PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Natural history and molecular evolution of demersal Mediterranean sharks and skates inferred by comparative phylogeographic and demographic analyses
items: Functional significance of cuckoo Cuculus canorus calls: responses of conspecifics, hosts and non-hosts
items: Neuroblastomas in Eastern China: a retrospective series study of 275 cases in a regional center
items: 60S dynamic state of bacterial ribosome is fixed by yeast mitochondrial initiation factor 3
items: Zooming into plant-flower visitor networks: an individual trait-based approach
items: Insomnia and intellect mask the positive link between schizotypal traits and creativity
items: Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales
items: Effects of income and residential area on survival of patients with head and neck cancers following radiotherapy: working age individuals in Taiwan
items: The influence of sample distribution on growth model output for a highly-exploited marine fish, the Gulf Corvina (Cynoscion othonopterus)
items: https://peerj.com/articles/5577

Natural history and molecular evolution of demersal Mediterranean sharks and skates inferred by comparative phylogeographic and demographic analyses
type: item
type: AcademicArticle
description: Background The unique and complex paleoclimatic and paleogeographic events which affected the Mediterranean Sea since late Miocene deeply influenced the distribution and evolution of marine organisms and shaped their genetic structure. Following the Messinian salinity crisis and the sea-level fluctuations during the Pleistocene, several Mediterranean marine species developed deep genetic differentiation, and some underwent rapid radiation. Here, we consider two of the most prioritized groups for conservation in the light of their evolutionary history: sharks and rays (elasmobranchs). This paper deals with a comparative multispecies analysis of phylogeographic structure and historical demography in two pairs of sympatric, phylogenetically- and ecologically-related elasmobranchs, two scyliorhinid catsharks (Galeus melastomus, Scyliorhinus canicula) and two rajid skates (Raja clavata, Raja miraletus). Sampling and experimental analyses were designed to primarily test if the Sicilian Channel can be considered as effective eco-physiological barrier for Mediterranean demersal sympatric elasmobranchs. Methods The phylogeography and the historical demography of target species were inferred by analysing the nucleotide variation of three mitochondrial DNA markers (i.e., partial sequence of COI, NADH2 and CR) obtained from a total of 248 individuals sampled in the Western and Eastern Mediterranean Sea as well as in the adjacent northeastern Atlantic Ocean. Phylogeographic analysis was performed by haplotype networking and testing spatial genetic differentiation of samples (i.e., analysis of molecular variance and of principal components). Demographic history of Mediterranean populations was reconstructed using mismatch distribution and Bayesian Skyline Plot analyses. Results No spatial genetic differentiation was identified in either catshark species, while phylogeographic structure of lineages was identified in both skates, with R. miraletus more structured than R. clavata. H…
format: application/pdf
format: text/html
creator: Alice Ferrari
creator: Fausto Tinti
creator: Victoria Bertucci Maresca
creator: Alessandro Velonà
creator: Rita Cannas
creator: Ioannis Thasitis
creator: Filipe Oliveira Costa
creator: Maria Cristina Follesa
creator: Daniel Golani
creator: Farid Hemida
creator: Sarah J. Helyar
creator: Cecilia Mancusi
creator: Antonello Mulas
creator: Fabrizio Serena
creator: Letizia Sion
creator: Marco Stagioni
creator: Alessia Cariani
subject: Biogeography
subject: Evolutionary Studies
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.5560
publisher: PeerJ Inc.
rights: © 2018 Ferrari et al.
abstract: Background The unique and complex paleoclimatic and paleogeographic events which affected the Mediterranean Sea since late Miocene deeply influenced the distribution and evolution of marine organisms and shaped their genetic structure. Following the Messinian salinity crisis and the sea-level fluctuations during the Pleistocene, several Mediterranean marine species developed deep genetic differentiation, and some underwent rapid radiation. Here, we consider two of the most prioritized groups for conservation in the light of their evolutionary history: sharks and rays (elasmobranchs). This paper deals with a comparative multispecies analysis of phylogeographic structure and historical demography in two pairs of sympatric, phylogenetically- and ecologically-related elasmobranchs, two scyliorhinid catsharks (Galeus melastomus, Scyliorhinus canicula) and two rajid skates (Raja clavata, Raja miraletus). Sampling and experimental analyses were designed to primarily test if the Sicilian Channel can be considered as effective eco-physiological barrier for Mediterranean demersal sympatric elasmobranchs. Methods The phylogeography and the historical demography of target species were inferred by analysing the nucleotide variation of three mitochondrial DNA markers (i.e., partial sequence of COI, NADH2 and CR) obtained from a total of 248 individuals sampled in the Western and Eastern Mediterranean Sea as well as in the adjacent northeastern Atlantic Ocean. Phylogeographic analysis was performed by haplotype networking and testing spatial genetic differentiation of samples (i.e., analysis of molecular variance and of principal components). Demographic history of Mediterranean populations was reconstructed using mismatch distribution and Bayesian Skyline Plot analyses. Results No spatial genetic differentiation was identified in either catshark species, while phylogeographic structure of lineages was identified in both skates, with R. miraletus more structured than R. clavata. H…
bibliographic citation: Ferrari et al. (2018) Natural history and molecular evolution of demersal Mediterranean sharks and skates inferred by comparative phylogeographic and demographic analyses. PeerJ 6:e5560 https://doi.org/10.7717/peerj.5560
date submitted: 2018-03-09
date accepted: 2018-08-09
issued: 2018-09-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferrari
  given name: Alice
author list: Agent
  family name: Tinti
  given name: Fausto
author list: Agent
  family name: Bertucci Maresca
  given name: Victoria
author list: Agent
  family name: Velonà
  given name: Alessandro
author list: Agent
  family name: Cannas
  given name: Rita
author list: Agent
  family name: Thasitis
  given name: Ioannis
author list: Agent
  family name: Costa
  given name: Filipe Oliveira
author list: Agent
  family name: Follesa
  given name: Maria Cristina
author list: Agent
  family name: Golani
  given name: Daniel
author list: Agent
  family name: Hemida
  given name: Farid
author list: Agent
  family name: Helyar
  given name: Sarah J.
author list: Agent
  family name: Mancusi
  given name: Cecilia
author list: Agent
  family name: Mulas
  given name: Antonello
author list: Agent
  family name: Serena
  given name: Fabrizio
author list: Agent
  family name: Sion
  given name: Letizia
author list: Agent
  family name: Stagioni
  given name: Marco
author list: Agent
  family name: Cariani
  given name: Alessia
doi: 10.7717/peerj.5560
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-18
copyright: ©2018 Ferrari et al.
attribution name: Ferrari et al.

Functional significance of cuckoo Cuculus canorus calls: responses of conspecifics, hosts and non-hosts
type: item
type: AcademicArticle
description: Male cuckoos Cuculus canorus produce calls that differ in number of syllables depending on environmental conditions and presence of male and female conspecifics. Why different males produce so repeatable calls that vary greatly in duration among males remains an open question. We used playback of cuckoo calls with few or many syllables (hereafter short and long calls), and woodpigeon calls (a control that also produces few or many syllables), predicting that playback of longer cuckoo calls should attract more male cuckoos (if males with such calls are dominant and successfully out-compete other males due to intraspecific competition), and attract more hosts mobbing male cuckoos (cuckoos with such calls and their females attract more hosts because of an increased risk of parasitism). Because cuckoos differentially parasitize hosts away from human habitation, we also tested whether the number of syllables in cuckoo calls differed with distance from buildings. Playback showed significant effects of number of syllables in cuckoo calls, but not woodpigeon Columba palumbus calls, with an additional effect of distance from human habitation decreasing the response to playback. These findings are consistent with the hypothesis that longer cuckoo calls, especially played back near human habitation, attract more conspecifics and hosts than shorter calls. To the best of knowledge this is the first study showing that cuckoo call response modified both other cuckoo individuals, as well as hosts response.
format: application/pdf
format: text/html
creator: Piotr Tryjanowski
creator: Federico Morelli
creator: Tomasz S. Osiejuk
creator: Anders Pape Møller
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.5302
publisher: PeerJ Inc.
rights: © 2018 Tryjanowski et al.
abstract: Male cuckoos Cuculus canorus produce calls that differ in number of syllables depending on environmental conditions and presence of male and female conspecifics. Why different males produce so repeatable calls that vary greatly in duration among males remains an open question. We used playback of cuckoo calls with few or many syllables (hereafter short and long calls), and woodpigeon calls (a control that also produces few or many syllables), predicting that playback of longer cuckoo calls should attract more male cuckoos (if males with such calls are dominant and successfully out-compete other males due to intraspecific competition), and attract more hosts mobbing male cuckoos (cuckoos with such calls and their females attract more hosts because of an increased risk of parasitism). Because cuckoos differentially parasitize hosts away from human habitation, we also tested whether the number of syllables in cuckoo calls differed with distance from buildings. Playback showed significant effects of number of syllables in cuckoo calls, but not woodpigeon Columba palumbus calls, with an additional effect of distance from human habitation decreasing the response to playback. These findings are consistent with the hypothesis that longer cuckoo calls, especially played back near human habitation, attract more conspecifics and hosts than shorter calls. To the best of knowledge this is the first study showing that cuckoo call response modified both other cuckoo individuals, as well as hosts response.
bibliographic citation: Tryjanowski et al. (2018) Functional significance of cuckoo Cuculus canorus calls: responses of conspecifics, hosts and non-hosts. PeerJ 6:e5302 https://doi.org/10.7717/peerj.5302
date submitted: 2018-04-03
date accepted: 2018-07-03
issued: 2018-09-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tryjanowski
  given name: Piotr
author list: Agent
  family name: Morelli
  given name: Federico
author list: Agent
  family name: Osiejuk
  given name: Tomasz S.
author list: Agent
  family name: Møller
  given name: Anders Pape
doi: 10.7717/peerj.5302
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-18
copyright: ©2018 Tryjanowski et al.
attribution name: Tryjanowski et al.

Neuroblastomas in Eastern China: a retrospective series study of 275 cases in a regional center
type: item
type: AcademicArticle
description: Purpose Most studies on neuroblastoma (NB) have been conducted in Western countries or Japan. The objective of our study was to analyze clinical and pathological features, MYCN status, surgical methods, and prognosis in Chinese NB patients. Methods A retrospective, single-center case series study of 275 NBs was implemented. Clinical manifestations, pathological features, MYCN status, and surgical treatment were analyzed. Log-rank test and Cox hazards models were used to assess overall survivals (OSs). Results The cohort consisted of 105 females and 170 males, with an age range of five days to 15 years. MYCN amplification was detected in 21.5% of all cases. The median OS was 15.0 months for MYCN amplified group. The five-year OS rates were 70.8% and 18.3% for MYCN unamplified and amplified groups, respectively, and the comparison of Kaplan–Meier curves for these two groups showed statistical significance (P < .001 by log-rank test). Gross total resection (GTR, n = 111) and subtotal resection (STR, n = 58) were administered in 169 patients at stages 3 and 4 who received chemotherapy and the comparison of Kaplan–Meier curves for different groups in these patients had statistical significance (STR vs. GTR, P = .009; MYCN unamplified vs. amplified, P < .001 by log-rank test, respectively).The multivariate survival analyses showed statistical significance (STR vs. GTR, P = .047; MYCN unamplified vs. amplified, P = .001 by Cox regression model). Conclusions MYCN amplification is an independently adverse prognostic factor in Chinese NB patients at stages 3 and 4 and GTR is associated with improved OS compared with STR in these patients.
format: application/pdf
format: text/html
creator: Yangyang Ma
creator: Jicui Zheng
creator: Jiayan Feng
creator: Lian Chen
creator: Kuiran Dong
creator: Xianmin Xiao
subject: Oncology
subject: Pediatrics
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.5665
publisher: PeerJ Inc.
rights: © 2018 Ma et al.
abstract: Purpose Most studies on neuroblastoma (NB) have been conducted in Western countries or Japan. The objective of our study was to analyze clinical and pathological features, MYCN status, surgical methods, and prognosis in Chinese NB patients. Methods A retrospective, single-center case series study of 275 NBs was implemented. Clinical manifestations, pathological features, MYCN status, and surgical treatment were analyzed. Log-rank test and Cox hazards models were used to assess overall survivals (OSs). Results The cohort consisted of 105 females and 170 males, with an age range of five days to 15 years. MYCN amplification was detected in 21.5% of all cases. The median OS was 15.0 months for MYCN amplified group. The five-year OS rates were 70.8% and 18.3% for MYCN unamplified and amplified groups, respectively, and the comparison of Kaplan–Meier curves for these two groups showed statistical significance (P < .001 by log-rank test). Gross total resection (GTR, n = 111) and subtotal resection (STR, n = 58) were administered in 169 patients at stages 3 and 4 who received chemotherapy and the comparison of Kaplan–Meier curves for different groups in these patients had statistical significance (STR vs. GTR, P = .009; MYCN unamplified vs. amplified, P < .001 by log-rank test, respectively).The multivariate survival analyses showed statistical significance (STR vs. GTR, P = .047; MYCN unamplified vs. amplified, P = .001 by Cox regression model). Conclusions MYCN amplification is an independently adverse prognostic factor in Chinese NB patients at stages 3 and 4 and GTR is associated with improved OS compared with STR in these patients.
bibliographic citation: Ma et al. (2018) Neuroblastomas in Eastern China: a retrospective series study of 275 cases in a regional center. PeerJ 6:e5665 https://doi.org/10.7717/peerj.5665
date submitted: 2018-06-27
date accepted: 2018-08-29
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Yangyang
author list: Agent
  family name: Zheng
  given name: Jicui
author list: Agent
  family name: Feng
  given name: Jiayan
author list: Agent
  family name: Chen
  given name: Lian
author list: Agent
  family name: Dong
  given name: Kuiran
author list: Agent
  family name: Xiao
  given name: Xianmin
doi: 10.7717/peerj.5665
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: ©2018 Ma et al.
attribution name: Ma et al.

60S dynamic state of bacterial ribosome is fixed by yeast mitochondrial initiation factor 3
type: item
type: AcademicArticle
description: The processes of association and dissociation of ribosomal subunits are of great importance for the protein biosynthesis. The mechanistic details of these processes, however, are not well known. In bacteria, upon translation termination, the ribosome dissociates into subunits which is necessary for its further involvement into new initiation step. The dissociated state of the ribosome is maintained by initiation factor 3 (IF3) which binds to free small subunits and prevents their premature association with large subunits. In this work, we have exchanged IF3 in Escherichia coli cells by its ortholog from Saccharomyces cerevisiae mitochondria (Aim23p) and showed that yeast protein cannot functionally substitute the bacterial one and is even slightly toxic for bacterial cells. Our in vitro experiments have demonstrated that Aim23p does not split E. coli ribosomes into subunits. Instead, it fixes a state of ribosomes characterized by sedimentation coefficient about 60S which is not a stable structure but rather reflects a shift of dynamic equilibrium between associated and dissociated states of the ribosome. Mitochondria-specific terminal extensions of Aim23p are necessary for “60S state” formation, and molecular modeling results point out that these extensions might stabilize the position of the protein on the bacterial ribosome.
format: application/pdf
format: text/html
creator: Sergey Levitskii
creator: Ksenia Derbikova
creator: Maria V. Baleva
creator: Anton Kuzmenko
creator: Andrey V. Golovin
creator: Ivan Chicherin
creator: Igor A. Krasheninnikov
creator: Piotr Kamenski
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.5620
publisher: PeerJ Inc.
rights: © 2018 Levitskii et al.
abstract: The processes of association and dissociation of ribosomal subunits are of great importance for the protein biosynthesis. The mechanistic details of these processes, however, are not well known. In bacteria, upon translation termination, the ribosome dissociates into subunits which is necessary for its further involvement into new initiation step. The dissociated state of the ribosome is maintained by initiation factor 3 (IF3) which binds to free small subunits and prevents their premature association with large subunits. In this work, we have exchanged IF3 in Escherichia coli cells by its ortholog from Saccharomyces cerevisiae mitochondria (Aim23p) and showed that yeast protein cannot functionally substitute the bacterial one and is even slightly toxic for bacterial cells. Our in vitro experiments have demonstrated that Aim23p does not split E. coli ribosomes into subunits. Instead, it fixes a state of ribosomes characterized by sedimentation coefficient about 60S which is not a stable structure but rather reflects a shift of dynamic equilibrium between associated and dissociated states of the ribosome. Mitochondria-specific terminal extensions of Aim23p are necessary for “60S state” formation, and molecular modeling results point out that these extensions might stabilize the position of the protein on the bacterial ribosome.
bibliographic citation: Levitskii et al. (2018) 60S dynamic state of bacterial ribosome is fixed by yeast mitochondrial initiation factor 3. PeerJ 6:e5620 https://doi.org/10.7717/peerj.5620
date submitted: 2018-06-14
date accepted: 2018-08-21
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Levitskii
  given name: Sergey
author list: Agent
  family name: Derbikova
  given name: Ksenia
author list: Agent
  family name: Baleva
  given name: Maria V.
author list: Agent
  family name: Kuzmenko
  given name: Anton
author list: Agent
  family name: Golovin
  given name: Andrey V.
author list: Agent
  family name: Chicherin
  given name: Ivan
author list: Agent
  family name: Krasheninnikov
  given name: Igor A.
author list: Agent
  family name: Kamenski
  given name: Piotr
doi: 10.7717/peerj.5620
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: © 2018 Levitskii et al.
attribution name: Levitskii et al.

Zooming into plant-flower visitor networks: an individual trait-based approach
type: item
type: AcademicArticle
description: Understanding how ecological communities are structured is a major goal in ecology. Ecological networks representing interaction patterns among species have become a powerful tool to capture the mechanisms underlying plant-animal assemblages. However, these networks largely do not account for inter-individual variability and thus may be limiting our development of a clear mechanistic understanding of community structure. In this study, we develop a new individual-trait based approach to examine the importance of individual plant and pollinator functional size traits (pollinator thorax width and plant nectar holder depth) in mutualistic networks. We performed hierarchical cluster analyses to group interacting individuals into classes, according to their similarity in functional size. We then compared the structure of bee-flower networks where nodes represented either species identity or trait sets. The individual trait-based network was almost twice as nested as its species-based equivalent and it had a more symmetric linkage pattern resulting from of a high degree of size-matching. In conclusion, we show that by constructing individual trait-based networks we can reveal important patterns otherwise difficult to observe in species-based networks and thus improve our understanding of community structure. We therefore recommend using both trait-based and species-based approaches together to develop a clearer understanding of the properties of ecological networks.
format: application/pdf
format: text/html
creator: Beatriz Rumeu
creator: Danny J. Sheath
creator: Joseph E. Hawes
creator: Thomas C. Ings
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.5618
publisher: PeerJ Inc.
rights: © 2018 Rumeu et al.
abstract: Understanding how ecological communities are structured is a major goal in ecology. Ecological networks representing interaction patterns among species have become a powerful tool to capture the mechanisms underlying plant-animal assemblages. However, these networks largely do not account for inter-individual variability and thus may be limiting our development of a clear mechanistic understanding of community structure. In this study, we develop a new individual-trait based approach to examine the importance of individual plant and pollinator functional size traits (pollinator thorax width and plant nectar holder depth) in mutualistic networks. We performed hierarchical cluster analyses to group interacting individuals into classes, according to their similarity in functional size. We then compared the structure of bee-flower networks where nodes represented either species identity or trait sets. The individual trait-based network was almost twice as nested as its species-based equivalent and it had a more symmetric linkage pattern resulting from of a high degree of size-matching. In conclusion, we show that by constructing individual trait-based networks we can reveal important patterns otherwise difficult to observe in species-based networks and thus improve our understanding of community structure. We therefore recommend using both trait-based and species-based approaches together to develop a clearer understanding of the properties of ecological networks.
bibliographic citation: Rumeu et al. (2018) Zooming into plant-flower visitor networks: an individual trait-based approach. PeerJ 6:e5618 https://doi.org/10.7717/peerj.5618
date submitted: 2018-03-09
date accepted: 2018-08-20
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rumeu
  given name: Beatriz
author list: Agent
  family name: Sheath
  given name: Danny J.
author list: Agent
  family name: Hawes
  given name: Joseph E.
author list: Agent
  family name: Ings
  given name: Thomas C.
doi: 10.7717/peerj.5618
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: ©2018 Rumeu et al.
attribution name: Rumeu et al.

Insomnia and intellect mask the positive link between schizotypal traits and creativity
type: item
type: AcademicArticle
description: Background Schizotypy is a set of personality traits that resemble the signs and symptoms of schizophrenia in the general population, and it is associated with various subclinical mental health problems, including sleep disturbances. Additionally, dimensions of schizotypy show specific but weak associations with creativity. Given that creativity demands cognitive control and mental health, and that sleep disturbances negatively impact cognitive control, we predicted that positive, impulsive and disorganised schizotypy will demonstrate stronger associations with indicators of creativity, if the effect of mental health, insomnia, and intellect are statistically controlled. Methods University students (N = 182) took part in the study. Schizotypy was assessed with the shortened Oxford-Liverpool Inventory of Feelings and Experiences (sO-LIFE). Creative achievements were measured with the Creative Achievement Questionnaire (CAQ), divergent thinking was assessed with the ‘Just suppose’ task, and remote association problem solving was tested with Compound Remote Associate (CRA) problems. Mental health was assessed with the 12-item version of the General Health Questionnaire (GHQ-12), and insomnia was examined with the Athens Insomnia Scale (AIS). Verbal short term memory was measured with the forward digit span task, and intellect was assessed with the Rational-Experiential Inventory (REI). Multiple linear regressions were performed to examine the relationship between creativity and schizotypy. Indicators of creativity were the dependent variables. In the first block, dimensions of schizotypy, age, gender and smoking were entered, and in the second block, the models were extended with mental health, insomnia, verbal short term memory, and intellect. Results Positive schizotypy positively predicted real-life creative achievements, independently from the positive effect of intellect. Follow-up analyses revealed that positive schizotypy predicted creative achievements in art, …
format: application/pdf
format: text/html
creator: Bertalan Polner
creator: Péter Simor
creator: Szabolcs Kéri
subject: Cognitive Disorders
subject: Global Health
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.5615
publisher: PeerJ Inc.
rights: © 2018 Polner et al.
abstract: Background Schizotypy is a set of personality traits that resemble the signs and symptoms of schizophrenia in the general population, and it is associated with various subclinical mental health problems, including sleep disturbances. Additionally, dimensions of schizotypy show specific but weak associations with creativity. Given that creativity demands cognitive control and mental health, and that sleep disturbances negatively impact cognitive control, we predicted that positive, impulsive and disorganised schizotypy will demonstrate stronger associations with indicators of creativity, if the effect of mental health, insomnia, and intellect are statistically controlled. Methods University students (N = 182) took part in the study. Schizotypy was assessed with the shortened Oxford-Liverpool Inventory of Feelings and Experiences (sO-LIFE). Creative achievements were measured with the Creative Achievement Questionnaire (CAQ), divergent thinking was assessed with the ‘Just suppose’ task, and remote association problem solving was tested with Compound Remote Associate (CRA) problems. Mental health was assessed with the 12-item version of the General Health Questionnaire (GHQ-12), and insomnia was examined with the Athens Insomnia Scale (AIS). Verbal short term memory was measured with the forward digit span task, and intellect was assessed with the Rational-Experiential Inventory (REI). Multiple linear regressions were performed to examine the relationship between creativity and schizotypy. Indicators of creativity were the dependent variables. In the first block, dimensions of schizotypy, age, gender and smoking were entered, and in the second block, the models were extended with mental health, insomnia, verbal short term memory, and intellect. Results Positive schizotypy positively predicted real-life creative achievements, independently from the positive effect of intellect. Follow-up analyses revealed that positive schizotypy predicted creative achievements in art, …
bibliographic citation: Polner et al. (2018) Insomnia and intellect mask the positive link between schizotypal traits and creativity. PeerJ 6:e5615 https://doi.org/10.7717/peerj.5615
date submitted: 2018-03-12
date accepted: 2018-08-21
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Polner
  given name: Bertalan
author list: Agent
  family name: Simor
  given name: Péter
author list: Agent
  family name: Kéri
  given name: Szabolcs
doi: 10.7717/peerj.5615
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: ©2018 Polner et al.
attribution name: Polner et al.

Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales
type: item
type: AcademicArticle
description: Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of the Methanomassiliicoccales and reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an uncultivated environmental clade of the Methanomassiliicoccales. Analysis of the ‘Lake Pavin cluster’ draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studied Methanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH) provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subse…
format: application/pdf
format: text/html
creator: Daan R. Speth
creator: Victoria J. Orphan
subject: Bioinformatics
subject: Microbiology
description: doi:10.7717/peerj.5614
publisher: PeerJ Inc.
rights: © 2018 Speth and Orphan
abstract: Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of the Methanomassiliicoccales and reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an uncultivated environmental clade of the Methanomassiliicoccales. Analysis of the ‘Lake Pavin cluster’ draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studied Methanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH) provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subse…
bibliographic citation: Speth et al. (2018) Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. PeerJ 6:e5614 https://doi.org/10.7717/peerj.5614
date submitted: 2018-06-08
date accepted: 2018-08-21
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Speth
  given name: Daan R.
author list: Agent
  family name: Orphan
  given name: Victoria J.
doi: 10.7717/peerj.5614
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: ©2018 Speth and Orphan
attribution name: Speth and Orphan

Effects of income and residential area on survival of patients with head and neck cancers following radiotherapy: working age individuals in Taiwan
type: item
type: AcademicArticle
description: Objectives The five-year survival rate of head and neck cancer (HNC) after radiotherapy (RT) varies widely from 35% to 89%. Many studies have addressed the effect of socioeconomic status and urban dwelling on the survival of HNC, but a limited number of studies have focused on the survival rate of HNC patients after RT. Materials and methods During the period of 2000–2013, 40,985 working age individuals (20 < age < 65 years) with HNC patients treated with RT were included in this study from a registry of patients with catastrophic illnesses maintained by the Taiwan National Health Insurance Research Database (NHIRD). Results The cumulative survival rate of HNC following RT in Taiwan was 53.2% (mean follow-up period, 3.75 ± 3.31 years). The combined effects of income and geographic effect on cumulative survival rates were as follows: high income group > medium income group > low income group and northern > central > southern > eastern Taiwan. Patients with moderate income levels had a 36.9% higher risk of mortality as compared with patients with high income levels (hazard ratio (HR) = 1.369; p < 0.001). Patients with low income levels had a 51.4% greater risk of mortality than patients with high income levels (HR = 1.514, p < 0.001). Conclusion In Taiwan, income and residential area significantly affected the survival rate of HNC patients receiving RT. The highest income level group had the best survival rate, regardless of the geographic area. The difference in survival between the low and high income groups was still pronounced in more deprived areas.
format: application/pdf
format: text/html
creator: Yu Cheng Lai
creator: Pei Ling Tang
creator: Chi Hsiang Chu
creator: Tsu Jen Kuo
subject: Dentistry
subject: Oncology
subject: Otorhinolaryngology
subject: Public Health
description: doi:10.7717/peerj.5591
publisher: PeerJ Inc.
rights: © 2018 Lai et al.
abstract: Objectives The five-year survival rate of head and neck cancer (HNC) after radiotherapy (RT) varies widely from 35% to 89%. Many studies have addressed the effect of socioeconomic status and urban dwelling on the survival of HNC, but a limited number of studies have focused on the survival rate of HNC patients after RT. Materials and methods During the period of 2000–2013, 40,985 working age individuals (20 < age < 65 years) with HNC patients treated with RT were included in this study from a registry of patients with catastrophic illnesses maintained by the Taiwan National Health Insurance Research Database (NHIRD). Results The cumulative survival rate of HNC following RT in Taiwan was 53.2% (mean follow-up period, 3.75 ± 3.31 years). The combined effects of income and geographic effect on cumulative survival rates were as follows: high income group > medium income group > low income group and northern > central > southern > eastern Taiwan. Patients with moderate income levels had a 36.9% higher risk of mortality as compared with patients with high income levels (hazard ratio (HR) = 1.369; p < 0.001). Patients with low income levels had a 51.4% greater risk of mortality than patients with high income levels (HR = 1.514, p < 0.001). Conclusion In Taiwan, income and residential area significantly affected the survival rate of HNC patients receiving RT. The highest income level group had the best survival rate, regardless of the geographic area. The difference in survival between the low and high income groups was still pronounced in more deprived areas.
bibliographic citation: Lai et al. (2018) Effects of income and residential area on survival of patients with head and neck cancers following radiotherapy: working age individuals in Taiwan. PeerJ 6:e5591 https://doi.org/10.7717/peerj.5591
date submitted: 2018-02-19
date accepted: 2018-08-16
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lai
  given name: Yu Cheng
author list: Agent
  family name: Tang
  given name: Pei Ling
author list: Agent
  family name: Chu
  given name: Chi Hsiang
author list: Agent
  family name: Kuo
  given name: Tsu Jen
doi: 10.7717/peerj.5591
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: ©2018 Lai et al.
attribution name: Lai et al.

The influence of sample distribution on growth model output for a highly-exploited marine fish, the Gulf Corvina (Cynoscion othonopterus)
type: item
type: AcademicArticle
description: Estimating the growth of fishes is critical to understanding their life history and conducting fisheries assessments. It is imperative to sufficiently sample each size and age class of fishes to construct models that accurately reflect biological growth patterns, but this may be a challenging endeavor for highly-exploited species in which older fish are rare. Here, we use the Gulf Corvina (Cynoscion othonopterus), a vulnerable marine fish that has been persistently overfished for two decades, as a model species to compare the performance of several growth models. We fit the von Bertalanffy, Gompertz, logistic, Schnute, and Schnute–Richards growth models to length-at-age data by nonlinear least squares regression and used simple indicators to reveal biased data and ensure our results were biologically feasible. We then explored the consequences of selecting a biased growth model with a per-recruit model that estimated female spawning-stock-biomass-per-recruit and yield-per-recruit. Based on statistics alone, we found that the Schnute–Richards model described our data best. However, it was evident that our data were biased by a bimodal distribution of samples and underrepresentation of large, old individuals, and we found the Schnute–Richards model output to be biologically implausible. By simulating an equal distribution of samples across all age classes, we found that sample distribution distinctly influenced model output for all growth models tested. Consequently, we determined that the growth pattern of the Gulf Corvina was best described by the von Bertalanffy growth model, which was the most robust to biased data, comparable across studies, and statistically comparable to the Schnute–Richards model. Growth model selection had important consequences for assessment, as the per-recruit model employing the Schnute–Richards model fit to raw data predicted the stock to be in a much healthier state than per-recruit models employing other growth models. Our results serv…
format: application/pdf
format: text/html
creator: Derek G. Bolser
creator: Arnaud Grüss
creator: Mark A. Lopez
creator: Erin M. Reed
creator: Ismael Mascareñas-Osorio
creator: Brad E. Erisman
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
subject: Statistics
description: doi:10.7717/peerj.5582
publisher: PeerJ Inc.
rights: © 2018 Bolser et al.
abstract: Estimating the growth of fishes is critical to understanding their life history and conducting fisheries assessments. It is imperative to sufficiently sample each size and age class of fishes to construct models that accurately reflect biological growth patterns, but this may be a challenging endeavor for highly-exploited species in which older fish are rare. Here, we use the Gulf Corvina (Cynoscion othonopterus), a vulnerable marine fish that has been persistently overfished for two decades, as a model species to compare the performance of several growth models. We fit the von Bertalanffy, Gompertz, logistic, Schnute, and Schnute–Richards growth models to length-at-age data by nonlinear least squares regression and used simple indicators to reveal biased data and ensure our results were biologically feasible. We then explored the consequences of selecting a biased growth model with a per-recruit model that estimated female spawning-stock-biomass-per-recruit and yield-per-recruit. Based on statistics alone, we found that the Schnute–Richards model described our data best. However, it was evident that our data were biased by a bimodal distribution of samples and underrepresentation of large, old individuals, and we found the Schnute–Richards model output to be biologically implausible. By simulating an equal distribution of samples across all age classes, we found that sample distribution distinctly influenced model output for all growth models tested. Consequently, we determined that the growth pattern of the Gulf Corvina was best described by the von Bertalanffy growth model, which was the most robust to biased data, comparable across studies, and statistically comparable to the Schnute–Richards model. Growth model selection had important consequences for assessment, as the per-recruit model employing the Schnute–Richards model fit to raw data predicted the stock to be in a much healthier state than per-recruit models employing other growth models. Our results serv…
bibliographic citation: Bolser et al. (2018) The influence of sample distribution on growth model output for a highly-exploited marine fish, the Gulf Corvina (Cynoscion othonopterus). PeerJ 6:e5582 https://doi.org/10.7717/peerj.5582
date submitted: 2018-04-13
date accepted: 2018-08-13
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bolser
  given name: Derek G.
author list: Agent
  family name: Grüss
  given name: Arnaud
author list: Agent
  family name: Lopez
  given name: Mark A.
author list: Agent
  family name: Reed
  given name: Erin M.
author list: Agent
  family name: Mascareñas-Osorio
  given name: Ismael
author list: Agent
  family name: Erisman
  given name: Brad E.
doi: 10.7717/peerj.5582
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: ©2018 Bolser et al.
attribution name: Bolser et al.

https://peerj.com/articles/5577
type: item
type: AcademicArticle
title: The role of miRNAs 34a, 146a, 320a and 542 in the synergistic anticancer effects of methyl 2-(5-fluoro-2-hydroxyphenyl)-1H- benzo[d]imidazole-5-carboxylate (MBIC) with doxorubicin in breast cancer cells
description: Combination Index (CI) analysis suggested that MBIC and doxorubicin synergistically inhibited up to 97% of cell proliferation in ER+/PR+MCF-7 and triple negative MDA-MB-231 breast cancer cell lines. Moreover, treatment of the breast cancer cells with the combined drugs resulted in lower IC50 values in contrast to the individual drug treatment. Small noncoding microRNAs (miRNA) may function as non-mutational gene regulators at post-transcriptional level of protein synthesis. In the present study, the effect of the combined treatment of MBIC and doxorubicin on the expression level of several miRNAs including miR-34a, miR-146a, miR-320a and miR-542 were evaluated in MCF-7 and MDA-MB-231 breast cancer cell lines. These miRNAs have the potential to alter the protein level of survivin, the anti-apoptotic protein and reduce the metastatic activity in human breast cancer cell lines by interfering with the nuclear accumulation of NF-κB. Our results demonstrated the several fold changes in expression of miRNAs, which is drug and cell line dependent. This finding demonstrated a functional synergistic network between miR-34a, miR-320a and miR-542 that are negatively involved in post-transcriptional regulation of survivin in MCF-7 cells. While in MDA-MB-231 cells, changes in expression level of miR-146a was correlated with inhibition of the nuclear translocation of NF-κB. The overall result suggested that alteration in protein level and location of survivin and NF-κB by miR-34a, miR-320a, miR-146a and miR-542, remarkably influenced the synergistic enhancement of combined MBIC and doxorubicin in treatment of aggressive and less aggressive human breast cancer cell lines.
format: application/pdf
format: text/html
creator: Mohadeseh Hasanpourghadi
creator: Nazia Abdul Majid
creator: Mohd Rais Mustafa
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.5577
publisher: PeerJ Inc.
rights: © 2018 Hasanpourghadi et al.
abstract: Combination Index (CI) analysis suggested that MBIC and doxorubicin synergistically inhibited up to 97% of cell proliferation in ER+/PR+MCF-7 and triple negative MDA-MB-231 breast cancer cell lines. Moreover, treatment of the breast cancer cells with the combined drugs resulted in lower IC50 values in contrast to the individual drug treatment. Small noncoding microRNAs (miRNA) may function as non-mutational gene regulators at post-transcriptional level of protein synthesis. In the present study, the effect of the combined treatment of MBIC and doxorubicin on the expression level of several miRNAs including miR-34a, miR-146a, miR-320a and miR-542 were evaluated in MCF-7 and MDA-MB-231 breast cancer cell lines. These miRNAs have the potential to alter the protein level of survivin, the anti-apoptotic protein and reduce the metastatic activity in human breast cancer cell lines by interfering with the nuclear accumulation of NF-κB. Our results demonstrated the several fold changes in expression of miRNAs, which is drug and cell line dependent. This finding demonstrated a functional synergistic network between miR-34a, miR-320a and miR-542 that are negatively involved in post-transcriptional regulation of survivin in MCF-7 cells. While in MDA-MB-231 cells, changes in expression level of miR-146a was correlated with inhibition of the nuclear translocation of NF-κB. The overall result suggested that alteration in protein level and location of survivin and NF-κB by miR-34a, miR-320a, miR-146a and miR-542, remarkably influenced the synergistic enhancement of combined MBIC and doxorubicin in treatment of aggressive and less aggressive human breast cancer cell lines.
bibliographic citation: Hasanpourghadi et al. (2018) The role of miRNAs 34a, 146a, 320a and 542 in the synergistic anticancer effects of methyl 2-(5-fluoro-2-hydroxyphenyl)-1H- benzo[d]imidazole-5-carboxylate (MBIC) with doxorubicin in breast cancer cells. PeerJ 6:e5577 https://doi.org/10.7717/peerj.5577
date submitted: 2018-03-13
date accepted: 2018-08-14
issued: 2018-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hasanpourghadi
  given name: Mohadeseh
author list: Agent
  family name: Abdul Majid
  given name: Nazia
author list: Agent
  family name: Rais Mustafa
  given name: Mohd
doi: 10.7717/peerj.5577
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-17
copyright: ©2018 Hasanpourghadi et al.
attribution name: Hasanpourghadi et al.

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