of spray. Results. In Dhaka, over 18 days there were only 4 infestations in the piperonal group and 8 in the placebo group. This difference was not significant (p = 0.312). In North London, there were 41 cases of infestation over the course of the study. Although there were fewer infestations in the piperonal group, analysis of time to first infestation showed a no significant (p = 0.4368) difference between groups. Conclusion. Routine use of 2% piperonal spray in communities with a high prevalence of head louse infestation may provide some protection from infestation. However, the difference between use of the product and no active intervention was sufficiently small that regular checking for presence of lice is likely to be a more practical and cost effective approach to pre…
format: application/pdf
format: text/html
creator: Ian F. Burgess
creator: Christine M. Brown
creator: Nazma A. Burgess
creator: Judith Kaufman
subject: Entomology
subject: Parasitology
subject: Epidemiology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.351
publisher: PeerJ Inc.
rights: © 2014 Burgess et al.
abstract: Background. Many families find regular checking of children’s heads for head louse infestation too onerous and would prefer to be able to prevent infestation by use of a topical application that deters lice from infesting the head. Identification in the laboratory of a repellent activity for piperonal provided the basis for developing a spray product to repel lice. Methods. A proof of principle field study in Dhaka, Bangladesh, compared the effect of using 2% piperonal spray with that of a placebo in 105 children and adults from three communities with infestation levels close to 100%. All participants were treated for infestation and subsequent incidence of reinfestation monitored daily by investigators. A second randomised, controlled, double blind, study in North London, UK, evaluated the effect of the product in normal use. One hundred and sixty-three children from schools with a high level (20–25%) of infestation were treated and confirmed louse free and randomly divided between 2% piperonal, a placebo spray, and a control group for up to 22 weeks. Parents applied the spray and monitored for infestation. Regular investigator visits confirmed the parental monitoring and replenished supplies of spray. Results. In Dhaka, over 18 days there were only 4 infestations in the piperonal group and 8 in the placebo group. This difference was not significant (p = 0.312). In North London, there were 41 cases of infestation over the course of the study. Although there were fewer infestations in the piperonal group, analysis of time to first infestation showed a no significant (p = 0.4368) difference between groups. Conclusion. Routine use of 2% piperonal spray in communities with a high prevalence of head louse infestation may provide some protection from infestation. However, the difference between use of the product and no active intervention was sufficiently small that regular checking for presence of lice is likely to be a more practical and cost effective approach to pre…
bibliographic citation: Burgess et al. (2014) Can head louse repellents really work? Field studies of piperonal 2% spray. PeerJ 2:e351 https://doi.org/10.7717/peerj.351
date submitted: 2014-01-17
date accepted: 2014-03-28
issued: 2014-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Burgess
  given name: Ian F.
author list: Agent
  family name: Brown
  given name: Christine M.
author list: Agent
  family name: Burgess
  given name: Nazma A.
author list: Agent
  family name: Kaufman
  given name: Judith
doi: 10.7717/peerj.351
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-17
copyright: © 2014 Burgess et al.
attribution name: Burgess et al.

The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica
type: item
type: AcademicArticle
description: Evolutionary studies of clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (cas) genes can provide insights into host-pathogen co-evolutionary dynamics and the frequency at which different genomic events (e.g., horizontal vs. vertical transmission) occur. Within this study, we used whole genome sequence (WGS) data to determine the evolutionary history and genetic diversity of CRISPR loci and cas genes among a diverse set of 427 Salmonella enterica ssp. enterica isolates representing 64 different serovars. We also evaluated the performance of CRISPR loci for typing when compared to whole genome and multilocus sequence typing (MLST) approaches. We found that there was high diversity in array length within both CRISPR1 (median = 22; min = 3; max = 79) and CRISPR2 (median = 27; min = 2; max = 221). There was also much diversity within serovars (e.g., arrays differed by as many as 50 repeat-spacer units among Salmonella ser. Senftenberg isolates). Interestingly, we found that there are two general cas gene profiles that do not track phylogenetic relationships, which suggests that non-vertical transmission events have occurred frequently throughout the evolutionary history of the sampled isolates. There is also considerable variation among the ranges of pairwise distances estimated within each cas gene, which may be indicative of the strength of natural selection acting on those genes. We developed a novel clustering approach based on CRISPR spacer content, but found that typing based on CRISPRs was less accurate than the MLST-based alternative; typing based on WGS data was the most accurate. Notwithstanding cost and accessibility, we anticipate that draft genome sequencing, due to its greater discriminatory power, will eventually become routine for traceback investigations.
format: application/pdf
format: text/html
creator: James B. Pettengill
creator: Ruth E. Timme
creator: Rodolphe Barrangou
creator: Magaly Toro
creator: Marc W. Allard
creator: Errol Strain
creator: Steven M. Musser
creator: Eric W. Brown
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.340
publisher: PeerJ Inc.
rights: © 2014 Pettengill et al.
abstract: Evolutionary studies of clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (cas) genes can provide insights into host-pathogen co-evolutionary dynamics and the frequency at which different genomic events (e.g., horizontal vs. vertical transmission) occur. Within this study, we used whole genome sequence (WGS) data to determine the evolutionary history and genetic diversity of CRISPR loci and cas genes among a diverse set of 427 Salmonella enterica ssp. enterica isolates representing 64 different serovars. We also evaluated the performance of CRISPR loci for typing when compared to whole genome and multilocus sequence typing (MLST) approaches. We found that there was high diversity in array length within both CRISPR1 (median = 22; min = 3; max = 79) and CRISPR2 (median = 27; min = 2; max = 221). There was also much diversity within serovars (e.g., arrays differed by as many as 50 repeat-spacer units among Salmonella ser. Senftenberg isolates). Interestingly, we found that there are two general cas gene profiles that do not track phylogenetic relationships, which suggests that non-vertical transmission events have occurred frequently throughout the evolutionary history of the sampled isolates. There is also considerable variation among the ranges of pairwise distances estimated within each cas gene, which may be indicative of the strength of natural selection acting on those genes. We developed a novel clustering approach based on CRISPR spacer content, but found that typing based on CRISPRs was less accurate than the MLST-based alternative; typing based on WGS data was the most accurate. Notwithstanding cost and accessibility, we anticipate that draft genome sequencing, due to its greater discriminatory power, will eventually become routine for traceback investigations.
bibliographic citation: Pettengill et al. (2014) The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica. PeerJ 2:e340 https://doi.org/10.7717/peerj.340
date submitted: 2014-01-03
date accepted: 2014-03-21
issued: 2014-04-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Pettengill
  given name: James B.
author list: Agent
  family name: Timme
  given name: Ruth E.
author list: Agent
  family name: Barrangou
  given name: Rodolphe
author list: Agent
  family name: Toro
  given name: Magaly
author list: Agent
  family name: Allard
  given name: Marc W.
author list: Agent
  family name: Strain
  given name: Errol
author list: Agent
  family name: Musser
  given name: Steven M.
author list: Agent
  family name: Brown
  given name: Eric W.
doi: 10.7717/peerj.340
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-17
copyright: © 2014 Pettengill et al.
attribution name: Pettengill et al.

Diet and kwashiorkor: a prospective study from rural DR Congo
type: item
type: AcademicArticle
description: The etiology of kwashiorkor remains enigmatic and longitudinal studies examining potential causes of kwashiorkor are scarce. Using historical, longitudinal study data from the rural area of Bwamanda, Democratic Republic of Congo, we investigated the potential causal association between diet and the development of kwashiorkor in 5 657 preschool children followed 3-monthly during 15 months. We compared dietary risk factors for kwashiorkor with those of marasmus. Kwashiorkor was diagnosed as pitting oedema of the ankles; marasmus as abnormal visibility of skeletal structures and palpable wasting of the gluteus muscle. A 24-h recall was administered 3-monthly to record the consumption of the 41 locally most frequent food items. We specified Hanley–Miettinen smooth-in-time risk models containing potential causal factors, including food items, special meals prepared for the child, breastfeeding, disease status, nutritional status, birth rank, age, season and number of meals. Bayesian Information Criteria identified the most plausible causal model of why some children developed kwashiorkor. In a descriptive analysis of the diet at the last dietary assessment prior to development of kwashiorkor, the diet of children who developed kwashiorkor was characterized by low consumption of sweet potatoes, papaya and “other vegetables” [0.0% , 2.3% (95% CI [0.4, 12.1]) and 2.3% (95% CI [0.4, 12.1])] in comparison with children who did not develop kwashiorkor [6.8% (95% CI [6.4, 7.2]), 15.5% (95% CI [15, 16.1]) and 15.1% (95% CI [14.6, 15.7])] or children who developed marasmus [4.5% (95% CI [2.6, 7.5]) 11.8% (95% CI [8.5, 16.0]) and 17.6% (95% CI [13.7, 22.5])]. Sweet potatoes and papayas have high β-carotene content and so may some of “the other vegetables”. We found that a risk model containing an age function, length/height-for age Z-score, consumption of sweet potatoes, papaya or other vegetables, duration of this consumption and its interaction term, was the most plausible model…
format: application/pdf
format: text/html
creator: Hallgeir Kismul
creator: Jan Van den Broeck
creator: Torleif Markussen Lunde
subject: Epidemiology
subject: Global Health
subject: Nutrition
description: doi:10.7717/peerj.350
publisher: PeerJ Inc.
rights: © 2014 Kismul et al.
abstract: The etiology of kwashiorkor remains enigmatic and longitudinal studies examining potential causes of kwashiorkor are scarce. Using historical, longitudinal study data from the rural area of Bwamanda, Democratic Republic of Congo, we investigated the potential causal association between diet and the development of kwashiorkor in 5 657 preschool children followed 3-monthly during 15 months. We compared dietary risk factors for kwashiorkor with those of marasmus. Kwashiorkor was diagnosed as pitting oedema of the ankles; marasmus as abnormal visibility of skeletal structures and palpable wasting of the gluteus muscle. A 24-h recall was administered 3-monthly to record the consumption of the 41 locally most frequent food items. We specified Hanley–Miettinen smooth-in-time risk models containing potential causal factors, including food items, special meals prepared for the child, breastfeeding, disease status, nutritional status, birth rank, age, season and number of meals. Bayesian Information Criteria identified the most plausible causal model of why some children developed kwashiorkor. In a descriptive analysis of the diet at the last dietary assessment prior to development of kwashiorkor, the diet of children who developed kwashiorkor was characterized by low consumption of sweet potatoes, papaya and “other vegetables” [0.0% , 2.3% (95% CI [0.4, 12.1]) and 2.3% (95% CI [0.4, 12.1])] in comparison with children who did not develop kwashiorkor [6.8% (95% CI [6.4, 7.2]), 15.5% (95% CI [15, 16.1]) and 15.1% (95% CI [14.6, 15.7])] or children who developed marasmus [4.5% (95% CI [2.6, 7.5]) 11.8% (95% CI [8.5, 16.0]) and 17.6% (95% CI [13.7, 22.5])]. Sweet potatoes and papayas have high β-carotene content and so may some of “the other vegetables”. We found that a risk model containing an age function, length/height-for age Z-score, consumption of sweet potatoes, papaya or other vegetables, duration of this consumption and its interaction term, was the most plausible model…
bibliographic citation: Kismul et al. (2014) Diet and kwashiorkor: a prospective study from rural DR Congo. PeerJ 2:e350 https://doi.org/10.7717/peerj.350
date submitted: 2013-11-22
date accepted: 2014-03-27
issued: 2014-04-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Kismul
  given name: Hallgeir
author list: Agent
  family name: Van den Broeck
  given name: Jan
author list: Agent
  family name: Lunde
  given name: Torleif Markussen
doi: 10.7717/peerj.350
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-15
copyright: © 2014 Kismul et al.
attribution name: Kismul et al.

Re-examining the relationship between invasive lionfish and native grouper in the Caribbean
type: item
type: AcademicArticle
description: Biotic resistance is the idea that native species negatively affect the invasion success of introduced species, but whether this can occur at large spatial scales is poorly understood. Here we re-evaluated the hypothesis that native large-bodied grouper and other predators are controlling the abundance of exotic lionfish (Pterois volitans/miles) on Caribbean coral reefs. We assessed the relationship between the biomass of lionfish and native predators at 71 reefs in three biogeographic regions while taking into consideration several cofactors that may affect fish abundance, including among others, proxies for fishing pressure and habitat structural complexity. Our results indicate that the abundance of lionfish, large-bodied grouper and other predators were not negatively related. Lionfish abundance was instead controlled by several physical site characteristics, and possibly by culling. Taken together, our results suggest that managers cannot rely on current native grouper populations to control the lionfish invasion.
format: application/pdf
format: text/html
creator: Abel Valdivia
creator: John F. Bruno
creator: Courtney E. Cox
creator: Serena Hackerott
creator: Stephanie J. Green
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
description: doi:10.7717/peerj.348
publisher: PeerJ Inc.
rights: © 2014 Valdivia et al.
abstract: Biotic resistance is the idea that native species negatively affect the invasion success of introduced species, but whether this can occur at large spatial scales is poorly understood. Here we re-evaluated the hypothesis that native large-bodied grouper and other predators are controlling the abundance of exotic lionfish (Pterois volitans/miles) on Caribbean coral reefs. We assessed the relationship between the biomass of lionfish and native predators at 71 reefs in three biogeographic regions while taking into consideration several cofactors that may affect fish abundance, including among others, proxies for fishing pressure and habitat structural complexity. Our results indicate that the abundance of lionfish, large-bodied grouper and other predators were not negatively related. Lionfish abundance was instead controlled by several physical site characteristics, and possibly by culling. Taken together, our results suggest that managers cannot rely on current native grouper populations to control the lionfish invasion.
bibliographic citation: Valdivia et al. (2014) Re-examining the relationship between invasive lionfish and native grouper in the Caribbean. PeerJ 2:e348 https://doi.org/10.7717/peerj.348
date submitted: 2014-02-03
date accepted: 2014-03-25
issued: 2014-04-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valdivia
  given name: Abel
author list: Agent
  family name: Bruno
  given name: John F.
author list: Agent
  family name: Cox
  given name: Courtney E.
author list: Agent
  family name: Hackerott
  given name: Serena
author list: Agent
  family name: Green
  given name: Stephanie J.
doi: 10.7717/peerj.348
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-15
copyright: © 2014 Valdivia et al.
attribution name: Valdivia et al.

There and back again: putting the vectorial movement planning hypothesis to a critical test
type: item
type: AcademicArticle
description: Based on psychophysical evidence about how learning of visuomotor transformation generalizes, it has been suggested that movements are planned on the basis of movement direction and magnitude, i.e., the vector connecting movement origin and targets. This notion is also known under the term “vectorial planning hypothesis”. Previous psychophysical studies, however, have included separate areas of the workspace for training movements and testing the learning. This study eliminates this confounding factor by investigating the transfer of learning from forward to backward movements in a center-out-and-back task, in which the workspace for both movements is completely identical. Visual feedback allowed for learning only during movements towards the target (forward movements) and not while moving back to the origin (backward movements). When subjects learned the visuomotor rotation in forward movements, initial directional errors in backward movements also decreased to some degree. This learning effect in backward movements occurred predominantly when backward movements featured the same movement directions as the ones trained in forward movements (i.e., when opposite targets were presented). This suggests that learning was transferred in a direction specific way, supporting the notion that movement direction is the most prominent parameter used for motor planning.
format: application/pdf
format: text/html
creator: Eva-Maria Kobak
creator: Simone Cardoso de Oliveira
subject: Neuroscience
description: doi:10.7717/peerj.342
publisher: PeerJ Inc.
rights: © 2014 Kobak and Cardoso de Oliveira
abstract: Based on psychophysical evidence about how learning of visuomotor transformation generalizes, it has been suggested that movements are planned on the basis of movement direction and magnitude, i.e., the vector connecting movement origin and targets. This notion is also known under the term “vectorial planning hypothesis”. Previous psychophysical studies, however, have included separate areas of the workspace for training movements and testing the learning. This study eliminates this confounding factor by investigating the transfer of learning from forward to backward movements in a center-out-and-back task, in which the workspace for both movements is completely identical. Visual feedback allowed for learning only during movements towards the target (forward movements) and not while moving back to the origin (backward movements). When subjects learned the visuomotor rotation in forward movements, initial directional errors in backward movements also decreased to some degree. This learning effect in backward movements occurred predominantly when backward movements featured the same movement directions as the ones trained in forward movements (i.e., when opposite targets were presented). This suggests that learning was transferred in a direction specific way, supporting the notion that movement direction is the most prominent parameter used for motor planning.
bibliographic citation: Kobak et al. (2014) There and back again: putting the vectorial movement planning hypothesis to a critical test. PeerJ 2:e342 https://doi.org/10.7717/peerj.342
date submitted: 2013-11-22
date accepted: 2014-03-24
issued: 2014-04-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Kobak
  given name: Eva-Maria
author list: Agent
  family name: Cardoso de Oliveira
  given name: Simone
doi: 10.7717/peerj.342
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-15
copyright: © 2014 Kobak and Cardoso de Oliveira
attribution name: Kobak and Cardoso de Oliveira

Castration modulates singing patterns and electrophysiological properties of RA projection neurons in adult male zebra finches
type: item
type: AcademicArticle
description: Castration can change levels of plasma testosterone. Androgens such as testosterone play an important role in stabilizing birdsong. The robust nucleus of the arcopallium (RA) is an important premotor nucleus critical for singing. In this study, we investigated the effect of castration on singing patterns and electrophysiological properties of projection neurons (PNs) in the RA of adult male zebra finches. Adult male zebra finches were castrated and the changes in bird song assessed. We also recorded the electrophysiological changes from RA PNs using patch clamp recording. We found that the plasma levels of testosterone were significantly decreased, song syllable’s entropy was increased and the similarity of motif was decreased after castration. Spontaneous and evoked firing rates, membrane time constants, and membrane capacitance of RA PNs in the castration group were lower than those of the control and the sham groups. Afterhyperpolarization AHP time to peak of spontaneous action potential (AP) was prolonged after castration.These findings suggest that castration decreases song stereotypy and excitability of RA PNs in male zebra finches.
format: application/pdf
format: text/html
creator: Songhua Wang
creator: Congshu Liao
creator: Fengling Li
creator: Shaoyi Liu
creator: Wei Meng
creator: Dongfeng Li
subject: Animal Behavior
subject: Neuroscience
description: doi:10.7717/peerj.352
publisher: PeerJ Inc.
rights: © 2014 Wang et al.
abstract: Castration can change levels of plasma testosterone. Androgens such as testosterone play an important role in stabilizing birdsong. The robust nucleus of the arcopallium (RA) is an important premotor nucleus critical for singing. In this study, we investigated the effect of castration on singing patterns and electrophysiological properties of projection neurons (PNs) in the RA of adult male zebra finches. Adult male zebra finches were castrated and the changes in bird song assessed. We also recorded the electrophysiological changes from RA PNs using patch clamp recording. We found that the plasma levels of testosterone were significantly decreased, song syllable’s entropy was increased and the similarity of motif was decreased after castration. Spontaneous and evoked firing rates, membrane time constants, and membrane capacitance of RA PNs in the castration group were lower than those of the control and the sham groups. Afterhyperpolarization AHP time to peak of spontaneous action potential (AP) was prolonged after castration.These findings suggest that castration decreases song stereotypy and excitability of RA PNs in male zebra finches.
bibliographic citation: Wang et al. (2014) Castration modulates singing patterns and electrophysiological properties of RA projection neurons in adult male zebra finches. PeerJ 2:e352 https://doi.org/10.7717/peerj.352
date submitted: 2014-02-11
date accepted: 2014-03-28
issued: 2014-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Songhua
author list: Agent
  family name: Liao
  given name: Congshu
author list: Agent
  family name: Li
  given name: Fengling
author list: Agent
  family name: Liu
  given name: Shaoyi
author list: Agent
  family name: Meng
  given name: Wei
author list: Agent
  family name: Li
  given name: Dongfeng
doi: 10.7717/peerj.352
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-10
copyright: © 2014 Wang et al.
attribution name: Wang et al.

TMEM65 is a mitochondrial inner-membrane protein
type: item
type: AcademicArticle
description: It has been reported that the expression of TMEM65 is regulated by steroid receptor RNA activator (SRA). To date, however, the localization and function of TMEM65 remained unknown. We analyzed the intracellular localization of TMEM65. Immunoblot and immunostaining analysis revealed mitochondrial localization of TMEM65. Alkali extraction analysis and digitonin extraction test using isolated mitochondria revealed that TMEM65 is an integral membrane protein that localizes to the inner-membrane of mitochondria. Analysis using deletion mutants of TMEM65 suggested that the N-terminal region (1–20) of this protein is sufficient for mitochondrial targeting and that this mitochondrial targeting signal (MTS) is cleaved between the amino acid positions 35 and 64, which contain a putative recognition site of matrix processing protease (MPP). Together, these results suggest that TMEM65 is imported into the mitochondria, integrated into mitochondrial inner-membrane, and processed into its mature form by an MPP.
format: application/pdf
format: text/html
creator: Naotaka Nishimura
creator: Tomomi Gotoh
creator: Yuichi Oike
creator: Masato Yano
subject: Biochemistry
subject: Cell Biology
description: doi:10.7717/peerj.349
publisher: PeerJ Inc.
rights: © 2014 Nishimura et al.
abstract: It has been reported that the expression of TMEM65 is regulated by steroid receptor RNA activator (SRA). To date, however, the localization and function of TMEM65 remained unknown. We analyzed the intracellular localization of TMEM65. Immunoblot and immunostaining analysis revealed mitochondrial localization of TMEM65. Alkali extraction analysis and digitonin extraction test using isolated mitochondria revealed that TMEM65 is an integral membrane protein that localizes to the inner-membrane of mitochondria. Analysis using deletion mutants of TMEM65 suggested that the N-terminal region (1–20) of this protein is sufficient for mitochondrial targeting and that this mitochondrial targeting signal (MTS) is cleaved between the amino acid positions 35 and 64, which contain a putative recognition site of matrix processing protease (MPP). Together, these results suggest that TMEM65 is imported into the mitochondria, integrated into mitochondrial inner-membrane, and processed into its mature form by an MPP.
bibliographic citation: Nishimura et al. (2014) TMEM65 is a mitochondrial inner-membrane protein. PeerJ 2:e349 https://doi.org/10.7717/peerj.349
date submitted: 2014-02-25
date accepted: 2014-03-26
issued: 2014-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nishimura
  given name: Naotaka
author list: Agent
  family name: Gotoh
  given name: Tomomi
author list: Agent
  family name: Oike
  given name: Yuichi
author list: Agent
  family name: Yano
  given name: Masato
doi: 10.7717/peerj.349
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-10
copyright: © 2014 Nishimura et al.
attribution name: Nishimura et al.

Fluvial transport potential of shed and root-bearing dinosaur teeth from the late Jurassic Morrison Formation
type: item
type: AcademicArticle
description: Shed dinosaur teeth are commonly collected microvertebrate remains that have been used for interpretations of dinosaur feeding behaviors, paleoecology, and population studies. However, such interpretations may be biased by taphonomic processes such as fluvial sorting influenced by tooth shape: shed teeth, removed from the skull during life, and teeth possessing roots, removed from the skull after death. As such, teeth may behave differently in fluvial systems due to their differences in shape. In order to determine the influence of fluvial processes on the preservation and distribution of shed and root-bearing dinosaur teeth, the hydrodynamic behaviors of high-density urethane resin casts of shed and root-bearing Allosaurus and Camarasaurus teeth were experimentally tested for relative transport distances at increasing flow velocities in an artificial fluviatile environment. Results show that tooth cast specimens exhibited comparable patterns of transport at lower velocities, though the shed Camarasaurus teeth transported considerably farther in medium to higher flow velocities. Two-Way ANOVA tests indicate significant differences in the mean transport distances of tooth casts oriented perpendicular to flow (p < 0.05) with varying tooth morphologies and flow velocities. The differences exhibited in the transportability of shed and root-bearing teeth has important implications for taphonomic reconstructions, as well as future studies on dinosaur population dynamics, paleoecology, and feeding behaviors.
format: application/pdf
format: text/html
creator: Joseph E. Peterson
creator: Jason J. Coenen
creator: Christopher R. Noto
subject: Paleontology
description: doi:10.7717/peerj.347
publisher: PeerJ Inc.
rights: © 2014 Peterson et al.
abstract: Shed dinosaur teeth are commonly collected microvertebrate remains that have been used for interpretations of dinosaur feeding behaviors, paleoecology, and population studies. However, such interpretations may be biased by taphonomic processes such as fluvial sorting influenced by tooth shape: shed teeth, removed from the skull during life, and teeth possessing roots, removed from the skull after death. As such, teeth may behave differently in fluvial systems due to their differences in shape. In order to determine the influence of fluvial processes on the preservation and distribution of shed and root-bearing dinosaur teeth, the hydrodynamic behaviors of high-density urethane resin casts of shed and root-bearing Allosaurus and Camarasaurus teeth were experimentally tested for relative transport distances at increasing flow velocities in an artificial fluviatile environment. Results show that tooth cast specimens exhibited comparable patterns of transport at lower velocities, though the shed Camarasaurus teeth transported considerably farther in medium to higher flow velocities. Two-Way ANOVA tests indicate significant differences in the mean transport distances of tooth casts oriented perpendicular to flow (p < 0.05) with varying tooth morphologies and flow velocities. The differences exhibited in the transportability of shed and root-bearing teeth has important implications for taphonomic reconstructions, as well as future studies on dinosaur population dynamics, paleoecology, and feeding behaviors.
bibliographic citation: Peterson et al. (2014) Fluvial transport potential of shed and root-bearing dinosaur teeth from the late Jurassic Morrison Formation. PeerJ 2:e347 https://doi.org/10.7717/peerj.347
date submitted: 2014-02-23
date accepted: 2014-03-25
issued: 2014-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peterson
  given name: Joseph E.
author list: Agent
  family name: Coenen
  given name: Jason J.
author list: Agent
  family name: Noto
  given name: Christopher R.
doi: 10.7717/peerj.347
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-10
copyright: © 2014 Peterson et al.
attribution name: Peterson et al.

Vertebrate blood cell volume increases with temperature: implications for aerobic activity
type: item
type: AcademicArticle
description: Aerobic activity levels increase with body temperature across vertebrates. Differences in these levels, from highly active to sedentary, are reflected in their ecology and behavior. Yet, the changes in the cardiovascular system that allow for greater oxygen supply at higher temperatures, and thus greater aerobic activity, remain unclear. Here we show that the total volume of red blood cells in the body increases exponentially with temperature across vertebrates, after controlling for effects of body size and taxonomy. These changes are accompanied by increases in relative heart mass, an indicator of aerobic activity. The results point to one way vertebrates may increase oxygen supply to meet the demands of greater activity at higher temperatures.
format: application/pdf
format: text/html
creator: James F. Gillooly
creator: Rosana Zenil-Ferguson
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.346
publisher: PeerJ Inc.
rights: © 2014 Gillooly and Zenil-Ferguson
abstract: Aerobic activity levels increase with body temperature across vertebrates. Differences in these levels, from highly active to sedentary, are reflected in their ecology and behavior. Yet, the changes in the cardiovascular system that allow for greater oxygen supply at higher temperatures, and thus greater aerobic activity, remain unclear. Here we show that the total volume of red blood cells in the body increases exponentially with temperature across vertebrates, after controlling for effects of body size and taxonomy. These changes are accompanied by increases in relative heart mass, an indicator of aerobic activity. The results point to one way vertebrates may increase oxygen supply to meet the demands of greater activity at higher temperatures.
bibliographic citation: Gillooly et al. (2014) Vertebrate blood cell volume increases with temperature: implications for aerobic activity. PeerJ 2:e346 https://doi.org/10.7717/peerj.346
date submitted: 2013-12-07
date accepted: 2014-03-25
issued: 2014-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Gillooly
  given name: James F.
author list: Agent
  family name: Zenil-Ferguson
  given name: Rosana
doi: 10.7717/peerj.346
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-10
copyright: © 2014 Gillooly and Zenil-Ferguson
attribution name: Gillooly and Zenil-Ferguson

Peruvians’ sleep duration: analysis of a population-based survey on adolescents and adults
type: item
type: AcademicArticle
description: Background. Sleep duration, either short or long, has been associated with diseases such as obesity, type-2 diabetes and cardiovascular diseases. Characterizing the prevalence and patterns of sleep duration at the population-level, especially in resource-constrained settings, will provide informative evidence on a potentially modifiable risk factor. The aim of this study was to explore the patterns of sleep duration in the Peruvian adult and adolescent population, together with its socio-demographic profile. Material and Methods. A total of 12,424 subjects, mean age 35.8 years (SD ±17.7), 50.6% males, were included in the analysis. This is a cross-sectional study, secondary analysis of the Use of Time National Survey conducted in 2010. We used weighted means and proportions to describe sleep duration according to socio-demographic variables (area and region; sex; age; education attainment; asset index; martial and job status). We used Poisson regressions, taking into account the multistage sampling design of the survey, to calculate crude and adjusted prevalence ratios (PR) and 95% confidence intervals (95% CI). Main outcomes were short- (<6 h) and long-sleep duration (≥ 9 h). Results. On average, Peruvians slept 7.7 h (95% CI [7.4–8.0]) on weekdays and 8.0 h (95% CI [7.8–8.1]) during weekends. The proportions of short- and long-sleep, during weekdays, were 4.3% (95% CI [2.9%–6.3%]) and 22.4% (95% CI [14.9%–32.1%]), respectively. Regarding urban and rural areas, a much higher proportion of short-sleep was observed in the former (92.0% vs. 8.0%); both for weekdays and weekends. On the multivariable analysis, compared to regular-sleepers (≥ 6 to <9 h), short-sleepers were twice more likely to be older and to have higher educational status, and 50% more likely to be currently employed. Similarly, relative to regular-sleep, long-sleepers were more likely to have a lower socioeconomic status as per educational attainment. Conclusions. In this nationally representative sa…
format: application/pdf
format: text/html
creator: Rodrigo M. Carrillo-Larco
creator: Antonio Bernabé-Ortiz
creator: J. Jaime Miranda
creator: Jorge Rey de Castro
subject: Epidemiology
subject: Global Health
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.345
publisher: PeerJ Inc.
rights: © 2014 Carrillo-Larco et al.
abstract: Background. Sleep duration, either short or long, has been associated with diseases such as obesity, type-2 diabetes and cardiovascular diseases. Characterizing the prevalence and patterns of sleep duration at the population-level, especially in resource-constrained settings, will provide informative evidence on a potentially modifiable risk factor. The aim of this study was to explore the patterns of sleep duration in the Peruvian adult and adolescent population, together with its socio-demographic profile. Material and Methods. A total of 12,424 subjects, mean age 35.8 years (SD ±17.7), 50.6% males, were included in the analysis. This is a cross-sectional study, secondary analysis of the Use of Time National Survey conducted in 2010. We used weighted means and proportions to describe sleep duration according to socio-demographic variables (area and region; sex; age; education attainment; asset index; martial and job status). We used Poisson regressions, taking into account the multistage sampling design of the survey, to calculate crude and adjusted prevalence ratios (PR) and 95% confidence intervals (95% CI). Main outcomes were short- (<6 h) and long-sleep duration (≥ 9 h). Results. On average, Peruvians slept 7.7 h (95% CI [7.4–8.0]) on weekdays and 8.0 h (95% CI [7.8–8.1]) during weekends. The proportions of short- and long-sleep, during weekdays, were 4.3% (95% CI [2.9%–6.3%]) and 22.4% (95% CI [14.9%–32.1%]), respectively. Regarding urban and rural areas, a much higher proportion of short-sleep was observed in the former (92.0% vs. 8.0%); both for weekdays and weekends. On the multivariable analysis, compared to regular-sleepers (≥ 6 to <9 h), short-sleepers were twice more likely to be older and to have higher educational status, and 50% more likely to be currently employed. Similarly, relative to regular-sleep, long-sleepers were more likely to have a lower socioeconomic status as per educational attainment. Conclusions. In this nationally representative sa…
bibliographic citation: Carrillo-Larco et al. (2014) Peruvians’ sleep duration: analysis of a population-based survey on adolescents and adults. PeerJ 2:e345 https://doi.org/10.7717/peerj.345
date submitted: 2013-12-20
date accepted: 2014-03-25
issued: 2014-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Carrillo-Larco
  given name: Rodrigo M.
author list: Agent
  family name: Bernabé-Ortiz
  given name: Antonio
author list: Agent
  family name: Miranda
  given name: J. Jaime
author list: Agent
  family name: Rey de Castro
  given name: Jorge
doi: 10.7717/peerj.345
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-10
copyright: © 2014 Carrillo-Larco et al.
attribution name: Carrillo-Larco et al.

Red deer synchronise their activity with close neighbours
type: item
type: AcademicArticle
description: Models of collective animal behaviour frequently make assumptions about the effects of neighbours on the behaviour of focal individuals, but these assumptions are rarely tested. One such set of assumptions is that the switch between active and inactive behaviour seen in herding animals is influenced by the activity of close neighbours, where neighbouring animals show a higher degree of behavioural synchrony than would be expected by chance. We tested this assumption by observing the simultaneous behaviour of paired individuals within a herd of red deer Cervus elaphus. Focal individuals were more synchronised with their two closest neighbours than with the third closest or randomly selected individuals from the herd. Our results suggest that the behaviour of individual deer is influenced by immediate neighbours. Even if we assume that there are no social relationships between individuals, this suggests that the assumptions made in models about the influence of neighbours may be appropriate.
format: application/pdf
format: text/html
creator: Sean A. Rands
creator: Hayley Muir
creator: Naomi L. Terry
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.344
publisher: PeerJ Inc.
rights: © 2014 Rands et al.
abstract: Models of collective animal behaviour frequently make assumptions about the effects of neighbours on the behaviour of focal individuals, but these assumptions are rarely tested. One such set of assumptions is that the switch between active and inactive behaviour seen in herding animals is influenced by the activity of close neighbours, where neighbouring animals show a higher degree of behavioural synchrony than would be expected by chance. We tested this assumption by observing the simultaneous behaviour of paired individuals within a herd of red deer Cervus elaphus. Focal individuals were more synchronised with their two closest neighbours than with the third closest or randomly selected individuals from the herd. Our results suggest that the behaviour of individual deer is influenced by immediate neighbours. Even if we assume that there are no social relationships between individuals, this suggests that the assumptions made in models about the influence of neighbours may be appropriate.
bibliographic citation: Rands et al. (2014) Red deer synchronise their activity with close neighbours. PeerJ 2:e344 https://doi.org/10.7717/peerj.344
date submitted: 2013-12-20
date accepted: 2014-03-25
issued: 2014-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Rands
  given name: Sean A.
author list: Agent
  family name: Muir
  given name: Hayley
author list: Agent
  family name: Terry
  given name: Naomi L.
doi: 10.7717/peerj.344
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-10
copyright: © 2014 Rands et al.
attribution name: Rands et al.

Automated electronic medical record sepsis detection in the emergency department
type: item
type: AcademicArticle
description: Background. While often first treated in the emergency department (ED), identification of sepsis is difficult. Electronic medical record (EMR) clinical decision tools offer a novel strategy for identifying patients with sepsis. The objective of this study was to test the accuracy of an EMR-based, automated sepsis identification system. Methods. We tested an EMR-based sepsis identification tool at a major academic, urban ED with 64,000 annual visits. The EMR system collected vital sign and laboratory test information on all ED patients, triggering a “sepsis alert” for those with ≥2 SIRS (systemic inflammatory response syndrome) criteria (fever, tachycardia, tachypnea, leukocytosis) plus ≥1 major organ dysfunction (SBP ≤ 90 mm Hg, lactic acid ≥2.0 mg/dL). We confirmed the presence of sepsis through manual review of physician, nursing, and laboratory records. We also reviewed a random selection of ED cases that did not trigger a sepsis alert. We evaluated the diagnostic accuracy of the sepsis identification tool. Results. From January 1 through March 31, 2012, there were 795 automated sepsis alerts. We randomly selected 300 cases without a sepsis alert from the same period. The true prevalence of sepsis was 355/795 (44.7%) among alerts and 0/300 (0%) among non-alerts. The positive predictive value of the sepsis alert was 44.7% (95% CI [41.2–48.2%]). Pneumonia and respiratory infections (38%) and urinary tract infection (32.7%) were the most common infections among the 355 patients with true sepsis (true positives). Among false-positive sepsis alerts, the most common medical conditions were gastrointestinal (26.1%), traumatic (25.7%), and cardiovascular (20.0%) conditions. Rates of hospital admission were: true-positive sepsis alert 91.0%, false-positive alert 83.0%, no sepsis alert 5.7%. Conclusions. This ED EMR-based automated sepsis identification system was able to detect cases with sepsis. Automated EMR-based detection may provide a viable strategy for identifying …
format: application/pdf
format: text/html
creator: Su Q. Nguyen
creator: Edwin Mwakalindile
creator: James S. Booth
creator: Vicki Hogan
creator: Jordan Morgan
creator: Charles T. Prickett
creator: John P. Donnelly
creator: Henry E. Wang
subject: Emergency and Critical Care
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.343
publisher: PeerJ Inc.
rights: © 2014 Nguyen et al.
abstract: Background. While often first treated in the emergency department (ED), identification of sepsis is difficult. Electronic medical record (EMR) clinical decision tools offer a novel strategy for identifying patients with sepsis. The objective of this study was to test the accuracy of an EMR-based, automated sepsis identification system. Methods. We tested an EMR-based sepsis identification tool at a major academic, urban ED with 64,000 annual visits. The EMR system collected vital sign and laboratory test information on all ED patients, triggering a “sepsis alert” for those with ≥2 SIRS (systemic inflammatory response syndrome) criteria (fever, tachycardia, tachypnea, leukocytosis) plus ≥1 major organ dysfunction (SBP ≤ 90 mm Hg, lactic acid ≥2.0 mg/dL). We confirmed the presence of sepsis through manual review of physician, nursing, and laboratory records. We also reviewed a random selection of ED cases that did not trigger a sepsis alert. We evaluated the diagnostic accuracy of the sepsis identification tool. Results. From January 1 through March 31, 2012, there were 795 automated sepsis alerts. We randomly selected 300 cases without a sepsis alert from the same period. The true prevalence of sepsis was 355/795 (44.7%) among alerts and 0/300 (0%) among non-alerts. The positive predictive value of the sepsis alert was 44.7% (95% CI [41.2–48.2%]). Pneumonia and respiratory infections (38%) and urinary tract infection (32.7%) were the most common infections among the 355 patients with true sepsis (true positives). Among false-positive sepsis alerts, the most common medical conditions were gastrointestinal (26.1%), traumatic (25.7%), and cardiovascular (20.0%) conditions. Rates of hospital admission were: true-positive sepsis alert 91.0%, false-positive alert 83.0%, no sepsis alert 5.7%. Conclusions. This ED EMR-based automated sepsis identification system was able to detect cases with sepsis. Automated EMR-based detection may provide a viable strategy for identifying …
bibliographic citation: Nguyen et al. (2014) Automated electronic medical record sepsis detection in the emergency department. PeerJ 2:e343 https://doi.org/10.7717/peerj.343
date submitted: 2013-10-31
date accepted: 2014-03-25
issued: 2014-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Nguyen
  given name: Su Q.
author list: Agent
  family name: Mwakalindile
  given name: Edwin
author list: Agent
  family name: Booth
  given name: James S.
author list: Agent
  family name: Hogan
  given name: Vicki
author list: Agent
  family name: Morgan
  given name: Jordan
author list: Agent
  family name: Prickett
  given name: Charles T.
author list: Agent
  family name: Donnelly
  given name: John P.
author list: Agent
  family name: Wang
  given name: Henry E.
doi: 10.7717/peerj.343
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-10
copyright: © 2014 Nguyen et al.
attribution name: Nguyen et al.

The challenge of evaluating pain and a pre-incisional local anesthetic block
type: item
type: AcademicArticle
description: Background. Our objective was to test the effectiveness of a local anesthetic line block administered before surgery in reducing postoperative pain scores in dogs undergoing ovariohysterectomy (OVHX). Methods. This study is a prospective, randomized, blinded, clinical trial involving 59 healthy female dogs. An algometric pressure-measuring device was used to determine nociceptive threshold, and compared to three subjective pain scales. Group L/B received a line block of lidocaine (4 mg/kg) and bupivacaine (1 mg/kg) subcutaneously in the area of the incision site and saline subcutaneously as premedication; group L/BM (positive control) received a similar block and morphine (0.5 mg/kg) subcutaneously for premedication; and group SS (negative control) received a saline line block and saline premedication. Criteria for rescue analgesia were defined before the study. Dogs were assessed prior to surgery, at extubation (time 0) and at 2, 4, 6, 8 and 24 h post-recovery. The data were analyzed with one-way ANOVA, and a Split Plot Repeated Measures ANOVA with one grouping factor and one repeat factor (time). P < 0.05 was considered statistically significant. Results. Approximately 33% of dogs required rescue analgesia at some point during the study, with no significant difference between groups. There was no significant difference between treatment groups with any assessment method. Conclusions. As there were no statistically significant differences between positive and negative controls, the outcome of this technique cannot be proven.
format: application/pdf
format: text/html
creator: Carolyn M. McKune
creator: Peter J. Pascoe
creator: B. Duncan X. Lascelles
creator: Philip H. Kass
subject: Anesthesiology and Pain Management
subject: Surgery and Surgical Specialties
subject: Veterinary Medicine
description: doi:10.7717/peerj.341
publisher: PeerJ Inc.
rights: © 2014 McKune et al.
abstract: Background. Our objective was to test the effectiveness of a local anesthetic line block administered before surgery in reducing postoperative pain scores in dogs undergoing ovariohysterectomy (OVHX). Methods. This study is a prospective, randomized, blinded, clinical trial involving 59 healthy female dogs. An algometric pressure-measuring device was used to determine nociceptive threshold, and compared to three subjective pain scales. Group L/B received a line block of lidocaine (4 mg/kg) and bupivacaine (1 mg/kg) subcutaneously in the area of the incision site and saline subcutaneously as premedication; group L/BM (positive control) received a similar block and morphine (0.5 mg/kg) subcutaneously for premedication; and group SS (negative control) received a saline line block and saline premedication. Criteria for rescue analgesia were defined before the study. Dogs were assessed prior to surgery, at extubation (time 0) and at 2, 4, 6, 8 and 24 h post-recovery. The data were analyzed with one-way ANOVA, and a Split Plot Repeated Measures ANOVA with one grouping factor and one repeat factor (time). P < 0.05 was considered statistically significant. Results. Approximately 33% of dogs required rescue analgesia at some point during the study, with no significant difference between groups. There was no significant difference between treatment groups with any assessment method. Conclusions. As there were no statistically significant differences between positive and negative controls, the outcome of this technique cannot be proven.
bibliographic citation: McKune et al. (2014) The challenge of evaluating pain and a pre-incisional local anesthetic block. PeerJ 2:e341 https://doi.org/10.7717/peerj.341
date submitted: 2013-12-31
date accepted: 2014-03-23
issued: 2014-04-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: McKune
  given name: Carolyn M.
author list: Agent
  family name: Pascoe
  given name: Peter J.
author list: Agent
  family name: Lascelles
  given name: B. Duncan X.
author list: Agent
  family name: Kass
  given name: Philip H.
doi: 10.7717/peerj.341
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-10
copyright: © 2014 McKune et al.
attribution name: McKune et al.

In situ effects of simulated overfishing and eutrophication on settlement of benthic coral reef invertebrates in the Central Red Sea
type: item
type: AcademicArticle
description: In the Central Red Sea, healthy coral reefs meet intense coastal development, but data on the effects of related stressors for reef functioning are lacking. This in situ study therefore investigated the independent and combined effects of simulated overfishing through predator/grazer exclusion and simulated eutrophication through fertilizer addition on settlement of reef associated invertebrates on light-exposed and -shaded tiles over 4 months. At the end of the study period invertebrates had almost exclusively colonized shaded tiles. Algae were superior settling competitors on light-exposed tiles. On the shaded tiles, simulated overfishing prevented settlement of hard corals, but significantly increased settlement of polychaetes, while simulated eutrophication only significantly decreased hard coral settlement relative to controls. The combined treatment significantly increased settlement of bryozoans and bivalves compared to controls and individual manipulations, but significantly decreased polychaetes compared to simulated overfishing. These results suggest settlement of polychaetes and hard corals as potential bioindicators for overfishing and eutrophication, respectively, and settlement of bivalves and bryozoans for a combination of both. Therefore, if the investigated stressors are not controlled, phase shifts from dominance by hard corals to that by other invertebrates may occur at shaded reef locations in the Central Red Sea.
format: application/pdf
format: text/html
creator: Christian Jessen
creator: Christian R. Voolstra
creator: Christian Wild
subject: Biosphere Interactions
subject: Ecology
subject: Marine Biology
subject: Science and Medical Education
subject: Zoology
description: doi:10.7717/peerj.339
publisher: PeerJ Inc.
rights: © 2014 Jessen et al.
abstract: In the Central Red Sea, healthy coral reefs meet intense coastal development, but data on the effects of related stressors for reef functioning are lacking. This in situ study therefore investigated the independent and combined effects of simulated overfishing through predator/grazer exclusion and simulated eutrophication through fertilizer addition on settlement of reef associated invertebrates on light-exposed and -shaded tiles over 4 months. At the end of the study period invertebrates had almost exclusively colonized shaded tiles. Algae were superior settling competitors on light-exposed tiles. On the shaded tiles, simulated overfishing prevented settlement of hard corals, but significantly increased settlement of polychaetes, while simulated eutrophication only significantly decreased hard coral settlement relative to controls. The combined treatment significantly increased settlement of bryozoans and bivalves compared to controls and individual manipulations, but significantly decreased polychaetes compared to simulated overfishing. These results suggest settlement of polychaetes and hard corals as potential bioindicators for overfishing and eutrophication, respectively, and settlement of bivalves and bryozoans for a combination of both. Therefore, if the investigated stressors are not controlled, phase shifts from dominance by hard corals to that by other invertebrates may occur at shaded reef locations in the Central Red Sea.
bibliographic citation: Jessen et al. (2014) In situ effects of simulated overfishing and eutrophication on settlement of benthic coral reef invertebrates in the Central Red Sea. PeerJ 2:e339 https://doi.org/10.7717/peerj.339
date submitted: 2014-02-02
date accepted: 2014-03-21
issued: 2014-04-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jessen
  given name: Christian
author list: Agent
  family name: Voolstra
  given name: Christian R.
author list: Agent
  family name: Wild
  given name: Christian
doi: 10.7717/peerj.339
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-08
copyright: © 2014 Jessen et al.
attribution name: Jessen et al.

Evaluation of granular anaerobic ammonium oxidation process for the disposal of pre-treated swine manure
type: item
type: AcademicArticle
description: With rising environmental concerns on potable water safety and eutrophication, increased media attention and tighter environmental regulations, managing animal waste in an environmentally responsible and economically feasible way can be a challenge. In this study, the possibility of using granular anammox process for ammonia removal from swine waste treatment water was investigated. A rapid decrease of NO2−–N and NH4+–N was observed during incubation with wastewater from an activated sludge deodorization reactor and anaerobic digestion-partial oxidation treatment process treating swine manure and its corresponding control artificial wastewaters. Ammonium removal dropped from 98.0 ± 0.6% to 66.9 ± 2.7% and nearly absent when the organic load in the feeding increased from 232 mg COD/L to 1160 mg COD/L and 2320 mg COD/L. The presence of organic carbon had limited effect on nitrite and total nitrogen removal. At a COD to N ratio of 0.9, COD inhibitory organic load threshold concentration was 727 mg COD/L. Mass balance indicated that denitrifiers played an important role in nitrite, nitrate and organic carbon removal. These results demonstrated that anammox system had the potential to effectively treat swine manure that can achieve high nitrogen standards at reduced costs.
format: application/pdf
format: text/html
creator: Shou-Qing Ni
creator: Ning Yang
subject: Biotechnology
subject: Environmental Contamination and Remediation
subject: Environmental Sciences
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.336
publisher: PeerJ Inc.
rights: © 2014 Ni and Yang
abstract: With rising environmental concerns on potable water safety and eutrophication, increased media attention and tighter environmental regulations, managing animal waste in an environmentally responsible and economically feasible way can be a challenge. In this study, the possibility of using granular anammox process for ammonia removal from swine waste treatment water was investigated. A rapid decrease of NO2−–N and NH4+–N was observed during incubation with wastewater from an activated sludge deodorization reactor and anaerobic digestion-partial oxidation treatment process treating swine manure and its corresponding control artificial wastewaters. Ammonium removal dropped from 98.0 ± 0.6% to 66.9 ± 2.7% and nearly absent when the organic load in the feeding increased from 232 mg COD/L to 1160 mg COD/L and 2320 mg COD/L. The presence of organic carbon had limited effect on nitrite and total nitrogen removal. At a COD to N ratio of 0.9, COD inhibitory organic load threshold concentration was 727 mg COD/L. Mass balance indicated that denitrifiers played an important role in nitrite, nitrate and organic carbon removal. These results demonstrated that anammox system had the potential to effectively treat swine manure that can achieve high nitrogen standards at reduced costs.
bibliographic citation: Ni et al. (2014) Evaluation of granular anaerobic ammonium oxidation process for the disposal of pre-treated swine manure. PeerJ 2:e336 https://doi.org/10.7717/peerj.336
date submitted: 2013-12-31
date accepted: 2014-03-17
issued: 2014-04-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Ni
  given name: Shou-Qing
author list: Agent
  family name: Yang
  given name: Ning
doi: 10.7717/peerj.336
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-08
copyright: © 2014 Ni and Yang
attribution name: Ni and Yang

Comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus DNA in fluids and tissues
type: item
type: AcademicArticle
description: Testing for cytomegalovirus (CMV) DNA is increasingly being used for specimen types other than plasma or whole blood. However, few studies have investigated the performance of different nucleic acid extraction protocols in such specimens. In this study, CMV extraction using the Cell-free 1000 and Pathogen Complex 400 protocols on the QIAsymphony Sample Processing (SP) system were compared using bronchoalveolar lavage fluid (BAL), tissue samples, and urine. The QIAsymphonyAssay Set-up (AS) system was used to assemble reactions using artus CMV PCR reagents and amplification was carried out on the Rotor-Gene Q. Samples from 93 patients previously tested for CMV DNA and negative samples spiked with CMV AD-169 were used to evaluate assay performance. The Pathogen Complex 400 protocol yielded the following results: BAL, sensitivity 100% (33/33), specificity 87% (20/23); tissue, sensitivity 100% (25/25), specificity 100% (20/20); urine, sensitivity 100% (21/21), specificity 100% (20/20). Cell-free 1000 extraction gave comparable results for BAL and tissue, however, for urine, the sensitivity was 86% (18/21) and specimen quantitation was inaccurate. Comparative studies of different extraction protocols and DNA detection methods in body fluids and tissues are needed, as assays optimized for blood or plasma will not necessarily perform well on other specimen types.
format: application/pdf
format: text/html
creator: Jesse J. Waggoner
creator: Benjamin A. Pinsky
subject: Infectious Diseases
subject: Pathology
description: doi:10.7717/peerj.334
publisher: PeerJ Inc.
rights: © 2014 Waggoner and Pinsky
abstract: Testing for cytomegalovirus (CMV) DNA is increasingly being used for specimen types other than plasma or whole blood. However, few studies have investigated the performance of different nucleic acid extraction protocols in such specimens. In this study, CMV extraction using the Cell-free 1000 and Pathogen Complex 400 protocols on the QIAsymphony Sample Processing (SP) system were compared using bronchoalveolar lavage fluid (BAL), tissue samples, and urine. The QIAsymphonyAssay Set-up (AS) system was used to assemble reactions using artus CMV PCR reagents and amplification was carried out on the Rotor-Gene Q. Samples from 93 patients previously tested for CMV DNA and negative samples spiked with CMV AD-169 were used to evaluate assay performance. The Pathogen Complex 400 protocol yielded the following results: BAL, sensitivity 100% (33/33), specificity 87% (20/23); tissue, sensitivity 100% (25/25), specificity 100% (20/20); urine, sensitivity 100% (21/21), specificity 100% (20/20). Cell-free 1000 extraction gave comparable results for BAL and tissue, however, for urine, the sensitivity was 86% (18/21) and specimen quantitation was inaccurate. Comparative studies of different extraction protocols and DNA detection methods in body fluids and tissues are needed, as assays optimized for blood or plasma will not necessarily perform well on other specimen types.
bibliographic citation: Waggoner et al. (2014) Comparison of automated nucleic acid extraction methods for the detection of cytomegalovirus DNA in fluids and tissues. PeerJ 2:e334 https://doi.org/10.7717/peerj.334
date submitted: 2013-12-27
date accepted: 2014-03-16
issued: 2014-04-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Waggoner
  given name: Jesse J.
author list: Agent
  family name: Pinsky
  given name: Benjamin A.
doi: 10.7717/peerj.334
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-08
copyright: © 2014 Waggoner and Pinsky
attribution name: Waggoner and Pinsky

A cross-ocean comparison of responses to settlement cues in reef-building corals
type: item
type: AcademicArticle
description: Caribbean coral reefs have deteriorated substantially over the past 30 years, which is broadly attributable to the effects of global climate change. In the same time, Indo-Pacific reefs maintain higher coral cover and typically recover rapidly after disturbances. This difference in reef resilience is largely due to much higher coral recruitment rates in the Pacific. We hypothesized that the lack of Caribbean recruitment might be explained by diminishing quality of settlement cues and/or impaired sensitivity of Caribbean coral larvae to those cues, relative to the Pacific. To evaluate this hypothesis, we assembled a collection of bulk samples of reef encrusting communities, mostly consisting of crustose coralline algae (CCA), from various reefs around the world and tested them as settlement cues for several coral species originating from different ocean provinces. Cue samples were meta-barcoded to evaluate their taxonomic diversity. We observed no systematic differences either in cue potency or in strength of larval responses depending on the ocean province, and no preference of coral larvae towards cues from the same ocean. Instead, we detected significant differences in cue preferences among coral species, even for corals originating from the same reef. We conclude that the region-wide disruption of the settlement process is unlikely to be the major cause of Caribbean reef loss. However, due to their high sensitivity to the effects of climate change, shifts in the composition of CCA-associated communities, combined with pronounced differences in cue preferences among coral species, could substantially influence future coral community structure.
format: application/pdf
format: text/html
creator: Sarah W. Davies
creator: Eli Meyer
creator: Sarah M. Guermond
creator: Mikhail V. Matz
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.333
publisher: PeerJ Inc.
rights: © 2014 Davies et al.
abstract: Caribbean coral reefs have deteriorated substantially over the past 30 years, which is broadly attributable to the effects of global climate change. In the same time, Indo-Pacific reefs maintain higher coral cover and typically recover rapidly after disturbances. This difference in reef resilience is largely due to much higher coral recruitment rates in the Pacific. We hypothesized that the lack of Caribbean recruitment might be explained by diminishing quality of settlement cues and/or impaired sensitivity of Caribbean coral larvae to those cues, relative to the Pacific. To evaluate this hypothesis, we assembled a collection of bulk samples of reef encrusting communities, mostly consisting of crustose coralline algae (CCA), from various reefs around the world and tested them as settlement cues for several coral species originating from different ocean provinces. Cue samples were meta-barcoded to evaluate their taxonomic diversity. We observed no systematic differences either in cue potency or in strength of larval responses depending on the ocean province, and no preference of coral larvae towards cues from the same ocean. Instead, we detected significant differences in cue preferences among coral species, even for corals originating from the same reef. We conclude that the region-wide disruption of the settlement process is unlikely to be the major cause of Caribbean reef loss. However, due to their high sensitivity to the effects of climate change, shifts in the composition of CCA-associated communities, combined with pronounced differences in cue preferences among coral species, could substantially influence future coral community structure.
bibliographic citation: Davies et al. (2014) A cross-ocean comparison of responses to settlement cues in reef-building corals. PeerJ 2:e333 https://doi.org/10.7717/peerj.333
date submitted: 2013-12-30
date accepted: 2014-03-15
issued: 2014-04-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Davies
  given name: Sarah W.
author list: Agent
  family name: Meyer
  given name: Eli
author list: Agent
  family name: Guermond
  given name: Sarah M.
author list: Agent
  family name: Matz
  given name: Mikhail V.
doi: 10.7717/peerj.333
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-08
copyright: © 2014 Davies et al.
attribution name: Davies et al.

Can resistant coral-Symbiodinium associations enable coral communities to survive climate change? A study of a site exposed to long-term hot water input
type: item
type: AcademicArticle
description: Climate change has led to a decline in the health of corals and coral reefs around the world. Studies have shown that, while some corals can cope with natural and anthropogenic stressors either through resistance mechanisms of coral hosts or through sustainable relationships with Symbiodinium clades or types, many coral species cannot. Here, we show that the corals present in a reef in southern Taiwan, and exposed to long-term elevated seawater temperatures due to the presence of a nuclear power plant outlet (NPP OL), are unique in terms of species and associated Symbiodinium types. At shallow depths (<3 m), eleven coral genera elsewhere in Kenting predominantly found with Symbiodinium types C1 and C3 (stress sensitive) were instead hosting Symbiodinium type D1a (stress tolerant) or a mixture of Symbiodinium type C1/C3/C21a/C15 and Symbiodinium type D1a. Of the 16 coral genera that dominate the local reefs, two that are apparently unable to associate with Symbiodinium type D1a are not present at NPP OL at depths of <3 m. Two other genera present at NPP OL and other locations host a specific type of Symbiodinium type C15. These data imply that coral assemblages may have the capacity to maintain their presence at the generic level against long-term disturbances such as elevated seawater temperatures by acclimatization through successful association with a stress-tolerant Symbiodinium over time. However, at the community level it comes at the cost of some coral genera being lost, suggesting that species unable to associate with a stress-tolerant Symbiodinium are likely to become extinct locally and unfavorable shifts in coral communities are likely to occur under the impact of climate change.
format: application/pdf
format: text/html
creator: Shashank Keshavmurthy
creator: Pei-Jie Meng
creator: Jih-Terng Wang
creator: Chao-Yang Kuo
creator: Sung-Yin Yang
creator: Chia-Min Hsu
creator: Chai-Hsia Gan
creator: Chang-Feng Dai
creator: Chaolun Allen Chen
subject: Climate Change Biology
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.327
publisher: PeerJ Inc.
rights: © 2014 Keshavmurthy et al.
abstract: Climate change has led to a decline in the health of corals and coral reefs around the world. Studies have shown that, while some corals can cope with natural and anthropogenic stressors either through resistance mechanisms of coral hosts or through sustainable relationships with Symbiodinium clades or types, many coral species cannot. Here, we show that the corals present in a reef in southern Taiwan, and exposed to long-term elevated seawater temperatures due to the presence of a nuclear power plant outlet (NPP OL), are unique in terms of species and associated Symbiodinium types. At shallow depths (<3 m), eleven coral genera elsewhere in Kenting predominantly found with Symbiodinium types C1 and C3 (stress sensitive) were instead hosting Symbiodinium type D1a (stress tolerant) or a mixture of Symbiodinium type C1/C3/C21a/C15 and Symbiodinium type D1a. Of the 16 coral genera that dominate the local reefs, two that are apparently unable to associate with Symbiodinium type D1a are not present at NPP OL at depths of <3 m. Two other genera present at NPP OL and other locations host a specific type of Symbiodinium type C15. These data imply that coral assemblages may have the capacity to maintain their presence at the generic level against long-term disturbances such as elevated seawater temperatures by acclimatization through successful association with a stress-tolerant Symbiodinium over time. However, at the community level it comes at the cost of some coral genera being lost, suggesting that species unable to associate with a stress-tolerant Symbiodinium are likely to become extinct locally and unfavorable shifts in coral communities are likely to occur under the impact of climate change.
bibliographic citation: Keshavmurthy et al. (2014) Can resistant coral-Symbiodinium associations enable coral communities to survive climate change? A study of a site exposed to long-term hot water input. PeerJ 2:e327 https://doi.org/10.7717/peerj.327
date submitted: 2013-08-30
date accepted: 2014-03-11
issued: 2014-04-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Keshavmurthy
  given name: Shashank
author list: Agent
  family name: Meng
  given name: Pei-Jie
author list: Agent
  family name: Wang
  given name: Jih-Terng
author list: Agent
  family name: Kuo
  given name: Chao-Yang
author list: Agent
  family name: Yang
  given name: Sung-Yin
author list: Agent
  family name: Hsu
  given name: Chia-Min
author list: Agent
  family name: Gan
  given name: Chai-Hsia
author list: Agent
  family name: Dai
  given name: Chang-Feng
author list: Agent
  family name: Chen
  given name: Chaolun Allen
doi: 10.7717/peerj.327
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-08
copyright: © 2014 Keshavmurthy et al.
attribution name: Keshavmurthy et al.

Bone microstructure and the evolution of growth patterns in Permo-Triassic therocephalians (Amniota, Therapsida) of South Africa
type: item
type: AcademicArticle
description: Therocephalians were a speciose clade of nonmammalian therapsids whose ecological diversity and survivorship of the end-Permian mass extinction offer the potential to investigate the evolution of growth patterns across the clade and their underlying influences on post-extinction body size reductions, or ‘Lilliput effects’. We present a phylogenetic survey of limb bone histology and growth patterns in therocephalians from the Middle Permian through Middle Triassic of the Karoo Basin, South Africa. Histologic sections were prepared from 80 limb bones representing 11 genera of therocephalians. Histologic indicators of skeletal growth, including cortical vascularity (%CV) and mean primary osteon diameters (POD), were evaluated in a phylogenetic framework and assessed for correlations with other biologically significant variables (e.g., size and robusticity). Changes in %CV and POD correlated strongly with evolutionary changes in body size (i.e., smaller-bodied descendants tended to have lower %CV than their larger-bodied ancestors across the tree). Bone wall thickness tended to be high in early therocephalians and lower in the gracile-limbed baurioids, but showed no general correlation with cross-sectional area or degree of vascularity (and, thus, growth). Clade-level patterns, however, deviated from previously studied within-lineage patterns. For example, Moschorhinus, one of few therapsid genera to have survived the extinction boundary, demonstrated higher %CV in the Triassic than in the Permian despite its smaller size in the extinction aftermath. Results support a synergistic model of size reductions for Triassic therocephalians, influenced both by within-lineage heterochronic shifts in survivor taxa (as reported in Moschorhinus and the dicynodont Lystrosaurus) and phylogenetically inferred survival of small-bodied taxa that had evolved short growth durations (e.g., baurioids). These findings mirror the multi-causal Lilliput patterns described in marine faunas, but …
format: application/pdf
format: text/html
creator: Adam K. Huttenlocker
creator: Jennifer Botha-Brink
subject: Evolutionary Studies
subject: Histology
subject: Paleontology
description: doi:10.7717/peerj.325
publisher: PeerJ Inc.
rights: © 2014 Huttenlocker and Botha-Brink
abstract: Therocephalians were a speciose clade of nonmammalian therapsids whose ecological diversity and survivorship of the end-Permian mass extinction offer the potential to investigate the evolution of growth patterns across the clade and their underlying influences on post-extinction body size reductions, or ‘Lilliput effects’. We present a phylogenetic survey of limb bone histology and growth patterns in therocephalians from the Middle Permian through Middle Triassic of the Karoo Basin, South Africa. Histologic sections were prepared from 80 limb bones representing 11 genera of therocephalians. Histologic indicators of skeletal growth, including cortical vascularity (%CV) and mean primary osteon diameters (POD), were evaluated in a phylogenetic framework and assessed for correlations with other biologically significant variables (e.g., size and robusticity). Changes in %CV and POD correlated strongly with evolutionary changes in body size (i.e., smaller-bodied descendants tended to have lower %CV than their larger-bodied ancestors across the tree). Bone wall thickness tended to be high in early therocephalians and lower in the gracile-limbed baurioids, but showed no general correlation with cross-sectional area or degree of vascularity (and, thus, growth). Clade-level patterns, however, deviated from previously studied within-lineage patterns. For example, Moschorhinus, one of few therapsid genera to have survived the extinction boundary, demonstrated higher %CV in the Triassic than in the Permian despite its smaller size in the extinction aftermath. Results support a synergistic model of size reductions for Triassic therocephalians, influenced both by within-lineage heterochronic shifts in survivor taxa (as reported in Moschorhinus and the dicynodont Lystrosaurus) and phylogenetically inferred survival of small-bodied taxa that had evolved short growth durations (e.g., baurioids). These findings mirror the multi-causal Lilliput patterns described in marine faunas, but …
bibliographic citation: Huttenlocker et al. (2014) Bone microstructure and the evolution of growth patterns in Permo-Triassic therocephalians (Amniota, Therapsida) of South Africa. PeerJ 2:e325 https://doi.org/10.7717/peerj.325
date submitted: 2013-11-22
date accepted: 2014-03-10
issued: 2014-04-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Huttenlocker
  given name: Adam K.
author list: Agent
  family name: Botha-Brink
  given name: Jennifer
doi: 10.7717/peerj.325
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-08
copyright: © 2014 Huttenlocker and Botha-Brink
attribution name: Huttenlocker and Botha-Brink

Honey bee sting pain index by body location
type: item
type: AcademicArticle
description: The Schmidt Sting Pain Index rates the painfulness of 78 Hymenoptera species, using the honey bee as a reference point. However, the question of how sting painfulness varies depending on body location remains unanswered. This study rated the painfulness of honey bee stings over 25 body locations in one subject (the author). Pain was rated on a 1–10 scale, relative to an internal standard, the forearm. In the single subject, pain ratings were consistent over three repetitions. Sting location was a significant predictor of the pain rating in a linear model (p < 0.0001, DF = 25, 94, F = 27.4). The three least painful locations were the skull, middle toe tip, and upper arm (all scoring a 2.3). The three most painful locations were the nostril, upper lip, and penis shaft (9.0, 8.7, and 7.3, respectively). This study provides an index of how the painfulness of a honey bee sting varies depending on body location.
format: application/pdf
format: text/html
creator: Michael L. Smith
subject: Anesthesiology and Pain Management
subject: Entomology
description: doi:10.7717/peerj.338
publisher: PeerJ Inc.
rights: © 2014 Smith
abstract: The Schmidt Sting Pain Index rates the painfulness of 78 Hymenoptera species, using the honey bee as a reference point. However, the question of how sting painfulness varies depending on body location remains unanswered. This study rated the painfulness of honey bee stings over 25 body locations in one subject (the author). Pain was rated on a 1–10 scale, relative to an internal standard, the forearm. In the single subject, pain ratings were consistent over three repetitions. Sting location was a significant predictor of the pain rating in a linear model (p < 0.0001, DF = 25, 94, F = 27.4). The three least painful locations were the skull, middle toe tip, and upper arm (all scoring a 2.3). The three most painful locations were the nostril, upper lip, and penis shaft (9.0, 8.7, and 7.3, respectively). This study provides an index of how the painfulness of a honey bee sting varies depending on body location.
bibliographic citation: Smith (2014) Honey bee sting pain index by body location. PeerJ 2:e338 https://doi.org/10.7717/peerj.338
date submitted: 2014-01-02
date accepted: 2014-03-18
issued: 2014-04-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Smith
  given name: Michael L.
doi: 10.7717/peerj.338
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-03
copyright: © 2014 Smith
attribution name: Smith

Sense of presence and anxiety during virtual social interactions between a human and virtual humans
type: item
type: AcademicArticle
description: Virtual reality exposure therapy (VRET) has been shown to be effective in treatment of anxiety disorders. Yet, there is lack of research on the extent to which interaction between the individual and virtual humans can be successfully implanted to increase levels of anxiety for therapeutic purposes. This proof-of-concept pilot study aimed at examining levels of the sense of presence and anxiety during exposure to virtual environments involving social interaction with virtual humans and using different virtual reality displays. A non-clinical sample of 38 participants was randomly assigned to either a head-mounted display (HMD) with motion tracker and sterescopic view condition or a one-screen projection-based virtual reality display condition. Participants in both conditions engaged in free speech dialogues with virtual humans controlled by research assistants. It was hypothesized that exposure to virtual social interactions will elicit moderate levels of sense of presence and anxiety in both groups. Further it was expected that participants in the HMD condition will report higher scores of sense of presence and anxiety than participants in the one-screen projection-based display condition. Results revealed that in both conditions virtual social interactions were associated with moderate levels of sense of presence and anxiety. Additionally, participants in the HMD condition reported significantly higher levels of presence than those in the one-screen projection-based display condition (p = .001). However, contrary to the expectations neither the average level of anxiety nor the highest level of anxiety during exposure to social virtual environments differed between the groups (p = .97 and p = .75, respectively). The findings suggest that virtual social interactions can be successfully applied in VRET to enhance sense of presence and anxiety. Furthermore, our results indicate that one-screen projection-based displays can successfully activate levels of anxiety in soc…
format: application/pdf
format: text/html
creator: Nexhmedin Morina
creator: Willem-Paul Brinkman
creator: Dwi Hartanto
creator: Paul M.G. Emmelkamp
subject: Human-Computer Interaction
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.337
publisher: PeerJ Inc.
rights: © 2014 Morina et al.
abstract: Virtual reality exposure therapy (VRET) has been shown to be effective in treatment of anxiety disorders. Yet, there is lack of research on the extent to which interaction between the individual and virtual humans can be successfully implanted to increase levels of anxiety for therapeutic purposes. This proof-of-concept pilot study aimed at examining levels of the sense of presence and anxiety during exposure to virtual environments involving social interaction with virtual humans and using different virtual reality displays. A non-clinical sample of 38 participants was randomly assigned to either a head-mounted display (HMD) with motion tracker and sterescopic view condition or a one-screen projection-based virtual reality display condition. Participants in both conditions engaged in free speech dialogues with virtual humans controlled by research assistants. It was hypothesized that exposure to virtual social interactions will elicit moderate levels of sense of presence and anxiety in both groups. Further it was expected that participants in the HMD condition will report higher scores of sense of presence and anxiety than participants in the one-screen projection-based display condition. Results revealed that in both conditions virtual social interactions were associated with moderate levels of sense of presence and anxiety. Additionally, participants in the HMD condition reported significantly higher levels of presence than those in the one-screen projection-based display condition (p = .001). However, contrary to the expectations neither the average level of anxiety nor the highest level of anxiety during exposure to social virtual environments differed between the groups (p = .97 and p = .75, respectively). The findings suggest that virtual social interactions can be successfully applied in VRET to enhance sense of presence and anxiety. Furthermore, our results indicate that one-screen projection-based displays can successfully activate levels of anxiety in soc…
bibliographic citation: Morina et al. (2014) Sense of presence and anxiety during virtual social interactions between a human and virtual humans. PeerJ 2:e337 https://doi.org/10.7717/peerj.337
date submitted: 2014-02-27
date accepted: 2014-03-17
issued: 2014-04-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Morina
  given name: Nexhmedin
author list: Agent
  family name: Brinkman
  given name: Willem-Paul
author list: Agent
  family name: Hartanto
  given name: Dwi
author list: Agent
  family name: Emmelkamp
  given name: Paul M.G.
doi: 10.7717/peerj.337
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-03
copyright: © 2014 Morina et al.
attribution name: Morina et al.

Leishmania amazonensis promastigotes in 3D Collagen I culture: an in vitro physiological environment for the study of extracellular matrix and host cell interactions
type: item
type: AcademicArticle
description: Leishmania amazonensis is the causative agent of American cutaneous leishmaniasis, an important neglected tropical disease. Once Leishmania amazonensis is inoculated into the human host, promastigotes are exposed to the extracellular matrix (ECM) of the dermis. However, little is known about the interaction between the ECM and Leishmania promastigotes. In this study we established L. amazonensis promastigote culture in a three-dimensional (3D) environment mainly composed of Collagen I (COL I). This 3D culture recreates in vitro some aspects of the human host infection site, enabling the study of the interaction mechanisms of L. amazonensis with the host ECM. Promastigotes exhibited “freeze and run” migration in the 3D COL I matrix, which is completely different from the conventional in vitro swimming mode of migration. Moreover, L. amazonensis promastigotes were able to invade, migrate inside, and remodel the 3D COL I matrix. Promastigote trans-matrix invasion and the freeze and run migration mode were also observed when macrophages were present in the matrix. At least two classes of proteases, metallo- and cysteine proteases, are involved in the 3D COL I matrix degradation caused by Leishmania. Treatment with a mixture of protease inhibitors significantly reduced promastigote invasion and migration through this matrix. Together our results demonstrate that L. amazonensis promastigotes release proteases and actively remodel their 3D environment, facilitating their migration. This raises the possibility that promastigotes actively interact with their 3D environment during the search for their cellular “home”—macrophages. Supporting this hypothesis, promastigotes migrated faster than macrophages in a novel 3D co-culture model.
format: application/pdf
format: text/html
creator: Debora B. Petropolis
creator: Juliany C.F. Rodrigues
creator: Nathan B. Viana
creator: Bruno Pontes
creator: Camila F.A. Pereira
creator: Fernando C. Silva-Filho
subject: Cell Biology
subject: Parasitology
description: doi:10.7717/peerj.317
publisher: PeerJ Inc.
rights: © 2014 Petropolis et al.
abstract: Leishmania amazonensis is the causative agent of American cutaneous leishmaniasis, an important neglected tropical disease. Once Leishmania amazonensis is inoculated into the human host, promastigotes are exposed to the extracellular matrix (ECM) of the dermis. However, little is known about the interaction between the ECM and Leishmania promastigotes. In this study we established L. amazonensis promastigote culture in a three-dimensional (3D) environment mainly composed of Collagen I (COL I). This 3D culture recreates in vitro some aspects of the human host infection site, enabling the study of the interaction mechanisms of L. amazonensis with the host ECM. Promastigotes exhibited “freeze and run” migration in the 3D COL I matrix, which is completely different from the conventional in vitro swimming mode of migration. Moreover, L. amazonensis promastigotes were able to invade, migrate inside, and remodel the 3D COL I matrix. Promastigote trans-matrix invasion and the freeze and run migration mode were also observed when macrophages were present in the matrix. At least two classes of proteases, metallo- and cysteine proteases, are involved in the 3D COL I matrix degradation caused by Leishmania. Treatment with a mixture of protease inhibitors significantly reduced promastigote invasion and migration through this matrix. Together our results demonstrate that L. amazonensis promastigotes release proteases and actively remodel their 3D environment, facilitating their migration. This raises the possibility that promastigotes actively interact with their 3D environment during the search for their cellular “home”—macrophages. Supporting this hypothesis, promastigotes migrated faster than macrophages in a novel 3D co-culture model.
bibliographic citation: Petropolis et al. (2014) Leishmania amazonensis promastigotes in 3D Collagen I culture: an in vitro physiological environment for the study of extracellular matrix and host cell interactions. PeerJ 2:e317 https://doi.org/10.7717/peerj.317
date submitted: 2013-09-07
date accepted: 2014-03-04
issued: 2014-04-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Petropolis
  given name: Debora B.
author list: Agent
  family name: Rodrigues
  given name: Juliany C.F.
author list: Agent
  family name: Viana
  given name: Nathan B.
author list: Agent
  family name: Pontes
  given name: Bruno
author list: Agent
  family name: Pereira
  given name: Camila F.A.
author list: Agent
  family name: Silva-Filho
  given name: Fernando C.
doi: 10.7717/peerj.317
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-03
copyright: © 2014 Petropolis et al.
attribution name: Petropolis et al.

Internet publicity of data problems in the bioscience literature correlates with enhanced corrective action
type: item
type: AcademicArticle
description: Several online forums exist to facilitate open and/or anonymous discussion of the peer-reviewed scientific literature. Data integrity is a common discussion topic, and it is widely assumed that publicity surrounding such matters will accelerate correction of the scientific record. This study aimed to test this assumption by examining a collection of 497 papers for which data integrity had been questioned either in public or in private. As such, the papers were divided into two sub-sets: a public set of 274 papers discussed online, and the remainder a private set of 223 papers not publicized. The sources of alleged data problems, as well as criteria for defining problem data, and communication of problems to journals and appropriate institutions, were similar between the sets. The number of laboratory groups represented in each set was also similar (75 in public, 62 in private), as was the number of problem papers per laboratory group (3.65 in public, 3.54 in private). Over a study period of 18 months, public papers were retracted 6.5-fold more, and corrected 7.7-fold more, than those in the private set. Parsing the results by laboratory group, 28 laboratory groups in the public set had papers which received corrective action, versus 6 laboratory groups in the private set. For those laboratory groups in the public set with corrected/retracted papers, the fraction of their papers acted on was 62% of those initially flagged, whereas in the private set this fraction was 27%. Such clustering of actions suggests a pattern in which correction/retraction of one paper from a group correlates with more corrections/retractions from the same group, with this pattern being stronger in the public set. It is therefore concluded that online discussion enhances levels of corrective action in the scientific literature. Nevertheless, anecdotal discussion reveals substantial room for improvement in handling of such matters.
format: application/pdf
format: text/html
creator: Paul S. Brookes
subject: Ethical Issues
subject: Science Policy
description: doi:10.7717/peerj.313
publisher: PeerJ Inc.
rights: © 2014 Brookes
abstract: Several online forums exist to facilitate open and/or anonymous discussion of the peer-reviewed scientific literature. Data integrity is a common discussion topic, and it is widely assumed that publicity surrounding such matters will accelerate correction of the scientific record. This study aimed to test this assumption by examining a collection of 497 papers for which data integrity had been questioned either in public or in private. As such, the papers were divided into two sub-sets: a public set of 274 papers discussed online, and the remainder a private set of 223 papers not publicized. The sources of alleged data problems, as well as criteria for defining problem data, and communication of problems to journals and appropriate institutions, were similar between the sets. The number of laboratory groups represented in each set was also similar (75 in public, 62 in private), as was the number of problem papers per laboratory group (3.65 in public, 3.54 in private). Over a study period of 18 months, public papers were retracted 6.5-fold more, and corrected 7.7-fold more, than those in the private set. Parsing the results by laboratory group, 28 laboratory groups in the public set had papers which received corrective action, versus 6 laboratory groups in the private set. For those laboratory groups in the public set with corrected/retracted papers, the fraction of their papers acted on was 62% of those initially flagged, whereas in the private set this fraction was 27%. Such clustering of actions suggests a pattern in which correction/retraction of one paper from a group correlates with more corrections/retractions from the same group, with this pattern being stronger in the public set. It is therefore concluded that online discussion enhances levels of corrective action in the scientific literature. Nevertheless, anecdotal discussion reveals substantial room for improvement in handling of such matters.
bibliographic citation: Brookes (2014) Internet publicity of data problems in the bioscience literature correlates with enhanced corrective action. PeerJ 2:e313 https://doi.org/10.7717/peerj.313
date submitted: 2013-11-28
date accepted: 2014-02-27
issued: 2014-04-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Brookes
  given name: Paul S.
doi: 10.7717/peerj.313
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-03
copyright: © 2014 Brookes
attribution name: Brookes

Predicting changes in language skills between 2 and 3 years in the EDEN mother–child cohort
type: item
type: AcademicArticle
description: Objective. To examine the factors predicting changes in language skills between 2 and 3 years. Methods. By using longitudinal data concerning 1002 children from the EDEN study, linear regression was used to predict 3-year language performance from 2-year language performance and the risk factors associated with language delays. Logistic regressions were performed to examine two change trajectories: children who fall below the 10th percentile of language skills between 2 and 3 years (declining trajectory), and those who rose above the 10th percentile (resilient trajectory). Results. The final linear model accounted for 43% of the variance in 3-year language scores, with 2-year language scores accounting for 22%. Exposure to alcohol during pregnancy, earlier birth term, lower level of parental education and lower frequency of maternal stimulation were associated with the declining trajectory. Breastfeeding was associated with the resilient trajectory. Conclusions. This study provides a better understanding of the natural history of early language delays by identifying biological and social factors that predict changes in language skills between the ages of 2 and 3 years.
format: application/pdf
format: text/html
creator: Hugo Peyre
creator: Jonathan Y. Bernard
creator: Anne Forhan
creator: Marie-Aline Charles
creator: Maria De Agostini
creator: Barbara Heude
creator: Franck Ramus
subject: Neuroscience
subject: Cognitive Disorders
subject: Epidemiology
description: doi:10.7717/peerj.335
publisher: PeerJ Inc.
rights: © 2014 Peyre et al.
abstract: Objective. To examine the factors predicting changes in language skills between 2 and 3 years. Methods. By using longitudinal data concerning 1002 children from the EDEN study, linear regression was used to predict 3-year language performance from 2-year language performance and the risk factors associated with language delays. Logistic regressions were performed to examine two change trajectories: children who fall below the 10th percentile of language skills between 2 and 3 years (declining trajectory), and those who rose above the 10th percentile (resilient trajectory). Results. The final linear model accounted for 43% of the variance in 3-year language scores, with 2-year language scores accounting for 22%. Exposure to alcohol during pregnancy, earlier birth term, lower level of parental education and lower frequency of maternal stimulation were associated with the declining trajectory. Breastfeeding was associated with the resilient trajectory. Conclusions. This study provides a better understanding of the natural history of early language delays by identifying biological and social factors that predict changes in language skills between the ages of 2 and 3 years.
bibliographic citation: Peyre et al. (2014) Predicting changes in language skills between 2 and 3 years in the EDEN mother–child cohort. PeerJ 2:e335 https://doi.org/10.7717/peerj.335
date submitted: 2013-12-12
date accepted: 2014-03-16
issued: 2014-04-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Peyre
  given name: Hugo
author list: Agent
  family name: Bernard
  given name: Jonathan Y.
author list: Agent
  family name: Forhan
  given name: Anne
author list: Agent
  family name: Charles
  given name: Marie-Aline
author list: Agent
  family name: De Agostini
  given name: Maria
author list: Agent
  family name: Heude
  given name: Barbara
author list: Agent
  family name: Ramus
  given name: Franck
doi: 10.7717/peerj.335
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-01
copyright: © 2014 Peyre et al.
attribution name: Peyre et al.

The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes
type: item
type: AcademicArticle
description: Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the rapid, large-scale, full-genome comparative analyses carried out by LS-BSR. Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 min using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in 27–57 h, depending upon the alignment method, using 16 processors. Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical di…
format: application/pdf
format: text/html
creator: Jason W. Sahl
creator: J. Gregory Caporaso
creator: David A. Rasko
creator: Paul Keim
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.332
publisher: PeerJ Inc.
rights: © 2014 Sahl et al.
abstract: Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the rapid, large-scale, full-genome comparative analyses carried out by LS-BSR. Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 min using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in 27–57 h, depending upon the alignment method, using 16 processors. Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical di…
bibliographic citation: Sahl et al. (2014) The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. PeerJ 2:e332 https://doi.org/10.7717/peerj.332
date submitted: 2014-02-11
date accepted: 2014-03-14
issued: 2014-04-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sahl
  given name: Jason W.
author list: Agent
  family name: Caporaso
  given name: J. Gregory
author list: Agent
  family name: Rasko
  given name: David A.
author list: Agent
  family name: Keim
  given name: Paul
doi: 10.7717/peerj.332
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-01
copyright: © 2014 Sahl et al.
attribution name: Sahl et al.

Association between shell morphology of micro-land snails (genus Plectostoma) and their predator’s predatory behaviour
type: item
type: AcademicArticle
description: Predator–prey interactions are among the main ecological interactions that shape the diversity of biological form. In many cases, the evolution of the mollusc shell form is presumably driven by predation. However, the adaptive significance of several uncommon, yet striking, shell traits of land snails are still poorly known. These include the distorted coiled “tuba” and the protruded radial ribs that can be found in micro-landsnails of the genus Plectostoma. Here, we experimentally tested whether these shell traits may act as defensive adaptations against predators. We characterised and quantified the possible anti-predation behaviour and shell traits of Plectostoma snails both in terms of their properties and efficiencies in defending against the Atopos slug predatory strategies, namely, shell-apertural entry and shell-drilling. The results showed that Atopos slugs would first attack the snail by shell-apertural entry, and, should this fail, shift to the energetically more costly shell-drilling strategy. We found that the shell tuba of Plectostoma snails is an effective defensive trait against shell-apertural entry attack. None of the snail traits, such as resting behaviour, shell thickness, shell tuba shape, shell rib density and intensity can fully protect the snail from the slug’s shell-drilling attack. However, these traits could increase the predation costs to the slug. Further analysis on the shell traits revealed that the lack of effectiveness in these anti-predation shell traits may be caused by a functional trade-off between shell traits under selection of two different predatory strategies.
format: application/pdf
format: text/html
creator: Thor-Seng Liew
creator: Menno Schilthuizen
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.329
publisher: PeerJ Inc.
rights: © 2014 Liew and Schilthuizen
abstract: Predator–prey interactions are among the main ecological interactions that shape the diversity of biological form. In many cases, the evolution of the mollusc shell form is presumably driven by predation. However, the adaptive significance of several uncommon, yet striking, shell traits of land snails are still poorly known. These include the distorted coiled “tuba” and the protruded radial ribs that can be found in micro-landsnails of the genus Plectostoma. Here, we experimentally tested whether these shell traits may act as defensive adaptations against predators. We characterised and quantified the possible anti-predation behaviour and shell traits of Plectostoma snails both in terms of their properties and efficiencies in defending against the Atopos slug predatory strategies, namely, shell-apertural entry and shell-drilling. The results showed that Atopos slugs would first attack the snail by shell-apertural entry, and, should this fail, shift to the energetically more costly shell-drilling strategy. We found that the shell tuba of Plectostoma snails is an effective defensive trait against shell-apertural entry attack. None of the snail traits, such as resting behaviour, shell thickness, shell tuba shape, shell rib density and intensity can fully protect the snail from the slug’s shell-drilling attack. However, these traits could increase the predation costs to the slug. Further analysis on the shell traits revealed that the lack of effectiveness in these anti-predation shell traits may be caused by a functional trade-off between shell traits under selection of two different predatory strategies.
bibliographic citation: Liew et al. (2014) Association between shell morphology of micro-land snails (genus Plectostoma) and their predator’s predatory behaviour. PeerJ 2:e329 https://doi.org/10.7717/peerj.329
date submitted: 2013-10-23
date accepted: 2014-03-12
issued: 2014-04-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Liew
  given name: Thor-Seng
author list: Agent
  family name: Schilthuizen
  given name: Menno
doi: 10.7717/peerj.329
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-01
copyright: © 2014 Liew and Schilthuizen
attribution name: Liew and Schilthuizen

Tumor vascular disruption using various radiation types
type: item
type: AcademicArticle
description: The feasibility of disrupting a tumor’s vascular structure with various radiation types and radionuclides is investigated. Calculated absorbed dose profiles for photons and 4He ions suggest that low-energy beta-gamma and alpha emitting radionuclides can deposit sufficient absorbed dose to disrupt a tumor’s vascular structure while minimizing the dose outside the blood vessel. Candidate radionuclides uniformly distributed in microspheres are theoretically investigated with respect to their vascular disruption potential and to offer an alternative to 90Y microsphere therapy. Requisite activities of candidate low-energy beta-gamma and alpha emitting radionuclides to facilitate vascular disruption are calculated.
format: application/pdf
format: text/html
creator: JJ Bevelacqua
subject: Biophysics
subject: Biotechnology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.320
publisher: PeerJ Inc.
rights: © 2014 Bevelacqua
abstract: The feasibility of disrupting a tumor’s vascular structure with various radiation types and radionuclides is investigated. Calculated absorbed dose profiles for photons and 4He ions suggest that low-energy beta-gamma and alpha emitting radionuclides can deposit sufficient absorbed dose to disrupt a tumor’s vascular structure while minimizing the dose outside the blood vessel. Candidate radionuclides uniformly distributed in microspheres are theoretically investigated with respect to their vascular disruption potential and to offer an alternative to 90Y microsphere therapy. Requisite activities of candidate low-energy beta-gamma and alpha emitting radionuclides to facilitate vascular disruption are calculated.
bibliographic citation: Bevelacqua (2014) Tumor vascular disruption using various radiation types. PeerJ 2:e320 https://doi.org/10.7717/peerj.320
date submitted: 2013-11-28
date accepted: 2014-03-04
issued: 2014-04-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Bevelacqua
  given name: JJ
doi: 10.7717/peerj.320
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-04-01
copyright: © 2014 Bevelacqua
attribution name: Bevelacqua

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