PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effect of the environment on horizontal gene transfer between bacteria and archaea
items: Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?
items: A prospective study of the motivational and health dynamics of Internet Gaming Disorder
items: Unraveling the diversification history of grasshoppers belonging to the “Trimerotropis pallidipennis” (Oedipodinae: Acrididae) species group: a hotspot of biodiversity in the Central Andes
items: The relationship between sustained attention and aerobic fitness in a group of young adults
items: Extracorporeal life support with left ventricular decompression—improved survival in severe cardiogenic shock: results from a retrospective study
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

Effect of the environment on horizontal gene transfer between bacteria and archaea
type: item
type: AcademicArticle
description: Background Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted). Results We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids. Conclusions Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the a…
format: application/pdf
format: text/html
creator: Clara A. Fuchsman
creator: Roy Eric Collins
creator: Gabrielle Rocap
creator: William J. Brazelton
subject: Environmental Sciences
subject: Genomics
subject: Microbiology
subject: Natural Resource Management
description: doi:10.7717/peerj.3865
publisher: PeerJ Inc.
rights: © 2017 Fuchsman et al.
abstract: Background Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted). Results We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids. Conclusions Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the a…
bibliographic citation: Fuchsman et al. (2017) Effect of the environment on horizontal gene transfer between bacteria and archaea. PeerJ 5:e3865 https://doi.org/10.7717/peerj.3865
date submitted: 2017-04-06
date accepted: 2017-09-08
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fuchsman
  given name: Clara A.
author list: Agent
  family name: Collins
  given name: Roy Eric
author list: Agent
  family name: Rocap
  given name: Gabrielle
author list: Agent
  family name: Brazelton
  given name: William J.
doi: 10.7717/peerj.3865
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Fuchsman et al.
attribution name: Fuchsman et al.

Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?
type: item
type: AcademicArticle
description: Background Fragmentation of native forests is a highly visible result of human land-use throughout the world. In this study, we evaluated the effects of landscape fragmentation and matrix features on the genetic diversity and structure of Oligoryzomys longicaudatus, the natural reservoir of Hantavirus in southern South America. We focused our work in the Valdivian Rainforest where human activities have produced strong change of natural habitats, with an important number of human cases of Hantavirus. Methods We sampled specimens of O. longicaudatus from five native forest patches surrounded by silvoagropecuary matrix from Panguipulli, Los Rios Region, Chile. Using the hypervariable domain I (mtDNA), we characterized the genetic diversity and evaluated the effect of fragmentation and landscape matrix on the genetic structure of O. longicaudatus. For the latter, we used three approaches: (i) Isolation by Distance (IBD) as null model, (ii) Least-cost Path (LCP) where genetic distances between patch pairs increase with cost-weighted distances, and (iii) Isolation by Resistance (IBR) where the resistance distance is the average number of steps that is needed to commute between the patches during a random walk. Results We found low values of nucleotide diversity (π) for the five patches surveyed, ranging from 0.012 to 0.015, revealing that the 73 sampled specimens of this study belong to two populations but with low values of genetic distance (γST) ranging from 0.022 to 0.099. Likewise, we found that there are no significant associations between genetic distance and geographic distance for IBD and IBR. However, we found for the LCP approach, a significant positive relationship (r = 0.737, p = 0.05), with shortest least-cost paths traced through native forest and arborescent shrublands. Discussion In this work we found that, at this reduced geographical scale, Oligoryzomys longicaudatus shows genetic signs of fragmentation. In addition, we found that connectivity between fu…
format: application/pdf
format: text/html
creator: Daniela Lazo-Cancino
creator: Selim S. Musleh
creator: Cristian E. Hernandez
creator: Eduardo Palma
creator: Enrique Rodriguez-Serrano
subject: Biodiversity
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.3842
publisher: PeerJ Inc.
rights: © 2017 Lazo-Cancino et al.
abstract: Background Fragmentation of native forests is a highly visible result of human land-use throughout the world. In this study, we evaluated the effects of landscape fragmentation and matrix features on the genetic diversity and structure of Oligoryzomys longicaudatus, the natural reservoir of Hantavirus in southern South America. We focused our work in the Valdivian Rainforest where human activities have produced strong change of natural habitats, with an important number of human cases of Hantavirus. Methods We sampled specimens of O. longicaudatus from five native forest patches surrounded by silvoagropecuary matrix from Panguipulli, Los Rios Region, Chile. Using the hypervariable domain I (mtDNA), we characterized the genetic diversity and evaluated the effect of fragmentation and landscape matrix on the genetic structure of O. longicaudatus. For the latter, we used three approaches: (i) Isolation by Distance (IBD) as null model, (ii) Least-cost Path (LCP) where genetic distances between patch pairs increase with cost-weighted distances, and (iii) Isolation by Resistance (IBR) where the resistance distance is the average number of steps that is needed to commute between the patches during a random walk. Results We found low values of nucleotide diversity (π) for the five patches surveyed, ranging from 0.012 to 0.015, revealing that the 73 sampled specimens of this study belong to two populations but with low values of genetic distance (γST) ranging from 0.022 to 0.099. Likewise, we found that there are no significant associations between genetic distance and geographic distance for IBD and IBR. However, we found for the LCP approach, a significant positive relationship (r = 0.737, p = 0.05), with shortest least-cost paths traced through native forest and arborescent shrublands. Discussion In this work we found that, at this reduced geographical scale, Oligoryzomys longicaudatus shows genetic signs of fragmentation. In addition, we found that connectivity between fu…
bibliographic citation: Lazo-Cancino et al. (2017) Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?. PeerJ 5:e3842 https://doi.org/10.7717/peerj.3842
date submitted: 2017-03-29
date accepted: 2017-09-01
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lazo-Cancino
  given name: Daniela
author list: Agent
  family name: Musleh
  given name: Selim S.
author list: Agent
  family name: Hernandez
  given name: Cristian E.
author list: Agent
  family name: Palma
  given name: Eduardo
author list: Agent
  family name: Rodriguez-Serrano
  given name: Enrique
doi: 10.7717/peerj.3842
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Lazo-Cancino et al.
attribution name: Lazo-Cancino et al.

A prospective study of the motivational and health dynamics of Internet Gaming Disorder
type: item
type: AcademicArticle
description: The American Psychiatric Association has identified Internet Gaming Disorder (IGD) as a potential psychiatric condition and called for research to investigate its etiology, stability, and impacts on health and behavior. The present study recruited 5,777 American adults and applied self-determination theory to examine how motivational factors influence, and are influenced by, IGD and health across a six month period. Following a preregistered analysis plan, results confirmed our hypotheses that IGD criteria are moderately stable and that they and basic psychological need satisfaction have a reciprocal relationship over time. Results also showed need satisfaction promoted health and served as a protective factor against IGD. Contrary to what was hypothesized, results provided no evidence directly linking IGD to health over time. Exploratory analyses suggested that IGD may have indirect effects on health by way of its impact on basic needs. Implications are discussed in terms of existing gaming addiction and motivational frameworks.
format: application/pdf
format: text/html
creator: Netta Weinstein
creator: Andrew K. Przybylski
creator: Kou Murayama
subject: Human-Computer Interaction
subject: Psychiatry and Psychology
subject: Science Policy
description: doi:10.7717/peerj.3838
publisher: PeerJ Inc.
rights: © 2017 Weinstein et al.
abstract: The American Psychiatric Association has identified Internet Gaming Disorder (IGD) as a potential psychiatric condition and called for research to investigate its etiology, stability, and impacts on health and behavior. The present study recruited 5,777 American adults and applied self-determination theory to examine how motivational factors influence, and are influenced by, IGD and health across a six month period. Following a preregistered analysis plan, results confirmed our hypotheses that IGD criteria are moderately stable and that they and basic psychological need satisfaction have a reciprocal relationship over time. Results also showed need satisfaction promoted health and served as a protective factor against IGD. Contrary to what was hypothesized, results provided no evidence directly linking IGD to health over time. Exploratory analyses suggested that IGD may have indirect effects on health by way of its impact on basic needs. Implications are discussed in terms of existing gaming addiction and motivational frameworks.
bibliographic citation: Weinstein et al. (2017) A prospective study of the motivational and health dynamics of Internet Gaming Disorder. PeerJ 5:e3838 https://doi.org/10.7717/peerj.3838
date submitted: 2017-07-07
date accepted: 2017-09-01
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weinstein
  given name: Netta
author list: Agent
  family name: Przybylski
  given name: Andrew K.
author list: Agent
  family name: Murayama
  given name: Kou
doi: 10.7717/peerj.3838
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Weinstein et al.
attribution name: Weinstein et al.

Unraveling the diversification history of grasshoppers belonging to the “Trimerotropis pallidipennis” (Oedipodinae: Acrididae) species group: a hotspot of biodiversity in the Central Andes
type: item
type: AcademicArticle
description: The Andean Mountain range has been recognized as one of the biodiversity hotspots of the world. The proposed mechanisms for such species diversification, among others, are due to the elevation processes occurring during the Miocene and the intensive glacial action during the Pleistocene. In this study we investigated the diversification history of the grasshopper Trimerotropis pallidipennis species complex which shows a particularly wide latitudinal and altitudinal distribution range across the northern, central and southern Andes in South America. Many genetic lineages of this complex have been so far discovered, making it an excellent model to investigate the role of the central Andes Mountains together with climatic fluctuations as drivers of speciation. Phylogenetics, biogeographic and molecular clock analyses using a multi-locus dataset revealed that in Peru there are at least two, and possibly four genetic lineages. Two different stocks originated from a common ancestor from North/Central America—would have dispersed toward southern latitudes favored by the closure of the Panama Isthmus giving rise to two lineages, the coastal and mountain lineages, which still coexist in Peru (i.e., T. pallidipennis and T. andeana). Subsequent vicariant and dispersal events continued the differentiation process, giving rise to three to six genetic lineages (i.e., clades) detected in this study, which were geographically restricted to locations dispersed over the central Andes Mountains in South America. Our results provide another interesting example of “island diversification” motored by the topography plus unstable climatic conditions during the Pleistocene, pointing out the presence of a hotspot of diversification in the Andean region of Peru.
format: application/pdf
format: text/html
creator: Noelia Verónica Guzmán
creator: Silvia Mónica Pietrokovsky
creator: Maria Marta Cigliano
creator: Viviana Andrea Confalonieri
subject: Entomology
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.3835
publisher: PeerJ Inc.
rights: © 2017 Guzmán et al.
abstract: The Andean Mountain range has been recognized as one of the biodiversity hotspots of the world. The proposed mechanisms for such species diversification, among others, are due to the elevation processes occurring during the Miocene and the intensive glacial action during the Pleistocene. In this study we investigated the diversification history of the grasshopper Trimerotropis pallidipennis species complex which shows a particularly wide latitudinal and altitudinal distribution range across the northern, central and southern Andes in South America. Many genetic lineages of this complex have been so far discovered, making it an excellent model to investigate the role of the central Andes Mountains together with climatic fluctuations as drivers of speciation. Phylogenetics, biogeographic and molecular clock analyses using a multi-locus dataset revealed that in Peru there are at least two, and possibly four genetic lineages. Two different stocks originated from a common ancestor from North/Central America—would have dispersed toward southern latitudes favored by the closure of the Panama Isthmus giving rise to two lineages, the coastal and mountain lineages, which still coexist in Peru (i.e., T. pallidipennis and T. andeana). Subsequent vicariant and dispersal events continued the differentiation process, giving rise to three to six genetic lineages (i.e., clades) detected in this study, which were geographically restricted to locations dispersed over the central Andes Mountains in South America. Our results provide another interesting example of “island diversification” motored by the topography plus unstable climatic conditions during the Pleistocene, pointing out the presence of a hotspot of diversification in the Andean region of Peru.
bibliographic citation: Guzmán et al. (2017) Unraveling the diversification history of grasshoppers belonging to the “Trimerotropis pallidipennis” (Oedipodinae: Acrididae) species group: a hotspot of biodiversity in the Central Andes. PeerJ 5:e3835 https://doi.org/10.7717/peerj.3835
date submitted: 2017-06-29
date accepted: 2017-08-30
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guzmán
  given name: Noelia Verónica
author list: Agent
  family name: Pietrokovsky
  given name: Silvia Mónica
author list: Agent
  family name: Cigliano
  given name: Maria Marta
author list: Agent
  family name: Confalonieri
  given name: Viviana Andrea
doi: 10.7717/peerj.3835
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Guzmán et al.
attribution name: Guzmán et al.

The relationship between sustained attention and aerobic fitness in a group of young adults
type: item
type: AcademicArticle
description: Background A growing set of studies has shown a positive relationship between aerobic fitness and a broad array of cognitive functions. However, few studies have focused on sustained attention, which has been considered a fundamental cognitive process that underlies most everyday activities. The purpose of this study was to investigate the role of aerobic fitness as a key factor in sustained attention capacities in young adults. Methods Forty-four young adults (18–23 years) were divided into two groups as a function of the level of aerobic fitness (high-fit and low-fit). Participants completed the Psychomotor Vigilance Task (PVT) and an oddball task where they had to detect infrequent targets presented among frequent non-targets. Results The analysis of variance (ANOVA) showed faster responses for the high-fit group than for the low-fit group in the PVT, replicating previous accounts. In the oddball task, the high-fit group maintained their accuracy (ACC) rate of target detection over time, while the low-fit group suffered a significant decline of response ACC throughout the task. Discussion Importantly, the results show that the greater sustained attention capacity of high-fit young adults is not specific to a reaction time (RT) sustained attention task like the PVT, but it is also evident in an ACC oddball task. In sum, the present findings point to the important role of aerobic fitness on sustained attention capacities in young adults.
format: application/pdf
format: text/html
creator: Luis F. Ciria
creator: Pandelis Perakakis
creator: Antonio Luque-Casado
creator: Cristina Morato
creator: Daniel Sanabria
subject: Neuroscience
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.3831
publisher: PeerJ Inc.
rights: © 2017 Ciria et al.
abstract: Background A growing set of studies has shown a positive relationship between aerobic fitness and a broad array of cognitive functions. However, few studies have focused on sustained attention, which has been considered a fundamental cognitive process that underlies most everyday activities. The purpose of this study was to investigate the role of aerobic fitness as a key factor in sustained attention capacities in young adults. Methods Forty-four young adults (18–23 years) were divided into two groups as a function of the level of aerobic fitness (high-fit and low-fit). Participants completed the Psychomotor Vigilance Task (PVT) and an oddball task where they had to detect infrequent targets presented among frequent non-targets. Results The analysis of variance (ANOVA) showed faster responses for the high-fit group than for the low-fit group in the PVT, replicating previous accounts. In the oddball task, the high-fit group maintained their accuracy (ACC) rate of target detection over time, while the low-fit group suffered a significant decline of response ACC throughout the task. Discussion Importantly, the results show that the greater sustained attention capacity of high-fit young adults is not specific to a reaction time (RT) sustained attention task like the PVT, but it is also evident in an ACC oddball task. In sum, the present findings point to the important role of aerobic fitness on sustained attention capacities in young adults.
bibliographic citation: Ciria et al. (2017) The relationship between sustained attention and aerobic fitness in a group of young adults. PeerJ 5:e3831 https://doi.org/10.7717/peerj.3831
date submitted: 2017-05-16
date accepted: 2017-08-30
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ciria
  given name: Luis F.
author list: Agent
  family name: Perakakis
  given name: Pandelis
author list: Agent
  family name: Luque-Casado
  given name: Antonio
author list: Agent
  family name: Morato
  given name: Cristina
author list: Agent
  family name: Sanabria
  given name: Daniel
doi: 10.7717/peerj.3831
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Ciria et al.
attribution name: Ciria et al.

Extracorporeal life support with left ventricular decompression—improved survival in severe cardiogenic shock: results from a retrospective study
type: item
type: AcademicArticle
description: Objective Extracorporeal life support (ECLS) is a life-saving procedure used in the treatment of severe cardiogenic shock. Within this retrospective single centre study, we examined our experience in this critically ill patient cohort to assess outcomes and clinical parameters by comparison of ECLS with or without selective left ventricular decompression. Methods Between 2004 and 2014 we evaluated 48 adult patients with INTERMACS level 1 heart failure (age 49.7 ± 19.5 years), who received either central ECLS with (n = 20, 41.7%) or ECLS without (n = 28, 58.3%, including 10 peripheral ECLS) integrated left ventricular vent in our retrospective single centre trial. Results Follow up was 100% with a mean of 0.83 ± 1.85 years. Bridge to ventricular assist device was feasible in 29.2% (n = 14), bridge to transplant in 10.4% (n = 5) and bridge to recovery in 8.3% (n = 4). Overall 30-day survival was 37.5%, 6-month survival 27.1% and 1-year survival 25.0%. ECLS support with left ventricular decompression showed favourable 30-day survival compared to ECLS without left ventricular decompression (p = 0.034). Thirty-day as well as long-term survival did not differ between the subgroups (central ECLS with vent, ECLS without vent and peripheral ECLS without vent). Multivariate logistic regression adjusted for age and gender revealed ECLS without vent as independent factor influencing 30-day survival. Conclusion ECLS is an established therapy for patients in severe cardiogenic shock. Independent of the ECLS approach, 30-day mortality is still high but with superior 30-day survival for patients with ECLS and left ventricular venting. Moreover, by unloading the ventricle, left ventricular decompression may provide an important time window for recovery or further treatment, such as bridge to bridge or bridge to transplant.
format: application/pdf
format: text/html
creator: Bastian Schmack
creator: Philipp Seppelt
creator: Alexander Weymann
creator: Christina Alt
creator: Mina Farag
creator: Rawa Arif
creator: Andreas O. Doesch
creator: Philip W. Raake
creator: Klaus Kallenbach
creator: Ashham Mansur
creator: Aron-Frederik Popov
creator: Matthias Karck
creator: Arjang Ruhparwar
subject: Cardiology
subject: Clinical Trials
subject: Emergency and Critical Care
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.3813
publisher: PeerJ Inc.
rights: © 2017 Schmack et al.
abstract: Objective Extracorporeal life support (ECLS) is a life-saving procedure used in the treatment of severe cardiogenic shock. Within this retrospective single centre study, we examined our experience in this critically ill patient cohort to assess outcomes and clinical parameters by comparison of ECLS with or without selective left ventricular decompression. Methods Between 2004 and 2014 we evaluated 48 adult patients with INTERMACS level 1 heart failure (age 49.7 ± 19.5 years), who received either central ECLS with (n = 20, 41.7%) or ECLS without (n = 28, 58.3%, including 10 peripheral ECLS) integrated left ventricular vent in our retrospective single centre trial. Results Follow up was 100% with a mean of 0.83 ± 1.85 years. Bridge to ventricular assist device was feasible in 29.2% (n = 14), bridge to transplant in 10.4% (n = 5) and bridge to recovery in 8.3% (n = 4). Overall 30-day survival was 37.5%, 6-month survival 27.1% and 1-year survival 25.0%. ECLS support with left ventricular decompression showed favourable 30-day survival compared to ECLS without left ventricular decompression (p = 0.034). Thirty-day as well as long-term survival did not differ between the subgroups (central ECLS with vent, ECLS without vent and peripheral ECLS without vent). Multivariate logistic regression adjusted for age and gender revealed ECLS without vent as independent factor influencing 30-day survival. Conclusion ECLS is an established therapy for patients in severe cardiogenic shock. Independent of the ECLS approach, 30-day mortality is still high but with superior 30-day survival for patients with ECLS and left ventricular venting. Moreover, by unloading the ventricle, left ventricular decompression may provide an important time window for recovery or further treatment, such as bridge to bridge or bridge to transplant.
bibliographic citation: Schmack et al. (2017) Extracorporeal life support with left ventricular decompression—improved survival in severe cardiogenic shock: results from a retrospective study. PeerJ 5:e3813 https://doi.org/10.7717/peerj.3813
date submitted: 2017-07-10
date accepted: 2017-08-25
issued: 2017-09-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schmack
  given name: Bastian
author list: Agent
  family name: Seppelt
  given name: Philipp
author list: Agent
  family name: Weymann
  given name: Alexander
author list: Agent
  family name: Alt
  given name: Christina
author list: Agent
  family name: Farag
  given name: Mina
author list: Agent
  family name: Arif
  given name: Rawa
author list: Agent
  family name: Doesch
  given name: Andreas O.
author list: Agent
  family name: Raake
  given name: Philip W.
author list: Agent
  family name: Kallenbach
  given name: Klaus
author list: Agent
  family name: Mansur
  given name: Ashham
author list: Agent
  family name: Popov
  given name: Aron-Frederik
author list: Agent
  family name: Karck
  given name: Matthias
author list: Agent
  family name: Ruhparwar
  given name: Arjang
doi: 10.7717/peerj.3813
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-09-29
copyright: ©2017 Schmack et al.
attribution name: Schmack et al.

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

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