PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The non-avian theropod quadrate I: standardized terminology with an overview of the anatomy and function
items: A practical guide and power analysis for GLMMs: detecting among treatment variation in random effects
items: APOE genotype and age modifies the correlation between cognitive status and metabolites from hippocampus by a 2D 1H-MRS in non-demented elders
items: MaqFACS (Macaque Facial Action Coding System) can be used to document facial movements in Barbary macaques (Macaca sylvanus)
items: An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system
items: Pursuit tracks chase: exploring the role of eye movements in the detection of chasing
items: Integrated probability of coronary heart disease subject to the −308 tumor necrosis factor-alpha SNP: a Bayesian meta-analysis
items: Survivorship and feeding preferences among size classes of outplanted sea urchins, Tripneustes gratilla, and possible use as biocontrol for invasive alien algae
items: Registered report: androgen receptor splice variants determine taxane sensitivity in prostate cancer
items: Registered report: the androgen receptor induces a distinct transcriptional program in castration-resistant prostate cancer in man

The non-avian theropod quadrate I: standardized terminology with an overview of the anatomy and function
type: item
type: AcademicArticle
description: The quadrate of reptiles and most other tetrapods plays an important morphofunctional role by allowing the articulation of the mandible with the cranium. In Theropoda, the morphology of the quadrate is particularly complex and varies importantly among different clades of non-avian theropods, therefore conferring a strong taxonomic potential. Inconsistencies in the notation and terminology used in discussions of the theropod quadrate anatomy have been noticed, including at least one instance when no less than eight different terms were given to the same structure. A standardized list of terms and notations for each quadrate anatomical entity is proposed here, with the goal of facilitating future descriptions of this important cranial bone. In addition, an overview of the literature on quadrate function and pneumaticity in non-avian theropods is presented, along with a discussion of the inferences that could be made from this research. Specifically, the quadrate of the large majority of non-avian theropods is akinetic but the diagonally oriented intercondylar sulcus of the mandibular articulation allowed both rami of the mandible to move laterally when opening the mouth in many of theropods. Pneumaticity of the quadrate is also present in most averostran clades and the pneumatic chamber—invaded by the quadrate diverticulum of the mandibular arch pneumatic system—was connected to one or several pneumatic foramina on the medial, lateral, posterior, anterior or ventral sides of the quadrate.
format: application/pdf
format: text/html
creator: Christophe Hendrickx
creator: Ricardo Araújo
creator: Octávio Mateus
subject: Paleontology
description: doi:10.7717/peerj.1245
publisher: PeerJ Inc.
rights: © 2015 Hendrickx et al.
abstract: The quadrate of reptiles and most other tetrapods plays an important morphofunctional role by allowing the articulation of the mandible with the cranium. In Theropoda, the morphology of the quadrate is particularly complex and varies importantly among different clades of non-avian theropods, therefore conferring a strong taxonomic potential. Inconsistencies in the notation and terminology used in discussions of the theropod quadrate anatomy have been noticed, including at least one instance when no less than eight different terms were given to the same structure. A standardized list of terms and notations for each quadrate anatomical entity is proposed here, with the goal of facilitating future descriptions of this important cranial bone. In addition, an overview of the literature on quadrate function and pneumaticity in non-avian theropods is presented, along with a discussion of the inferences that could be made from this research. Specifically, the quadrate of the large majority of non-avian theropods is akinetic but the diagonally oriented intercondylar sulcus of the mandibular articulation allowed both rami of the mandible to move laterally when opening the mouth in many of theropods. Pneumaticity of the quadrate is also present in most averostran clades and the pneumatic chamber—invaded by the quadrate diverticulum of the mandibular arch pneumatic system—was connected to one or several pneumatic foramina on the medial, lateral, posterior, anterior or ventral sides of the quadrate.
bibliographic citation: Hendrickx et al. (2015) The non-avian theropod quadrate I: standardized terminology with an overview of the anatomy and function. PeerJ 3:e1245 https://doi.org/10.7717/peerj.1245
date submitted: 2014-05-04
date accepted: 2015-08-25
issued: 2015-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hendrickx
  given name: Christophe
author list: Agent
  family name: Araújo
  given name: Ricardo
author list: Agent
  family name: Mateus
  given name: Octávio
doi: 10.7717/peerj.1245
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-17
copyright: © 2015 Hendrickx et al.
attribution name: Hendrickx et al.

A practical guide and power analysis for GLMMs: detecting among treatment variation in random effects
type: item
type: AcademicArticle
description: In ecology and evolution generalized linear mixed models (GLMMs) are becoming increasingly used to test for differences in variation by treatment at multiple hierarchical levels. Yet, the specific sampling schemes that optimize the power of an experiment to detect differences in random effects by treatment/group remain unknown. In this paper we develop a blueprint for conducting power analyses for GLMMs focusing on detecting differences in variance by treatment. We present parameterization and power analyses for random-intercepts and random-slopes GLMMs because of their generality as focal parameters for most applications and because of their immediate applicability to emerging questions in the field of behavioral ecology. We focus on the extreme case of hierarchically structured binomial data, though the framework presented here generalizes easily to any error distribution model. First, we determine the optimal ratio of individuals to repeated measures within individuals that maximizes power to detect differences by treatment in among-individual variation in intercept, among-individual variation in slope, and within-individual variation in intercept. Second, we explore how power to detect differences in target variance parameters is affected by total variation. Our results indicate heterogeneity in power across ratios of individuals to repeated measures with an optimal ratio determined by both the target variance parameter and total sample size. Additionally, power to detect each variance parameter was low overall (in most cases >1,000 total observations per treatment needed to achieve 80% power) and decreased with increasing variance in non-target random effects. With growing interest in variance as the parameter of inquiry, these power analyses provide a crucial component for designing experiments focused on detecting differences in variance. We hope to inspire novel experimental designs in ecology and evolution investigating the causes and implications of indivi…
format: application/pdf
format: text/html
creator: Morgan P. Kain
creator: Ben M. Bolker
creator: Michael W. McCoy
subject: Ecology
subject: Mathematical Biology
subject: Statistics
description: doi:10.7717/peerj.1226
publisher: PeerJ Inc.
rights: © 2015 Kain et al.
abstract: In ecology and evolution generalized linear mixed models (GLMMs) are becoming increasingly used to test for differences in variation by treatment at multiple hierarchical levels. Yet, the specific sampling schemes that optimize the power of an experiment to detect differences in random effects by treatment/group remain unknown. In this paper we develop a blueprint for conducting power analyses for GLMMs focusing on detecting differences in variance by treatment. We present parameterization and power analyses for random-intercepts and random-slopes GLMMs because of their generality as focal parameters for most applications and because of their immediate applicability to emerging questions in the field of behavioral ecology. We focus on the extreme case of hierarchically structured binomial data, though the framework presented here generalizes easily to any error distribution model. First, we determine the optimal ratio of individuals to repeated measures within individuals that maximizes power to detect differences by treatment in among-individual variation in intercept, among-individual variation in slope, and within-individual variation in intercept. Second, we explore how power to detect differences in target variance parameters is affected by total variation. Our results indicate heterogeneity in power across ratios of individuals to repeated measures with an optimal ratio determined by both the target variance parameter and total sample size. Additionally, power to detect each variance parameter was low overall (in most cases >1,000 total observations per treatment needed to achieve 80% power) and decreased with increasing variance in non-target random effects. With growing interest in variance as the parameter of inquiry, these power analyses provide a crucial component for designing experiments focused on detecting differences in variance. We hope to inspire novel experimental designs in ecology and evolution investigating the causes and implications of indivi…
bibliographic citation: Kain et al. (2015) A practical guide and power analysis for GLMMs: detecting among treatment variation in random effects. PeerJ 3:e1226 https://doi.org/10.7717/peerj.1226
date submitted: 2015-06-16
date accepted: 2015-08-11
issued: 2015-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kain
  given name: Morgan P.
author list: Agent
  family name: Bolker
  given name: Ben M.
author list: Agent
  family name: McCoy
  given name: Michael W.
doi: 10.7717/peerj.1226
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-17
copyright: © 2015 Kain et al.
attribution name: Kain et al.

APOE genotype and age modifies the correlation between cognitive status and metabolites from hippocampus by a 2D 1H-MRS in non-demented elders
type: item
type: AcademicArticle
description: Purpose. To examine the associations among age, Apolipoprotein E (APOE) genotype, metabolic changes in the hippocampus detected by 2D 1H magnetic resonance spectroscopy (MRS), and neuropsychological measures of cognition in non-demented elders. Materials and Methods. We studied a cohort of 16 cognitively normal controls (CN) and 11 amnestic mild cognitive impairment (aMCI) patients between 66 and 88 years old who were genotyped for APOE genetic polymorphism. Measurements of 2D1H-MRS metabolites were obtained in the hippocampus region. Adjusting by age among all subjects, the association between metabolic changes and cognitive function was measured by Spearman partial rank-order correlation. The effect of APOE status was measured by separating the subjects into APOE genotype subgroups, including the APOEε4 carriers and APOEε4 non-carriers. Results. In contrast to the CN group matched with age, gender, and education, aMCI patients showed increased myo-inositol (mI)/Creatine (Cr) ratio only in the right hippocampus. No differences were noted on N-acetylaspartate (NAA)/Cr and mI/NAA from bilateral hippocampus, and so was mI/Cr ratio in left hippocampus between aMCI and CN. The mI/Cr ratio from the right hippocampus in non-demented elders was negatively correlated with Montreal Cognitive Assessment (MoCA) scores. Whether ε4 genotype or age was added as a covariate, none of the correlation effects remained significant. Additionally, adjusting for age and APOE genotype together, there was no significant correlation between them. Conclusion. Since the higher mI/Cr from the right hippocampus of the patients with aMCI than those from CN, the mI/Cr could be a more specific predictor of general cognitive function in aMCI patients. There is an association between higher mI/Cr in right hippocampus and worse cognitive function for the non-demented older adults, and the correlation could be modified by APOE status and age. That provided a window on objectively understanding the mec…
format: application/pdf
format: text/html
creator: Zhenyu Yin
creator: Wenbo Wu
creator: Renyuan Liu
creator: Xue Liang
creator: Tingting Yu
creator: Xiaoling Chen
creator: Jie Feng
creator: Aibin Guo
creator: Yu Xie
creator: Haiyan Yang
creator: Mingmin Huang
creator: Chuanshuai Tian
creator: Bing Zhang
creator: Yun Xu
subject: Neuroscience
subject: Diabetes and Endocrinology
subject: Geriatrics
subject: Metabolic Sciences
description: doi:10.7717/peerj.1202
publisher: PeerJ Inc.
rights: © 2015 Yin et al.
abstract: Purpose. To examine the associations among age, Apolipoprotein E (APOE) genotype, metabolic changes in the hippocampus detected by 2D 1H magnetic resonance spectroscopy (MRS), and neuropsychological measures of cognition in non-demented elders. Materials and Methods. We studied a cohort of 16 cognitively normal controls (CN) and 11 amnestic mild cognitive impairment (aMCI) patients between 66 and 88 years old who were genotyped for APOE genetic polymorphism. Measurements of 2D1H-MRS metabolites were obtained in the hippocampus region. Adjusting by age among all subjects, the association between metabolic changes and cognitive function was measured by Spearman partial rank-order correlation. The effect of APOE status was measured by separating the subjects into APOE genotype subgroups, including the APOEε4 carriers and APOEε4 non-carriers. Results. In contrast to the CN group matched with age, gender, and education, aMCI patients showed increased myo-inositol (mI)/Creatine (Cr) ratio only in the right hippocampus. No differences were noted on N-acetylaspartate (NAA)/Cr and mI/NAA from bilateral hippocampus, and so was mI/Cr ratio in left hippocampus between aMCI and CN. The mI/Cr ratio from the right hippocampus in non-demented elders was negatively correlated with Montreal Cognitive Assessment (MoCA) scores. Whether ε4 genotype or age was added as a covariate, none of the correlation effects remained significant. Additionally, adjusting for age and APOE genotype together, there was no significant correlation between them. Conclusion. Since the higher mI/Cr from the right hippocampus of the patients with aMCI than those from CN, the mI/Cr could be a more specific predictor of general cognitive function in aMCI patients. There is an association between higher mI/Cr in right hippocampus and worse cognitive function for the non-demented older adults, and the correlation could be modified by APOE status and age. That provided a window on objectively understanding the mec…
bibliographic citation: Yin et al. (2015) APOE genotype and age modifies the correlation between cognitive status and metabolites from hippocampus by a 2D 1H-MRS in non-demented elders. PeerJ 3:e1202 https://doi.org/10.7717/peerj.1202
date submitted: 2015-04-30
date accepted: 2015-07-30
issued: 2015-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Zhenyu
author list: Agent
  family name: Wu
  given name: Wenbo
author list: Agent
  family name: Liu
  given name: Renyuan
author list: Agent
  family name: Liang
  given name: Xue
author list: Agent
  family name: Yu
  given name: Tingting
author list: Agent
  family name: Chen
  given name: Xiaoling
author list: Agent
  family name: Feng
  given name: Jie
author list: Agent
  family name: Guo
  given name: Aibin
author list: Agent
  family name: Xie
  given name: Yu
author list: Agent
  family name: Yang
  given name: Haiyan
author list: Agent
  family name: Huang
  given name: Mingmin
author list: Agent
  family name: Tian
  given name: Chuanshuai
author list: Agent
  family name: Zhang
  given name: Bing
author list: Agent
  family name: Xu
  given name: Yun
doi: 10.7717/peerj.1202
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-17
copyright: © 2015 Yin et al.
attribution name: Yin et al.

MaqFACS (Macaque Facial Action Coding System) can be used to document facial movements in Barbary macaques (Macaca sylvanus)
type: item
type: AcademicArticle
description: Human and non-human primates exhibit facial movements or displays to communicate with one another. The evolution of form and function of those displays could be better understood through multispecies comparisons. Anatomically based coding systems (Facial Action Coding Systems: FACS) are developed to enable such comparisons because they are standardized and systematic and aid identification of homologous expressions underpinned by similar muscle contractions. To date, FACS has been developed for humans, and subsequently modified for chimpanzees, rhesus macaques, orangutans, hylobatids, dogs, and cats. Here, we wanted to test whether the MaqFACS system developed in rhesus macaques (Macaca mulatta) could be used to code facial movements in Barbary macaques (M. sylvanus), a species phylogenetically close to the rhesus macaques. The findings show that the facial movement capacity of Barbary macaques can be reliably coded using the MaqFACS. We found differences in use and form of some movements, most likely due to specializations in the communicative repertoire of each species, rather than morphological differences.
format: application/pdf
format: text/html
creator: Églantine Julle-Danière
creator: Jérôme Micheletta
creator: Jamie Whitehouse
creator: Marine Joly
creator: Carolin Gass
creator: Anne M. Burrows
creator: Bridget M. Waller
subject: Animal Behavior
description: doi:10.7717/peerj.1248
publisher: PeerJ Inc.
rights: © 2015 Julle-Danière et al.
abstract: Human and non-human primates exhibit facial movements or displays to communicate with one another. The evolution of form and function of those displays could be better understood through multispecies comparisons. Anatomically based coding systems (Facial Action Coding Systems: FACS) are developed to enable such comparisons because they are standardized and systematic and aid identification of homologous expressions underpinned by similar muscle contractions. To date, FACS has been developed for humans, and subsequently modified for chimpanzees, rhesus macaques, orangutans, hylobatids, dogs, and cats. Here, we wanted to test whether the MaqFACS system developed in rhesus macaques (Macaca mulatta) could be used to code facial movements in Barbary macaques (M. sylvanus), a species phylogenetically close to the rhesus macaques. The findings show that the facial movement capacity of Barbary macaques can be reliably coded using the MaqFACS. We found differences in use and form of some movements, most likely due to specializations in the communicative repertoire of each species, rather than morphological differences.
bibliographic citation: Julle-Danière et al. (2015) MaqFACS (Macaque Facial Action Coding System) can be used to document facial movements in Barbary macaques (Macaca sylvanus). PeerJ 3:e1248 https://doi.org/10.7717/peerj.1248
date submitted: 2015-06-15
date accepted: 2015-08-27
issued: 2015-09-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Julle-Danière
  given name: Églantine
author list: Agent
  family name: Micheletta
  given name: Jérôme
author list: Agent
  family name: Whitehouse
  given name: Jamie
author list: Agent
  family name: Joly
  given name: Marine
author list: Agent
  family name: Gass
  given name: Carolin
author list: Agent
  family name: Burrows
  given name: Anne M.
author list: Agent
  family name: Waller
  given name: Bridget M.
doi: 10.7717/peerj.1248
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-15
copyright: © 2015 Julle-Danière et al.
attribution name: Julle-Danière et al.

An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system
type: item
type: AcademicArticle
description: Biological containment is a genetic technique that programs dangerous organisms to grow only in the laboratory and to die in the natural environment. Auxotrophy for a substance not found in the natural environment is an ideal biological containment. Here, we constructed an Escherichia coli strain that cannot survive in the absence of the unnatural amino acid 3-iodo-L-tyrosine. This synthetic auxotrophy was achieved by conditional production of the antidote protein against the highly toxic enzyme colicin E3. An amber stop codon was inserted in the antidote gene. The translation of the antidote mRNA was controlled by a translational switch using amber-specific 3-iodo-L-tyrosine incorporation. The antidote is synthesized only when 3-iodo-L-tyrosine is present in the culture medium. The viability of this strain rapidly decreased with less than a 1 h half-life after removal of 3-iodo-L-tyrosine, suggesting that the decay of the antidote causes the host killing by activated colicin E3 in the absence of this unnatural amino acid. The contained strain grew 1.5 times more slowly than the parent strains. The escaper frequency was estimated to be 1.4 mutations (95% highest posterior density 1.1–1.8) per 105 cell divisions. This containment system can be constructed by only plasmid introduction without genome editing, suggesting that this system may be applicable to other microbes carrying toxin-antidote systems similar to that of colicin E3.
format: application/pdf
format: text/html
creator: Yusuke Kato
subject: Bioengineering
subject: Biotechnology
subject: Environmental Sciences
subject: Microbiology
description: doi:10.7717/peerj.1247
publisher: PeerJ Inc.
rights: © 2015 Kato
abstract: Biological containment is a genetic technique that programs dangerous organisms to grow only in the laboratory and to die in the natural environment. Auxotrophy for a substance not found in the natural environment is an ideal biological containment. Here, we constructed an Escherichia coli strain that cannot survive in the absence of the unnatural amino acid 3-iodo-L-tyrosine. This synthetic auxotrophy was achieved by conditional production of the antidote protein against the highly toxic enzyme colicin E3. An amber stop codon was inserted in the antidote gene. The translation of the antidote mRNA was controlled by a translational switch using amber-specific 3-iodo-L-tyrosine incorporation. The antidote is synthesized only when 3-iodo-L-tyrosine is present in the culture medium. The viability of this strain rapidly decreased with less than a 1 h half-life after removal of 3-iodo-L-tyrosine, suggesting that the decay of the antidote causes the host killing by activated colicin E3 in the absence of this unnatural amino acid. The contained strain grew 1.5 times more slowly than the parent strains. The escaper frequency was estimated to be 1.4 mutations (95% highest posterior density 1.1–1.8) per 105 cell divisions. This containment system can be constructed by only plasmid introduction without genome editing, suggesting that this system may be applicable to other microbes carrying toxin-antidote systems similar to that of colicin E3.
bibliographic citation: Kato (2015) An engineered bacterium auxotrophic for an unnatural amino acid: a novel biological containment system. PeerJ 3:e1247 https://doi.org/10.7717/peerj.1247
date submitted: 2015-04-22
date accepted: 2015-08-27
issued: 2015-09-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kato
  given name: Yusuke
doi: 10.7717/peerj.1247
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-15
copyright: © 2015 Kato
attribution name: Kato

Pursuit tracks chase: exploring the role of eye movements in the detection of chasing
type: item
type: AcademicArticle
description: We explore the role of eye movements in a chase detection task. Unlike the previous studies, which focused on overall performance as indicated by response speed and chase detection accuracy, we decompose the search process into gaze events such as smooth eye movements and use a data-driven approach to separately describe these gaze events. We measured eye movements of four human subjects engaged in a chase detection task displayed on a computer screen. The subjects were asked to detect two chasing rings among twelve other randomly moving rings. Using principal component analysis and support vector machines, we looked at the template and classification images that describe various stages of the detection process. We showed that the subjects mostly search for pairs of rings that move one after another in the same direction with a distance of 3.5–3.8 degrees. To find such pairs, the subjects first looked for regions with a high ring density and then pursued the rings in this region. Most of these groups consisted of two rings. Three subjects preferred to pursue the pair as a single object, while the remaining subject pursued the group by alternating the gaze between the two individual rings. In the discussion, we argue that subjects do not compare the movement of the pursued pair to a singular preformed template that describes a chasing motion. Rather, subjects bring certain hypotheses about what motion may qualify as chase and then, through feedback, they learn to look for a motion pattern that maximizes their performance.
format: application/pdf
format: text/html
creator: Matúš Šimkovic
creator: Birgit Träuble
subject: Neuroscience
subject: Ophthalmology
subject: Psychiatry and Psychology
subject: Computational Science
description: doi:10.7717/peerj.1243
publisher: PeerJ Inc.
rights: © 2015 Šimkovic and Träuble
abstract: We explore the role of eye movements in a chase detection task. Unlike the previous studies, which focused on overall performance as indicated by response speed and chase detection accuracy, we decompose the search process into gaze events such as smooth eye movements and use a data-driven approach to separately describe these gaze events. We measured eye movements of four human subjects engaged in a chase detection task displayed on a computer screen. The subjects were asked to detect two chasing rings among twelve other randomly moving rings. Using principal component analysis and support vector machines, we looked at the template and classification images that describe various stages of the detection process. We showed that the subjects mostly search for pairs of rings that move one after another in the same direction with a distance of 3.5–3.8 degrees. To find such pairs, the subjects first looked for regions with a high ring density and then pursued the rings in this region. Most of these groups consisted of two rings. Three subjects preferred to pursue the pair as a single object, while the remaining subject pursued the group by alternating the gaze between the two individual rings. In the discussion, we argue that subjects do not compare the movement of the pursued pair to a singular preformed template that describes a chasing motion. Rather, subjects bring certain hypotheses about what motion may qualify as chase and then, through feedback, they learn to look for a motion pattern that maximizes their performance.
bibliographic citation: Šimkovic et al. (2015) Pursuit tracks chase: exploring the role of eye movements in the detection of chasing. PeerJ 3:e1243 https://doi.org/10.7717/peerj.1243
date submitted: 2015-02-19
date accepted: 2015-08-25
issued: 2015-09-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Šimkovic
  given name: Matúš
author list: Agent
  family name: Träuble
  given name: Birgit
doi: 10.7717/peerj.1243
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-15
copyright: © 2015 Šimkovic and Träuble
attribution name: Šimkovic and Träuble

Integrated probability of coronary heart disease subject to the −308 tumor necrosis factor-alpha SNP: a Bayesian meta-analysis
type: item
type: AcademicArticle
description: We present a meta-analysis of independent studies on the potential implication in the occurrence of coronary heart disease (CHD) of the single-nucleotide polymorphism (SNP) at the −308 position of the tumor necrosis factor alpha (TNF-alpha) gene. We use Bayesian analysis to integrate independent data sets and to infer statistically robust measurements of correlation. Bayesian hypothesis testing indicates that there is no preference for the hypothesis that the −308 TNF-alpha SNP is related to the occurrence of CHD, in the Caucasian or in the Asian population, over the null hypothesis. As a measure of correlation, we use the probability of occurrence of CHD conditional on the presence of the SNP, derived as the posterior probability of the Bayesian meta-analysis. The conditional probability indicates that CHD is not more likely to occur when the SNP is present, which suggests that the −308 TNF-alpha SNP is not implicated in the occurrence of CHD.
format: application/pdf
format: text/html
creator: C. Sofia Carvalho
subject: Bioinformatics
subject: Cardiology
subject: Statistics
description: doi:10.7717/peerj.1236
publisher: PeerJ Inc.
rights: © 2015 Carvalho
abstract: We present a meta-analysis of independent studies on the potential implication in the occurrence of coronary heart disease (CHD) of the single-nucleotide polymorphism (SNP) at the −308 position of the tumor necrosis factor alpha (TNF-alpha) gene. We use Bayesian analysis to integrate independent data sets and to infer statistically robust measurements of correlation. Bayesian hypothesis testing indicates that there is no preference for the hypothesis that the −308 TNF-alpha SNP is related to the occurrence of CHD, in the Caucasian or in the Asian population, over the null hypothesis. As a measure of correlation, we use the probability of occurrence of CHD conditional on the presence of the SNP, derived as the posterior probability of the Bayesian meta-analysis. The conditional probability indicates that CHD is not more likely to occur when the SNP is present, which suggests that the −308 TNF-alpha SNP is not implicated in the occurrence of CHD.
bibliographic citation: Carvalho (2015) Integrated probability of coronary heart disease subject to the −308 tumor necrosis factor-alpha SNP: a Bayesian meta-analysis. PeerJ 3:e1236 https://doi.org/10.7717/peerj.1236
date submitted: 2015-06-18
date accepted: 2015-08-21
issued: 2015-09-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carvalho
  given name: C. Sofia
doi: 10.7717/peerj.1236
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-15
copyright: © 2015 Carvalho
attribution name: Carvalho

Survivorship and feeding preferences among size classes of outplanted sea urchins, Tripneustes gratilla, and possible use as biocontrol for invasive alien algae
type: item
type: AcademicArticle
description: We investigate the survivorship, growth and diet preferences of hatchery-raised juvenile urchins, Tripneustes gratilla, to evaluate the efficacy of their use as biocontrol agents in the efforts to reduce alien invasive algae. In flow-through tanks, we measured urchin growth rates, feeding rates and feeding preferences among diets of the most common invasive algae found in Kāneʻohe Bay, Hawaiʻi: Acanthophora spicifera, Gracilaria salicornia, Eucheuma denticulatum and Kappaphycus clade B. Post-transport survivorship of outplanted urchins was measured in paired open and closed cages in three different reef environments (lagoon, reef flat and reef slope) for a month. Survivorship in closed cages was highest on the reef flat (∼75%), and intermediate in the lagoon and reef slope (∼50%). In contrast, open cages showed similar survivorship on the reef flat and in the lagoon, but only 20% of juvenile urchins survived in open cages placed on the reef slope. Urchins grew significantly faster on diets of G. salicornia (1.58 mm/week ± 0.14 SE) and Kappaphycus clade B (1.69 ± 0.14 mm/wk) than on E. denticulatum (0.97 ± 0.14 mm/wk), with intermediate growth when fed on A. spicifera (1.23 ± 0.11 mm/wk). Interestingly, urchins display size-specific feeding preferences. In non-choice feeding trials, small urchins (17.5–22.5 mm test diameter) consumed G. salicornia fastest (6.08 g/day ± 0.19 SE), with A. spicifera (4.25 ± 0.02 g/day) and Kappaphycus clade B (3.83 ± 0.02 g/day) intermediate, and E. denticulatum was clearly the least consumed (2.32 ± 0.37 g/day). Medium-sized (29.8–43.8 mm) urchins likewise preferentially consumed G. salicornia (12.60 ± 0.08 g/day), with less clear differences among the other species in which E. denticulatum was still consumed least (9.35 ± 0.90 g/day). In contrast, large urchins (45.0–65.0 mm) showed no significant preferences among the different algae species at all (12.43–15.24 g/day). Overall consumption rates in non-choice trials were roughly equal…
format: application/pdf
format: text/html
creator: Charley E. Westbrook
creator: Rory R. Ringang
creator: Sean Michael A. Cantero
creator: Robert J. Toonen
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
description: doi:10.7717/peerj.1235
publisher: PeerJ Inc.
rights: © 2015 Westbrook et al.
abstract: We investigate the survivorship, growth and diet preferences of hatchery-raised juvenile urchins, Tripneustes gratilla, to evaluate the efficacy of their use as biocontrol agents in the efforts to reduce alien invasive algae. In flow-through tanks, we measured urchin growth rates, feeding rates and feeding preferences among diets of the most common invasive algae found in Kāneʻohe Bay, Hawaiʻi: Acanthophora spicifera, Gracilaria salicornia, Eucheuma denticulatum and Kappaphycus clade B. Post-transport survivorship of outplanted urchins was measured in paired open and closed cages in three different reef environments (lagoon, reef flat and reef slope) for a month. Survivorship in closed cages was highest on the reef flat (∼75%), and intermediate in the lagoon and reef slope (∼50%). In contrast, open cages showed similar survivorship on the reef flat and in the lagoon, but only 20% of juvenile urchins survived in open cages placed on the reef slope. Urchins grew significantly faster on diets of G. salicornia (1.58 mm/week ± 0.14 SE) and Kappaphycus clade B (1.69 ± 0.14 mm/wk) than on E. denticulatum (0.97 ± 0.14 mm/wk), with intermediate growth when fed on A. spicifera (1.23 ± 0.11 mm/wk). Interestingly, urchins display size-specific feeding preferences. In non-choice feeding trials, small urchins (17.5–22.5 mm test diameter) consumed G. salicornia fastest (6.08 g/day ± 0.19 SE), with A. spicifera (4.25 ± 0.02 g/day) and Kappaphycus clade B (3.83 ± 0.02 g/day) intermediate, and E. denticulatum was clearly the least consumed (2.32 ± 0.37 g/day). Medium-sized (29.8–43.8 mm) urchins likewise preferentially consumed G. salicornia (12.60 ± 0.08 g/day), with less clear differences among the other species in which E. denticulatum was still consumed least (9.35 ± 0.90 g/day). In contrast, large urchins (45.0–65.0 mm) showed no significant preferences among the different algae species at all (12.43–15.24 g/day). Overall consumption rates in non-choice trials were roughly equal…
bibliographic citation: Westbrook et al. (2015) Survivorship and feeding preferences among size classes of outplanted sea urchins, Tripneustes gratilla, and possible use as biocontrol for invasive alien algae. PeerJ 3:e1235 https://doi.org/10.7717/peerj.1235
date submitted: 2015-05-07
date accepted: 2015-08-18
issued: 2015-09-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Westbrook
  given name: Charley E.
author list: Agent
  family name: Ringang
  given name: Rory R.
author list: Agent
  family name: Cantero
  given name: Sean Michael A.
author list: Agent
  family name: Toonen
  given name: Robert J.
doi: 10.7717/peerj.1235
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-15
copyright: © 2015 Westbrook et al.
attribution name: Westbrook et al.

Registered report: androgen receptor splice variants determine taxane sensitivity in prostate cancer
type: item
type: AcademicArticle
description: The Prostate Cancer Foundation-Movember Foundation Reproducibility Initiative seeks to address growing concerns about reproducibility in scientific research by conducting replications of recent papers in the field of prostate cancer. This Registered Report describes the proposed replication plan of key experiments from “Androgen Receptor Splice Variants Determine Taxane Sensitivity in Prostate Cancer” by Thadani-Mulero and colleagues (2014) published in Cancer Research in 2014. The experiment that will be replicated is reported in Fig. 6A. Thadani-Mulero and colleagues generated xenografts from two prostate cancer cell lines; LuCaP 86.2, which expresses predominantly the ARv567 splice variant of the androgen receptor (AR), and LuCaP 23.1, which expresses the full length AR as well as the ARv7 variant. Treatment of the tumors with the taxane docetaxel showed that the drug inhibited tumor growth of the LuCaP 86.2 cells but not of the LuCaP 23.1 cells, indicating that expression of splice variants of the AR can affect sensitivity to docetaxel. The Prostate Cancer Foundation-Movember Foundation Reproducibility Initiative is a collaboration between the Prostate Cancer Foundation, the Movember Foundation and Science Exchange, and the results of the replications will be published by PeerJ.
format: application/pdf
format: text/html
creator: Xiaochuan Shan
creator: Gwenn Danet-Desnoyers
creator: Juan José Fung
creator: Alan H. Kosaka
creator: Fraser Tan
creator: Nicole Perfito
creator: Joelle Lomax
creator: Elizabeth Iorns
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.1232
publisher: PeerJ Inc.
rights: © 2015 Shan et al.
abstract: The Prostate Cancer Foundation-Movember Foundation Reproducibility Initiative seeks to address growing concerns about reproducibility in scientific research by conducting replications of recent papers in the field of prostate cancer. This Registered Report describes the proposed replication plan of key experiments from “Androgen Receptor Splice Variants Determine Taxane Sensitivity in Prostate Cancer” by Thadani-Mulero and colleagues (2014) published in Cancer Research in 2014. The experiment that will be replicated is reported in Fig. 6A. Thadani-Mulero and colleagues generated xenografts from two prostate cancer cell lines; LuCaP 86.2, which expresses predominantly the ARv567 splice variant of the androgen receptor (AR), and LuCaP 23.1, which expresses the full length AR as well as the ARv7 variant. Treatment of the tumors with the taxane docetaxel showed that the drug inhibited tumor growth of the LuCaP 86.2 cells but not of the LuCaP 23.1 cells, indicating that expression of splice variants of the AR can affect sensitivity to docetaxel. The Prostate Cancer Foundation-Movember Foundation Reproducibility Initiative is a collaboration between the Prostate Cancer Foundation, the Movember Foundation and Science Exchange, and the results of the replications will be published by PeerJ.
bibliographic citation: Shan et al. (2015) Registered report: androgen receptor splice variants determine taxane sensitivity in prostate cancer. PeerJ 3:e1232 https://doi.org/10.7717/peerj.1232
date submitted: 2015-05-23
date accepted: 2015-08-17
issued: 2015-09-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shan
  given name: Xiaochuan
author list: Agent
  family name: Danet-Desnoyers
  given name: Gwenn
author list: Agent
  family name: Fung
  given name: Juan José
author list: Agent
  family name: Kosaka
  given name: Alan H.
author list: Agent
  family name: Tan
  given name: Fraser
author list: Agent
  family name: Perfito
  given name: Nicole
author list: Agent
  family name: Lomax
  given name: Joelle
author list: Agent
  family name: Iorns
  given name: Elizabeth
doi: 10.7717/peerj.1232
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-15
copyright: © 2015 Shan et al.
attribution name: Shan et al.

Registered report: the androgen receptor induces a distinct transcriptional program in castration-resistant prostate cancer in man
type: item
type: AcademicArticle
description: The Prostate Cancer Foundation-Movember Foundation Reproducibility Initiative (PCFMFRI) seeks to address growing concerns about reproducibility in scientific research by conducting replications of recent papers in the field of prostate cancer. This Registered Report describes the proposed replication plan of key experiments from “The Androgen Receptor Induces a Distinct Transcriptional Program in Castration-Resistant Prostate Cancer in Man” by Sharma and colleagues (2013), published in Cancer Cell in 2013. Of thousands of targets for the androgen receptor (AR), the authors elucidated a subset of 16 core genes that were consistently downregulated with castration and re-emerged with castration resistance. These 16 AR binding sites were distinct from those observed in cells in culture. The authors suggested that cellular context can have dramatic effects on downstream transcriptional regulation of AR binding sites. The present study will attempt to replicate Fig. 7C by comparing gene expression of the 16 core genes identified by Sharma and colleagues in xenograft tumor tissue compared to androgen treated LNCaP cells in vitro. The Prostate Cancer Foundation-Movember Foundation Reproducibility Initiative is a collaboration between the Prostate Cancer Foundation, the Movember Initiative, and Science Exchange, and the results of the replications will be published by PeerJ.
format: application/pdf
format: text/html
creator: Denise Chronscinski
creator: Srujana Cherukeri
creator: Fraser Tan
creator: Nicole Perfito
creator: Joelle Lomax
creator: Elizabeth Iorns
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.1231
publisher: PeerJ Inc.
rights: © 2015 Chronscinski et al.
abstract: The Prostate Cancer Foundation-Movember Foundation Reproducibility Initiative (PCFMFRI) seeks to address growing concerns about reproducibility in scientific research by conducting replications of recent papers in the field of prostate cancer. This Registered Report describes the proposed replication plan of key experiments from “The Androgen Receptor Induces a Distinct Transcriptional Program in Castration-Resistant Prostate Cancer in Man” by Sharma and colleagues (2013), published in Cancer Cell in 2013. Of thousands of targets for the androgen receptor (AR), the authors elucidated a subset of 16 core genes that were consistently downregulated with castration and re-emerged with castration resistance. These 16 AR binding sites were distinct from those observed in cells in culture. The authors suggested that cellular context can have dramatic effects on downstream transcriptional regulation of AR binding sites. The present study will attempt to replicate Fig. 7C by comparing gene expression of the 16 core genes identified by Sharma and colleagues in xenograft tumor tissue compared to androgen treated LNCaP cells in vitro. The Prostate Cancer Foundation-Movember Foundation Reproducibility Initiative is a collaboration between the Prostate Cancer Foundation, the Movember Initiative, and Science Exchange, and the results of the replications will be published by PeerJ.
bibliographic citation: Chronscinski et al. (2015) Registered report: the androgen receptor induces a distinct transcriptional program in castration-resistant prostate cancer in man. PeerJ 3:e1231 https://doi.org/10.7717/peerj.1231
date submitted: 2015-05-22
date accepted: 2015-08-17
issued: 2015-09-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chronscinski
  given name: Denise
author list: Agent
  family name: Cherukeri
  given name: Srujana
author list: Agent
  family name: Tan
  given name: Fraser
author list: Agent
  family name: Perfito
  given name: Nicole
author list: Agent
  family name: Lomax
  given name: Joelle
author list: Agent
  family name: Iorns
  given name: Elizabeth
doi: 10.7717/peerj.1231
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-15
copyright: © 2015 Chronscinski et al.
attribution name: Chronscinski et al.

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