PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: No association between autistic traits and contextual influences on eye-movements during reading
items: Drivers of macroinvertebrate community structure in unmodified streams
items: The impact of maths support tutorials on mathematics confidence and academic performance in a cohort of HE Animal Science students
items: Characterisation of the interaction of neuropilin-1 with heparin and a heparan sulfate mimetic library of heparin-derived sugars
items: Bird-window collisions in the summer breeding season
items: Out of control mortality matters: the effect of perceived uncontrollable mortality risk on a health-related decision
items: Unexplained abdominal pain as a driver for inappropriate therapeutics: an audit on the use of intravenous proton pump inhibitors
items: You can’t teach speed: sprinters falsify the deliberate practice model of expertise
items: QSpec: online control and data analysis system for single-cell Raman spectroscopy
items: Beyond birth-weight: early growth and adolescent blood pressure in a Peruvian population
items: Single cell transcriptional analysis reveals novel innate immune cell types
items: Mobile phones carry the personal microbiome of their owners
items: Functional connectivity in task-negative network of the Deaf: effects of sign language experience
items: Facelock: familiarity-based graphical authentication
items: scikit-image: image processing in Python
items: A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+
items: Identification of MHCII variants associated with chlamydial disease in the koala (Phascolarctos cinereus)
items: Photobacterium sanctipauli sp. nov. isolated from bleached Madracis decactis (Scleractinia) in the St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil
items: Movement and ranging patterns of the Common Chaffinch in heterogeneous forest landscapes
items: Digital dissection of the masticatory muscles of the naked mole-rat, Heterocephalus glaber (Mammalia, Rodentia)
items: Cascading effects of a highly specialized beech-aphid–fungus interaction on forest regeneration
items: Effectiveness of accommodation and constant resistance training on maximal strength and power in trained athletes
items: Laboratory generation of new parthenogenetic lineages supports contagious parthenogenesis in Artemia
items: Prediction uncertainty assessment of a systems biology model requires a sample of the full probability distribution of its parameters
items: SHAPS-C: the Snaith-Hamilton pleasure scale modified for clinician administration
items: Geographic variation in the advertisement calls of Hyla eximia and its possible explanations
items: Diversity and antimicrobial potential of culturable heterotrophic bacteria associated with the endemic marine sponge Arenosclera brasiliensis
items: Limited geographic genetic structure detected in a widespread Palearctic corvid, Nucifraga caryocatactes
items: Modelling the impacts of an invasive species across landscapes: a step-wise approach
items: First evidence of bryophyte diaspores in the plumage of transequatorial migrant birds
items: Ape duos and trios: spontaneous cooperation with free partner choice in chimpanzees
items: Continental variation in wing pigmentation in Calopteryx damselflies is related to the presence of heterospecifics
items: How male sound pressure level influences phonotaxis in virgin female Jamaican field crickets (Gryllus assimilis)
items: Immune stimulation reduces sleep and memory ability in Drosophila melanogaster
items: dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms
items: Diversity of introduced terrestrial flatworms in the Iberian Peninsula: a cautionary tale
items: Interannual and spatial variability of maple syrup yield as related to climatic factors
items: Oral health status among long-term hospitalized adults: a cross sectional study
items: Forms of Melanoplus bowditchi (Orthoptera: Acrididae) collected from different host plants are indistinguishable genetically and in aedeagal morphology
items: Regulation of KCa2.3 and endothelium-dependent hyperpolarization (EDH) in the rat middle cerebral artery: the role of lipoxygenase metabolites and isoprostanes
items: Molecular cytogenetic analyses of Epinephelus bruneus and Epinephelus moara (Perciformes, Epinephelidae)
items: Tree mortality from a short-duration freezing event and global-change-type drought in a Southwestern piñon-juniper woodland, USA
items: Stability of commercial glucanase and β-glucosidase preparations under hydrolysis conditions
items: The salivary secretome of the biting midge, Culicoides sonorensis
items: FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares
items: Swedish high-school pupils’ attitudes towards drugs in relation to drug usage, impulsiveness and other risk factors
items: Quantification of intraskeletal histovariability in Alligator mississippiensis and implications for vertebrate osteohistology
items: BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU
items: Rape and the prevalence of hybrids in broadly sympatric species: a case study using albatrosses
items: Compliance with vessel speed restrictions to protect North Atlantic right whales

No association between autistic traits and contextual influences on eye-movements during reading
type: item
type: AcademicArticle
description: Individuals with autism spectrum disorders are claimed to show a local cognitive bias, termed “weak central coherence”, which manifests in a reduced influence of contextual information on linguistic processing. Here, we investigated whether this bias might also be demonstrated by individuals who exhibit sub-clinical levels of autistic traits, as has been found for other aspects of autistic cognition. The eye-movements of 71 university students were monitored as they completed a reading comprehension task. Consistent with previous studies, participants made shorter fixations on words that were highly predicted on the basis of preceding sentence context. However, contrary to the weak central coherence account, this effect was not reduced amongst individuals with high levels of autistic traits, as measured by the Autism Spectrum Quotient (AQ). Further exploratory analyses revealed that participants with high AQ scores fixated longer on words that resolved the meaning of an earlier homograph. However, this was only the case for sentences where the two potential meanings of the homograph result in different pronunciations. The results provide tentative evidence for differences in reading style that are associated with autistic traits, but fail to support the notion of weak central coherence extending into the non-autistic population.
format: application/pdf
format: text/html
creator: Nathan Caruana
creator: Jon Brock
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.466
publisher: PeerJ Inc.
rights: © 2014 Caruana and Brock
abstract: Individuals with autism spectrum disorders are claimed to show a local cognitive bias, termed “weak central coherence”, which manifests in a reduced influence of contextual information on linguistic processing. Here, we investigated whether this bias might also be demonstrated by individuals who exhibit sub-clinical levels of autistic traits, as has been found for other aspects of autistic cognition. The eye-movements of 71 university students were monitored as they completed a reading comprehension task. Consistent with previous studies, participants made shorter fixations on words that were highly predicted on the basis of preceding sentence context. However, contrary to the weak central coherence account, this effect was not reduced amongst individuals with high levels of autistic traits, as measured by the Autism Spectrum Quotient (AQ). Further exploratory analyses revealed that participants with high AQ scores fixated longer on words that resolved the meaning of an earlier homograph. However, this was only the case for sentences where the two potential meanings of the homograph result in different pronunciations. The results provide tentative evidence for differences in reading style that are associated with autistic traits, but fail to support the notion of weak central coherence extending into the non-autistic population.
bibliographic citation: Caruana et al. (2014) No association between autistic traits and contextual influences on eye-movements during reading. PeerJ 2:e466 https://doi.org/10.7717/peerj.466
date submitted: 2014-04-01
date accepted: 2014-06-12
issued: 2014-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Caruana
  given name: Nathan
author list: Agent
  family name: Brock
  given name: Jon
doi: 10.7717/peerj.466
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-26
copyright: © 2014 Caruana and Brock
attribution name: Caruana and Brock

Drivers of macroinvertebrate community structure in unmodified streams
type: item
type: AcademicArticle
description: Often simple metrics are used to summarise complex patterns in stream benthic ecology, thus it is important to understand how well these metrics can explain the finer-scale underlying environmental variation often hidden by coarser-scale influences. I sampled 47 relatively pristine streams in the central North Island of New Zealand in 2007 and (1) evaluated the local-scale drivers of macroinvertebrate community structure as well as both diversity and biomonitoring metrics in this unmodified landscape, and (2) assessed whether these drivers were similar for commonly used univariate metrics and multivariate structure. The drivers of community metrics and multivariate structure were largely similar, with % canopy cover and resource supply metrics the most commonly identified environmental drivers in these pristine streams. For an area with little to no anthropogenic influence, substantial variation was explained in the macroinvertebrate community (up to 70% on the first two components of a partial least squares regression), with both uni- and multivariate approaches. This research highlights two important points: (1) the importance of considering natural underlying environmental variation when assessing the response to coarse environmental gradients, and (2) the importance of considering canopy cover presence when assessing the impact of stressors on stream macroinvertebrate communities.
format: application/pdf
format: text/html
creator: Jonathan D. Tonkin
subject: Biodiversity
subject: Ecohydrology
subject: Ecology
subject: Entomology
subject: Environmental Sciences
description: doi:10.7717/peerj.465
publisher: PeerJ Inc.
rights: © 2014 Tonkin
abstract: Often simple metrics are used to summarise complex patterns in stream benthic ecology, thus it is important to understand how well these metrics can explain the finer-scale underlying environmental variation often hidden by coarser-scale influences. I sampled 47 relatively pristine streams in the central North Island of New Zealand in 2007 and (1) evaluated the local-scale drivers of macroinvertebrate community structure as well as both diversity and biomonitoring metrics in this unmodified landscape, and (2) assessed whether these drivers were similar for commonly used univariate metrics and multivariate structure. The drivers of community metrics and multivariate structure were largely similar, with % canopy cover and resource supply metrics the most commonly identified environmental drivers in these pristine streams. For an area with little to no anthropogenic influence, substantial variation was explained in the macroinvertebrate community (up to 70% on the first two components of a partial least squares regression), with both uni- and multivariate approaches. This research highlights two important points: (1) the importance of considering natural underlying environmental variation when assessing the response to coarse environmental gradients, and (2) the importance of considering canopy cover presence when assessing the impact of stressors on stream macroinvertebrate communities.
bibliographic citation: Tonkin (2014) Drivers of macroinvertebrate community structure in unmodified streams. PeerJ 2:e465 https://doi.org/10.7717/peerj.465
date submitted: 2014-04-01
date accepted: 2014-06-12
issued: 2014-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tonkin
  given name: Jonathan D.
doi: 10.7717/peerj.465
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-26
copyright: © 2014 Tonkin
attribution name: Tonkin

The impact of maths support tutorials on mathematics confidence and academic performance in a cohort of HE Animal Science students
type: item
type: AcademicArticle
description: Students embarking on a bioscience degree course, such as Animal Science, often do not have sufficient experience in mathematics. However, mathematics forms an essential and integral part of any bioscience degree and is essential to enhance employability. This paper presents the findings of a project looking at the effect of mathematics tutorials on a cohort of first year animal science and management students. The results of a questionnaire, focus group discussions and academic performance analysis indicate that small group tutorials enhance students’ confidence in maths and improve students’ academic performance. Furthermore, student feedback on the tutorial programme provides a deeper insight into student experiences and the value students assign to the tutorials.
format: application/pdf
format: text/html
creator: Nieky van Veggel
creator: Jonathan Amory
subject: Agricultural Science
subject: Zoology
subject: Science and Medical Education
description: doi:10.7717/peerj.463
publisher: PeerJ Inc.
rights: © 2014 van Veggel and Amory
abstract: Students embarking on a bioscience degree course, such as Animal Science, often do not have sufficient experience in mathematics. However, mathematics forms an essential and integral part of any bioscience degree and is essential to enhance employability. This paper presents the findings of a project looking at the effect of mathematics tutorials on a cohort of first year animal science and management students. The results of a questionnaire, focus group discussions and academic performance analysis indicate that small group tutorials enhance students’ confidence in maths and improve students’ academic performance. Furthermore, student feedback on the tutorial programme provides a deeper insight into student experiences and the value students assign to the tutorials.
bibliographic citation: van Veggel et al. (2014) The impact of maths support tutorials on mathematics confidence and academic performance in a cohort of HE Animal Science students. PeerJ 2:e463 https://doi.org/10.7717/peerj.463
date submitted: 2014-03-31
date accepted: 2014-06-11
issued: 2014-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: van Veggel
  given name: Nieky
author list: Agent
  family name: Amory
  given name: Jonathan
doi: 10.7717/peerj.463
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-26
copyright: © 2014 van Veggel and Amory
attribution name: van Veggel and Amory

Characterisation of the interaction of neuropilin-1 with heparin and a heparan sulfate mimetic library of heparin-derived sugars
type: item
type: AcademicArticle
description: Background. Neuropilin-1 (NRP-1) is a multidomain membrane protein with soluble isoforms interacting with a complex network of other membrane receptors, their respective ligands and heparan sulfate (HS). It is involved in the development of vasculature, neural patterning, immunological responses and pathological angiogenesis. Methods. We have characterised the binding of a Fc fusion of rat NRP-1 (Fc rNRP-1) and of a soluble isoform, corresponding to the first four extracellular domains of human NRP-1, shNRP-1, using optical biosensor-based binding assays with a library of heparin derivatives. Selective labelling of lysines protected upon heparin binding allowed their identification by mass spectrometry. Results. Fc rNRP-1 bound to heparin with high affinity (2.5 nM) and fast ka (9.8 × 106 M−1s−1). Unusually, NRP-1 bound both highly sulfated and completely desulfated stretches of heparin and exhibited a complex pattern of preferences for chemically modified heparins possessing one or two sulfate groups, e.g., it bound heparin with just a 6-O sulfate group better than heparin with any two of N-sulfate, 6-O sulfate and 2-O sulfate. Mass-spectrometry based mapping identified that, in addition to the expected the b1 domain, the a1, and c domains and the L2 linker were also involved in the interaction. In contrast, shNRP-1 bound heparin far more weakly. This could only be shown by affinity chromatography and by differential scanning fluorimetry. Discussion. The results suggest that the interaction of NRP-1 with HS is more complex than anticipated and involving a far greater extent of the protein than just the b1–b2 domains. NRP-1’s preference for binding long saccharide structures suggests it has the potential to bind large segments of HS chains and so organise their local structure. In contrast, the four domain soluble isoform, shNRP-1 binds heparin weakly and so would be expected to diffuse away rapidly from the source cell.
format: application/pdf
format: text/html
creator: Katarzyna A. Uniewicz
creator: Alessandro Ori
creator: Yassir A. Ahmed
creator: Edwin A. Yates
creator: David G. Fernig
subject: Biochemistry
description: doi:10.7717/peerj.461
publisher: PeerJ Inc.
rights: © 2014 Uniewicz et al.
abstract: Background. Neuropilin-1 (NRP-1) is a multidomain membrane protein with soluble isoforms interacting with a complex network of other membrane receptors, their respective ligands and heparan sulfate (HS). It is involved in the development of vasculature, neural patterning, immunological responses and pathological angiogenesis. Methods. We have characterised the binding of a Fc fusion of rat NRP-1 (Fc rNRP-1) and of a soluble isoform, corresponding to the first four extracellular domains of human NRP-1, shNRP-1, using optical biosensor-based binding assays with a library of heparin derivatives. Selective labelling of lysines protected upon heparin binding allowed their identification by mass spectrometry. Results. Fc rNRP-1 bound to heparin with high affinity (2.5 nM) and fast ka (9.8 × 106 M−1s−1). Unusually, NRP-1 bound both highly sulfated and completely desulfated stretches of heparin and exhibited a complex pattern of preferences for chemically modified heparins possessing one or two sulfate groups, e.g., it bound heparin with just a 6-O sulfate group better than heparin with any two of N-sulfate, 6-O sulfate and 2-O sulfate. Mass-spectrometry based mapping identified that, in addition to the expected the b1 domain, the a1, and c domains and the L2 linker were also involved in the interaction. In contrast, shNRP-1 bound heparin far more weakly. This could only be shown by affinity chromatography and by differential scanning fluorimetry. Discussion. The results suggest that the interaction of NRP-1 with HS is more complex than anticipated and involving a far greater extent of the protein than just the b1–b2 domains. NRP-1’s preference for binding long saccharide structures suggests it has the potential to bind large segments of HS chains and so organise their local structure. In contrast, the four domain soluble isoform, shNRP-1 binds heparin weakly and so would be expected to diffuse away rapidly from the source cell.
bibliographic citation: Uniewicz et al. (2014) Characterisation of the interaction of neuropilin-1 with heparin and a heparan sulfate mimetic library of heparin-derived sugars. PeerJ 2:e461 https://doi.org/10.7717/peerj.461
date submitted: 2014-03-31
date accepted: 2014-06-09
issued: 2014-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Uniewicz
  given name: Katarzyna A.
author list: Agent
  family name: Ori
  given name: Alessandro
author list: Agent
  family name: Ahmed
  given name: Yassir A.
author list: Agent
  family name: Yates
  given name: Edwin A.
author list: Agent
  family name: Fernig
  given name: David G.
doi: 10.7717/peerj.461
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-26
copyright: © 2014 Uniewicz et al.
attribution name: Uniewicz et al.

Bird-window collisions in the summer breeding season
type: item
type: AcademicArticle
description: Birds that reside in urban settings face numerous human-related threats to survival, including mortality from bird-window collisions (BWCs). Our current understanding of this issue has largely been driven by data collected during spring and fall migration, and patterns of collision mortality during the summer breeding season remain relatively unexplored. We assessed BWCs during four breeding seasons (2009–2012) at a site in northwestern Illinois, USA, by comparing the abundance, richness, migratory class, and age of the species living around buildings to species mortally wounded by window collisions. We also systematically assessed the daily timing of BWCs throughout the breeding season. We documented BWCs in 4 of 25 (16%) species and 7 of 21 (33%) species in 2009 and 2010, respectively. The relationship between BWCs and abundance depended on age. For adults, BWCs were highest in the least abundant species, e.g., Red-eyed Vireo (Vireo olivaceus), and lowest in species with high abundance values, e.g., Chipping Sparrow (Spizella passerina). For juveniles, mortality was greatest for the most abundant species, and the American Robin (Turdus migratorius) accounted for 62% of all juvenile carcasses. Early in the breeding season, collision mortality was restricted to adults of Long-distance Migrants, whereas juveniles of all three migratory guilds (Long-distance and Short-distance Migrants and Permanent Residents) died at windows from late June through early August. Daily mortality for all species was highest between sunrise–1600 h and lowest from 1600 h–sunrise the next day. Generally, the species observed as carcasses matched birds considered a ‘high risk’ for BWCs, e.g., Ruby-throated Hummingbird (Archilochus colubris), and those considered ‘low risk’ were not observed as carcasses, e.g., Blue-gray Gnatcatcher (Polioptila caerulea). Our results suggest that the number of BWCs during the breeding season does not necessarily increase with abundance, but rather appears re…
format: application/pdf
format: text/html
creator: Stephen B. Hager
creator: Matthew E. Craig
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.460
publisher: PeerJ Inc.
rights: © 2014 Hager and Craig
abstract: Birds that reside in urban settings face numerous human-related threats to survival, including mortality from bird-window collisions (BWCs). Our current understanding of this issue has largely been driven by data collected during spring and fall migration, and patterns of collision mortality during the summer breeding season remain relatively unexplored. We assessed BWCs during four breeding seasons (2009–2012) at a site in northwestern Illinois, USA, by comparing the abundance, richness, migratory class, and age of the species living around buildings to species mortally wounded by window collisions. We also systematically assessed the daily timing of BWCs throughout the breeding season. We documented BWCs in 4 of 25 (16%) species and 7 of 21 (33%) species in 2009 and 2010, respectively. The relationship between BWCs and abundance depended on age. For adults, BWCs were highest in the least abundant species, e.g., Red-eyed Vireo (Vireo olivaceus), and lowest in species with high abundance values, e.g., Chipping Sparrow (Spizella passerina). For juveniles, mortality was greatest for the most abundant species, and the American Robin (Turdus migratorius) accounted for 62% of all juvenile carcasses. Early in the breeding season, collision mortality was restricted to adults of Long-distance Migrants, whereas juveniles of all three migratory guilds (Long-distance and Short-distance Migrants and Permanent Residents) died at windows from late June through early August. Daily mortality for all species was highest between sunrise–1600 h and lowest from 1600 h–sunrise the next day. Generally, the species observed as carcasses matched birds considered a ‘high risk’ for BWCs, e.g., Ruby-throated Hummingbird (Archilochus colubris), and those considered ‘low risk’ were not observed as carcasses, e.g., Blue-gray Gnatcatcher (Polioptila caerulea). Our results suggest that the number of BWCs during the breeding season does not necessarily increase with abundance, but rather appears re…
bibliographic citation: Hager et al. (2014) Bird-window collisions in the summer breeding season. PeerJ 2:e460 https://doi.org/10.7717/peerj.460
date submitted: 2014-05-08
date accepted: 2014-06-08
issued: 2014-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hager
  given name: Stephen B.
author list: Agent
  family name: Craig
  given name: Matthew E.
doi: 10.7717/peerj.460
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-26
copyright: © 2014 Hager and Craig
attribution name: Hager and Craig

Out of control mortality matters: the effect of perceived uncontrollable mortality risk on a health-related decision
type: item
type: AcademicArticle
description: Prior evidence from the public health literature suggests that both control beliefs and perceived threats to life are important for health behaviour. Our previously presented theoretical model generated the more specific hypothesis that uncontrollable, but not controllable, personal mortality risk should alter the payoff from investment in health protection behaviours. We carried out three experiments to test whether altering the perceived controllability of mortality risk would affect a health-related decision. Experiment 1 demonstrated that a mortality prime could be used to alter a health-related decision: the choice between a healthier food reward (fruit) and an unhealthy alternative (chocolate). Experiment 2 demonstrated that it is the controllability of the mortality risk being primed that generates the effect, rather than mortality risk per se. Experiment 3 showed that the effect could be seen in a surreptitious experiment that was not explicitly health related. Our results suggest that perceptions about the controllability of mortality risk may be an important factor in people’s health-related decisions. Thus, techniques for adjusting perceptions about mortality risk could be important tools for use in health interventions. More importantly, tackling those sources of mortality that people perceive to be uncontrollable could have a dual purpose: making neighbourhoods and workplaces safer would have the primary benefit of reducing uncontrollable mortality risk, which could lead to a secondary benefit from improved health behaviours.
format: application/pdf
format: text/html
creator: Gillian V. Pepper
creator: Daniel Nettle
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.459
publisher: PeerJ Inc.
rights: © 2014 Pepper and Nettle
abstract: Prior evidence from the public health literature suggests that both control beliefs and perceived threats to life are important for health behaviour. Our previously presented theoretical model generated the more specific hypothesis that uncontrollable, but not controllable, personal mortality risk should alter the payoff from investment in health protection behaviours. We carried out three experiments to test whether altering the perceived controllability of mortality risk would affect a health-related decision. Experiment 1 demonstrated that a mortality prime could be used to alter a health-related decision: the choice between a healthier food reward (fruit) and an unhealthy alternative (chocolate). Experiment 2 demonstrated that it is the controllability of the mortality risk being primed that generates the effect, rather than mortality risk per se. Experiment 3 showed that the effect could be seen in a surreptitious experiment that was not explicitly health related. Our results suggest that perceptions about the controllability of mortality risk may be an important factor in people’s health-related decisions. Thus, techniques for adjusting perceptions about mortality risk could be important tools for use in health interventions. More importantly, tackling those sources of mortality that people perceive to be uncontrollable could have a dual purpose: making neighbourhoods and workplaces safer would have the primary benefit of reducing uncontrollable mortality risk, which could lead to a secondary benefit from improved health behaviours.
bibliographic citation: Pepper et al. (2014) Out of control mortality matters: the effect of perceived uncontrollable mortality risk on a health-related decision. PeerJ 2:e459 https://doi.org/10.7717/peerj.459
date submitted: 2014-04-03
date accepted: 2014-06-08
issued: 2014-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pepper
  given name: Gillian V.
author list: Agent
  family name: Nettle
  given name: Daniel
doi: 10.7717/peerj.459
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-26
copyright: © 2014 Pepper and Nettle
attribution name: Pepper and Nettle

Unexplained abdominal pain as a driver for inappropriate therapeutics: an audit on the use of intravenous proton pump inhibitors
type: item
type: AcademicArticle
description: Background. Proton pump inhibitors (PPIs) are currently the most effective agents for acid-related disorders. However, studies show that 25–75% of patients receiving intravenous PPIs had no appropriate justification, indicating high rates of inappropriate prescribing. Objective. To examine the appropriate use of intravenous PPIs in accordance with guidelines and the efficacy of a prescribing awareness intervention at an Asian teaching institution. Setting. Prospective audit in a tertiary hospital in Malaysia. Method. Every 4th intravenous PPI prescription received in the pharmacy was screened against hospital guidelines. Interventions for incorrect indication/dose/duration were performed. Patients’ demographic data, medical history and the use of intravenous PPI were collected. Included were all adult inpatients prescribed intravenous PPI. Main Outcome Measure. Proportion of appropriate IV PPI prescriptions. Results. Data for 106 patients were collected. Most patients were male [65(61.3%)], Chinese [50(47.2%)], with mean age ± SD = 60.3 ± 18.0 years. Most intravenous PPI prescriptions were initiated by junior doctors from the surgical [47(44.3%)] and medical [42(39.6%)] departments. Only 50/106(47.2%) patients had upper gastrointestinal endoscopy/surgery performed to verify the source of bleeding. Unexplained abdominal pain [81(76.4%)] was the main driver for prescribing intravenous PPIs empirically, out of which 73(68.9%) were for suspected upper gastrointestinal bleed. Overall, intravenous PPI was found to be inappropriately prescribed in 56(52.8%) patients for indication, dose or duration. Interventions on the use of intravenous PPI were most effective when performed by senior doctors (100%), followed by clinical pharmacists (50%), and inpatient pharmacists (37.5%, p = 0.027). Conclusion. Inappropriate intravenous PPI usage is still prevalent despite the enforcement of hospital guidelines. The promotion of prescribing awareness and evidence-based prescribing thro…
format: application/pdf
format: text/html
creator: Pauline Siew Mei Lai
creator: Yin Yen Wong
creator: Yong Chia Low
creator: Hui Ling Lau
creator: Kin-Fah Chin
creator: Sanjiv Mahadeva
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.451
publisher: PeerJ Inc.
rights: © 2014 Lai et al.
abstract: Background. Proton pump inhibitors (PPIs) are currently the most effective agents for acid-related disorders. However, studies show that 25–75% of patients receiving intravenous PPIs had no appropriate justification, indicating high rates of inappropriate prescribing. Objective. To examine the appropriate use of intravenous PPIs in accordance with guidelines and the efficacy of a prescribing awareness intervention at an Asian teaching institution. Setting. Prospective audit in a tertiary hospital in Malaysia. Method. Every 4th intravenous PPI prescription received in the pharmacy was screened against hospital guidelines. Interventions for incorrect indication/dose/duration were performed. Patients’ demographic data, medical history and the use of intravenous PPI were collected. Included were all adult inpatients prescribed intravenous PPI. Main Outcome Measure. Proportion of appropriate IV PPI prescriptions. Results. Data for 106 patients were collected. Most patients were male [65(61.3%)], Chinese [50(47.2%)], with mean age ± SD = 60.3 ± 18.0 years. Most intravenous PPI prescriptions were initiated by junior doctors from the surgical [47(44.3%)] and medical [42(39.6%)] departments. Only 50/106(47.2%) patients had upper gastrointestinal endoscopy/surgery performed to verify the source of bleeding. Unexplained abdominal pain [81(76.4%)] was the main driver for prescribing intravenous PPIs empirically, out of which 73(68.9%) were for suspected upper gastrointestinal bleed. Overall, intravenous PPI was found to be inappropriately prescribed in 56(52.8%) patients for indication, dose or duration. Interventions on the use of intravenous PPI were most effective when performed by senior doctors (100%), followed by clinical pharmacists (50%), and inpatient pharmacists (37.5%, p = 0.027). Conclusion. Inappropriate intravenous PPI usage is still prevalent despite the enforcement of hospital guidelines. The promotion of prescribing awareness and evidence-based prescribing thro…
bibliographic citation: Lai et al. (2014) Unexplained abdominal pain as a driver for inappropriate therapeutics: an audit on the use of intravenous proton pump inhibitors. PeerJ 2:e451 https://doi.org/10.7717/peerj.451
date submitted: 2014-04-16
date accepted: 2014-06-04
issued: 2014-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lai
  given name: Pauline Siew Mei
author list: Agent
  family name: Wong
  given name: Yin Yen
author list: Agent
  family name: Low
  given name: Yong Chia
author list: Agent
  family name: Lau
  given name: Hui Ling
author list: Agent
  family name: Chin
  given name: Kin-Fah
author list: Agent
  family name: Mahadeva
  given name: Sanjiv
doi: 10.7717/peerj.451
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-26
copyright: © 2014 Lai et al.
attribution name: Lai et al.

You can’t teach speed: sprinters falsify the deliberate practice model of expertise
type: item
type: AcademicArticle
description: Many scientists agree that expertise requires both innate talent and proper training. Nevertheless, the highly influential deliberate practice model (DPM) of expertise holds that talent does not exist or makes a negligible contribution to performance. It predicts that initial performance will be unrelated to achieving expertise and that 10 years of deliberate practice is necessary. We tested these predictions in the domain of sprinting. In Studies 1 and 2 we reviewed biographies of 15 Olympic champions and the 20 fastest American men in U.S. history. In all documented cases, sprinters were exceptional prior to initiating training, and most reached world class status rapidly (Study 1 median = 3 years; Study 2 = 7.5). In Study 3 we surveyed U.S. national collegiate championships qualifiers in sprinters (n = 20) and throwers (n = 44). Sprinters recalled being faster as youths than did throwers, whereas throwers recalled greater strength and throwing ability. Sprinters’ best performances in their first season of high school, generally the onset of formal training, were consistently faster than 95–99% of their peers. Collectively, these results falsify the DPM for sprinting. Because speed is foundational for many sports, they challenge the DPM generally.
format: application/pdf
format: text/html
creator: Michael P. Lombardo
creator: Robert O. Deaner
subject: Evolutionary Studies
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.445
publisher: PeerJ Inc.
rights: © 2014 Lombardo and Deaner
abstract: Many scientists agree that expertise requires both innate talent and proper training. Nevertheless, the highly influential deliberate practice model (DPM) of expertise holds that talent does not exist or makes a negligible contribution to performance. It predicts that initial performance will be unrelated to achieving expertise and that 10 years of deliberate practice is necessary. We tested these predictions in the domain of sprinting. In Studies 1 and 2 we reviewed biographies of 15 Olympic champions and the 20 fastest American men in U.S. history. In all documented cases, sprinters were exceptional prior to initiating training, and most reached world class status rapidly (Study 1 median = 3 years; Study 2 = 7.5). In Study 3 we surveyed U.S. national collegiate championships qualifiers in sprinters (n = 20) and throwers (n = 44). Sprinters recalled being faster as youths than did throwers, whereas throwers recalled greater strength and throwing ability. Sprinters’ best performances in their first season of high school, generally the onset of formal training, were consistently faster than 95–99% of their peers. Collectively, these results falsify the DPM for sprinting. Because speed is foundational for many sports, they challenge the DPM generally.
bibliographic citation: Lombardo et al. (2014) You can’t teach speed: sprinters falsify the deliberate practice model of expertise. PeerJ 2:e445 https://doi.org/10.7717/peerj.445
date submitted: 2014-04-11
date accepted: 2014-06-02
issued: 2014-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lombardo
  given name: Michael P.
author list: Agent
  family name: Deaner
  given name: Robert O.
doi: 10.7717/peerj.445
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-26
copyright: © 2014 Lombardo and Deaner
attribution name: Lombardo and Deaner

QSpec: online control and data analysis system for single-cell Raman spectroscopy
type: item
type: AcademicArticle
description: Single-cell phenotyping is critical to the success of biological reductionism. Raman-activated cell sorting (RACS) has shown promise in resolving the dynamics of living cells at the individual level and to uncover population heterogeneities in comparison to established approaches such as fluorescence-activated cell sorting (FACS). Given that the number of single-cells would be massive in any experiment, the power of Raman profiling technique for single-cell analysis would be fully utilized only when coupled with a high-throughput and intelligent process control and data analysis system. In this work, we established QSpec, an automatic system that supports high-throughput Raman-based single-cell phenotyping. Additionally, a single-cell Raman profile database has been established upon which data-mining could be applied to discover the heterogeneity among single-cells under different conditions. To test the effectiveness of this control and data analysis system, a sub-system was also developed to simulate the phenotypes of single-cells as well as the device features.
format: application/pdf
format: text/html
creator: Lihui Ren
creator: Xiaoquan Su
creator: Yun Wang
creator: Jian Xu
creator: Kang Ning
subject: Bioinformatics
subject: Biotechnology
subject: Computational Biology
description: doi:10.7717/peerj.436
publisher: PeerJ Inc.
rights: © 2014 Ren et al.
abstract: Single-cell phenotyping is critical to the success of biological reductionism. Raman-activated cell sorting (RACS) has shown promise in resolving the dynamics of living cells at the individual level and to uncover population heterogeneities in comparison to established approaches such as fluorescence-activated cell sorting (FACS). Given that the number of single-cells would be massive in any experiment, the power of Raman profiling technique for single-cell analysis would be fully utilized only when coupled with a high-throughput and intelligent process control and data analysis system. In this work, we established QSpec, an automatic system that supports high-throughput Raman-based single-cell phenotyping. Additionally, a single-cell Raman profile database has been established upon which data-mining could be applied to discover the heterogeneity among single-cells under different conditions. To test the effectiveness of this control and data analysis system, a sub-system was also developed to simulate the phenotypes of single-cells as well as the device features.
bibliographic citation: Ren et al. (2014) QSpec: online control and data analysis system for single-cell Raman spectroscopy. PeerJ 2:e436 https://doi.org/10.7717/peerj.436
date submitted: 2014-04-02
date accepted: 2014-05-29
issued: 2014-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Lihui
author list: Agent
  family name: Su
  given name: Xiaoquan
author list: Agent
  family name: Wang
  given name: Yun
author list: Agent
  family name: Xu
  given name: Jian
author list: Agent
  family name: Ning
  given name: Kang
doi: 10.7717/peerj.436
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-26
copyright: © 2014 Ren et al.
attribution name: Ren et al.

Beyond birth-weight: early growth and adolescent blood pressure in a Peruvian population
type: item
type: AcademicArticle
description: Background. Longitudinal investigations into the origins of adult essential hypertension have found elevated blood pressure in children to accurately track into adulthood, however the direct causes of essential hypertension in adolescence and adulthood remains unclear. Methods. We revisited 152 Peruvian adolescents from a birth cohort tracked from 0 to 30 months of age, and evaluated growth via monthly anthropometric measurements between 1995 and 1998, and obtained anthropometric and blood pressure measurements 11–14 years later. We used multivariable regression models to study the effects of infantile and childhood growth trends on blood pressure and central obesity in early adolescence. Results. In regression models adjusted for interim changes in weight and height, each 0.1 SD increase in weight for length from 0 to 5 months of age, and 1 SD increase from 6 to 30 months of age, was associated with decreased adolescent systolic blood pressure by 1.3 mm Hg (95% CI −2.4 to −0.1) and 2.5 mm Hg (95% CI −4.9 to 0.0), and decreased waist circumference by 0.6 (95% CI −1.1 to 0.0) and 1.2 cm (95% CI −2.3 to −0.1), respectively. Growth in infancy and early childhood was not significantly associated with adolescent waist-to-hip ratio. Conclusions. Rapid compensatory growth in early life has been posited to increase the risk of long-term cardiovascular morbidities such that nutritional interventions may do more harm than good. However, we found increased weight growth during infancy and early childhood to be associated with decreased systolic blood pressure and central adiposity in adolescence.
format: application/pdf
format: text/html
creator: Robie Sterling
creator: William Checkley
creator: Robert H. Gilman
creator: Lilia Cabrera
creator: Charles R. Sterling
creator: Caryn Bern
creator: J. Jaime Miranda
subject: Epidemiology
subject: Global Health
subject: Pediatrics
subject: Public Health
subject: Statistics
description: doi:10.7717/peerj.381
publisher: PeerJ Inc.
rights: © 2014 Sterling et al.
abstract: Background. Longitudinal investigations into the origins of adult essential hypertension have found elevated blood pressure in children to accurately track into adulthood, however the direct causes of essential hypertension in adolescence and adulthood remains unclear. Methods. We revisited 152 Peruvian adolescents from a birth cohort tracked from 0 to 30 months of age, and evaluated growth via monthly anthropometric measurements between 1995 and 1998, and obtained anthropometric and blood pressure measurements 11–14 years later. We used multivariable regression models to study the effects of infantile and childhood growth trends on blood pressure and central obesity in early adolescence. Results. In regression models adjusted for interim changes in weight and height, each 0.1 SD increase in weight for length from 0 to 5 months of age, and 1 SD increase from 6 to 30 months of age, was associated with decreased adolescent systolic blood pressure by 1.3 mm Hg (95% CI −2.4 to −0.1) and 2.5 mm Hg (95% CI −4.9 to 0.0), and decreased waist circumference by 0.6 (95% CI −1.1 to 0.0) and 1.2 cm (95% CI −2.3 to −0.1), respectively. Growth in infancy and early childhood was not significantly associated with adolescent waist-to-hip ratio. Conclusions. Rapid compensatory growth in early life has been posited to increase the risk of long-term cardiovascular morbidities such that nutritional interventions may do more harm than good. However, we found increased weight growth during infancy and early childhood to be associated with decreased systolic blood pressure and central adiposity in adolescence.
bibliographic citation: Sterling et al. (2014) Beyond birth-weight: early growth and adolescent blood pressure in a Peruvian population. PeerJ 2:e381 https://doi.org/10.7717/peerj.381
date submitted: 2013-12-30
date accepted: 2014-04-24
issued: 2014-06-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Sterling
  given name: Robie
author list: Agent
  family name: Checkley
  given name: William
author list: Agent
  family name: Gilman
  given name: Robert H.
author list: Agent
  family name: Cabrera
  given name: Lilia
author list: Agent
  family name: Sterling
  given name: Charles R.
author list: Agent
  family name: Bern
  given name: Caryn
author list: Agent
  family name: Miranda
  given name: J. Jaime
doi: 10.7717/peerj.381
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-26
copyright: © 2014 Sterling et al.
attribution name: Sterling et al.

Single cell transcriptional analysis reveals novel innate immune cell types
type: item
type: AcademicArticle
description: Single-cell analysis has the potential to provide us with a host of new knowledge about biological systems, but it comes with the challenge of correctly interpreting the biological information. While emerging techniques have made it possible to measure inter-cellular variability at the transcriptome level, no consensus yet exists on the most appropriate method of data analysis of such single cell data. Methods for analysis of transcriptional data at the population level are well established but are not well suited to single cell analysis due to their dependence on population averages. In order to address this question, we have systematically tested combinations of methods for primary data analysis on single cell transcription data generated from two types of primary immune cells, neutrophils and T lymphocytes. Cells were obtained from healthy individuals, and single cell transcript expression data was obtained by a combination of single cell sorting and nanoscale quantitative real time PCR (qRT-PCR) for markers of cell type, intracellular signaling, and immune functionality. Gene expression analysis was focused on hierarchical clustering to determine the existence of cellular subgroups within the populations. Nine combinations of criteria for data exclusion and normalization were tested and evaluated. Bimodality in gene expression indicated the presence of cellular subgroups which were also revealed by data clustering. We observed evidence for two clearly defined cellular subtypes in the neutrophil populations and at least two in the T lymphocyte populations. When normalizing the data by different methods, we observed varying outcomes with corresponding interpretations of the biological characteristics of the cell populations. Normalization of the data by linear standardization taking into account technical effects such as plate effects, resulted in interpretations that most closely matched biological expectations. Single cell transcription profiling provides eviden…
format: application/pdf
format: text/html
creator: Linda E. Kippner
creator: Jinhee Kim
creator: Greg Gibson
creator: Melissa L. Kemp
subject: Bioinformatics
subject: Immunology
description: doi:10.7717/peerj.452
publisher: PeerJ Inc.
rights: © 2014 Kippner et al.
abstract: Single-cell analysis has the potential to provide us with a host of new knowledge about biological systems, but it comes with the challenge of correctly interpreting the biological information. While emerging techniques have made it possible to measure inter-cellular variability at the transcriptome level, no consensus yet exists on the most appropriate method of data analysis of such single cell data. Methods for analysis of transcriptional data at the population level are well established but are not well suited to single cell analysis due to their dependence on population averages. In order to address this question, we have systematically tested combinations of methods for primary data analysis on single cell transcription data generated from two types of primary immune cells, neutrophils and T lymphocytes. Cells were obtained from healthy individuals, and single cell transcript expression data was obtained by a combination of single cell sorting and nanoscale quantitative real time PCR (qRT-PCR) for markers of cell type, intracellular signaling, and immune functionality. Gene expression analysis was focused on hierarchical clustering to determine the existence of cellular subgroups within the populations. Nine combinations of criteria for data exclusion and normalization were tested and evaluated. Bimodality in gene expression indicated the presence of cellular subgroups which were also revealed by data clustering. We observed evidence for two clearly defined cellular subtypes in the neutrophil populations and at least two in the T lymphocyte populations. When normalizing the data by different methods, we observed varying outcomes with corresponding interpretations of the biological characteristics of the cell populations. Normalization of the data by linear standardization taking into account technical effects such as plate effects, resulted in interpretations that most closely matched biological expectations. Single cell transcription profiling provides eviden…
bibliographic citation: Kippner et al. (2014) Single cell transcriptional analysis reveals novel innate immune cell types. PeerJ 2:e452 https://doi.org/10.7717/peerj.452
date submitted: 2014-03-13
date accepted: 2014-06-04
issued: 2014-06-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kippner
  given name: Linda E.
author list: Agent
  family name: Kim
  given name: Jinhee
author list: Agent
  family name: Gibson
  given name: Greg
author list: Agent
  family name: Kemp
  given name: Melissa L.
doi: 10.7717/peerj.452
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-24
copyright: © 2014 Kippner et al.
attribution name: Kippner et al.

Mobile phones carry the personal microbiome of their owners
type: item
type: AcademicArticle
description: Most people on the planet own mobile phones, and these devices are increasingly being utilized to gather data relevant to our personal health, behavior, and environment. During an educational workshop, we investigated the utility of mobile phones to gather data about the personal microbiome — the collection of microorganisms associated with the personal effects of an individual. We characterized microbial communities on smartphone touchscreens to determine whether there was significant overlap with the skin microbiome sampled directly from their owners. We found that about 22% of the bacterial taxa on participants’ fingers were also present on their own phones, as compared to 17% they shared on average with other people’s phones. When considered as a group, bacterial communities on men’s phones were significantly different from those on their fingers, while women’s were not. Yet when considered on an individual level, men and women both shared significantly more of their bacterial communities with their own phones than with anyone else’s. In fact, 82% of the OTUs were shared between a person’s index and phone when considering the dominant taxa (OTUs with more than 0.1% of the sequences in an individual’s dataset). Our results suggest that mobile phones hold untapped potential as personal microbiome sensors.
format: application/pdf
format: text/html
creator: James F. Meadow
creator: Adam E. Altrichter
creator: Jessica L. Green
subject: Ecology
subject: Microbiology
subject: Drugs and Devices
subject: Public Health
description: doi:10.7717/peerj.447
publisher: PeerJ Inc.
rights: © 2014 Meadow et al.
abstract: Most people on the planet own mobile phones, and these devices are increasingly being utilized to gather data relevant to our personal health, behavior, and environment. During an educational workshop, we investigated the utility of mobile phones to gather data about the personal microbiome — the collection of microorganisms associated with the personal effects of an individual. We characterized microbial communities on smartphone touchscreens to determine whether there was significant overlap with the skin microbiome sampled directly from their owners. We found that about 22% of the bacterial taxa on participants’ fingers were also present on their own phones, as compared to 17% they shared on average with other people’s phones. When considered as a group, bacterial communities on men’s phones were significantly different from those on their fingers, while women’s were not. Yet when considered on an individual level, men and women both shared significantly more of their bacterial communities with their own phones than with anyone else’s. In fact, 82% of the OTUs were shared between a person’s index and phone when considering the dominant taxa (OTUs with more than 0.1% of the sequences in an individual’s dataset). Our results suggest that mobile phones hold untapped potential as personal microbiome sensors.
bibliographic citation: Meadow et al. (2014) Mobile phones carry the personal microbiome of their owners. PeerJ 2:e447 https://doi.org/10.7717/peerj.447
date submitted: 2014-05-04
date accepted: 2014-06-03
issued: 2014-06-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meadow
  given name: James F.
author list: Agent
  family name: Altrichter
  given name: Adam E.
author list: Agent
  family name: Green
  given name: Jessica L.
doi: 10.7717/peerj.447
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-24
copyright: © 2014 Meadow et al.
attribution name: Meadow et al.

Functional connectivity in task-negative network of the Deaf: effects of sign language experience
type: item
type: AcademicArticle
description: Prior studies investigating cortical processing in Deaf signers suggest that life-long experience with sign language and/or auditory deprivation may alter the brain’s anatomical structure and the function of brain regions typically recruited for auditory processing (Emmorey et al., 2010; Pénicaud et al., 2013 inter alia). We report the first investigation of the task-negative network in Deaf signers and its functional connectivity—the temporal correlations among spatially remote neurophysiological events. We show that Deaf signers manifest increased functional connectivity between posterior cingulate/precuneus and left medial temporal gyrus (MTG), but also inferior parietal lobe and medial temporal gyrus in the right hemisphere- areas that have been found to show functional recruitment specifically during sign language processing. These findings suggest that the organization of the brain at the level of inter-network connectivity is likely affected by experience with processing visual language, although sensory deprivation could be another source of the difference. We hypothesize that connectivity alterations in the task negative network reflect predictive/automatized processing of the visual signal.
format: application/pdf
format: text/html
creator: Evie Malaia
creator: Thomas M. Talavage
creator: Ronnie B. Wilbur
subject: Neuroscience
description: doi:10.7717/peerj.446
publisher: PeerJ Inc.
rights: © 2014 Malaia et al.
abstract: Prior studies investigating cortical processing in Deaf signers suggest that life-long experience with sign language and/or auditory deprivation may alter the brain’s anatomical structure and the function of brain regions typically recruited for auditory processing (Emmorey et al., 2010; Pénicaud et al., 2013 inter alia). We report the first investigation of the task-negative network in Deaf signers and its functional connectivity—the temporal correlations among spatially remote neurophysiological events. We show that Deaf signers manifest increased functional connectivity between posterior cingulate/precuneus and left medial temporal gyrus (MTG), but also inferior parietal lobe and medial temporal gyrus in the right hemisphere- areas that have been found to show functional recruitment specifically during sign language processing. These findings suggest that the organization of the brain at the level of inter-network connectivity is likely affected by experience with processing visual language, although sensory deprivation could be another source of the difference. We hypothesize that connectivity alterations in the task negative network reflect predictive/automatized processing of the visual signal.
bibliographic citation: Malaia et al. (2014) Functional connectivity in task-negative network of the Deaf: effects of sign language experience. PeerJ 2:e446 https://doi.org/10.7717/peerj.446
date submitted: 2014-03-16
date accepted: 2014-06-02
issued: 2014-06-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malaia
  given name: Evie
author list: Agent
  family name: Talavage
  given name: Thomas M.
author list: Agent
  family name: Wilbur
  given name: Ronnie B.
doi: 10.7717/peerj.446
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-24
copyright: © 2014 Malaia et al.
attribution name: Malaia et al.

Facelock: familiarity-based graphical authentication
type: item
type: AcademicArticle
description: Authentication codes such as passwords and PIN numbers are widely used to control access to resources. One major drawback of these codes is that they are difficult to remember. Account holders are often faced with a choice between forgetting a code, which can be inconvenient, or writing it down, which compromises security. In two studies, we test a new knowledge-based authentication method that does not impose memory load on the user. Psychological research on face recognition has revealed an important distinction between familiar and unfamiliar face perception: When a face is familiar to the observer, it can be identified across a wide range of images. However, when the face is unfamiliar, generalisation across images is poor. This contrast can be used as the basis for a personalised ‘facelock’, in which authentication succeeds or fails based on image-invariant recognition of faces that are familiar to the account holder. In Study 1, account holders authenticated easily by detecting familiar targets among other faces (97.5% success rate), even after a one-year delay (86.1% success rate). Zero-acquaintance attackers were reduced to guessing (<1% success rate). Even personal attackers who knew the account holder well were rarely able to authenticate (6.6% success rate). In Study 2, we found that shoulder-surfing attacks by strangers could be defeated by presenting different photos of the same target faces in observed and attacked grids (1.9% success rate). Our findings suggest that the contrast between familiar and unfamiliar face recognition may be useful for developers of graphical authentication systems.
format: application/pdf
format: text/html
creator: Rob Jenkins
creator: Jane L. McLachlan
creator: Karen Renaud
subject: Human-Computer Interaction
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.444
publisher: PeerJ Inc.
rights: © 2014 Jenkins et al.
abstract: Authentication codes such as passwords and PIN numbers are widely used to control access to resources. One major drawback of these codes is that they are difficult to remember. Account holders are often faced with a choice between forgetting a code, which can be inconvenient, or writing it down, which compromises security. In two studies, we test a new knowledge-based authentication method that does not impose memory load on the user. Psychological research on face recognition has revealed an important distinction between familiar and unfamiliar face perception: When a face is familiar to the observer, it can be identified across a wide range of images. However, when the face is unfamiliar, generalisation across images is poor. This contrast can be used as the basis for a personalised ‘facelock’, in which authentication succeeds or fails based on image-invariant recognition of faces that are familiar to the account holder. In Study 1, account holders authenticated easily by detecting familiar targets among other faces (97.5% success rate), even after a one-year delay (86.1% success rate). Zero-acquaintance attackers were reduced to guessing (<1% success rate). Even personal attackers who knew the account holder well were rarely able to authenticate (6.6% success rate). In Study 2, we found that shoulder-surfing attacks by strangers could be defeated by presenting different photos of the same target faces in observed and attacked grids (1.9% success rate). Our findings suggest that the contrast between familiar and unfamiliar face recognition may be useful for developers of graphical authentication systems.
bibliographic citation: Jenkins et al. (2014) Facelock: familiarity-based graphical authentication. PeerJ 2:e444 https://doi.org/10.7717/peerj.444
date submitted: 2014-04-11
date accepted: 2014-06-02
issued: 2014-06-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jenkins
  given name: Rob
author list: Agent
  family name: McLachlan
  given name: Jane L.
author list: Agent
  family name: Renaud
  given name: Karen
doi: 10.7717/peerj.444
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-24
copyright: © 2014 Jenkins et al.
attribution name: Jenkins et al.

scikit-image: image processing in Python
type: item
type: AcademicArticle
description: scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org.
format: application/pdf
format: text/html
creator: Stéfan van der Walt
creator: Johannes L. Schönberger
creator: Juan Nunez-Iglesias
creator: François Boulogne
creator: Joshua D. Warner
creator: Neil Yager
creator: Emmanuelle Gouillart
creator: Tony Yu
subject: Bioinformatics
subject: Computational Biology
subject: Computational Science
subject: Human-Computer Interaction
subject: Science and Medical Education
description: doi:10.7717/peerj.453
publisher: PeerJ Inc.
rights: © 2014 Van der Walt et al.
abstract: scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org.
bibliographic citation: van der Walt et al. (2014) scikit-image: image processing in Python. PeerJ 2:e453 https://doi.org/10.7717/peerj.453
date submitted: 2014-04-02
date accepted: 2014-06-04
issued: 2014-06-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: van der Walt
  given name: Stéfan
author list: Agent
  family name: Schönberger
  given name: Johannes L.
author list: Agent
  family name: Nunez-Iglesias
  given name: Juan
author list: Agent
  family name: Boulogne
  given name: François
author list: Agent
  family name: Warner
  given name: Joshua D.
author list: Agent
  family name: Yager
  given name: Neil
author list: Agent
  family name: Gouillart
  given name: Emmanuelle
author list: Agent
  family name: Yu
  given name: Tony
doi: 10.7717/peerj.453
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-19
copyright: © 2014 Van der Walt et al.
attribution name: Van der Walt et al.

A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+
type: item
type: AcademicArticle
description: We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g., when computing vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent, compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible.
format: application/pdf
format: text/html
creator: Jimmy C. Kromann
creator: Anders S. Christensen
creator: Casper Steinmann
creator: Martin Korth
creator: Jan H. Jensen
subject: Biochemistry
subject: Computational Biology
subject: Computational Science
description: doi:10.7717/peerj.449
publisher: PeerJ Inc.
rights: © 2014 Kromann et al.
abstract: We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g., when computing vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent, compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible.
bibliographic citation: Kromann et al. (2014) A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+. PeerJ 2:e449 https://doi.org/10.7717/peerj.449
date submitted: 2014-04-04
date accepted: 2014-06-04
issued: 2014-06-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kromann
  given name: Jimmy C.
author list: Agent
  family name: Christensen
  given name: Anders S.
author list: Agent
  family name: Steinmann
  given name: Casper
author list: Agent
  family name: Korth
  given name: Martin
author list: Agent
  family name: Jensen
  given name: Jan H.
doi: 10.7717/peerj.449
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-19
copyright: © 2014 Kromann et al.
attribution name: Kromann et al.

Identification of MHCII variants associated with chlamydial disease in the koala (Phascolarctos cinereus)
type: item
type: AcademicArticle
description: Chlamydiosis, the most common infectious disease in koalas, can cause chronic urogenital tract fibrosis and infertility. High titres of serum immunoglobulin G against 10 kDa and 60 kDa chlamydial heat-shock proteins (c-hsp10 and c-hsp60) are associated with fibrous occlusion of the koala uterus and uterine tube. Murine and human studies have identified associations between specific major histocompatibility complex class II (MHCII) alleles or genotypes, and higher c-hsp 60 antibody levels or chlamydia-associated disease and infertility. In this study, we characterised partial MHCII DAB and DBB genes in female koalas (n = 94) from a single geographic population, and investigated associations among antibody responses to c-hsp60 quantified by ELISA, susceptibility to chlamydial infection, or age. The identification of three candidate MHCII variants provides additional support for the functional role of MHCII in the koala, and will inform more focused future studies. This is the first study to investigate an association between MHC genes with chlamydial pathogenesis in a non-model, free-ranging species.
format: application/pdf
format: text/html
creator: Quintin Lau
creator: Joanna E. Griffith
creator: Damien P. Higgins
subject: Conservation Biology
subject: Molecular Biology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.443
publisher: PeerJ Inc.
rights: © 2014 Lau et al.
abstract: Chlamydiosis, the most common infectious disease in koalas, can cause chronic urogenital tract fibrosis and infertility. High titres of serum immunoglobulin G against 10 kDa and 60 kDa chlamydial heat-shock proteins (c-hsp10 and c-hsp60) are associated with fibrous occlusion of the koala uterus and uterine tube. Murine and human studies have identified associations between specific major histocompatibility complex class II (MHCII) alleles or genotypes, and higher c-hsp 60 antibody levels or chlamydia-associated disease and infertility. In this study, we characterised partial MHCII DAB and DBB genes in female koalas (n = 94) from a single geographic population, and investigated associations among antibody responses to c-hsp60 quantified by ELISA, susceptibility to chlamydial infection, or age. The identification of three candidate MHCII variants provides additional support for the functional role of MHCII in the koala, and will inform more focused future studies. This is the first study to investigate an association between MHC genes with chlamydial pathogenesis in a non-model, free-ranging species.
bibliographic citation: Lau et al. (2014) Identification of MHCII variants associated with chlamydial disease in the koala (Phascolarctos cinereus). PeerJ 2:e443 https://doi.org/10.7717/peerj.443
date submitted: 2014-03-21
date accepted: 2014-06-02
issued: 2014-06-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lau
  given name: Quintin
author list: Agent
  family name: Griffith
  given name: Joanna E.
author list: Agent
  family name: Higgins
  given name: Damien P.
doi: 10.7717/peerj.443
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-19
copyright: © 2014 Lau et al.
attribution name: Lau et al.

Photobacterium sanctipauli sp. nov. isolated from bleached Madracis decactis (Scleractinia) in the St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil
type: item
type: AcademicArticle
description: Five novel strains of Photobacterium (A-394T, A-373, A-379, A-397 and A-398) were isolated from bleached coral Madracis decactis (scleractinian) in the remote St Peter & St Archipelago (SPSPA), Mid-Atlantic Ridge, Brazil. Healthy M. decactis specimens were also surveyed, but no strains were related to them. The novel isolates formed a distinct lineage based on the 16S rRNA, recA, and rpoA gene sequences analysis. Their closest phylogenetic neighbours were Photobacterium rosenbergii, P. gaetbulicola, and P. lutimaris, sharing 96.6 to 95.8% 16S rRNA gene sequence similarity. The novel species can be differentiated from the closest neighbours by several phenotypic and chemotaxonomic markers. It grows at pH 11, produces tryptophane deaminase, presents the fatty acid C18:0, but lacks C16:0 iso. The whole cell protein profile, based in MALDI-TOF MS, distinguished the strains of the novel species among each other and from the closest neighbors. In addition, we are releasing the whole genome sequence of the type strain. The name Photobacterium sanctipauli sp. nov. is proposed for this taxon. The G + C content of the type strain A-394T (= LMG27910T = CAIM1892T) is 48.2 mol%.
format: application/pdf
format: text/html
creator: Ana Paula B. Moreira
creator: Gwen Duytschaever
creator: Luciane A. Chimetto Tonon
creator: Adriana M. Fróes
creator: Louisi S. de Oliveira
creator: Gilberto M. Amado-Filho
creator: Ronaldo B. Francini-Filho
creator: Paul De Vos
creator: Jean Swings
creator: Cristiane C. Thompson
creator: Fabiano L. Thompson
subject: Biodiversity
subject: Genomics
subject: Marine Biology
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.427
publisher: PeerJ Inc.
rights: © 2014 Moreira et al.
abstract: Five novel strains of Photobacterium (A-394T, A-373, A-379, A-397 and A-398) were isolated from bleached coral Madracis decactis (scleractinian) in the remote St Peter & St Archipelago (SPSPA), Mid-Atlantic Ridge, Brazil. Healthy M. decactis specimens were also surveyed, but no strains were related to them. The novel isolates formed a distinct lineage based on the 16S rRNA, recA, and rpoA gene sequences analysis. Their closest phylogenetic neighbours were Photobacterium rosenbergii, P. gaetbulicola, and P. lutimaris, sharing 96.6 to 95.8% 16S rRNA gene sequence similarity. The novel species can be differentiated from the closest neighbours by several phenotypic and chemotaxonomic markers. It grows at pH 11, produces tryptophane deaminase, presents the fatty acid C18:0, but lacks C16:0 iso. The whole cell protein profile, based in MALDI-TOF MS, distinguished the strains of the novel species among each other and from the closest neighbors. In addition, we are releasing the whole genome sequence of the type strain. The name Photobacterium sanctipauli sp. nov. is proposed for this taxon. The G + C content of the type strain A-394T (= LMG27910T = CAIM1892T) is 48.2 mol%.
bibliographic citation: Moreira et al. (2014) Photobacterium sanctipauli sp. nov. isolated from bleached Madracis decactis (Scleractinia) in the St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil. PeerJ 2:e427 https://doi.org/10.7717/peerj.427
date submitted: 2014-03-18
date accepted: 2014-05-22
issued: 2014-06-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreira
  given name: Ana Paula B.
author list: Agent
  family name: Duytschaever
  given name: Gwen
author list: Agent
  family name: Chimetto Tonon
  given name: Luciane A.
author list: Agent
  family name: Fróes
  given name: Adriana M.
author list: Agent
  family name: de Oliveira
  given name: Louisi S.
author list: Agent
  family name: Amado-Filho
  given name: Gilberto M.
author list: Agent
  family name: Francini-Filho
  given name: Ronaldo B.
author list: Agent
  family name: De Vos
  given name: Paul
author list: Agent
  family name: Swings
  given name: Jean
author list: Agent
  family name: Thompson
  given name: Cristiane C.
author list: Agent
  family name: Thompson
  given name: Fabiano L.
doi: 10.7717/peerj.427
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-19
copyright: © 2014 Moreira et al.
attribution name: Moreira et al.

Movement and ranging patterns of the Common Chaffinch in heterogeneous forest landscapes
type: item
type: AcademicArticle
description: The partitioning of production forests into discretely managed forest stands confronts animals with diversity in forest attributes at scales from point-level tree assemblages to distinct forest patches and range-level forest cover. We have investigated the movement and ranging patterns of male Common Chaffinches, Fringilla coelebs, in heterogeneous forest production landscapes during spring and summer in south-western Germany. We radio-tracked a total of 15 adult males, each for up to six days, recording locations at 10-min intervals. We then performed point-level tree surveys at all tracking locations and classified forest stand attributes for the areal covering of birds’ ranges. Movement distances were shortest in beech forest stands and longer in spruce-mixed and non-spruce conifer stands. Movement distances increased with stand age in beech stands but not in others, an effect that was only detectable in a multilevel hierarchical model. We found negligible effects of point-level tree assemblages and temperature on movement distances. Daily range estimates were from 0.01 to 8.0 hectare (median of 0.86 ha) with no evident impact of forest attributes on ranging patterns but considerable intra-individual variation in range sizes over consecutive days. Most daily ranges covered more than one forest stand type. Our results show that forest management impacts the movement behaviour of chaffinches in heterogeneous production forest. Although point-level effects of movement distances are weak compared with stand-level effects in this study, the hierarchical organization of forest is an important aspect to consider when analysing fine-scale movement and might exert more differentiated effects on bird species that are more sensitive to habitat changes than the chaffinch.
format: application/pdf
format: text/html
creator: Katrin Kubiczek
creator: Swen C. Renner
creator: Stefan M. Böhm
creator: Elisabeth K.V. Kalko
creator: Konstans Wells
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
description: doi:10.7717/peerj.368
publisher: PeerJ Inc.
rights: © 2014 Kubiczek et al.
abstract: The partitioning of production forests into discretely managed forest stands confronts animals with diversity in forest attributes at scales from point-level tree assemblages to distinct forest patches and range-level forest cover. We have investigated the movement and ranging patterns of male Common Chaffinches, Fringilla coelebs, in heterogeneous forest production landscapes during spring and summer in south-western Germany. We radio-tracked a total of 15 adult males, each for up to six days, recording locations at 10-min intervals. We then performed point-level tree surveys at all tracking locations and classified forest stand attributes for the areal covering of birds’ ranges. Movement distances were shortest in beech forest stands and longer in spruce-mixed and non-spruce conifer stands. Movement distances increased with stand age in beech stands but not in others, an effect that was only detectable in a multilevel hierarchical model. We found negligible effects of point-level tree assemblages and temperature on movement distances. Daily range estimates were from 0.01 to 8.0 hectare (median of 0.86 ha) with no evident impact of forest attributes on ranging patterns but considerable intra-individual variation in range sizes over consecutive days. Most daily ranges covered more than one forest stand type. Our results show that forest management impacts the movement behaviour of chaffinches in heterogeneous production forest. Although point-level effects of movement distances are weak compared with stand-level effects in this study, the hierarchical organization of forest is an important aspect to consider when analysing fine-scale movement and might exert more differentiated effects on bird species that are more sensitive to habitat changes than the chaffinch.
bibliographic citation: Kubiczek et al. (2014) Movement and ranging patterns of the Common Chaffinch in heterogeneous forest landscapes. PeerJ 2:e368 https://doi.org/10.7717/peerj.368
date submitted: 2014-04-06
date accepted: 2014-04-11
issued: 2014-06-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kubiczek
  given name: Katrin
author list: Agent
  family name: Renner
  given name: Swen C.
author list: Agent
  family name: Böhm
  given name: Stefan M.
author list: Agent
  family name: Kalko
  given name: Elisabeth K.V.
author list: Agent
  family name: Wells
  given name: Konstans
doi: 10.7717/peerj.368
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-19
copyright: © 2014 Kubiczek et al.
attribution name: Kubiczek et al.

Digital dissection of the masticatory muscles of the naked mole-rat, Heterocephalus glaber (Mammalia, Rodentia)
type: item
type: AcademicArticle
description: The naked mole-rat, Heterocephalus glaber, of the family Bathyergidae is a subterranean rodent that feeds on underground roots and tubers and digs extensive tunnel systems with its incisors. It is a highly unusual mammal with regard to its social structure, longevity, pain insensitivity and cancer resistance, all of which have made it the subject of a great deal of research in recent years. Yet, much of the basic anatomy of this species remains undocumented. In this paper, we describe the morphology of the jaw-closing musculature of the naked mole-rat, as revealed by contrast-enhanced micro-computed tomography. This technique uses an iodine stain to enable the imaging of soft tissues with microCT. The iodine-enhanced scans were used to create 3D reconstructions of the naked mole-rat masticatory muscles from which muscle masses were calculated. The jaw-closing musculature of Heterocephalus glaber is relatively very large compared to other rodents and is dominated by the superficial masseter, the deep masseter and the temporalis. The temporalis in particular is large for a rodent, covering the entirety of the braincase and much of the rear part of the orbit. The morphology of the masseter complex described here differs from two other published descriptions of bathyergid masticatory muscles, but is more similar to the arrangement seen in other rodent families. The zygomaticomandibularis (ZM) muscle does not protrude through the infraorbital foramen on to the rostrum and thus the naked mole-rat should be considered protrogomorphous rather than hystricomorphous, and the morphology is consistent with secondarily lost hystricomorphy as has been previously suggested for Bathyergidae. Overall, the morphology of the masticatory musculature indicates a species with a high bite force and a wide gape–both important adaptations for a life dominated by digging with the incisors.
format: application/pdf
format: text/html
creator: Philip G. Cox
creator: Chris G. Faulkes
subject: Evolutionary Studies
subject: Zoology
subject: Anatomy and Physiology
description: doi:10.7717/peerj.448
publisher: PeerJ Inc.
rights: © 2014 Cox and Faulkes
abstract: The naked mole-rat, Heterocephalus glaber, of the family Bathyergidae is a subterranean rodent that feeds on underground roots and tubers and digs extensive tunnel systems with its incisors. It is a highly unusual mammal with regard to its social structure, longevity, pain insensitivity and cancer resistance, all of which have made it the subject of a great deal of research in recent years. Yet, much of the basic anatomy of this species remains undocumented. In this paper, we describe the morphology of the jaw-closing musculature of the naked mole-rat, as revealed by contrast-enhanced micro-computed tomography. This technique uses an iodine stain to enable the imaging of soft tissues with microCT. The iodine-enhanced scans were used to create 3D reconstructions of the naked mole-rat masticatory muscles from which muscle masses were calculated. The jaw-closing musculature of Heterocephalus glaber is relatively very large compared to other rodents and is dominated by the superficial masseter, the deep masseter and the temporalis. The temporalis in particular is large for a rodent, covering the entirety of the braincase and much of the rear part of the orbit. The morphology of the masseter complex described here differs from two other published descriptions of bathyergid masticatory muscles, but is more similar to the arrangement seen in other rodent families. The zygomaticomandibularis (ZM) muscle does not protrude through the infraorbital foramen on to the rostrum and thus the naked mole-rat should be considered protrogomorphous rather than hystricomorphous, and the morphology is consistent with secondarily lost hystricomorphy as has been previously suggested for Bathyergidae. Overall, the morphology of the masticatory musculature indicates a species with a high bite force and a wide gape–both important adaptations for a life dominated by digging with the incisors.
bibliographic citation: Cox et al. (2014) Digital dissection of the masticatory muscles of the naked mole-rat, Heterocephalus glaber (Mammalia, Rodentia). PeerJ 2:e448 https://doi.org/10.7717/peerj.448
date submitted: 2014-04-15
date accepted: 2014-06-03
issued: 2014-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cox
  given name: Philip G.
author list: Agent
  family name: Faulkes
  given name: Chris G.
doi: 10.7717/peerj.448
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-17
copyright: © 2014 Cox and Faulkes
attribution name: Cox and Faulkes

Cascading effects of a highly specialized beech-aphid–fungus interaction on forest regeneration
type: item
type: AcademicArticle
description: Specialist herbivores are thought to often enhance or maintain plant diversity within ecosystems, because they prevent their host species from becoming competitively dominant. In contrast, specialist herbivores are not generally expected to have negative impacts on non-hosts. However, we describe a cascade of indirect interactions whereby a specialist sooty mold (Scorias spongiosa) colonizes the honeydew from a specialist beech aphid (Grylloprociphilus imbricator), ultimately decreasing the survival of seedlings beneath American beech trees (Fagus grandifolia). A common garden experiment indicated that this mortality resulted from moldy honeydew impairing leaf function rather than from chemical or microbial changes to the soil. In addition, aphids consistently and repeatedly colonized the same large beech trees, suggesting that seedling-depauperate islands may form beneath these trees. Thus this highly specialized three-way beech-aphid–fungus interaction has the potential to negatively impact local forest regeneration via a cascade of indirect effects.
format: application/pdf
format: text/html
creator: Susan C. Cook-Patton
creator: Lauren Maynard
creator: Nathan P. Lemoine
creator: Jessica Shue
creator: John D. Parker
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.442
publisher: PeerJ Inc.
rights: © 2014 Cook-Patton et al.
abstract: Specialist herbivores are thought to often enhance or maintain plant diversity within ecosystems, because they prevent their host species from becoming competitively dominant. In contrast, specialist herbivores are not generally expected to have negative impacts on non-hosts. However, we describe a cascade of indirect interactions whereby a specialist sooty mold (Scorias spongiosa) colonizes the honeydew from a specialist beech aphid (Grylloprociphilus imbricator), ultimately decreasing the survival of seedlings beneath American beech trees (Fagus grandifolia). A common garden experiment indicated that this mortality resulted from moldy honeydew impairing leaf function rather than from chemical or microbial changes to the soil. In addition, aphids consistently and repeatedly colonized the same large beech trees, suggesting that seedling-depauperate islands may form beneath these trees. Thus this highly specialized three-way beech-aphid–fungus interaction has the potential to negatively impact local forest regeneration via a cascade of indirect effects.
bibliographic citation: Cook-Patton et al. (2014) Cascading effects of a highly specialized beech-aphid–fungus interaction on forest regeneration. PeerJ 2:e442 https://doi.org/10.7717/peerj.442
date submitted: 2014-04-01
date accepted: 2014-06-02
issued: 2014-06-17
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Cook-Patton
  given name: Susan C.
author list: Agent
  family name: Maynard
  given name: Lauren
author list: Agent
  family name: Lemoine
  given name: Nathan P.
author list: Agent
  family name: Shue
  given name: Jessica
author list: Agent
  family name: Parker
  given name: John D.
doi: 10.7717/peerj.442
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-17
copyright: © 2014 Cook-Patton et al.
attribution name: Cook-Patton et al.

Effectiveness of accommodation and constant resistance training on maximal strength and power in trained athletes
type: item
type: AcademicArticle
description: Accommodation resistance is a training technique that may improve strength and power gains beyond those achieved by traditional free weights. In this method, chains are either added on a free-weight bar and combined with traditional plates or added to the bar as the entire load. Purpose. The aim of the current study was to compare the effectiveness of accommodation and constant resistance training methods during a four-week period on maximal strength and power in trained athletes. Methods. This study was comprised of 24 trained athletes, including 16 trained males [8 Wushu athletes (Kung-Fu) and 8 wrestlers, age: 20.5 ± 2.00 yrs. old]. Participants were initially tested on weight, body circumference, fat percent, upper and lower body maximal strength, determined by the 1-repetition maximum (1RM) test, which determines the greatest amount of weight a person can successfully lift, and upper and lower body power. Participants were equally randomized to either accommodation or constant resistance training groups. Both groups underwent resistance training for a four-week period that consisted of three sessions per week. Multivariate repeated-measures analyses of variance of the data were used to verify significant differences in strength and power between groups. The modified Bonferroni post hoc test was used to compare the obtained results in pre-, mid-, and post test. Results. In the accommodation resistance group, there was a significant difference in lower body maximal strength compared to the constant group (163.12 ± 18.82 kg in the accommodation group vs. 142.25 ± 20.04 kg in the constant group, P = 0.04). No significant differences were found in upper body power, lower body power, and upper body maximal strength between the two groups (P > 0.05). Conclusion. Although there was only a significant difference in lower body maximal strength between groups, accommodation resistance training may induce a physiological training response by improving the strength and powe…
format: application/pdf
format: text/html
creator: Jalil Ataee
creator: Majid S. Koozehchian
creator: Richard B. Kreider
creator: Li Zuo
subject: Biophysics
subject: Kinesiology
description: doi:10.7717/peerj.441
publisher: PeerJ Inc.
rights: © 2014 Ataee et al.
abstract: Accommodation resistance is a training technique that may improve strength and power gains beyond those achieved by traditional free weights. In this method, chains are either added on a free-weight bar and combined with traditional plates or added to the bar as the entire load. Purpose. The aim of the current study was to compare the effectiveness of accommodation and constant resistance training methods during a four-week period on maximal strength and power in trained athletes. Methods. This study was comprised of 24 trained athletes, including 16 trained males [8 Wushu athletes (Kung-Fu) and 8 wrestlers, age: 20.5 ± 2.00 yrs. old]. Participants were initially tested on weight, body circumference, fat percent, upper and lower body maximal strength, determined by the 1-repetition maximum (1RM) test, which determines the greatest amount of weight a person can successfully lift, and upper and lower body power. Participants were equally randomized to either accommodation or constant resistance training groups. Both groups underwent resistance training for a four-week period that consisted of three sessions per week. Multivariate repeated-measures analyses of variance of the data were used to verify significant differences in strength and power between groups. The modified Bonferroni post hoc test was used to compare the obtained results in pre-, mid-, and post test. Results. In the accommodation resistance group, there was a significant difference in lower body maximal strength compared to the constant group (163.12 ± 18.82 kg in the accommodation group vs. 142.25 ± 20.04 kg in the constant group, P = 0.04). No significant differences were found in upper body power, lower body power, and upper body maximal strength between the two groups (P > 0.05). Conclusion. Although there was only a significant difference in lower body maximal strength between groups, accommodation resistance training may induce a physiological training response by improving the strength and powe…
bibliographic citation: Ataee et al. (2014) Effectiveness of accommodation and constant resistance training on maximal strength and power in trained athletes. PeerJ 2:e441 https://doi.org/10.7717/peerj.441
date submitted: 2014-03-26
date accepted: 2014-06-02
issued: 2014-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ataee
  given name: Jalil
author list: Agent
  family name: Koozehchian
  given name: Majid S.
author list: Agent
  family name: Kreider
  given name: Richard B.
author list: Agent
  family name: Zuo
  given name: Li
doi: 10.7717/peerj.441
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-17
copyright: © 2014 Ataee et al.
attribution name: Ataee et al.

Laboratory generation of new parthenogenetic lineages supports contagious parthenogenesis in Artemia
type: item
type: AcademicArticle
description: Contagious parthenogenesis—a process involving rare functional males produced by a parthenogenetic lineage which mate with coexisting sexual females resulting in fertile parthenogenetic offspring—is one of the most striking mechanisms responsible for the generation of new parthenogenetic lineages. Populations of the parthenogenetic diploid brine shrimp Artemia produce fully functional males in low proportions. The evolutionary role of these so-called Artemia rare males is, however, unknown. Here we investigate whether new parthenogenetic clones could be obtained in the laboratory by mating these rare males with sexual females. We assessed the survival and sex ratio of the hybrid ovoviviparous offspring from previous crosses between rare males and females from all Asiatic sexual species, carried out cross-mating experiments between F1 hybrid individuals to assess their fertility, and estimated the viability and the reproductive mode of the resulting F2 offspring. Molecular analysis confirmed the parentage of hybrid parthenogenetic F2. Our study documents the first laboratory synthesis of new parthenogenetic lineages in Artemia and supports a model for the contagious spread of parthenogenesis. Our results suggest recessive inheritance but further experiments are required to confirm the likelihood of the contagious parthenogenesis model.
format: application/pdf
format: text/html
creator: Marta Maccari
creator: Francisco Amat
creator: Francisco Hontoria
creator: Africa Gómez
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.439
publisher: PeerJ Inc.
rights: © 2014 Maccari et al.
abstract: Contagious parthenogenesis—a process involving rare functional males produced by a parthenogenetic lineage which mate with coexisting sexual females resulting in fertile parthenogenetic offspring—is one of the most striking mechanisms responsible for the generation of new parthenogenetic lineages. Populations of the parthenogenetic diploid brine shrimp Artemia produce fully functional males in low proportions. The evolutionary role of these so-called Artemia rare males is, however, unknown. Here we investigate whether new parthenogenetic clones could be obtained in the laboratory by mating these rare males with sexual females. We assessed the survival and sex ratio of the hybrid ovoviviparous offspring from previous crosses between rare males and females from all Asiatic sexual species, carried out cross-mating experiments between F1 hybrid individuals to assess their fertility, and estimated the viability and the reproductive mode of the resulting F2 offspring. Molecular analysis confirmed the parentage of hybrid parthenogenetic F2. Our study documents the first laboratory synthesis of new parthenogenetic lineages in Artemia and supports a model for the contagious spread of parthenogenesis. Our results suggest recessive inheritance but further experiments are required to confirm the likelihood of the contagious parthenogenesis model.
bibliographic citation: Maccari et al. (2014) Laboratory generation of new parthenogenetic lineages supports contagious parthenogenesis in Artemia. PeerJ 2:e439 https://doi.org/10.7717/peerj.439
date submitted: 2014-04-01
date accepted: 2014-05-31
issued: 2014-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maccari
  given name: Marta
author list: Agent
  family name: Amat
  given name: Francisco
author list: Agent
  family name: Hontoria
  given name: Francisco
author list: Agent
  family name: Gómez
  given name: Africa
doi: 10.7717/peerj.439
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-17
copyright: © 2014 Maccari et al.
attribution name: Maccari et al.

Prediction uncertainty assessment of a systems biology model requires a sample of the full probability distribution of its parameters
type: item
type: AcademicArticle
description: Multi-parameter models in systems biology are typically ‘sloppy’: some parameters or combinations of parameters may be hard to estimate from data, whereas others are not. One might expect that parameter uncertainty automatically leads to uncertain predictions, but this is not the case. We illustrate this by showing that the prediction uncertainty of each of six sloppy models varies enormously among different predictions. Statistical approximations of parameter uncertainty may lead to dramatic errors in prediction uncertainty estimation. We argue that prediction uncertainty assessment must therefore be performed on a per-prediction basis using a full computational uncertainty analysis. In practice this is feasible by providing a model with a sample or ensemble representing the distribution of its parameters. Within a Bayesian framework, such a sample may be generated by a Markov Chain Monte Carlo (MCMC) algorithm that infers the parameter distribution based on experimental data. Matlab code for generating the sample (with the Differential Evolution Markov Chain sampler) and the subsequent uncertainty analysis using such a sample, is supplied as Supplemental Information.
format: application/pdf
format: text/html
creator: Simon van Mourik
creator: Cajo ter Braak
creator: Hans Stigter
creator: Jaap Molenaar
subject: Bioinformatics
subject: Computational Biology
subject: Mathematical Biology
subject: Statistics
description: doi:10.7717/peerj.433
publisher: PeerJ Inc.
rights: © 2014 van Mourik et al.
abstract: Multi-parameter models in systems biology are typically ‘sloppy’: some parameters or combinations of parameters may be hard to estimate from data, whereas others are not. One might expect that parameter uncertainty automatically leads to uncertain predictions, but this is not the case. We illustrate this by showing that the prediction uncertainty of each of six sloppy models varies enormously among different predictions. Statistical approximations of parameter uncertainty may lead to dramatic errors in prediction uncertainty estimation. We argue that prediction uncertainty assessment must therefore be performed on a per-prediction basis using a full computational uncertainty analysis. In practice this is feasible by providing a model with a sample or ensemble representing the distribution of its parameters. Within a Bayesian framework, such a sample may be generated by a Markov Chain Monte Carlo (MCMC) algorithm that infers the parameter distribution based on experimental data. Matlab code for generating the sample (with the Differential Evolution Markov Chain sampler) and the subsequent uncertainty analysis using such a sample, is supplied as Supplemental Information.
bibliographic citation: van Mourik et al. (2014) Prediction uncertainty assessment of a systems biology model requires a sample of the full probability distribution of its parameters. PeerJ 2:e433 https://doi.org/10.7717/peerj.433
date submitted: 2014-03-10
date accepted: 2014-05-28
issued: 2014-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: van Mourik
  given name: Simon
author list: Agent
  family name: ter Braak
  given name: Cajo
author list: Agent
  family name: Stigter
  given name: Hans
author list: Agent
  family name: Molenaar
  given name: Jaap
doi: 10.7717/peerj.433
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-17
copyright: © 2014 van Mourik et al.
attribution name: van Mourik et al.

SHAPS-C: the Snaith-Hamilton pleasure scale modified for clinician administration
type: item
type: AcademicArticle
description: Anhedonia, a diminished or lack of ability to experience and anticipate pleasure represents a core psychiatric symptom in depression. Current clinician assessment of anhedonia is generally limited to one or two all-purpose questions and most well-known psychometric scales of anhedonia are relatively long, self-administered, typically not state sensitive, and are unsuitable for use in clinical settings. A user-friendly tool for a more in-depth clinician assessment of hedonic capacity is needed. The present study assessed the validity and reliability of a clinician administered version of the Snaith-Hamilton Pleasure Scale, the SHAPS-C, in 34 depressed subjects. We compared total and specific item scores on the SHAPS-C, SHAPS (self-report version), Montgomery-Åsberg Depression Rating Scale (MADRS), and the Inventory of Depressive Symptomatology-Self Rating version (IDS-SR). We also examined construct, content, concurrent, convergent, and discriminant validity, internal consistency, and split-half reliability of the SHAPS-C. The SHAPS-C was found to be valid and reliable. The SHAPS and the SHAPS-C were positively correlated with one another, with levels of depression severity, as measured by the MADRS, and the IDS-SR total scores, and with specific items of the MADRS and IDS-SR sensitive to measuring hedonic capacity. Our investigation indicates that the SHAPS-C is a user friendly, reliable, and valid tool for clinician assessment of hedonic capacity in depressed bipolar and unipolar patients.
format: application/pdf
format: text/html
creator: Rezvan Ameli
creator: David A. Luckenbaugh
creator: Neda F. Gould
creator: M. Kathleen Holmes
creator: Níall Lally
creator: Elizabeth D. Ballard
creator: Carlos A. Zarate
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.429
publisher: PeerJ Inc.
rights: © 2014 Ameli et al.
abstract: Anhedonia, a diminished or lack of ability to experience and anticipate pleasure represents a core psychiatric symptom in depression. Current clinician assessment of anhedonia is generally limited to one or two all-purpose questions and most well-known psychometric scales of anhedonia are relatively long, self-administered, typically not state sensitive, and are unsuitable for use in clinical settings. A user-friendly tool for a more in-depth clinician assessment of hedonic capacity is needed. The present study assessed the validity and reliability of a clinician administered version of the Snaith-Hamilton Pleasure Scale, the SHAPS-C, in 34 depressed subjects. We compared total and specific item scores on the SHAPS-C, SHAPS (self-report version), Montgomery-Åsberg Depression Rating Scale (MADRS), and the Inventory of Depressive Symptomatology-Self Rating version (IDS-SR). We also examined construct, content, concurrent, convergent, and discriminant validity, internal consistency, and split-half reliability of the SHAPS-C. The SHAPS-C was found to be valid and reliable. The SHAPS and the SHAPS-C were positively correlated with one another, with levels of depression severity, as measured by the MADRS, and the IDS-SR total scores, and with specific items of the MADRS and IDS-SR sensitive to measuring hedonic capacity. Our investigation indicates that the SHAPS-C is a user friendly, reliable, and valid tool for clinician assessment of hedonic capacity in depressed bipolar and unipolar patients.
bibliographic citation: Ameli et al. (2014) SHAPS-C: the Snaith-Hamilton pleasure scale modified for clinician administration. PeerJ 2:e429 https://doi.org/10.7717/peerj.429
date submitted: 2014-03-17
date accepted: 2014-05-26
issued: 2014-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ameli
  given name: Rezvan
author list: Agent
  family name: Luckenbaugh
  given name: David A.
author list: Agent
  family name: Gould
  given name: Neda F.
author list: Agent
  family name: Holmes
  given name: M. Kathleen
author list: Agent
  family name: Lally
  given name: Níall
author list: Agent
  family name: Ballard
  given name: Elizabeth D.
author list: Agent
  family name: Zarate
  given name: Carlos A.
doi: 10.7717/peerj.429
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-17
copyright: © 2014 Ameli et al.
attribution name: Ameli et al.

Geographic variation in the advertisement calls of Hyla eximia and its possible explanations
type: item
type: AcademicArticle
description: Populations of species occupying large geographic ranges are often phenotypically diverse as a consequence of variation in selective pressures and drift. This applies to attributes involved in mate choice, particularly when both geographic range and breeding biology overlap between related species. This condition may lead to interference of mating signals, which would in turn promote reproductive character displacement (RCD). We investigated whether variation in the advertisement call of the mountain treefrog (Hyla eximia) is linked to geographic distribution with respect to major Mexican river basins (Panuco, Lerma, Balsas and Magdalena), or to coexistence with its sister (the canyon treefrog, Hyla arenicolor) or another related species (the dwarf treefrog, Tlalocohyla smithii). We also evaluated whether call divergence across the main river basins could be linked to genetic structure. We found that the multidimensional acoustic space of calls from two basins where H. eximia currently interacts with T. smithii, was different from the acoustic space of calls from H. eximia elsewhere. Individuals from these two basins were also distinguishable from the rest by both the phylogeny inferred from mitochondrial sequences, and the genetic structure inferred from nuclear markers. The discordant divergence of H. eximia advertisement calls in the two separate basins where its geographic range overlaps that of T. smithii can be interpreted as the result of two independent events of RCD, presumably as a consequence of acoustic interference in the breeding choruses, although more data are required to evaluate this possibility.
format: application/pdf
format: text/html
creator: Ruth E. Rodríguez-Tejeda
creator: María Guadalupe Méndez-Cárdenas
creator: Valentina Islas-Villanueva
creator: Constantino Macías Garcia
subject: Animal Behavior
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.420
publisher: PeerJ Inc.
rights: © 2014 Rodríguez-Tejeda et al.
abstract: Populations of species occupying large geographic ranges are often phenotypically diverse as a consequence of variation in selective pressures and drift. This applies to attributes involved in mate choice, particularly when both geographic range and breeding biology overlap between related species. This condition may lead to interference of mating signals, which would in turn promote reproductive character displacement (RCD). We investigated whether variation in the advertisement call of the mountain treefrog (Hyla eximia) is linked to geographic distribution with respect to major Mexican river basins (Panuco, Lerma, Balsas and Magdalena), or to coexistence with its sister (the canyon treefrog, Hyla arenicolor) or another related species (the dwarf treefrog, Tlalocohyla smithii). We also evaluated whether call divergence across the main river basins could be linked to genetic structure. We found that the multidimensional acoustic space of calls from two basins where H. eximia currently interacts with T. smithii, was different from the acoustic space of calls from H. eximia elsewhere. Individuals from these two basins were also distinguishable from the rest by both the phylogeny inferred from mitochondrial sequences, and the genetic structure inferred from nuclear markers. The discordant divergence of H. eximia advertisement calls in the two separate basins where its geographic range overlaps that of T. smithii can be interpreted as the result of two independent events of RCD, presumably as a consequence of acoustic interference in the breeding choruses, although more data are required to evaluate this possibility.
bibliographic citation: Rodríguez-Tejeda et al. (2014) Geographic variation in the advertisement calls of Hyla eximia and its possible explanations. PeerJ 2:e420 https://doi.org/10.7717/peerj.420
date submitted: 2013-12-05
date accepted: 2014-05-19
issued: 2014-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Rodríguez-Tejeda
  given name: Ruth E.
author list: Agent
  family name: Méndez-Cárdenas
  given name: María Guadalupe
author list: Agent
  family name: Islas-Villanueva
  given name: Valentina
author list: Agent
  family name: Macías Garcia
  given name: Constantino
doi: 10.7717/peerj.420
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-17
copyright: © 2014 Rodríguez-Tejeda et al.
attribution name: Rodríguez-Tejeda et al.

Diversity and antimicrobial potential of culturable heterotrophic bacteria associated with the endemic marine sponge Arenosclera brasiliensis
type: item
type: AcademicArticle
description: Marine sponges are the oldest Metazoa, very often presenting a complex microbial consortium. Such is the case of the marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro State, Brazil. In this investigation we characterized the diversity of some of the culturable heterotrophic bacteria living in association with A. brasiliensis and determined their antimicrobial activity. The genera Endozoicomonas (N = 32), Bacillus (N = 26), Shewanella (N = 17), Pseudovibrio (N = 12), and Ruegeria (N = 8) were dominant among the recovered isolates, corresponding to 97% of all isolates. Approximately one third of the isolates living in association with A. brasiliensis produced antibiotics that inhibited the growth of Bacillus subtilis, suggesting that bacteria associated with this sponge play a role in its health.
format: application/pdf
format: text/html
creator: Cintia P.J. Rua
creator: Amaro E. Trindade-Silva
creator: Luciana R. Appolinario
creator: Tainá M. Venas
creator: Gizele D. Garcia
creator: Lucas S. Carvalho
creator: Alinne Lima
creator: Ricardo Kruger
creator: Renato C. Pereira
creator: Roberto G.S. Berlinck
creator: Rogério A.B. Valle
creator: Cristiane C. Thompson
creator: Fabiano Thompson
subject: Biodiversity
subject: Biotechnology
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.419
publisher: PeerJ Inc.
rights: © 2014 Rua et al.
abstract: Marine sponges are the oldest Metazoa, very often presenting a complex microbial consortium. Such is the case of the marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro State, Brazil. In this investigation we characterized the diversity of some of the culturable heterotrophic bacteria living in association with A. brasiliensis and determined their antimicrobial activity. The genera Endozoicomonas (N = 32), Bacillus (N = 26), Shewanella (N = 17), Pseudovibrio (N = 12), and Ruegeria (N = 8) were dominant among the recovered isolates, corresponding to 97% of all isolates. Approximately one third of the isolates living in association with A. brasiliensis produced antibiotics that inhibited the growth of Bacillus subtilis, suggesting that bacteria associated with this sponge play a role in its health.
bibliographic citation: Rua et al. (2014) Diversity and antimicrobial potential of culturable heterotrophic bacteria associated with the endemic marine sponge Arenosclera brasiliensis. PeerJ 2:e419 https://doi.org/10.7717/peerj.419
date submitted: 2014-03-19
date accepted: 2014-05-18
issued: 2014-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rua
  given name: Cintia P.J.
author list: Agent
  family name: Trindade-Silva
  given name: Amaro E.
author list: Agent
  family name: Appolinario
  given name: Luciana R.
author list: Agent
  family name: Venas
  given name: Tainá M.
author list: Agent
  family name: Garcia
  given name: Gizele D.
author list: Agent
  family name: Carvalho
  given name: Lucas S.
author list: Agent
  family name: Lima
  given name: Alinne
author list: Agent
  family name: Kruger
  given name: Ricardo
author list: Agent
  family name: Pereira
  given name: Renato C.
author list: Agent
  family name: Berlinck
  given name: Roberto G.S.
author list: Agent
  family name: Valle
  given name: Rogério A.B.
author list: Agent
  family name: Thompson
  given name: Cristiane C.
author list: Agent
  family name: Thompson
  given name: Fabiano
doi: 10.7717/peerj.419
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-17
copyright: © 2014 Rua et al.
attribution name: Rua et al.

Limited geographic genetic structure detected in a widespread Palearctic corvid, Nucifraga caryocatactes
type: item
type: AcademicArticle
description: The Eurasian or spotted nutcracker (Nucifraga caryocatactes) is a widespread resident corvid found throughout the Palearctic from Central Europe to Japan. Characterized by periodic bouts of irruptive dispersal in search of Pinus seed crops, this species has potential for high levels of gene flow across its range. Previous analysis of 11 individuals did not find significant range-wide population genetic structure. We investigated population structure using 924 base pairs of mitochondrial DNA control region sequence data from 62 individuals from 12 populations distributed throughout the nutcracker’s range. We complemented this analysis by incorporating additional genetic data from previously published sequences. High levels of genetic diversity and limited population genetic structure were detected suggesting that potential barriers to dispersal do not restrict gene flow in nutcrackers.
format: application/pdf
format: text/html
creator: Kimberly M. Dohms
creator: Theresa M. Burg
subject: Biogeography
subject: Ecology
subject: Evolutionary Studies
description: doi:10.7717/peerj.371
publisher: PeerJ Inc.
rights: © 2014 Dohms and Burg
abstract: The Eurasian or spotted nutcracker (Nucifraga caryocatactes) is a widespread resident corvid found throughout the Palearctic from Central Europe to Japan. Characterized by periodic bouts of irruptive dispersal in search of Pinus seed crops, this species has potential for high levels of gene flow across its range. Previous analysis of 11 individuals did not find significant range-wide population genetic structure. We investigated population structure using 924 base pairs of mitochondrial DNA control region sequence data from 62 individuals from 12 populations distributed throughout the nutcracker’s range. We complemented this analysis by incorporating additional genetic data from previously published sequences. High levels of genetic diversity and limited population genetic structure were detected suggesting that potential barriers to dispersal do not restrict gene flow in nutcrackers.
bibliographic citation: Dohms et al. (2014) Limited geographic genetic structure detected in a widespread Palearctic corvid, Nucifraga caryocatactes. PeerJ 2:e371 https://doi.org/10.7717/peerj.371
date submitted: 2013-10-31
date accepted: 2014-04-14
issued: 2014-06-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Dohms
  given name: Kimberly M.
author list: Agent
  family name: Burg
  given name: Theresa M.
doi: 10.7717/peerj.371
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-17
copyright: © 2014 Dohms and Burg
attribution name: Dohms and Burg

Modelling the impacts of an invasive species across landscapes: a step-wise approach
type: item
type: AcademicArticle
description: We estimate the extent of ecological impacts of the invasive Asian paper wasp across different landscapes in New Zealand. We used: (i) a baseline distribution layer (modelled via MaxEnt); (ii) Asian paper wasp nest density (from >460 field plots, related to their preferences for specific land cover categories); and (iii) and their foraging intensity (rates of foraging success, and the time available to forage on a seasonal basis). Using geographic information systems this information is combined and modelled across different landscapes in New Zealand in a step-wise selection process. The highest densities of Asian paper wasps were in herbaceous saline vegetation, followed closely by built-up areas, and then scrub and shrubland. Nest densities of 34 per ha, and occupancy rates of 0.27 were recorded for herbaceous saline vegetation habitats. However, the extent of impacts of the Asian paper wasp remains relatively restricted because of narrow climate tolerances and spatial restriction of preferred habitats. A step-wise process based on geographic information systems and species distribution models, in combination with factors such as distribution, density, and predation, create a useful tool that allows the extent of impacts of invasive species to be assessed across large spatial scales. These models will be useful for conservation managers as they provide easy visual interpretation of results, and can help prioritise where direct conservation action or control of the invader are required.
format: application/pdf
format: text/html
creator: Darren Ward
creator: Fraser Morgan
subject: Biodiversity
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.435
publisher: PeerJ Inc.
rights: © 2014 Ward and Morgan
abstract: We estimate the extent of ecological impacts of the invasive Asian paper wasp across different landscapes in New Zealand. We used: (i) a baseline distribution layer (modelled via MaxEnt); (ii) Asian paper wasp nest density (from >460 field plots, related to their preferences for specific land cover categories); and (iii) and their foraging intensity (rates of foraging success, and the time available to forage on a seasonal basis). Using geographic information systems this information is combined and modelled across different landscapes in New Zealand in a step-wise selection process. The highest densities of Asian paper wasps were in herbaceous saline vegetation, followed closely by built-up areas, and then scrub and shrubland. Nest densities of 34 per ha, and occupancy rates of 0.27 were recorded for herbaceous saline vegetation habitats. However, the extent of impacts of the Asian paper wasp remains relatively restricted because of narrow climate tolerances and spatial restriction of preferred habitats. A step-wise process based on geographic information systems and species distribution models, in combination with factors such as distribution, density, and predation, create a useful tool that allows the extent of impacts of invasive species to be assessed across large spatial scales. These models will be useful for conservation managers as they provide easy visual interpretation of results, and can help prioritise where direct conservation action or control of the invader are required.
bibliographic citation: Ward et al. (2014) Modelling the impacts of an invasive species across landscapes: a step-wise approach. PeerJ 2:e435 https://doi.org/10.7717/peerj.435
date submitted: 2014-04-01
date accepted: 2014-05-29
issued: 2014-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ward
  given name: Darren
author list: Agent
  family name: Morgan
  given name: Fraser
doi: 10.7717/peerj.435
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-12
copyright: © 2014 Ward and Morgan
attribution name: Ward and Morgan

First evidence of bryophyte diaspores in the plumage of transequatorial migrant birds
type: item
type: AcademicArticle
description: Correlations between transequatorial migratory bird routes and bipolar biogeographic disjunctions in bryophytes suggest that disjunctions between northern and southern high latitude regions may result from bird-mediated dispersal; supporting evidence is, however, exclusively circumstantial. Birds disperse plant units (diaspores) internally via ingestion (endozoochory) or externally by the attachment of diaspores to the body (ectozoochory). Endozoochory is known to be the primary means of bird-mediated dispersal for seeds and invertebrates at local, regional, and continental scales. Data supporting the role of bird-mediated endozoochory or ectozoochory in the long distance dispersal of bryophytes remain sparse, however, despite the large number of bryophytes displaying bipolar disjunctions. To determine if transequatorial migrant shorebirds may play a role in the ectozoochory of bryophyte diaspores, we developed a method for screening feathers of wild birds. We provide the first evidence of microscopic bryophyte diaspores, as well as those from non-bryophyte lineages, embedded in the plumage of long distance transequatorial migrant birds captured in their arctic breeding grounds. The number of diaspores recovered suggests that entire migratory populations may be departing their northern breeding grounds laden with potentially viable plant parts and that they could thereby play significant roles in bipolar range expansions of lineages previously ignored in the migrant bird dispersal literature.
format: application/pdf
format: text/html
creator: Lily R. Lewis
creator: Emily Behling
creator: Hannah Gousse
creator: Emily Qian
creator: Chris S. Elphick
creator: Jean-François Lamarre
creator: Joël Bêty
creator: Joe Liebezeit
creator: Ricardo Rozzi
creator: Bernard Goffinet
subject: Biogeography
subject: Ecology
description: doi:10.7717/peerj.424
publisher: PeerJ Inc.
rights: © 2014 Lewis et al.
abstract: Correlations between transequatorial migratory bird routes and bipolar biogeographic disjunctions in bryophytes suggest that disjunctions between northern and southern high latitude regions may result from bird-mediated dispersal; supporting evidence is, however, exclusively circumstantial. Birds disperse plant units (diaspores) internally via ingestion (endozoochory) or externally by the attachment of diaspores to the body (ectozoochory). Endozoochory is known to be the primary means of bird-mediated dispersal for seeds and invertebrates at local, regional, and continental scales. Data supporting the role of bird-mediated endozoochory or ectozoochory in the long distance dispersal of bryophytes remain sparse, however, despite the large number of bryophytes displaying bipolar disjunctions. To determine if transequatorial migrant shorebirds may play a role in the ectozoochory of bryophyte diaspores, we developed a method for screening feathers of wild birds. We provide the first evidence of microscopic bryophyte diaspores, as well as those from non-bryophyte lineages, embedded in the plumage of long distance transequatorial migrant birds captured in their arctic breeding grounds. The number of diaspores recovered suggests that entire migratory populations may be departing their northern breeding grounds laden with potentially viable plant parts and that they could thereby play significant roles in bipolar range expansions of lineages previously ignored in the migrant bird dispersal literature.
bibliographic citation: Lewis et al. (2014) First evidence of bryophyte diaspores in the plumage of transequatorial migrant birds. PeerJ 2:e424 https://doi.org/10.7717/peerj.424
date submitted: 2014-04-08
date accepted: 2014-05-20
issued: 2014-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lewis
  given name: Lily R.
author list: Agent
  family name: Behling
  given name: Emily
author list: Agent
  family name: Gousse
  given name: Hannah
author list: Agent
  family name: Qian
  given name: Emily
author list: Agent
  family name: Elphick
  given name: Chris S.
author list: Agent
  family name: Lamarre
  given name: Jean-François
author list: Agent
  family name: Bêty
  given name: Joël
author list: Agent
  family name: Liebezeit
  given name: Joe
author list: Agent
  family name: Rozzi
  given name: Ricardo
author list: Agent
  family name: Goffinet
  given name: Bernard
doi: 10.7717/peerj.424
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-12
copyright: © 2014 Lewis et al.
attribution name: Lewis et al.

Ape duos and trios: spontaneous cooperation with free partner choice in chimpanzees
type: item
type: AcademicArticle
description: The purpose of the present study was to push the boundaries of cooperation among captive chimpanzees (Pan troglodytes). There has been doubt about the level of cooperation that chimpanzees are able to spontaneously achieve or understand. Would they, without any pre-training or restrictions in partner choice, be able to develop successful joint action? And would they be able to extend cooperation to more than two partners, as they do in nature? Chimpanzees were given a chance to cooperate with multiple partners of their own choosing. All members of the group (N = 11) had simultaneous access to an apparatus that required two (dyadic condition) or three (triadic condition) individuals to pull in a tray baited with food. Without any training, the chimpanzees spontaneously solved the task a total of 3,565 times in both dyadic and triadic combinations. Their success rate and efficiency increased over time, whereas the amount of pulling in the absence of a partner decreased, demonstrating that they had learned the task contingencies. They preferentially approached the apparatus when kin or nonkin of similar rank were present, showing a preference for socially tolerant partners. The forced partner combinations typical of cooperation experiments cannot reveal these abilities, which demonstrate that in the midst of a complex social environment, chimpanzees spontaneously initiate and maintain a high level of cooperative behavior.
format: application/pdf
format: text/html
creator: Malini Suchak
creator: Timothy M. Eppley
creator: Matthew W. Campbell
creator: Frans B.M. de Waal
subject: Animal Behavior
description: doi:10.7717/peerj.417
publisher: PeerJ Inc.
rights: © 2014 Suchak et al.
abstract: The purpose of the present study was to push the boundaries of cooperation among captive chimpanzees (Pan troglodytes). There has been doubt about the level of cooperation that chimpanzees are able to spontaneously achieve or understand. Would they, without any pre-training or restrictions in partner choice, be able to develop successful joint action? And would they be able to extend cooperation to more than two partners, as they do in nature? Chimpanzees were given a chance to cooperate with multiple partners of their own choosing. All members of the group (N = 11) had simultaneous access to an apparatus that required two (dyadic condition) or three (triadic condition) individuals to pull in a tray baited with food. Without any training, the chimpanzees spontaneously solved the task a total of 3,565 times in both dyadic and triadic combinations. Their success rate and efficiency increased over time, whereas the amount of pulling in the absence of a partner decreased, demonstrating that they had learned the task contingencies. They preferentially approached the apparatus when kin or nonkin of similar rank were present, showing a preference for socially tolerant partners. The forced partner combinations typical of cooperation experiments cannot reveal these abilities, which demonstrate that in the midst of a complex social environment, chimpanzees spontaneously initiate and maintain a high level of cooperative behavior.
bibliographic citation: Suchak et al. (2014) Ape duos and trios: spontaneous cooperation with free partner choice in chimpanzees. PeerJ 2:e417 https://doi.org/10.7717/peerj.417
date submitted: 2014-03-09
date accepted: 2014-05-16
issued: 2014-06-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Suchak
  given name: Malini
author list: Agent
  family name: Eppley
  given name: Timothy M.
author list: Agent
  family name: Campbell
  given name: Matthew W.
author list: Agent
  family name: de Waal
  given name: Frans B.M.
doi: 10.7717/peerj.417
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-12
copyright: © 2014 Suchak et al.
attribution name: Suchak et al.

Continental variation in wing pigmentation in Calopteryx damselflies is related to the presence of heterospecifics
type: item
type: AcademicArticle
description: Wing pigmentation in Calopteryx damselflies, caused by the deposition of melanin, is energetically expensive to produce and enhances predation risk. However, patterns of melanisation are used in species identification, greater pigmentation is an accurate signal of male immune function in at least some species, and there may be a role for pigment in thermoregulation. This study tested two potential hypotheses to explain the presence of, and variation in, this pigmentation based on these three potential benefits using 907 male specimens of Calopteryx maculata collected from 49 sites (34 discrete populations) across the geographical range of the species in North America: (i) pigmentation varies with the presence of the closely related species, Calopteryx aequabilis, and (ii) pigment increases at higher latitudes as would be expected if it enhances thermoregulatory capacity. No gradual latitudinal pattern was observed, as might be expected if pigmentation was involved in thermoregulation. However, strong variation was observed between populations that were sympatric or allopatric with C. aequabilis. This variation was characterised by dark wings through allopatry in the south of the range and then a step change to much lighter wings at the southern border of sympatry. Pigmentation then increased further north into the sympatric zone, finally returning to allopatry levels at the northern range margin. These patterns are qualitatively similar to variation in pigmentation in C. aequabilis, meaning that the data are consistent with what would be expected from convergent character displacement. Overall, the results corroborate recent research that has suggested sexual selection as a primary driver behind the evolution of wing pigmentation in this group.
format: application/pdf
format: text/html
creator: Christopher Hassall
subject: Animal Behavior
subject: Biogeography
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
description: doi:10.7717/peerj.438
publisher: PeerJ Inc.
rights: © 2014 Hassall
abstract: Wing pigmentation in Calopteryx damselflies, caused by the deposition of melanin, is energetically expensive to produce and enhances predation risk. However, patterns of melanisation are used in species identification, greater pigmentation is an accurate signal of male immune function in at least some species, and there may be a role for pigment in thermoregulation. This study tested two potential hypotheses to explain the presence of, and variation in, this pigmentation based on these three potential benefits using 907 male specimens of Calopteryx maculata collected from 49 sites (34 discrete populations) across the geographical range of the species in North America: (i) pigmentation varies with the presence of the closely related species, Calopteryx aequabilis, and (ii) pigment increases at higher latitudes as would be expected if it enhances thermoregulatory capacity. No gradual latitudinal pattern was observed, as might be expected if pigmentation was involved in thermoregulation. However, strong variation was observed between populations that were sympatric or allopatric with C. aequabilis. This variation was characterised by dark wings through allopatry in the south of the range and then a step change to much lighter wings at the southern border of sympatry. Pigmentation then increased further north into the sympatric zone, finally returning to allopatry levels at the northern range margin. These patterns are qualitatively similar to variation in pigmentation in C. aequabilis, meaning that the data are consistent with what would be expected from convergent character displacement. Overall, the results corroborate recent research that has suggested sexual selection as a primary driver behind the evolution of wing pigmentation in this group.
bibliographic citation: Hassall (2014) Continental variation in wing pigmentation in Calopteryx damselflies is related to the presence of heterospecifics. PeerJ 2:e438 https://doi.org/10.7717/peerj.438
date submitted: 2014-03-28
date accepted: 2014-05-29
issued: 2014-06-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hassall
  given name: Christopher
doi: 10.7717/peerj.438
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-10
copyright: © 2014 Hassall
attribution name: Hassall

How male sound pressure level influences phonotaxis in virgin female Jamaican field crickets (Gryllus assimilis)
type: item
type: AcademicArticle
description: Understanding female mate preference is important for determining the strength and direction of sexual trait evolution. The sound pressure level (SPL) acoustic signalers use is often an important predictor of mating success because higher sound pressure levels are detectable at greater distances. If females are more attracted to signals produced at higher sound pressure levels, then the potential fitness impacts of signalling at higher sound pressure levels should be elevated beyond what would be expected from detection distance alone. Here we manipulated the sound pressure level of cricket mate attraction signals to determine how female phonotaxis was influenced. We examined female phonotaxis using two common experimental methods: spherical treadmills and open arenas. Both methods showed similar results, with females exhibiting greatest phonotaxis towards loud sound pressure levels relative to the standard signal (69 vs. 60 dB SPL) but showing reduced phonotaxis towards very loud sound pressure level signals relative to the standard (77 vs. 60 dB SPL). Reduced female phonotaxis towards supernormal stimuli may signify an acoustic startle response, an absence of other required sensory cues, or perceived increases in predation risk.
format: application/pdf
format: text/html
creator: Karen Pacheco
creator: Susan M. Bertram
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
description: doi:10.7717/peerj.437
publisher: PeerJ Inc.
rights: © 2014 Pacheco and Bertram
abstract: Understanding female mate preference is important for determining the strength and direction of sexual trait evolution. The sound pressure level (SPL) acoustic signalers use is often an important predictor of mating success because higher sound pressure levels are detectable at greater distances. If females are more attracted to signals produced at higher sound pressure levels, then the potential fitness impacts of signalling at higher sound pressure levels should be elevated beyond what would be expected from detection distance alone. Here we manipulated the sound pressure level of cricket mate attraction signals to determine how female phonotaxis was influenced. We examined female phonotaxis using two common experimental methods: spherical treadmills and open arenas. Both methods showed similar results, with females exhibiting greatest phonotaxis towards loud sound pressure levels relative to the standard signal (69 vs. 60 dB SPL) but showing reduced phonotaxis towards very loud sound pressure level signals relative to the standard (77 vs. 60 dB SPL). Reduced female phonotaxis towards supernormal stimuli may signify an acoustic startle response, an absence of other required sensory cues, or perceived increases in predation risk.
bibliographic citation: Pacheco et al. (2014) How male sound pressure level influences phonotaxis in virgin female Jamaican field crickets (Gryllus assimilis). PeerJ 2:e437 https://doi.org/10.7717/peerj.437
date submitted: 2014-03-30
date accepted: 2014-05-29
issued: 2014-06-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pacheco
  given name: Karen
author list: Agent
  family name: Bertram
  given name: Susan M.
doi: 10.7717/peerj.437
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-10
copyright: © 2014 Pacheco and Bertram
attribution name: Pacheco and Bertram

Immune stimulation reduces sleep and memory ability in Drosophila melanogaster
type: item
type: AcademicArticle
description: Psychoneuroimmunology studies the increasing number of connections between neurobiology, immunology and behaviour. We demonstrate the effects of the immune response on two fundamental behaviours: sleep and memory ability in Drosophila melanogaster. We used the Geneswitch system to upregulate peptidoglycan receptor protein (PGRP) expression, thereby stimulating the immune system in the absence of infection. Geneswitch was activated by feeding the steroid RU486, to the flies. We used an aversive classical conditioning paradigm to quantify memory and measures of activity to infer sleep. Immune stimulated flies exhibited reduced levels of sleep, which could not be explained by a generalised increase in waking activity. Immune stimulated flies also showed a reduction in memory abilities. These results lend support to Drosophila as a model for immune–neural interactions and provide a possible role for sleep in the interplay between the immune response and memory.
format: application/pdf
format: text/html
creator: Eamonn B. Mallon
creator: Akram Alghamdi
creator: Robert T.K. Holdbrook
creator: Ezio Rosato
subject: Animal Behavior
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.434
publisher: PeerJ Inc.
rights: © 2014 Mallon et al.
abstract: Psychoneuroimmunology studies the increasing number of connections between neurobiology, immunology and behaviour. We demonstrate the effects of the immune response on two fundamental behaviours: sleep and memory ability in Drosophila melanogaster. We used the Geneswitch system to upregulate peptidoglycan receptor protein (PGRP) expression, thereby stimulating the immune system in the absence of infection. Geneswitch was activated by feeding the steroid RU486, to the flies. We used an aversive classical conditioning paradigm to quantify memory and measures of activity to infer sleep. Immune stimulated flies exhibited reduced levels of sleep, which could not be explained by a generalised increase in waking activity. Immune stimulated flies also showed a reduction in memory abilities. These results lend support to Drosophila as a model for immune–neural interactions and provide a possible role for sleep in the interplay between the immune response and memory.
bibliographic citation: Mallon et al. (2014) Immune stimulation reduces sleep and memory ability in Drosophila melanogaster. PeerJ 2:e434 https://doi.org/10.7717/peerj.434
date submitted: 2014-03-13
date accepted: 2014-05-29
issued: 2014-06-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mallon
  given name: Eamonn B.
author list: Agent
  family name: Alghamdi
  given name: Akram
author list: Agent
  family name: Holdbrook
  given name: Robert T.K.
author list: Agent
  family name: Rosato
  given name: Ezio
doi: 10.7717/peerj.434
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-10
copyright: © 2014 Mallon et al.
attribution name: Mallon et al.

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms
type: item
type: AcademicArticle
description: Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com.
format: application/pdf
format: text/html
creator: Jonathan B. Puritz
creator: Christopher M. Hollenbeck
creator: John R. Gold
subject: Bioinformatics
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.431
publisher: PeerJ Inc.
rights: © 2014 Puritz et al.
abstract: Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for non-model organisms with large effective population sizes and high levels of genetic polymorphism. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is due to the fact that dDocent quality trims instead of filtering, incorporates both forward and reverse reads (including reads with INDEL polymorphisms) in assembly, mapping, and SNP calling. The pipeline and a comprehensive user guide can be found at http://dDocent.wordpress.com.
bibliographic citation: Puritz et al. (2014) dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ 2:e431 https://doi.org/10.7717/peerj.431
date submitted: 2014-03-28
date accepted: 2014-05-27
issued: 2014-06-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Puritz
  given name: Jonathan B.
author list: Agent
  family name: Hollenbeck
  given name: Christopher M.
author list: Agent
  family name: Gold
  given name: John R.
doi: 10.7717/peerj.431
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-10
copyright: © 2014 Puritz et al.
attribution name: Puritz et al.

Diversity of introduced terrestrial flatworms in the Iberian Peninsula: a cautionary tale
type: item
type: AcademicArticle
description: Many tropical terrestrial planarians (Platyhelminthes, Geoplanidae) have been introduced around the globe. One of these species is known to cause significant decline in earthworm populations, resulting in a reduction of ecological functions that earthworms provide. Flatworms, additionally, are a potential risk to other species that have the same dietary needs. Hence, the planarian invasion might cause significant economic losses in agriculture and damage to the ecosystem. In the Iberian Peninsula only Bipalium kewense Moseley, 1878 had been cited till 2007. From that year on, four more species have been cited, and several reports of the presence of these animals in particular gardens have been received. In the present study we have: (1) analyzed the animals sent by non-specialists and also the presence of terrestrial planarians in plant nurseries and garden centers; (2) identified their species through morphological and phylogenetic molecular analyses, including representatives of their areas of origin; (3) revised their dietary sources and (4) used Species Distribution Modeling (SDM) for one species to evaluate the risk of its introduction to natural areas. The results have shown the presence of at least ten species of alien terrestrial planarians, from all its phylogenetic range. International plant trade is the source of these animals, and many garden centers are acting as reservoirs. Also, landscape restoration to reintroduce autochthonous plants has facilitated their introduction close to natural forests and agricultural fields. In conclusion, there is a need to take measures on plant trade and to have special care in the treatment of restored habitats.
format: application/pdf
format: text/html
creator: Marta Álvarez-Presas
creator: Eduardo Mateos
creator: Àngels Tudó
creator: Hugh Jones
creator: Marta Riutort
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.430
publisher: PeerJ Inc.
rights: © 2014 Álvarez-Presas et al.
abstract: Many tropical terrestrial planarians (Platyhelminthes, Geoplanidae) have been introduced around the globe. One of these species is known to cause significant decline in earthworm populations, resulting in a reduction of ecological functions that earthworms provide. Flatworms, additionally, are a potential risk to other species that have the same dietary needs. Hence, the planarian invasion might cause significant economic losses in agriculture and damage to the ecosystem. In the Iberian Peninsula only Bipalium kewense Moseley, 1878 had been cited till 2007. From that year on, four more species have been cited, and several reports of the presence of these animals in particular gardens have been received. In the present study we have: (1) analyzed the animals sent by non-specialists and also the presence of terrestrial planarians in plant nurseries and garden centers; (2) identified their species through morphological and phylogenetic molecular analyses, including representatives of their areas of origin; (3) revised their dietary sources and (4) used Species Distribution Modeling (SDM) for one species to evaluate the risk of its introduction to natural areas. The results have shown the presence of at least ten species of alien terrestrial planarians, from all its phylogenetic range. International plant trade is the source of these animals, and many garden centers are acting as reservoirs. Also, landscape restoration to reintroduce autochthonous plants has facilitated their introduction close to natural forests and agricultural fields. In conclusion, there is a need to take measures on plant trade and to have special care in the treatment of restored habitats.
bibliographic citation: Álvarez-Presas et al. (2014) Diversity of introduced terrestrial flatworms in the Iberian Peninsula: a cautionary tale. PeerJ 2:e430 https://doi.org/10.7717/peerj.430
date submitted: 2014-04-27
date accepted: 2014-05-26
issued: 2014-06-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Álvarez-Presas
  given name: Marta
author list: Agent
  family name: Mateos
  given name: Eduardo
author list: Agent
  family name: Tudó
  given name: Àngels
author list: Agent
  family name: Jones
  given name: Hugh
author list: Agent
  family name: Riutort
  given name: Marta
doi: 10.7717/peerj.430
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-10
copyright: © 2014 Álvarez-Presas et al.
attribution name: Álvarez-Presas et al.

Interannual and spatial variability of maple syrup yield as related to climatic factors
type: item
type: AcademicArticle
description: Sugar maple syrup production is an important economic activity for eastern Canada and the northeastern United States. Since annual variations in syrup yield have been related to climate, there are concerns about the impacts of climatic change on the industry in the upcoming decades. Although the temporal variability of syrup yield has been studied for specific sites on different time scales or for large regions, a model capable of accounting for both temporal and regional differences in yield is still lacking. In the present study, we studied the factors responsible for interregional and interannual variability in maple syrup yield over the 2001–2012 period, by combining the data from 8 Quebec regions (Canada) and 10 U.S. states. The resulting model explained 44.5% of the variability in yield. It includes the effect of climatic conditions that precede the sapflow season (variables from the previous growing season and winter), the effect of climatic conditions during the current sapflow season, and terms accounting for intercountry and temporal variability. Optimal conditions for maple syrup production appear to be spatially restricted by less favourable climate conditions occurring during the growing season in the north, and in the south, by the warmer winter and earlier spring conditions. This suggests that climate change may favor maple syrup production northwards, while southern regions are more likely to be negatively affected by adverse spring conditions.
format: application/pdf
format: text/html
creator: Louis Duchesne
creator: Daniel Houle
subject: Agricultural Science
subject: Climate Change Biology
subject: Environmental Sciences
description: doi:10.7717/peerj.428
publisher: PeerJ Inc.
rights: © 2014 Duchesne and Houle
abstract: Sugar maple syrup production is an important economic activity for eastern Canada and the northeastern United States. Since annual variations in syrup yield have been related to climate, there are concerns about the impacts of climatic change on the industry in the upcoming decades. Although the temporal variability of syrup yield has been studied for specific sites on different time scales or for large regions, a model capable of accounting for both temporal and regional differences in yield is still lacking. In the present study, we studied the factors responsible for interregional and interannual variability in maple syrup yield over the 2001–2012 period, by combining the data from 8 Quebec regions (Canada) and 10 U.S. states. The resulting model explained 44.5% of the variability in yield. It includes the effect of climatic conditions that precede the sapflow season (variables from the previous growing season and winter), the effect of climatic conditions during the current sapflow season, and terms accounting for intercountry and temporal variability. Optimal conditions for maple syrup production appear to be spatially restricted by less favourable climate conditions occurring during the growing season in the north, and in the south, by the warmer winter and earlier spring conditions. This suggests that climate change may favor maple syrup production northwards, while southern regions are more likely to be negatively affected by adverse spring conditions.
bibliographic citation: Duchesne et al. (2014) Interannual and spatial variability of maple syrup yield as related to climatic factors. PeerJ 2:e428 https://doi.org/10.7717/peerj.428
date submitted: 2014-04-09
date accepted: 2014-05-26
issued: 2014-06-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duchesne
  given name: Louis
author list: Agent
  family name: Houle
  given name: Daniel
doi: 10.7717/peerj.428
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-10
copyright: © 2014 Duchesne and Houle
attribution name: Duchesne and Houle

Oral health status among long-term hospitalized adults: a cross sectional study
type: item
type: AcademicArticle
description: Background. Many Long-Term Care (LTC) institutionalized patients are the most frail and functionally dependent among the geriatric population and have significant oral health disparities.They often suffer from dental neglect due to limited access to appropriate professional dental care. These patients have chronic health situations and are treated with medications, which increase their risk of oral diseases. Despite the growth in elderly population in Israel, there is insufficient data regarding their oral health status and treatment needs. Objective. To describe the oral health status of the LTC hospitalized adults in a geriatric and psychiatric hospital in Israel. Methods. Data was recorded from LTC hospitalized adults with a physical and/or mental disabilities in a cross-sectional research design, which included general health anamnesis and clinical oral examination. Variables included gender, medicines, oral hygiene (OH), using dentures, number of caries lesions and residual teeth. Univariate analyses included Pearson χ2 and t-test analyses. Multivariate analyses included logistic and linear regressions while the outcome variables were categorical OH index and number of carious cavitations, number of residual teeth and carious teeth percentage. Results. 153 participants were included in the study with a mean age of 65.03 ± 18.67 years. 31.3% of the patients were edentulous, and only 14% had partial or full dentures. Females had a significantly higher number of caries cavitation than males (P = 0.044). The number of caries cavitation was higher among patients with poor OH (P < 0.001) and when taking Clonazepam (P = 0.018). Number of residual teeth was higher in the fair OH group (P < 0.001). Carious teeth percentage was higher among the poor OH group (P < 0.001).
format: application/pdf
format: text/html
creator: Leon Bilder
creator: Nirit Yavnai
creator: Avi Zini
subject: Dentistry
subject: Epidemiology
subject: Evidence Based Medicine
subject: Health Policy
subject: Public Health
description: doi:10.7717/peerj.423
publisher: PeerJ Inc.
rights: © 2014 Bilder et al.
abstract: Background. Many Long-Term Care (LTC) institutionalized patients are the most frail and functionally dependent among the geriatric population and have significant oral health disparities.They often suffer from dental neglect due to limited access to appropriate professional dental care. These patients have chronic health situations and are treated with medications, which increase their risk of oral diseases. Despite the growth in elderly population in Israel, there is insufficient data regarding their oral health status and treatment needs. Objective. To describe the oral health status of the LTC hospitalized adults in a geriatric and psychiatric hospital in Israel. Methods. Data was recorded from LTC hospitalized adults with a physical and/or mental disabilities in a cross-sectional research design, which included general health anamnesis and clinical oral examination. Variables included gender, medicines, oral hygiene (OH), using dentures, number of caries lesions and residual teeth. Univariate analyses included Pearson χ2 and t-test analyses. Multivariate analyses included logistic and linear regressions while the outcome variables were categorical OH index and number of carious cavitations, number of residual teeth and carious teeth percentage. Results. 153 participants were included in the study with a mean age of 65.03 ± 18.67 years. 31.3% of the patients were edentulous, and only 14% had partial or full dentures. Females had a significantly higher number of caries cavitation than males (P = 0.044). The number of caries cavitation was higher among patients with poor OH (P < 0.001) and when taking Clonazepam (P = 0.018). Number of residual teeth was higher in the fair OH group (P < 0.001). Carious teeth percentage was higher among the poor OH group (P < 0.001).
bibliographic citation: Bilder et al. (2014) Oral health status among long-term hospitalized adults: a cross sectional study. PeerJ 2:e423 https://doi.org/10.7717/peerj.423
date submitted: 2013-12-26
date accepted: 2014-05-20
issued: 2014-06-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Bilder
  given name: Leon
author list: Agent
  family name: Yavnai
  given name: Nirit
author list: Agent
  family name: Zini
  given name: Avi
doi: 10.7717/peerj.423
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-10
copyright: © 2014 Bilder et al.
attribution name: Bilder et al.

Forms of Melanoplus bowditchi (Orthoptera: Acrididae) collected from different host plants are indistinguishable genetically and in aedeagal morphology
type: item
type: AcademicArticle
description: The sagebrush grasshopper, Melanoplus bowditchi Scudder (Orthoptera: Acrididae), is a phytophilous species that is widely distributed in the western United States on sagebrush species. The geographical distribution of M. bowditchi is very similar to the range of its host plants and its feeding association varies in relation to sagebrush distribution. Melanoplus bowditchi bowditchi Scudder and M. bowditchi canus Hebard were described based on their feeding association with different sagebrush species, sand sagebrush and silver sagebrush, respectively. Recently, M. bowditchi have been observed feeding on other plant species in western Nebraska. We collected adult M. bowditchi feeding on four plant species, sand sagebrush, Artemisia filifolia, big sagebrush, A. tridentata, fringed sagebrush, A. frigidus, and winterfat, Krascheninnikovia lanata. We compared the specimens collected from the four plant species for their morphological and genetic differences. We observed no consistent differences among the aedeagal parameres or basal rings among the grasshoppers collected from different host plants. Amplified Fragment Length Polymorphism markers were used to test the genetic relationships among the grasshoppers. Analysis of Molecular Variance and distance-based Unweighted Pair Group Method with Arithmetic mean dendrogram failed to reveal significant differences. Although the forms showed behavioral and minor color and size differences, the genetic data suggest all forms under study likely interbreed, which indicates they are a single species instead of four species or subspecies. These results indicate that host plant use may influence melanopline phenotype and suggest the need of further genetic analysis of subspecies recognized based on morphology, distribution, and ecology.
format: application/pdf
format: text/html
creator: Muhammad Irfan Ullah
creator: Fatima Mustafa
creator: Kate M. Kneeland
creator: Mathew L. Brust
creator: W. Wyatt Hoback
creator: Shripat T. Kamble
creator: John E. Foster
subject: Ecology
subject: Entomology
subject: Genetics
description: doi:10.7717/peerj.418
publisher: PeerJ Inc.
rights: © 2014 Ullah et al.
abstract: The sagebrush grasshopper, Melanoplus bowditchi Scudder (Orthoptera: Acrididae), is a phytophilous species that is widely distributed in the western United States on sagebrush species. The geographical distribution of M. bowditchi is very similar to the range of its host plants and its feeding association varies in relation to sagebrush distribution. Melanoplus bowditchi bowditchi Scudder and M. bowditchi canus Hebard were described based on their feeding association with different sagebrush species, sand sagebrush and silver sagebrush, respectively. Recently, M. bowditchi have been observed feeding on other plant species in western Nebraska. We collected adult M. bowditchi feeding on four plant species, sand sagebrush, Artemisia filifolia, big sagebrush, A. tridentata, fringed sagebrush, A. frigidus, and winterfat, Krascheninnikovia lanata. We compared the specimens collected from the four plant species for their morphological and genetic differences. We observed no consistent differences among the aedeagal parameres or basal rings among the grasshoppers collected from different host plants. Amplified Fragment Length Polymorphism markers were used to test the genetic relationships among the grasshoppers. Analysis of Molecular Variance and distance-based Unweighted Pair Group Method with Arithmetic mean dendrogram failed to reveal significant differences. Although the forms showed behavioral and minor color and size differences, the genetic data suggest all forms under study likely interbreed, which indicates they are a single species instead of four species or subspecies. These results indicate that host plant use may influence melanopline phenotype and suggest the need of further genetic analysis of subspecies recognized based on morphology, distribution, and ecology.
bibliographic citation: Ullah et al. (2014) Forms of Melanoplus bowditchi (Orthoptera: Acrididae) collected from different host plants are indistinguishable genetically and in aedeagal morphology. PeerJ 2:e418 https://doi.org/10.7717/peerj.418
date submitted: 2014-01-10
date accepted: 2014-05-17
issued: 2014-06-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Ullah
  given name: Muhammad Irfan
author list: Agent
  family name: Mustafa
  given name: Fatima
author list: Agent
  family name: Kneeland
  given name: Kate M.
author list: Agent
  family name: Brust
  given name: Mathew L.
author list: Agent
  family name: Hoback
  given name: W. Wyatt
author list: Agent
  family name: Kamble
  given name: Shripat T.
author list: Agent
  family name: Foster
  given name: John E.
doi: 10.7717/peerj.418
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-10
copyright: © 2014 Ullah et al.
attribution name: Ullah et al.

Regulation of KCa2.3 and endothelium-dependent hyperpolarization (EDH) in the rat middle cerebral artery: the role of lipoxygenase metabolites and isoprostanes
type: item
type: AcademicArticle
description: Background and Purpose. In rat middle cerebral arteries, endothelium-dependent hyperpolarization (EDH) is mediated by activation of calcium-activated potassium (KCa) channels specifically KCa2.3 and KCa3.1. Lipoxygenase (LOX) products function as endothelium-derived hyperpolarizing factors (EDHFs) in rabbit arteries by stimulating KCa2.3. We investigated if LOX products contribute to EDH in rat cerebral arteries. Methods. Arachidonic acid (AA) metabolites produced in middle cerebral arteries were measured using HPLC and LC/MS. Vascular tension and membrane potential responses to SLIGRL were simultaneously recorded using wire myography and intracellular microelectrodes. Results. SLIGRL, an agonist at PAR2 receptors, caused EDH that was inhibited by a combination of KCa2.3 and KCa3.1 blockade. Non-selective LOX-inhibition reduced EDH, whereas inhibition of 12-LOX had no effect. Soluble epoxide hydrolase (sEH) inhibition enhanced the KCa2.3 component of EDH. Following NO synthase (NOS) inhibition, the KCa2.3 component of EDH was absent. Using HPLC, middle cerebral arteries metabolized 14C-AA to 15- and 12-LOX products under control conditions. With NOS inhibition, there was little change in LOX metabolites, but increased F-type isoprostanes. 8-iso-PGF2α inhibited the KCa2.3 component of EDH. Conclusions. LOX metabolites mediate EDH in rat middle cerebral arteries. Inhibition of sEH increases the KCa2.3 component of EDH. Following NOS inhibition, loss of KCa2.3 function is independent of changes in LOX production or sEH inhibition but due to increased isoprostane production and subsequent stimulation of TP receptors. These findings have important implications in diseases associated with loss of NO signaling such as stroke; where inhibition of sEH and/or isoprostane formation may of benefit.
format: application/pdf
format: text/html
creator: Kathryn M. Gauthier
creator: William B. Campbell
creator: Alister J. McNeish
subject: Biochemistry
subject: Biophysics
subject: Anatomy and Physiology
subject: Pharmacology
description: doi:10.7717/peerj.414
publisher: PeerJ Inc.
rights: © 2014 Gauthier et al.
abstract: Background and Purpose. In rat middle cerebral arteries, endothelium-dependent hyperpolarization (EDH) is mediated by activation of calcium-activated potassium (KCa) channels specifically KCa2.3 and KCa3.1. Lipoxygenase (LOX) products function as endothelium-derived hyperpolarizing factors (EDHFs) in rabbit arteries by stimulating KCa2.3. We investigated if LOX products contribute to EDH in rat cerebral arteries. Methods. Arachidonic acid (AA) metabolites produced in middle cerebral arteries were measured using HPLC and LC/MS. Vascular tension and membrane potential responses to SLIGRL were simultaneously recorded using wire myography and intracellular microelectrodes. Results. SLIGRL, an agonist at PAR2 receptors, caused EDH that was inhibited by a combination of KCa2.3 and KCa3.1 blockade. Non-selective LOX-inhibition reduced EDH, whereas inhibition of 12-LOX had no effect. Soluble epoxide hydrolase (sEH) inhibition enhanced the KCa2.3 component of EDH. Following NO synthase (NOS) inhibition, the KCa2.3 component of EDH was absent. Using HPLC, middle cerebral arteries metabolized 14C-AA to 15- and 12-LOX products under control conditions. With NOS inhibition, there was little change in LOX metabolites, but increased F-type isoprostanes. 8-iso-PGF2α inhibited the KCa2.3 component of EDH. Conclusions. LOX metabolites mediate EDH in rat middle cerebral arteries. Inhibition of sEH increases the KCa2.3 component of EDH. Following NOS inhibition, loss of KCa2.3 function is independent of changes in LOX production or sEH inhibition but due to increased isoprostane production and subsequent stimulation of TP receptors. These findings have important implications in diseases associated with loss of NO signaling such as stroke; where inhibition of sEH and/or isoprostane formation may of benefit.
bibliographic citation: Gauthier et al. (2014) Regulation of KCa2.3 and endothelium-dependent hyperpolarization (EDH) in the rat middle cerebral artery: the role of lipoxygenase metabolites and isoprostanes. PeerJ 2:e414 https://doi.org/10.7717/peerj.414
date submitted: 2014-02-28
date accepted: 2014-05-15
issued: 2014-06-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gauthier
  given name: Kathryn M.
author list: Agent
  family name: Campbell
  given name: William B.
author list: Agent
  family name: McNeish
  given name: Alister J.
doi: 10.7717/peerj.414
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-10
copyright: © 2014 Gauthier et al.
attribution name: Gauthier et al.

Molecular cytogenetic analyses of Epinephelus bruneus and Epinephelus moara (Perciformes, Epinephelidae)
type: item
type: AcademicArticle
description: Genus Epinephelus (Perciformes, Epinephelidae), commonly known as groupers, are usually difficult in species identification for the lack and/or change of morphological specialization. In this study, molecular cytogenetic analyses were firstly performed to identify the closely related species Epinephelus bruneus and E. moara in this genus. The species-specific differences of both fish species showed in karyotype, chromosomal distribution of nucleolar organizer regions (NORs) and localization of 18S rDNA. The heterochromatin (interstitial C-bands) and distribution pattern of telomere (TTAGGG)n in E. bruneus revealed the chromosomal rearrangements and different karyotypic evolutionary characteristics compared to those in E. moara. The cytogenetic data suggested that the lineages of E. bruneus and E. moara were recently derived within the genus Epinephelus, and E. moara exhibited more plesiomorphic features than E. bruneus. All results confirmed that E. moara, which has long been considered a synonym of E. bruneus, is a distinct species in the family Epinephelidae. In addition, molecular cytogenetic analyses are useful in species differentiation and phylogenetic reconstruction in groupers.
format: application/pdf
format: text/html
creator: Minglan Guo
creator: Shifeng Wang
creator: Yongquan Su
creator: Yongcan Zhou
creator: Min Liu
creator: Jun Wang
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Genetics
subject: Marine Biology
subject: Taxonomy
description: doi:10.7717/peerj.412
publisher: PeerJ Inc.
rights: © 2014 Guo et al.
abstract: Genus Epinephelus (Perciformes, Epinephelidae), commonly known as groupers, are usually difficult in species identification for the lack and/or change of morphological specialization. In this study, molecular cytogenetic analyses were firstly performed to identify the closely related species Epinephelus bruneus and E. moara in this genus. The species-specific differences of both fish species showed in karyotype, chromosomal distribution of nucleolar organizer regions (NORs) and localization of 18S rDNA. The heterochromatin (interstitial C-bands) and distribution pattern of telomere (TTAGGG)n in E. bruneus revealed the chromosomal rearrangements and different karyotypic evolutionary characteristics compared to those in E. moara. The cytogenetic data suggested that the lineages of E. bruneus and E. moara were recently derived within the genus Epinephelus, and E. moara exhibited more plesiomorphic features than E. bruneus. All results confirmed that E. moara, which has long been considered a synonym of E. bruneus, is a distinct species in the family Epinephelidae. In addition, molecular cytogenetic analyses are useful in species differentiation and phylogenetic reconstruction in groupers.
bibliographic citation: Guo et al. (2014) Molecular cytogenetic analyses of Epinephelus bruneus and Epinephelus moara (Perciformes, Epinephelidae). PeerJ 2:e412 https://doi.org/10.7717/peerj.412
date submitted: 2014-04-02
date accepted: 2014-05-13
issued: 2014-06-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Minglan
author list: Agent
  family name: Wang
  given name: Shifeng
author list: Agent
  family name: Su
  given name: Yongquan
author list: Agent
  family name: Zhou
  given name: Yongcan
author list: Agent
  family name: Liu
  given name: Min
author list: Agent
  family name: Wang
  given name: Jun
doi: 10.7717/peerj.412
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-10
copyright: © 2014 Guo et al.
attribution name: Guo et al.

Tree mortality from a short-duration freezing event and global-change-type drought in a Southwestern piñon-juniper woodland, USA
type: item
type: AcademicArticle
description: This study documents tree mortality in Big Bend National Park in Texas in response to the most acute one-year drought on record, which occurred following a five-day winter freeze. I estimated changes in forest stand structure and species composition due to freezing and drought in the Chisos Mountains of Big Bend National Park using permanent monitoring plot data. The drought killed over half (63%) of the sampled trees over the entire elevation gradient. Significant mortality occurred in trees up to 20 cm diameter (P < 0.05). Pinus cembroides Zucc. experienced the highest seedling and tree mortality (P < 0.0001) (55% of piñon pines died), and over five times as many standing dead pines were observed in 2012 than in 2009. Juniperus deppeana vonSteudal and Quercus emoryi Leibmann also experienced significant declines in tree density (P < 0.02) (30.9% and 20.7%, respectively). Subsequent droughts under climate change will likely cause even greater damage to trees that survived this record drought, especially if such events follow freezes. The results from this study highlight the vulnerability of trees in the Southwest to climatic change and that future shifts in forest structure can have large-scale community consequences.
format: application/pdf
format: text/html
creator: Helen M. Poulos
subject: Climate Change Biology
subject: Ecology
subject: Environmental Sciences
subject: Plant Science
description: doi:10.7717/peerj.404
publisher: PeerJ Inc.
rights: © 2014 Poulos
abstract: This study documents tree mortality in Big Bend National Park in Texas in response to the most acute one-year drought on record, which occurred following a five-day winter freeze. I estimated changes in forest stand structure and species composition due to freezing and drought in the Chisos Mountains of Big Bend National Park using permanent monitoring plot data. The drought killed over half (63%) of the sampled trees over the entire elevation gradient. Significant mortality occurred in trees up to 20 cm diameter (P < 0.05). Pinus cembroides Zucc. experienced the highest seedling and tree mortality (P < 0.0001) (55% of piñon pines died), and over five times as many standing dead pines were observed in 2012 than in 2009. Juniperus deppeana vonSteudal and Quercus emoryi Leibmann also experienced significant declines in tree density (P < 0.02) (30.9% and 20.7%, respectively). Subsequent droughts under climate change will likely cause even greater damage to trees that survived this record drought, especially if such events follow freezes. The results from this study highlight the vulnerability of trees in the Southwest to climatic change and that future shifts in forest structure can have large-scale community consequences.
bibliographic citation: Poulos (2014) Tree mortality from a short-duration freezing event and global-change-type drought in a Southwestern piñon-juniper woodland, USA. PeerJ 2:e404 https://doi.org/10.7717/peerj.404
date submitted: 2013-10-23
date accepted: 2014-05-07
issued: 2014-06-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Poulos
  given name: Helen M.
doi: 10.7717/peerj.404
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-10
copyright: © 2014 Poulos
attribution name: Poulos

Stability of commercial glucanase and β-glucosidase preparations under hydrolysis conditions
type: item
type: AcademicArticle
description: The cost of enzymes makes enzymatic hydrolysis one of the most expensive steps in the production of lignocellulosic ethanol. Diverse studies have used commercial enzyme cocktails assuming that change in total protein concentration during hydrolysis was solely due to adsorption of endo- and exoglucanases onto the substrate. Given the sensitivity of enzymes and proteins to media conditions this assumption was tested by evaluating and modeling the protein concentration of commercial cocktails at hydrolysis conditions. In the absence of solid substrate, the total protein concentration of a mixture of Celluclast 1.5 L and Novozyme 188 decreased by as much as 45% at 50 °C after 4 days. The individual cocktails as well as a mixture of both were stable at 20 °C. At 50 °C, the protein concentration of Celluclast 1.5 was relatively constant but Novozyme 188 decreased by as much as 77%. It was hypothesized that Novozyme 188 proteins suffer a structural change at 50 °C which leads to protein aggregation and precipitation. Lyophilized β-glucosidase (P-β-glucosidase) at 50 °C exhibited an aggregation rate which was successfully modeled using first order kinetics (R2 = 0.97). By incorporating the possible presence of chaperone proteins in Novozyme 188, the protein aggregation observed for this cocktail was successfully modeled (R2 = 0.96). To accurately model the increasing protein stability observed at high cocktail loadings, the model was modified to include the presence of additives in the cocktail (R2 = 0.98). By combining the measurement of total protein concentration with the proposed Novozyme 188 protein aggregation model, the endo- and exoglucanases concentration in the solid and liquid phases during hydrolysis can be more accurately determined. This methodology can be applied to various systems leading to optimization of enzyme loading by minimizing the excess of endo- and exoglucanases. In addition, the monitoring of endo- and exoglucanases concentrations can be used to …
format: application/pdf
format: text/html
creator: Oscar Rosales-Calderon
creator: Heather L. Trajano
creator: Sheldon J.B. Duff
subject: Biotechnology
subject: Microbiology
subject: Synthetic Biology
description: doi:10.7717/peerj.402
publisher: PeerJ Inc.
rights: © 2014 Rosales-Calderon et al.
abstract: The cost of enzymes makes enzymatic hydrolysis one of the most expensive steps in the production of lignocellulosic ethanol. Diverse studies have used commercial enzyme cocktails assuming that change in total protein concentration during hydrolysis was solely due to adsorption of endo- and exoglucanases onto the substrate. Given the sensitivity of enzymes and proteins to media conditions this assumption was tested by evaluating and modeling the protein concentration of commercial cocktails at hydrolysis conditions. In the absence of solid substrate, the total protein concentration of a mixture of Celluclast 1.5 L and Novozyme 188 decreased by as much as 45% at 50 °C after 4 days. The individual cocktails as well as a mixture of both were stable at 20 °C. At 50 °C, the protein concentration of Celluclast 1.5 was relatively constant but Novozyme 188 decreased by as much as 77%. It was hypothesized that Novozyme 188 proteins suffer a structural change at 50 °C which leads to protein aggregation and precipitation. Lyophilized β-glucosidase (P-β-glucosidase) at 50 °C exhibited an aggregation rate which was successfully modeled using first order kinetics (R2 = 0.97). By incorporating the possible presence of chaperone proteins in Novozyme 188, the protein aggregation observed for this cocktail was successfully modeled (R2 = 0.96). To accurately model the increasing protein stability observed at high cocktail loadings, the model was modified to include the presence of additives in the cocktail (R2 = 0.98). By combining the measurement of total protein concentration with the proposed Novozyme 188 protein aggregation model, the endo- and exoglucanases concentration in the solid and liquid phases during hydrolysis can be more accurately determined. This methodology can be applied to various systems leading to optimization of enzyme loading by minimizing the excess of endo- and exoglucanases. In addition, the monitoring of endo- and exoglucanases concentrations can be used to …
bibliographic citation: Rosales-Calderon et al. (2014) Stability of commercial glucanase and β-glucosidase preparations under hydrolysis conditions. PeerJ 2:e402 https://doi.org/10.7717/peerj.402
date submitted: 2014-03-28
date accepted: 2014-05-07
issued: 2014-06-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rosales-Calderon
  given name: Oscar
author list: Agent
  family name: Trajano
  given name: Heather L.
author list: Agent
  family name: Duff
  given name: Sheldon J.B.
doi: 10.7717/peerj.402
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-10
copyright: © 2014 Rosales-Calderon et al.
attribution name: Rosales-Calderon et al.

The salivary secretome of the biting midge, Culicoides sonorensis
type: item
type: AcademicArticle
description: Culicoides biting midges (Diptera: Ceratopogonidae) are hematophagous insects with over 1400 species distributed throughout the world. Many of these species are of particular agricultural importance as primary vectors of bluetongue and Schmallenberg viruses, yet little is known about Culicoides genomics and proteomics. Detailed studies of members from other blood-feeding Dipteran families, including those of mosquito (Culicidae) and black fly (Simuliidae), have shown that protein components within the insect’s saliva facilitate the blood feeding process. To determine the protein components in Culicoides sonorensis midges, secreted saliva was collected for peptide sequencing by tandem mass spectrometry. Forty-five secreted proteins were identified, including members of the D7 odorant binding protein family, Kunitz-like serine protease inhibitors, maltase, trypsin, and six novel proteins unique to C. sonorensis. Identifying the complex myriad of proteins in saliva from blood-feeding Dipteran species is critical for understanding their role in blood feeding, arbovirus transmission, and possibly the resulting disease pathogenesis.
format: application/pdf
format: text/html
creator: Christopher J. Lehiy
creator: Barbara S. Drolet
subject: Entomology
subject: Genomics
description: doi:10.7717/peerj.426
publisher: PeerJ Inc.
rights: © 2014 Lehiy and Drolet
abstract: Culicoides biting midges (Diptera: Ceratopogonidae) are hematophagous insects with over 1400 species distributed throughout the world. Many of these species are of particular agricultural importance as primary vectors of bluetongue and Schmallenberg viruses, yet little is known about Culicoides genomics and proteomics. Detailed studies of members from other blood-feeding Dipteran families, including those of mosquito (Culicidae) and black fly (Simuliidae), have shown that protein components within the insect’s saliva facilitate the blood feeding process. To determine the protein components in Culicoides sonorensis midges, secreted saliva was collected for peptide sequencing by tandem mass spectrometry. Forty-five secreted proteins were identified, including members of the D7 odorant binding protein family, Kunitz-like serine protease inhibitors, maltase, trypsin, and six novel proteins unique to C. sonorensis. Identifying the complex myriad of proteins in saliva from blood-feeding Dipteran species is critical for understanding their role in blood feeding, arbovirus transmission, and possibly the resulting disease pathogenesis.
bibliographic citation: Lehiy et al. (2014) The salivary secretome of the biting midge, Culicoides sonorensis. PeerJ 2:e426 https://doi.org/10.7717/peerj.426
date submitted: 2014-02-25
date accepted: 2014-05-21
issued: 2014-06-05
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Lehiy
  given name: Christopher J.
author list: Agent
  family name: Drolet
  given name: Barbara S.
doi: 10.7717/peerj.426
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-05
copyright: © 2014 Lehiy and Drolet
attribution name: Lehiy and Drolet

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares
type: item
type: AcademicArticle
description: One of the major goals in metagenomics is to identify the organisms present in a microbial community from unannotated shotgun sequencing reads. Taxonomic profiling has valuable applications in biological and medical research, including disease diagnostics. Most currently available approaches do not scale well with increasing data volumes, which is important because both the number and lengths of the reads provided by sequencing platforms keep increasing. Here we introduce FOCUS, an agile composition based approach using non-negative least squares (NNLS) to report the organisms present in metagenomic samples and profile their abundances. FOCUS was tested with simulated and real metagenomes, and the results show that our approach accurately predicts the organisms present in microbial communities. FOCUS was implemented in Python. The source code and web-sever are freely available at http://edwards.sdsu.edu/FOCUS.
format: application/pdf
format: text/html
creator: Genivaldo Gueiros Z. Silva
creator: Daniel A. Cuevas
creator: Bas E. Dutilh
creator: Robert A. Edwards
subject: Computational Biology
description: doi:10.7717/peerj.425
publisher: PeerJ Inc.
rights: © 2014 Silva et al.
abstract: One of the major goals in metagenomics is to identify the organisms present in a microbial community from unannotated shotgun sequencing reads. Taxonomic profiling has valuable applications in biological and medical research, including disease diagnostics. Most currently available approaches do not scale well with increasing data volumes, which is important because both the number and lengths of the reads provided by sequencing platforms keep increasing. Here we introduce FOCUS, an agile composition based approach using non-negative least squares (NNLS) to report the organisms present in metagenomic samples and profile their abundances. FOCUS was tested with simulated and real metagenomes, and the results show that our approach accurately predicts the organisms present in microbial communities. FOCUS was implemented in Python. The source code and web-sever are freely available at http://edwards.sdsu.edu/FOCUS.
bibliographic citation: Silva et al. (2014) FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares. PeerJ 2:e425 https://doi.org/10.7717/peerj.425
date submitted: 2014-03-19
date accepted: 2014-05-21
issued: 2014-06-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Genivaldo Gueiros Z.
author list: Agent
  family name: Cuevas
  given name: Daniel A.
author list: Agent
  family name: Dutilh
  given name: Bas E.
author list: Agent
  family name: Edwards
  given name: Robert A.
doi: 10.7717/peerj.425
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-05
copyright: © 2014 Silva et al.
attribution name: Silva et al.

Swedish high-school pupils’ attitudes towards drugs in relation to drug usage, impulsiveness and other risk factors
type: item
type: AcademicArticle
description: Background. Illicit drug use influences people’s lives and elicits unwanted behaviour. Current research shows that there is an increase in young people’s drug use in Sweden. The aim was to investigate Swedish high-school pupils’ attitudes, impulsiveness and gender differences linked to drug use. Risk and protective factors relative to drug use were also a focus of interest. Method. High school pupils (n = 146) aged 17–21 years, responded to the Adolescent Health and Development Inventory, Barratt Impulsiveness Scale and Knowledge, and the Attitudes and Beliefs. Direct logistic, multiple regression analyses, and Multivariate Analysis of Variance were used to analyze the data. Results. Positive Attitudes towards drugs were predicted by risk factors (odds ratio = 37.31) and gender (odds ratio = .32). Risk factors (odds ratio = 46.89), positive attitudes towards drugs (odds ratio = 4.63), and impulsiveness (odds ratio = 1.11) predicted drug usage. Risk factors dimensions Family, Friends and Individual Characteristic were positively related to impulsiveness among drug users. Moreover, although boys reported using drugs to a greater extent, girls expressed more positive attitude towards drugs and even reported more impulsiveness than boys. Conclusion. This study reinforces the notion that research ought to focus on gender differences relative to pro-drug attitudes along with testing for differences in the predictors of girls’ and boys’ delinquency and impulsiveness. Positive attitudes towards drugs among adolescents seem to be part of a vicious circle including risk factors, such as friendly drug environments (e.g., friends who use drugs) and unsupportive family environments, individual characteristics, and impulsiveness.
format: application/pdf
format: text/html
creator: Fariba Mousavi
creator: Danilo Garcia
creator: Alexander Jimmefors
creator: Trevor Archer
creator: Béatrice Ewalds-Kvist
subject: Drugs and Devices
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.410
publisher: PeerJ Inc.
rights: © 2014 Mousavi et al.
abstract: Background. Illicit drug use influences people’s lives and elicits unwanted behaviour. Current research shows that there is an increase in young people’s drug use in Sweden. The aim was to investigate Swedish high-school pupils’ attitudes, impulsiveness and gender differences linked to drug use. Risk and protective factors relative to drug use were also a focus of interest. Method. High school pupils (n = 146) aged 17–21 years, responded to the Adolescent Health and Development Inventory, Barratt Impulsiveness Scale and Knowledge, and the Attitudes and Beliefs. Direct logistic, multiple regression analyses, and Multivariate Analysis of Variance were used to analyze the data. Results. Positive Attitudes towards drugs were predicted by risk factors (odds ratio = 37.31) and gender (odds ratio = .32). Risk factors (odds ratio = 46.89), positive attitudes towards drugs (odds ratio = 4.63), and impulsiveness (odds ratio = 1.11) predicted drug usage. Risk factors dimensions Family, Friends and Individual Characteristic were positively related to impulsiveness among drug users. Moreover, although boys reported using drugs to a greater extent, girls expressed more positive attitude towards drugs and even reported more impulsiveness than boys. Conclusion. This study reinforces the notion that research ought to focus on gender differences relative to pro-drug attitudes along with testing for differences in the predictors of girls’ and boys’ delinquency and impulsiveness. Positive attitudes towards drugs among adolescents seem to be part of a vicious circle including risk factors, such as friendly drug environments (e.g., friends who use drugs) and unsupportive family environments, individual characteristics, and impulsiveness.
bibliographic citation: Mousavi et al. (2014) Swedish high-school pupils’ attitudes towards drugs in relation to drug usage, impulsiveness and other risk factors. PeerJ 2:e410 https://doi.org/10.7717/peerj.410
date submitted: 2014-02-19
date accepted: 2014-05-12
issued: 2014-06-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mousavi
  given name: Fariba
author list: Agent
  family name: Garcia
  given name: Danilo
author list: Agent
  family name: Jimmefors
  given name: Alexander
author list: Agent
  family name: Archer
  given name: Trevor
author list: Agent
  family name: Ewalds-Kvist
  given name: Béatrice
doi: 10.7717/peerj.410
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-05
copyright: © 2014 Mousavi et al.
attribution name: Mousavi et al.

Quantification of intraskeletal histovariability in Alligator mississippiensis and implications for vertebrate osteohistology
type: item
type: AcademicArticle
description: Bone microanalyses of extant vertebrates provide a necessary framework from which to form hypotheses regarding the growth and skeletochronology of extinct taxa. Here, we describe the bone microstructure and quantify the histovariability of appendicular elements and osteoderms from three juvenile American alligators (Alligator mississippiensis) to assess growth mark and tissue organization within and amongst individuals, with the intention of validating paleohistological interpretations. Results confirm previous observations that lamellar and parallel fibered tissue organization are typical of crocodylians, and also that crocodylians are capable of forming woven tissue for brief periods. Tissue organization and growth mark count varies across individual skeletal elements and reveal that the femur, tibia, and humerus had the highest annual apposition rates in each individual. Cyclical growth mark count also varies intraskeletally, but data suggest these inconsistencies are due to differing medullary cavity expansion rates. There was no appreciable difference in either diaphyseal circumference or cyclical growth mark circumferences between left and right element pairs from an individual if diaphyses were sampled from roughly the same location. The considerable intraskeletal data obtained here provide validation for long-held paleohistology assumptions, but because medullary expansion, cyclical growth mark formation, and variable intraskeletal growth rates are skeletal features found in tetrapod taxa living or extinct, the validations presented herein should be considered during any tetrapod bone microanalysis.
format: application/pdf
format: text/html
creator: Holly N. Woodward
creator: John R. Horner
creator: James O. Farlow
subject: Histology
subject: Paleontology
description: doi:10.7717/peerj.422
publisher: PeerJ Inc.
rights: © 2014 Woodward et al.
abstract: Bone microanalyses of extant vertebrates provide a necessary framework from which to form hypotheses regarding the growth and skeletochronology of extinct taxa. Here, we describe the bone microstructure and quantify the histovariability of appendicular elements and osteoderms from three juvenile American alligators (Alligator mississippiensis) to assess growth mark and tissue organization within and amongst individuals, with the intention of validating paleohistological interpretations. Results confirm previous observations that lamellar and parallel fibered tissue organization are typical of crocodylians, and also that crocodylians are capable of forming woven tissue for brief periods. Tissue organization and growth mark count varies across individual skeletal elements and reveal that the femur, tibia, and humerus had the highest annual apposition rates in each individual. Cyclical growth mark count also varies intraskeletally, but data suggest these inconsistencies are due to differing medullary cavity expansion rates. There was no appreciable difference in either diaphyseal circumference or cyclical growth mark circumferences between left and right element pairs from an individual if diaphyses were sampled from roughly the same location. The considerable intraskeletal data obtained here provide validation for long-held paleohistology assumptions, but because medullary expansion, cyclical growth mark formation, and variable intraskeletal growth rates are skeletal features found in tetrapod taxa living or extinct, the validations presented herein should be considered during any tetrapod bone microanalysis.
bibliographic citation: Woodward et al. (2014) Quantification of intraskeletal histovariability in Alligator mississippiensis and implications for vertebrate osteohistology. PeerJ 2:e422 https://doi.org/10.7717/peerj.422
date submitted: 2014-03-01
date accepted: 2014-05-19
issued: 2014-06-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Woodward
  given name: Holly N.
author list: Agent
  family name: Horner
  given name: John R.
author list: Agent
  family name: Farlow
  given name: James O.
doi: 10.7717/peerj.422
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-03
copyright: © 2014 Woodward et al.
attribution name: Woodward et al.

BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU
type: item
type: AcademicArticle
description: This paper reports an integrated solution, called BALSA, for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis. From raw reads to variants (including SNPs and Indels), BALSA, using just a single computing node with a commodity GPU board, takes 5.5 h to process 50-fold whole genome sequencing (∼750 million 100 bp paired-end reads), or just 25 min for 210-fold whole exome sequencing. BALSA’s speed is rooted at its parallel algorithms to effectively exploit a GPU to speed up processes like alignment, realignment and statistical testing. BALSA incorporates a 16-genotype model to support the calling of SNPs and Indels and achieves competitive variant calling accuracy and sensitivity when compared to the ensemble of six popular variant callers. BALSA also supports efficient identification of somatic SNVs and CNVs; experiments showed that BALSA recovers all the previously validated somatic SNVs and CNVs, and it is more sensitive for somatic Indel detection. BALSA outputs variants in VCF format. A pileup-like SNAPSHOT format, while maintaining the same fidelity as BAM in variant calling, enables efficient storage and indexing, and facilitates the App development of downstream analyses. BALSA is available at: http://sourceforge.net/p/balsa.
format: application/pdf
format: text/html
creator: Ruibang Luo
creator: Yiu-Lun Wong
creator: Wai-Chun Law
creator: Lap-Kei Lee
creator: Jeanno Cheung
creator: Chi-Man Liu
creator: Tak-Wah Lam
subject: Bioinformatics
subject: Genomics
subject: Computational Science
description: doi:10.7717/peerj.421
publisher: PeerJ Inc.
rights: © 2014 Luo et al.
abstract: This paper reports an integrated solution, called BALSA, for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis. From raw reads to variants (including SNPs and Indels), BALSA, using just a single computing node with a commodity GPU board, takes 5.5 h to process 50-fold whole genome sequencing (∼750 million 100 bp paired-end reads), or just 25 min for 210-fold whole exome sequencing. BALSA’s speed is rooted at its parallel algorithms to effectively exploit a GPU to speed up processes like alignment, realignment and statistical testing. BALSA incorporates a 16-genotype model to support the calling of SNPs and Indels and achieves competitive variant calling accuracy and sensitivity when compared to the ensemble of six popular variant callers. BALSA also supports efficient identification of somatic SNVs and CNVs; experiments showed that BALSA recovers all the previously validated somatic SNVs and CNVs, and it is more sensitive for somatic Indel detection. BALSA outputs variants in VCF format. A pileup-like SNAPSHOT format, while maintaining the same fidelity as BAM in variant calling, enables efficient storage and indexing, and facilitates the App development of downstream analyses. BALSA is available at: http://sourceforge.net/p/balsa.
bibliographic citation: Luo et al. (2014) BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU. PeerJ 2:e421 https://doi.org/10.7717/peerj.421
date submitted: 2014-04-25
date accepted: 2014-05-19
issued: 2014-06-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Ruibang
author list: Agent
  family name: Wong
  given name: Yiu-Lun
author list: Agent
  family name: Law
  given name: Wai-Chun
author list: Agent
  family name: Lee
  given name: Lap-Kei
author list: Agent
  family name: Cheung
  given name: Jeanno
author list: Agent
  family name: Liu
  given name: Chi-Man
author list: Agent
  family name: Lam
  given name: Tak-Wah
doi: 10.7717/peerj.421
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-03
copyright: © 2014 Luo et al.
attribution name: Luo et al.

Rape and the prevalence of hybrids in broadly sympatric species: a case study using albatrosses
type: item
type: AcademicArticle
description: Conspecific rape often increases male reproductive success. However, the haste and aggression of forced copulations suggests that males may sometimes rape heterospecific females, thus making rape a likely, but undocumented, source of hybrids between broadly sympatric species. We present evidence that heterospecific rape may be the source of hybrids between Black-footed and Laysan Albatrosses (Phoebastria nigripes, and P. immutabilis, respectively). Extensive field studies have shown that paired (but not unpaired) males of both of these albatross species use rape as a supplemental reproductive strategy. Between species differences in size, timing of laying, and aggressiveness suggest that Black-footed Albatrosses should be more successful than Laysan Albatrosses in heteropspecific rape attempts, and male Black-footed Albatrosses have been observed attempting to force copulations on female Laysan Albatrosses. Nuclear markers showed that the six hybrids we studied were F1s and mitochondrial markers showed that male Black-footed Albatrosses sired all six hybrids. Long-term gene exchange between these species has been from Black-footed Albatrosses into Laysan Albatrosses, suggesting that the siring asymmetry found in our hybrids has long persisted. If hybrids are sired in heterospecific rapes, they presumably would be raised and sexually imprinted on Laysan Albatrosses, and two unmated hybrids in a previous study courted only Laysan Albatrosses.
format: application/pdf
format: text/html
creator: Sievert Rohwer
creator: Rebecca B. Harris
creator: Hollie E. Walsh
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.409
publisher: PeerJ Inc.
rights: © 2014 Rohwer et al.
abstract: Conspecific rape often increases male reproductive success. However, the haste and aggression of forced copulations suggests that males may sometimes rape heterospecific females, thus making rape a likely, but undocumented, source of hybrids between broadly sympatric species. We present evidence that heterospecific rape may be the source of hybrids between Black-footed and Laysan Albatrosses (Phoebastria nigripes, and P. immutabilis, respectively). Extensive field studies have shown that paired (but not unpaired) males of both of these albatross species use rape as a supplemental reproductive strategy. Between species differences in size, timing of laying, and aggressiveness suggest that Black-footed Albatrosses should be more successful than Laysan Albatrosses in heteropspecific rape attempts, and male Black-footed Albatrosses have been observed attempting to force copulations on female Laysan Albatrosses. Nuclear markers showed that the six hybrids we studied were F1s and mitochondrial markers showed that male Black-footed Albatrosses sired all six hybrids. Long-term gene exchange between these species has been from Black-footed Albatrosses into Laysan Albatrosses, suggesting that the siring asymmetry found in our hybrids has long persisted. If hybrids are sired in heterospecific rapes, they presumably would be raised and sexually imprinted on Laysan Albatrosses, and two unmated hybrids in a previous study courted only Laysan Albatrosses.
bibliographic citation: Rohwer et al. (2014) Rape and the prevalence of hybrids in broadly sympatric species: a case study using albatrosses. PeerJ 2:e409 https://doi.org/10.7717/peerj.409
date submitted: 2014-02-13
date accepted: 2014-05-12
issued: 2014-06-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rohwer
  given name: Sievert
author list: Agent
  family name: Harris
  given name: Rebecca B.
author list: Agent
  family name: Walsh
  given name: Hollie E.
doi: 10.7717/peerj.409
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-03
copyright: © 2014 Rohwer et al.
attribution name: Rohwer et al.

Compliance with vessel speed restrictions to protect North Atlantic right whales
type: item
type: AcademicArticle
description: Environmental regulations can only be effective if they are adhered to, but the motivations for regulatory compliance are not always clear. We assessed vessel operator compliance with a December 2008 regulation aimed at reducing collisions with the endangered North Atlantic right whale that requires vessels 65 feet or greater in length to travel at speeds of 10 knots or less at prescribed times and locations along the U.S. eastern seaboard. Extensive outreach efforts were undertaken to notify affected entities both before and after the regulation went into effect. Vessel speeds of 201,862 trips made between November 2008 and August 2013 by 8,009 individual vessels were quantified remotely, constituting a nearly complete census of transits made by the regulated population. Of these, 437 vessels (or their parent companies), some of whom had been observed exceeding the speed limit, were contacted through one of four non-punitive information programs. A fraction (n = 26 vessels/companies) received citations and fines. Despite the efforts to inform mariners, initial compliance was low (<5% of the trips were completely <10 knots) but improved in the latter part of the study. Each notification/enforcement program improved compliance to some degree and some may have influenced compliance across the entire regulated community. Citations/fines appeared to have the greatest influence on improving compliance in notified vessels/companies, followed in order of effectiveness by enforcement-office information letters, monthly summaries of vessel operations, and direct at-sea radio contact. Trips by cargo vessels exhibited the greatest change in behavior followed by tanker and passenger vessels. These results have application to other regulatory systems, especially where remote monitoring is feasible, and any setting where regulatory compliance is sought.
format: application/pdf
format: text/html
creator: Gregory K. Silber
creator: Jeffrey D. Adams
creator: Christopher J. Fonnesbeck
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.399
publisher: PeerJ Inc.
rights: © 2014 Silber et al.
abstract: Environmental regulations can only be effective if they are adhered to, but the motivations for regulatory compliance are not always clear. We assessed vessel operator compliance with a December 2008 regulation aimed at reducing collisions with the endangered North Atlantic right whale that requires vessels 65 feet or greater in length to travel at speeds of 10 knots or less at prescribed times and locations along the U.S. eastern seaboard. Extensive outreach efforts were undertaken to notify affected entities both before and after the regulation went into effect. Vessel speeds of 201,862 trips made between November 2008 and August 2013 by 8,009 individual vessels were quantified remotely, constituting a nearly complete census of transits made by the regulated population. Of these, 437 vessels (or their parent companies), some of whom had been observed exceeding the speed limit, were contacted through one of four non-punitive information programs. A fraction (n = 26 vessels/companies) received citations and fines. Despite the efforts to inform mariners, initial compliance was low (<5% of the trips were completely <10 knots) but improved in the latter part of the study. Each notification/enforcement program improved compliance to some degree and some may have influenced compliance across the entire regulated community. Citations/fines appeared to have the greatest influence on improving compliance in notified vessels/companies, followed in order of effectiveness by enforcement-office information letters, monthly summaries of vessel operations, and direct at-sea radio contact. Trips by cargo vessels exhibited the greatest change in behavior followed by tanker and passenger vessels. These results have application to other regulatory systems, especially where remote monitoring is feasible, and any setting where regulatory compliance is sought.
bibliographic citation: Silber et al. (2014) Compliance with vessel speed restrictions to protect North Atlantic right whales. PeerJ 2:e399 https://doi.org/10.7717/peerj.399
date submitted: 2014-03-14
date accepted: 2014-05-07
issued: 2014-06-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silber
  given name: Gregory K.
author list: Agent
  family name: Adams
  given name: Jeffrey D.
author list: Agent
  family name: Fonnesbeck
  given name: Christopher J.
doi: 10.7717/peerj.399
volume: 2
issn: 2167-8359
publication name: PeerJ
publication date: 2014-06-03
copyright: © 2014 Silber et al.
attribution name: Silber et al.

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