PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Trichoplax adhaerens reveals a network of nuclear receptors sensitive to 9-cis-retinoic acid at the base of metazoan evolution
items: The World (of Warcraft) through the eyes of an expert
items: Multi-scale immunoepidemiological modeling of within-host and between-host HIV dynamics: systematic review of mathematical models
items: An exploration of strategies used by dressage horses to control moments around the center of mass when performing passage
items: Slower EEG alpha generation, synchronization and “flow”—possible biomarkers of cognitive impairment and neuropathology of minor stroke
items: Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data
items: Advances in the study of nodavirus
items: A probe-based qRT-PCR method to profile immunological gene expression in blood of captive beluga whales (Delphinapterus leucas)
items: The Spanish version of the Fatigue Assessment Scale: reliability and validity assessment in postpartum women
items: Estimating the age of Heliconius butterflies from calibrated photographs

Trichoplax adhaerens reveals a network of nuclear receptors sensitive to 9-cis-retinoic acid at the base of metazoan evolution
type: item
type: AcademicArticle
description: Trichoplax adhaerens, the only known species of Placozoa is likely to be closely related to an early metazoan that preceded branching of Cnidaria and Bilateria. This animal species is surprisingly well adapted to free life in the World Ocean inhabiting tidal costal zones of oceans and seas with warm to moderate temperatures and shallow waters. The genome of T. adhaerens (sp. Grell) includes four nuclear receptors, namely orthologue of RXR (NR2B), HNF4 (NR2A), COUP-TF (NR2F) and ERR (NR3B) that show a high degree of similarity with human orthologues. In the case of RXR, the sequence identity to human RXR alpha reaches 81% in the DNA binding domain and 70% in the ligand binding domain. We show that T. adhaerens RXR (TaRXR) binds 9-cis retinoic acid (9-cis-RA) with high affinity, as well as high specificity and that exposure of T. adhaerens to 9-cis-RA regulates the expression of the putative T. adhaerens orthologue of vertebrate L-malate-NADP+ oxidoreductase (EC 1.1.1.40) which in vertebrates is regulated by a heterodimer of RXR and thyroid hormone receptor. Treatment by 9-cis-RA alters the relative expression profile of T. adhaerens nuclear receptors, suggesting the existence of natural ligands. Keeping with this, algal food composition has a profound effect on T. adhaerens growth and appearance. We show that nanomolar concentrations of 9-cis-RA interfere with T. adhaerens growth response to specific algal food and causes growth arrest. Our results uncover an endocrine-like network of nuclear receptors sensitive to 9-cis-RA in T. adhaerens and support the existence of a ligand-sensitive network of nuclear receptors at the base of metazoan evolution.
format: application/pdf
format: text/html
creator: Jan Philipp Novotný
creator: Ahmed Ali Chughtai
creator: Markéta Kostrouchová
creator: Veronika Kostrouchová
creator: David Kostrouch
creator: Filip Kaššák
creator: Radek Kaňa
creator: Bernd Schierwater
creator: Marta Kostrouchová
creator: Zdenek Kostrouch
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.3789
publisher: PeerJ Inc.
rights: © 2017 Novotný et al.
abstract: Trichoplax adhaerens, the only known species of Placozoa is likely to be closely related to an early metazoan that preceded branching of Cnidaria and Bilateria. This animal species is surprisingly well adapted to free life in the World Ocean inhabiting tidal costal zones of oceans and seas with warm to moderate temperatures and shallow waters. The genome of T. adhaerens (sp. Grell) includes four nuclear receptors, namely orthologue of RXR (NR2B), HNF4 (NR2A), COUP-TF (NR2F) and ERR (NR3B) that show a high degree of similarity with human orthologues. In the case of RXR, the sequence identity to human RXR alpha reaches 81% in the DNA binding domain and 70% in the ligand binding domain. We show that T. adhaerens RXR (TaRXR) binds 9-cis retinoic acid (9-cis-RA) with high affinity, as well as high specificity and that exposure of T. adhaerens to 9-cis-RA regulates the expression of the putative T. adhaerens orthologue of vertebrate L-malate-NADP+ oxidoreductase (EC 1.1.1.40) which in vertebrates is regulated by a heterodimer of RXR and thyroid hormone receptor. Treatment by 9-cis-RA alters the relative expression profile of T. adhaerens nuclear receptors, suggesting the existence of natural ligands. Keeping with this, algal food composition has a profound effect on T. adhaerens growth and appearance. We show that nanomolar concentrations of 9-cis-RA interfere with T. adhaerens growth response to specific algal food and causes growth arrest. Our results uncover an endocrine-like network of nuclear receptors sensitive to 9-cis-RA in T. adhaerens and support the existence of a ligand-sensitive network of nuclear receptors at the base of metazoan evolution.
bibliographic citation: Novotný et al. (2017) Trichoplax adhaerens reveals a network of nuclear receptors sensitive to 9-cis-retinoic acid at the base of metazoan evolution. PeerJ 5:e3789 https://doi.org/10.7717/peerj.3789
date submitted: 2017-04-21
date accepted: 2017-08-18
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Novotný
  given name: Jan Philipp
author list: Agent
  family name: Chughtai
  given name: Ahmed Ali
author list: Agent
  family name: Kostrouchová
  given name: Markéta
author list: Agent
  family name: Kostrouchová
  given name: Veronika
author list: Agent
  family name: Kostrouch
  given name: David
author list: Agent
  family name: Kaššák
  given name: Filip
author list: Agent
  family name: Kaňa
  given name: Radek
author list: Agent
  family name: Schierwater
  given name: Bernd
author list: Agent
  family name: Kostrouchová
  given name: Marta
author list: Agent
  family name: Kostrouch
  given name: Zdenek
doi: 10.7717/peerj.3789
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Novotný et al.
attribution name: Novotný et al.

The World (of Warcraft) through the eyes of an expert
type: item
type: AcademicArticle
description: Negative correlations between pupil size and the tendency to look at salient locations were found in recent studies (e.g., Mathôt et al., 2015). It is hypothesized that this negative correlation might be explained by the mental effort put by participants in the task that leads in return to pupil dilation. Here we present an exploratory study on the effect of expertise on eye-movement behavior. Because there is no available standard tool to evaluate WoW players’ expertise, we built an off-game questionnaire testing players’ knowledge about WoW and acquired skills through completed raids, highest rated battlegrounds, Skill Points, etc. Experts (N = 4) and novices (N = 4) in the massively multiplayer online role-playing game World of Warcraft (WoW) viewed 24 designed video segments from the game that differ in regards with their content (i.e, informative locations) and visual complexity (i.e, salient locations). Consistent with previous studies, we found a negative correlation between pupil size and the tendency to look at salient locations (experts, r = − .17, p < .0001, and novices, r = − .09, p < .0001). This correlation has been interpreted in terms of mental effort: People are inherently biased to look at salient locations (sharp corners, bright lights, etc.), but are able (i.e., experts) to overcome this bias if they invest sufficient mental effort. Crucially, we observed that this correlation was stronger for expert WoW players than novice players (Z = − 3.3, p = .0011). This suggests that experts learned to improve control over eye-movement behavior by guiding their eyes towards informative, but potentially low-salient areas of the screen. These findings may contribute to our understanding of what makes an expert an expert.
format: application/pdf
format: text/html
creator: Yousri Marzouki
creator: Valériane Dusaucy
creator: Myriam Chanceaux
creator: Sebastiaan Mathôt
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3783
publisher: PeerJ Inc.
rights: © 2017 Marzouki et al.
abstract: Negative correlations between pupil size and the tendency to look at salient locations were found in recent studies (e.g., Mathôt et al., 2015). It is hypothesized that this negative correlation might be explained by the mental effort put by participants in the task that leads in return to pupil dilation. Here we present an exploratory study on the effect of expertise on eye-movement behavior. Because there is no available standard tool to evaluate WoW players’ expertise, we built an off-game questionnaire testing players’ knowledge about WoW and acquired skills through completed raids, highest rated battlegrounds, Skill Points, etc. Experts (N = 4) and novices (N = 4) in the massively multiplayer online role-playing game World of Warcraft (WoW) viewed 24 designed video segments from the game that differ in regards with their content (i.e, informative locations) and visual complexity (i.e, salient locations). Consistent with previous studies, we found a negative correlation between pupil size and the tendency to look at salient locations (experts, r = − .17, p < .0001, and novices, r = − .09, p < .0001). This correlation has been interpreted in terms of mental effort: People are inherently biased to look at salient locations (sharp corners, bright lights, etc.), but are able (i.e., experts) to overcome this bias if they invest sufficient mental effort. Crucially, we observed that this correlation was stronger for expert WoW players than novice players (Z = − 3.3, p = .0011). This suggests that experts learned to improve control over eye-movement behavior by guiding their eyes towards informative, but potentially low-salient areas of the screen. These findings may contribute to our understanding of what makes an expert an expert.
bibliographic citation: Marzouki et al. (2017) The World (of Warcraft) through the eyes of an expert. PeerJ 5:e3783 https://doi.org/10.7717/peerj.3783
date submitted: 2016-01-15
date accepted: 2017-08-18
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marzouki
  given name: Yousri
author list: Agent
  family name: Dusaucy
  given name: Valériane
author list: Agent
  family name: Chanceaux
  given name: Myriam
author list: Agent
  family name: Mathôt
  given name: Sebastiaan
doi: 10.7717/peerj.3783
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Marzouki et al.
attribution name: Marzouki et al.

Multi-scale immunoepidemiological modeling of within-host and between-host HIV dynamics: systematic review of mathematical models
type: item
type: AcademicArticle
description: Objective The objective of this study is to conduct a systematic review of multi-scale HIV immunoepidemiological models to improve our understanding of the synergistic impact between the HIV viral-immune dynamics at the individual level and HIV transmission dynamics at the population level. Background While within-host and between-host models of HIV dynamics have been well studied at a single scale, connecting the immunological and epidemiological scales through multi-scale models is an emerging method to infer the synergistic dynamics of HIV at the individual and population levels. Methods We reviewed nine articles using the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) framework that focused on the synergistic dynamics of HIV immunoepidemiological models at the individual and population levels. Results HIV immunoepidemiological models simulate viral immune dynamics at the within-host scale and the epidemiological transmission dynamics at the between-host scale. They account for longitudinal changes in the immune viral dynamics of HIV+ individuals, and their corresponding impact on the transmission dynamics in the population. They are useful to analyze the dynamics of HIV super-infection, co-infection, drug resistance, evolution, and treatment in HIV+ individuals, and their impact on the epidemic pathways in the population. We illustrate the coupling mechanisms of the within-host and between-host scales, their mathematical implementation, and the clinical and public health problems that are appropriate for analysis using HIV immunoepidemiological models. Conclusion HIV immunoepidemiological models connect the within-host immune dynamics at the individual level and the epidemiological transmission dynamics at the population level. While multi-scale models add complexity over a single-scale model, they account for the time varying immune viral response of HIV+ individuals, and the corresponding impact on the time-varying risk of transmis…
format: application/pdf
format: text/html
creator: Nargesalsadat Dorratoltaj
creator: Ryan Nikin-Beers
creator: Stanca M. Ciupe
creator: Stephen G. Eubank
creator: Kaja M. Abbas
subject: Computational Biology
subject: Mathematical Biology
subject: Epidemiology
subject: HIV
subject: Immunology
description: doi:10.7717/peerj.3877
publisher: PeerJ Inc.
rights: © 2017 Dorratoltaj et al.
abstract: Objective The objective of this study is to conduct a systematic review of multi-scale HIV immunoepidemiological models to improve our understanding of the synergistic impact between the HIV viral-immune dynamics at the individual level and HIV transmission dynamics at the population level. Background While within-host and between-host models of HIV dynamics have been well studied at a single scale, connecting the immunological and epidemiological scales through multi-scale models is an emerging method to infer the synergistic dynamics of HIV at the individual and population levels. Methods We reviewed nine articles using the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) framework that focused on the synergistic dynamics of HIV immunoepidemiological models at the individual and population levels. Results HIV immunoepidemiological models simulate viral immune dynamics at the within-host scale and the epidemiological transmission dynamics at the between-host scale. They account for longitudinal changes in the immune viral dynamics of HIV+ individuals, and their corresponding impact on the transmission dynamics in the population. They are useful to analyze the dynamics of HIV super-infection, co-infection, drug resistance, evolution, and treatment in HIV+ individuals, and their impact on the epidemic pathways in the population. We illustrate the coupling mechanisms of the within-host and between-host scales, their mathematical implementation, and the clinical and public health problems that are appropriate for analysis using HIV immunoepidemiological models. Conclusion HIV immunoepidemiological models connect the within-host immune dynamics at the individual level and the epidemiological transmission dynamics at the population level. While multi-scale models add complexity over a single-scale model, they account for the time varying immune viral response of HIV+ individuals, and the corresponding impact on the time-varying risk of transmis…
bibliographic citation: Dorratoltaj et al. (2017) Multi-scale immunoepidemiological modeling of within-host and between-host HIV dynamics: systematic review of mathematical models. PeerJ 5:e3877 https://doi.org/10.7717/peerj.3877
date submitted: 2017-07-06
date accepted: 2017-09-11
issued: 2017-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dorratoltaj
  given name: Nargesalsadat
author list: Agent
  family name: Nikin-Beers
  given name: Ryan
author list: Agent
  family name: Ciupe
  given name: Stanca M.
author list: Agent
  family name: Eubank
  given name: Stephen G.
author list: Agent
  family name: Abbas
  given name: Kaja M.
doi: 10.7717/peerj.3877
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-28
copyright: ©2017 Dorratoltaj et al.
attribution name: Dorratoltaj et al.

An exploration of strategies used by dressage horses to control moments around the center of mass when performing passage
type: item
type: AcademicArticle
description: Background Locomotion results from the generation of ground reaction forces (GRF) that cause translations of the center of mass (COM) and generate moments that rotate the body around the COM. The trot is a diagonally-synchronized gait performed by horses at intermediate locomotor speeds. Passage is a variant of the trot performed by highly-trained dressage horses. It is distinguished from trot by having a slow speed of progression combined with great animation of the limbs in the swing phase. The slow speed of passage challenges the horse’s ability to control the sagittal-plane moments around the COM. Footfall patterns and peak GRF are known to differ between passage and trot, but their effects on balance management, which we define here as the ability to control nose-up/nose-down pitching moments around the horse’s COM to maintain a state of equilibrium, are not known. The objective was to investigate which biomechanical variables influence pitching moments around the COM in passage. Methods Three highly-trained dressage horses were captured by a 10-camera motion analysis system (120 Hz) as they were ridden in passage over four force platforms (960 Hz). A full-body marker set was used to track the horse’s COM and measure balance variables including total body center of pressure (COP), pitching moments, diagonal dissociation timing, peak force production, limb protraction–retraction, and trunk posture. A total of twenty passage steps were extracted and partial correlation (accounting for horse) was used to investigate significant (P < 0.05) relationships between variables. Results Hindlimb mean protraction–retraction correlated significantly with peak hindlimb propulsive forces (R = 0.821; P < 0.01), mean pitching moments (R = 0.546, P = 0.016), trunk range of motion, COM craniocaudal location and diagonal dissociation time (P < 0.05). Discussion Pitching moments around the COM were controlled by a combination of kinematic and kinetic adjustments that involve coordi…
format: application/pdf
format: text/html
creator: Hilary M. Clayton
creator: Sarah Jane Hobbs
subject: Animal Behavior
subject: Bioengineering
subject: Veterinary Medicine
subject: Zoology
subject: Kinesiology
description: doi:10.7717/peerj.3866
publisher: PeerJ Inc.
rights: © 2017 Clayton and Hobbs
abstract: Background Locomotion results from the generation of ground reaction forces (GRF) that cause translations of the center of mass (COM) and generate moments that rotate the body around the COM. The trot is a diagonally-synchronized gait performed by horses at intermediate locomotor speeds. Passage is a variant of the trot performed by highly-trained dressage horses. It is distinguished from trot by having a slow speed of progression combined with great animation of the limbs in the swing phase. The slow speed of passage challenges the horse’s ability to control the sagittal-plane moments around the COM. Footfall patterns and peak GRF are known to differ between passage and trot, but their effects on balance management, which we define here as the ability to control nose-up/nose-down pitching moments around the horse’s COM to maintain a state of equilibrium, are not known. The objective was to investigate which biomechanical variables influence pitching moments around the COM in passage. Methods Three highly-trained dressage horses were captured by a 10-camera motion analysis system (120 Hz) as they were ridden in passage over four force platforms (960 Hz). A full-body marker set was used to track the horse’s COM and measure balance variables including total body center of pressure (COP), pitching moments, diagonal dissociation timing, peak force production, limb protraction–retraction, and trunk posture. A total of twenty passage steps were extracted and partial correlation (accounting for horse) was used to investigate significant (P < 0.05) relationships between variables. Results Hindlimb mean protraction–retraction correlated significantly with peak hindlimb propulsive forces (R = 0.821; P < 0.01), mean pitching moments (R = 0.546, P = 0.016), trunk range of motion, COM craniocaudal location and diagonal dissociation time (P < 0.05). Discussion Pitching moments around the COM were controlled by a combination of kinematic and kinetic adjustments that involve coordi…
bibliographic citation: Clayton et al. (2017) An exploration of strategies used by dressage horses to control moments around the center of mass when performing passage. PeerJ 5:e3866 https://doi.org/10.7717/peerj.3866
date submitted: 2017-07-21
date accepted: 2017-09-08
issued: 2017-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clayton
  given name: Hilary M.
author list: Agent
  family name: Hobbs
  given name: Sarah Jane
doi: 10.7717/peerj.3866
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-28
copyright: ©2017 Clayton and Hobbs
attribution name: Clayton and Hobbs

Slower EEG alpha generation, synchronization and “flow”—possible biomarkers of cognitive impairment and neuropathology of minor stroke
type: item
type: AcademicArticle
description: Background We investigated EEG rhythms, particularly alpha activity, and their relationship to post-stroke neuropathology and cognitive functions in the subacute and chronic stages of minor strokes. Methods We included 10 patients with right middle cerebral artery (MCA) ischemic strokes and 11 healthy controls. All the assessments of stroke patients were done both in the subacute and chronic stages. Neurological impairment was measured using the National Institute of Health Stroke Scale (NIHSS), whereas cognitive functions were assessed using the Montreal Cognitive Assessment (MoCA) and MoCA memory index (MoCA-MIS). The EEG was recorded using a 19 channel EEG system with standard EEG electrode placement. In particular, we analyzed the EEGs derived from the four lateral frontal (F3, F7, F4, F8), and corresponding lateral posterior (P3, P4, T5, T6) electrodes. Quantitative EEG analysis included: the group FFT spectra, the weighted average of alpha frequency (αAVG), the group probability density distributions of all conventional EEG frequency band relative amplitudes (EEG microstructure), the inter- and intra-hemispheric coherences, and the topographic distribution of alpha carrier frequency phase potentials (PPs). Statistical analysis was done using a Kruskal–Wallis ANOVA with a post-hoc Mann–Whitney U two-tailed test, and Spearman’s correlation. Results We demonstrated transient cognitive impairment alongside a slower alpha frequency (αAVG) in the subacute right MCA stroke patients vs. the controls. This slower alpha frequency showed no amplitude change, but was highly synchronized intra-hemispherically, overlying the ipsi-lesional hemisphere, and inter-hemispherically, overlying the frontal cortex. In addition, the disturbances in EEG alpha activity in subacute stroke patients were expressed as a decrease in alpha PPs over the frontal cortex and an altered “alpha flow”, indicating the sustained augmentation of inter-hemispheric interactions. Although the stroke indu…
format: application/pdf
format: text/html
creator: Jelena Petrovic
creator: Vuk Milosevic
creator: Miroslava Zivkovic
creator: Dragan Stojanov
creator: Olga Milojkovic
creator: Aleksandar Kalauzi
creator: Jasna Saponjic
subject: Cognitive Disorders
subject: Neurology
description: doi:10.7717/peerj.3839
publisher: PeerJ Inc.
rights: © 2017 Petrovic et al.
abstract: Background We investigated EEG rhythms, particularly alpha activity, and their relationship to post-stroke neuropathology and cognitive functions in the subacute and chronic stages of minor strokes. Methods We included 10 patients with right middle cerebral artery (MCA) ischemic strokes and 11 healthy controls. All the assessments of stroke patients were done both in the subacute and chronic stages. Neurological impairment was measured using the National Institute of Health Stroke Scale (NIHSS), whereas cognitive functions were assessed using the Montreal Cognitive Assessment (MoCA) and MoCA memory index (MoCA-MIS). The EEG was recorded using a 19 channel EEG system with standard EEG electrode placement. In particular, we analyzed the EEGs derived from the four lateral frontal (F3, F7, F4, F8), and corresponding lateral posterior (P3, P4, T5, T6) electrodes. Quantitative EEG analysis included: the group FFT spectra, the weighted average of alpha frequency (αAVG), the group probability density distributions of all conventional EEG frequency band relative amplitudes (EEG microstructure), the inter- and intra-hemispheric coherences, and the topographic distribution of alpha carrier frequency phase potentials (PPs). Statistical analysis was done using a Kruskal–Wallis ANOVA with a post-hoc Mann–Whitney U two-tailed test, and Spearman’s correlation. Results We demonstrated transient cognitive impairment alongside a slower alpha frequency (αAVG) in the subacute right MCA stroke patients vs. the controls. This slower alpha frequency showed no amplitude change, but was highly synchronized intra-hemispherically, overlying the ipsi-lesional hemisphere, and inter-hemispherically, overlying the frontal cortex. In addition, the disturbances in EEG alpha activity in subacute stroke patients were expressed as a decrease in alpha PPs over the frontal cortex and an altered “alpha flow”, indicating the sustained augmentation of inter-hemispheric interactions. Although the stroke indu…
bibliographic citation: Petrovic et al. (2017) Slower EEG alpha generation, synchronization and “flow”—possible biomarkers of cognitive impairment and neuropathology of minor stroke. PeerJ 5:e3839 https://doi.org/10.7717/peerj.3839
date submitted: 2017-04-13
date accepted: 2017-09-01
issued: 2017-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Petrovic
  given name: Jelena
author list: Agent
  family name: Milosevic
  given name: Vuk
author list: Agent
  family name: Zivkovic
  given name: Miroslava
author list: Agent
  family name: Stojanov
  given name: Dragan
author list: Agent
  family name: Milojkovic
  given name: Olga
author list: Agent
  family name: Kalauzi
  given name: Aleksandar
author list: Agent
  family name: Saponjic
  given name: Jasna
doi: 10.7717/peerj.3839
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-28
copyright: ©2017 Petrovic et al.
attribution name: Petrovic et al.

Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data
type: item
type: AcademicArticle
description: We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks H2AZ and H3K4me3 were measured over time using ChIP-Seq experiments in MCF7 cells stimulated with estrogen. A Bayesian classifier was developed which uses the correlation of temporal binding patterns at enhancers and promoters and genomic proximity as features to predict interactions. This method was trained using experimentally determined interactions from the same system and was shown to achieve much higher precision than predictions based on the genomic proximity of nearest ERα binding. We use the method to identify a genome-wide confident set of ERα target genes and their regulatory enhancers genome-wide. Validation with publicly available GRO-Seq data demonstrates that our predicted targets are much more likely to show early nascent transcription than predictions based on genomic ERα binding proximity alone.
format: application/pdf
format: text/html
creator: Tomasz Dzida
creator: Mudassar Iqbal
creator: Iryna Charapitsa
creator: George Reid
creator: Henk Stunnenberg
creator: Filomena Matarese
creator: Korbinian Grote
creator: Antti Honkela
creator: Magnus Rattray
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
description: doi:10.7717/peerj.3742
publisher: PeerJ Inc.
rights: © 2017 Dzida et al.
abstract: We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks H2AZ and H3K4me3 were measured over time using ChIP-Seq experiments in MCF7 cells stimulated with estrogen. A Bayesian classifier was developed which uses the correlation of temporal binding patterns at enhancers and promoters and genomic proximity as features to predict interactions. This method was trained using experimentally determined interactions from the same system and was shown to achieve much higher precision than predictions based on the genomic proximity of nearest ERα binding. We use the method to identify a genome-wide confident set of ERα target genes and their regulatory enhancers genome-wide. Validation with publicly available GRO-Seq data demonstrates that our predicted targets are much more likely to show early nascent transcription than predictions based on genomic ERα binding proximity alone.
bibliographic citation: Dzida et al. (2017) Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data. PeerJ 5:e3742 https://doi.org/10.7717/peerj.3742
date submitted: 2017-03-20
date accepted: 2017-08-07
issued: 2017-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dzida
  given name: Tomasz
author list: Agent
  family name: Iqbal
  given name: Mudassar
author list: Agent
  family name: Charapitsa
  given name: Iryna
author list: Agent
  family name: Reid
  given name: George
author list: Agent
  family name: Stunnenberg
  given name: Henk
author list: Agent
  family name: Matarese
  given name: Filomena
author list: Agent
  family name: Grote
  given name: Korbinian
author list: Agent
  family name: Honkela
  given name: Antti
author list: Agent
  family name: Rattray
  given name: Magnus
doi: 10.7717/peerj.3742
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-28
copyright: ©2017 Dzida et al.
attribution name: Dzida et al.

Advances in the study of nodavirus
type: item
type: AcademicArticle
description: Nodaviruses are small bipartite RNA viruses which belong to the family of Nodaviridae. They are categorized into alpha-nodavirus, which infects insects, and beta-nodavirus, which infects fishes. Another distinct group of nodavirus infects shrimps and prawns, which has been proposed to be categorized as gamma-nodavirus. Our current review focuses mainly on recent studies performed on nodaviruses. Nodavirus can be transmitted vertically and horizontally. Recent outbreaks have been reported in China, Indonesia, Singapore and India, affecting the aquaculture industry. It also decreased mullet stock in the Caspian Sea. Histopathology and transmission electron microscopy (TEM) are used to examine the presence of nodaviruses in infected fishes and prawns. For classification, virus isolation followed by nucleotide sequencing are required. In contrast to partial sequence identification, profiling the whole transcriptome using next generation sequencing (NGS) offers a more comprehensive comparison and characterization of the virus. For rapid diagnosis of nodavirus, assays targeting the viral RNA based on reverse-transcription PCR (RT-PCR) such as microfluidic chips, reverse-transcription loop-mediated isothermal amplification (RT-LAMP) and RT-LAMP coupled with lateral flow dipstick (RT-LAMP-LFD) have been developed. Besides viral RNA detections, diagnosis based on immunological assays such as enzyme-linked immunosorbent assay (ELISA), immunodot and Western blotting have also been reported. In addition, immune responses of fish and prawn are also discussed. Overall, in fish, innate immunity, cellular type I interferon immunity and humoral immunity cooperatively prevent nodavirus infections, whereas prawns and shrimps adopt different immune mechanisms against nodavirus infections, through upregulation of superoxide anion, prophenoloxidase, superoxide dismutase (SOD), crustin, peroxinectin, anti-lipopolysaccharides and heat shock proteins (HSP). Potential vaccines for fishes and…
format: application/pdf
format: text/html
creator: Chean Yeah Yong
creator: Swee Keong Yeap
creator: Abdul Rahman Omar
creator: Wen Siang Tan
subject: Aquaculture, Fisheries and Fish Science
subject: Virology
subject: Immunology
description: doi:10.7717/peerj.3841
publisher: PeerJ Inc.
rights: © 2017 Yong et al.
abstract: Nodaviruses are small bipartite RNA viruses which belong to the family of Nodaviridae. They are categorized into alpha-nodavirus, which infects insects, and beta-nodavirus, which infects fishes. Another distinct group of nodavirus infects shrimps and prawns, which has been proposed to be categorized as gamma-nodavirus. Our current review focuses mainly on recent studies performed on nodaviruses. Nodavirus can be transmitted vertically and horizontally. Recent outbreaks have been reported in China, Indonesia, Singapore and India, affecting the aquaculture industry. It also decreased mullet stock in the Caspian Sea. Histopathology and transmission electron microscopy (TEM) are used to examine the presence of nodaviruses in infected fishes and prawns. For classification, virus isolation followed by nucleotide sequencing are required. In contrast to partial sequence identification, profiling the whole transcriptome using next generation sequencing (NGS) offers a more comprehensive comparison and characterization of the virus. For rapid diagnosis of nodavirus, assays targeting the viral RNA based on reverse-transcription PCR (RT-PCR) such as microfluidic chips, reverse-transcription loop-mediated isothermal amplification (RT-LAMP) and RT-LAMP coupled with lateral flow dipstick (RT-LAMP-LFD) have been developed. Besides viral RNA detections, diagnosis based on immunological assays such as enzyme-linked immunosorbent assay (ELISA), immunodot and Western blotting have also been reported. In addition, immune responses of fish and prawn are also discussed. Overall, in fish, innate immunity, cellular type I interferon immunity and humoral immunity cooperatively prevent nodavirus infections, whereas prawns and shrimps adopt different immune mechanisms against nodavirus infections, through upregulation of superoxide anion, prophenoloxidase, superoxide dismutase (SOD), crustin, peroxinectin, anti-lipopolysaccharides and heat shock proteins (HSP). Potential vaccines for fishes and…
bibliographic citation: Yong et al. (2017) Advances in the study of nodavirus. PeerJ 5:e3841 https://doi.org/10.7717/peerj.3841
date submitted: 2017-06-16
date accepted: 2017-09-01
issued: 2017-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yong
  given name: Chean Yeah
author list: Agent
  family name: Yeap
  given name: Swee Keong
author list: Agent
  family name: Omar
  given name: Abdul Rahman
author list: Agent
  family name: Tan
  given name: Wen Siang
doi: 10.7717/peerj.3841
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-27
copyright: ©2017 Yong et al.
attribution name: Yong et al.

A probe-based qRT-PCR method to profile immunological gene expression in blood of captive beluga whales (Delphinapterus leucas)
type: item
type: AcademicArticle
description: Cytokines are fundamental for a functioning immune system, and thus potentially serve as important indicators of animal health. Quantitation of mRNA using quantitative reverse transcription polymerase chain reaction (qRT-PCR) is an established immunological technique. It is particularly suitable for detecting the expression of proteins against which monoclonal antibodies are not available. In this study, we developed a probe-based quantitative gene expression assay for immunological assessment of captive beluga whales (Delphinapterus leucas) that is one of the most common cetacean species on display in aquariums worldwide. Six immunologically relevant genes (IL-2Rα, -4, -10, -12, TNFα, and IFNγ) were selected for analysis, and two validated housekeeping genes (PGK1 and RPL4) with stable expression were used as reference genes. Sixteen blood samples were obtained from four animals with different health conditions and stored in RNAlater™ solution. These samples were used for RNA extraction followed by qRT-PCR analysis. Analysis of gene transcripts was performed by relative quantitation using the comparative Cq method with the integration of amplification efficiency and two reference genes. The expression levels of each gene in the samples from clinically healthy animals were normally distributed. Transcript outliers for IL-2Rα, IL-4, IL-12, TNFα, and IFNγ were noticed in four samples collected from two clinically unhealthy animals. This assay has the potential to identify immune system deviation from normal state, which is caused by health problems. Furthermore, knowing the immune status of captive cetaceans could help both trainers and veterinarians in implementing preventive approaches prior to disease onset.
format: application/pdf
format: text/html
creator: Ming-An Tsai
creator: I-Hua Chen
creator: Jiann-Hsiung Wang
creator: Shih-Jen Chou
creator: Tsung-Hsien Li
creator: Ming-Yih Leu
creator: Hsiao-Kuan Ho
creator: Wei Cheng Yang
subject: Marine Biology
subject: Molecular Biology
subject: Veterinary Medicine
subject: Immunology
description: doi:10.7717/peerj.3840
publisher: PeerJ Inc.
rights: © 2017 Tsai et al.
abstract: Cytokines are fundamental for a functioning immune system, and thus potentially serve as important indicators of animal health. Quantitation of mRNA using quantitative reverse transcription polymerase chain reaction (qRT-PCR) is an established immunological technique. It is particularly suitable for detecting the expression of proteins against which monoclonal antibodies are not available. In this study, we developed a probe-based quantitative gene expression assay for immunological assessment of captive beluga whales (Delphinapterus leucas) that is one of the most common cetacean species on display in aquariums worldwide. Six immunologically relevant genes (IL-2Rα, -4, -10, -12, TNFα, and IFNγ) were selected for analysis, and two validated housekeeping genes (PGK1 and RPL4) with stable expression were used as reference genes. Sixteen blood samples were obtained from four animals with different health conditions and stored in RNAlater™ solution. These samples were used for RNA extraction followed by qRT-PCR analysis. Analysis of gene transcripts was performed by relative quantitation using the comparative Cq method with the integration of amplification efficiency and two reference genes. The expression levels of each gene in the samples from clinically healthy animals were normally distributed. Transcript outliers for IL-2Rα, IL-4, IL-12, TNFα, and IFNγ were noticed in four samples collected from two clinically unhealthy animals. This assay has the potential to identify immune system deviation from normal state, which is caused by health problems. Furthermore, knowing the immune status of captive cetaceans could help both trainers and veterinarians in implementing preventive approaches prior to disease onset.
bibliographic citation: Tsai et al. (2017) A probe-based qRT-PCR method to profile immunological gene expression in blood of captive beluga whales (Delphinapterus leucas). PeerJ 5:e3840 https://doi.org/10.7717/peerj.3840
date submitted: 2017-01-18
date accepted: 2017-09-01
issued: 2017-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tsai
  given name: Ming-An
author list: Agent
  family name: Chen
  given name: I-Hua
author list: Agent
  family name: Wang
  given name: Jiann-Hsiung
author list: Agent
  family name: Chou
  given name: Shih-Jen
author list: Agent
  family name: Li
  given name: Tsung-Hsien
author list: Agent
  family name: Leu
  given name: Ming-Yih
author list: Agent
  family name: Ho
  given name: Hsiao-Kuan
author list: Agent
  family name: Yang
  given name: Wei Cheng
doi: 10.7717/peerj.3840
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-27
copyright: ©2017 Tsai et al.
attribution name: Tsai et al.

The Spanish version of the Fatigue Assessment Scale: reliability and validity assessment in postpartum women
type: item
type: AcademicArticle
description: Background Fatigue is the most widely reported symptom by women during pregnancy, labour, the postpartum period, and early parenting. The objective was to translate the Fatigue Assessment Scale (FAS) into Spanish and assess its psychometric properties. Methods Instrumental Design. The FAS was translated into Spanish (FAS-e) using forward and back translation. A convenience sample was constituted with 870 postpartum women recruited at discharge from 17 public hospitals in Eastern Spain. Data was obtained from clinical records and self-administered questionnaires at discharge. Internal consistency, factor structure, comparisons between known groups and correlations with other variables were assessed. Results Cronbach’s alpha coefficient was .80. Findings on the dimensionality of the FAS-e scale indicated that it was sufficiently unidimensional. FAS-e scores were higher among women who had undergone caesarean births (p < .05), had a higher level of postpartum pain (p < .01), experienced difficulties during breastfeeding (p < .01) and had lower levels of self-efficacy for breastfeeding (p < .01). Conclusions An equivalent Spanish version of the FAS was obtained with good reliability and validity properties. FAS-e is an appropriate tool to measure postpartum fatigue.
format: application/pdf
format: text/html
creator: Antoni Cano-Climent
creator: Antonio Oliver-Roig
creator: Julio Cabrero-García
creator: Jolanda de Vries
creator: Miguel Richart-Martínez
subject: Nursing
subject: Psychiatry and Psychology
subject: Women's Health
description: doi:10.7717/peerj.3832
publisher: PeerJ Inc.
rights: © 2017 Cano-Climent et al.
abstract: Background Fatigue is the most widely reported symptom by women during pregnancy, labour, the postpartum period, and early parenting. The objective was to translate the Fatigue Assessment Scale (FAS) into Spanish and assess its psychometric properties. Methods Instrumental Design. The FAS was translated into Spanish (FAS-e) using forward and back translation. A convenience sample was constituted with 870 postpartum women recruited at discharge from 17 public hospitals in Eastern Spain. Data was obtained from clinical records and self-administered questionnaires at discharge. Internal consistency, factor structure, comparisons between known groups and correlations with other variables were assessed. Results Cronbach’s alpha coefficient was .80. Findings on the dimensionality of the FAS-e scale indicated that it was sufficiently unidimensional. FAS-e scores were higher among women who had undergone caesarean births (p < .05), had a higher level of postpartum pain (p < .01), experienced difficulties during breastfeeding (p < .01) and had lower levels of self-efficacy for breastfeeding (p < .01). Conclusions An equivalent Spanish version of the FAS was obtained with good reliability and validity properties. FAS-e is an appropriate tool to measure postpartum fatigue.
bibliographic citation: Cano-Climent et al. (2017) The Spanish version of the Fatigue Assessment Scale: reliability and validity assessment in postpartum women. PeerJ 5:e3832 https://doi.org/10.7717/peerj.3832
date submitted: 2017-04-28
date accepted: 2017-08-30
issued: 2017-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cano-Climent
  given name: Antoni
author list: Agent
  family name: Oliver-Roig
  given name: Antonio
author list: Agent
  family name: Cabrero-García
  given name: Julio
author list: Agent
  family name: de Vries
  given name: Jolanda
author list: Agent
  family name: Richart-Martínez
  given name: Miguel
doi: 10.7717/peerj.3832
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-27
copyright: ©2017 Cano-Climent et al.
attribution name: Cano-Climent et al.

Estimating the age of Heliconius butterflies from calibrated photographs
type: item
type: AcademicArticle
description: Mating behaviour and predation avoidance in Heliconius involve visual colour signals; however, there is considerable inter-individual phenotypic variation in the appearance of colours. In particular, the red pigment varies from bright crimson to faded red. It has been thought that this variation is primarily due to pigment fading with age, although this has not been explicitly tested. Previous studies have shown the importance of red patterns in mate choice and that birds and butterflies might perceive these small colour differences. Using digital photography and calibrated colour images, we investigated whether the hue variation in the forewing dorsal red band of Heliconius melpomene rosina corresponds with age. We found that the red hue and age were highly associated, suggesting that red colour can indeed be used as a proxy for age in the study of wild-caught butterflies.
format: application/pdf
format: text/html
creator: Denise Dalbosco Dell’Aglio
creator: Derya Akkaynak
creator: W. Owen McMillan
creator: Chris D. Jiggins
subject: Animal Behavior
subject: Bioinformatics
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.3821
publisher: PeerJ Inc.
rights: © 2017 Dalbosco Dell’Aglio et al.
abstract: Mating behaviour and predation avoidance in Heliconius involve visual colour signals; however, there is considerable inter-individual phenotypic variation in the appearance of colours. In particular, the red pigment varies from bright crimson to faded red. It has been thought that this variation is primarily due to pigment fading with age, although this has not been explicitly tested. Previous studies have shown the importance of red patterns in mate choice and that birds and butterflies might perceive these small colour differences. Using digital photography and calibrated colour images, we investigated whether the hue variation in the forewing dorsal red band of Heliconius melpomene rosina corresponds with age. We found that the red hue and age were highly associated, suggesting that red colour can indeed be used as a proxy for age in the study of wild-caught butterflies.
bibliographic citation: Dalbosco Dell’Aglio et al. (2017) Estimating the age of Heliconius butterflies from calibrated photographs. PeerJ 5:e3821 https://doi.org/10.7717/peerj.3821
date submitted: 2017-06-01
date accepted: 2017-08-28
issued: 2017-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dalbosco Dell’Aglio
  given name: Denise
author list: Agent
  family name: Akkaynak
  given name: Derya
author list: Agent
  family name: McMillan
  given name: W. Owen
author list: Agent
  family name: Jiggins
  given name: Chris D.
doi: 10.7717/peerj.3821
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-27
copyright: ©2017 Dalbosco Dell’Aglio et al.
attribution name: Dalbosco Dell’Aglio et al.

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