PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Mental disorder recovery correlated with centralities and interactions on an online social network
items: Environmental influences on the Indo–Pacific octocoral Isis hippuris Linnaeus 1758 (Alcyonacea: Isididae): genetic fixation or phenotypic plasticity?
items: In vitro biomechanical evaluation of internal fixation techniques on the canine lumbosacral junction
items: Coalescent: an open-science framework for importance sampling in coalescent theory
items: Biological and ecological traits of marine species
items: The application of fractional Mel cepstral coefficient in deceptive speech detection
items: Perivascular mast cells regulate vein graft neointimal formation and remodeling
items: Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota
items: Ichthyoplankton assemblage structure of springs in the Yangtze Estuary revealed by biological and environmental visions
items: Face matching in a long task: enforced rest and desk-switching cannot maintain identification accuracy

Mental disorder recovery correlated with centralities and interactions on an online social network
type: item
type: AcademicArticle
description: Recent research has established both a theoretical basis and strong empirical evidence that effective social behavior plays a beneficial role in the maintenance of physical and psychological well-being of people. To test whether social behavior and well-being are also associated in online communities, we studied the correlations between the recovery of patients with mental disorders and their behaviors in online social media. As the source of the data related to the social behavior and progress of mental recovery, we used PatientsLikeMe (PLM), the world’s first open-participation research platform for the development of patient-centered health outcome measures. We first constructed an online social network structure based on patient-to-patient ties among 200 patients obtained from PLM. We then characterized patients’ online social activities by measuring the numbers of “posts and views” and “helpful marks” each patient obtained. The patients’ recovery data were obtained from their self-reported status information that was also available on PLM. We found that some node properties (in-degree, eigenvector centrality and PageRank) and the two online social activity measures were significantly correlated with patients’ recovery. Furthermore, we re-collected the patients’ recovery data two months after the first data collection. We found significant correlations between the patients’ social behaviors and the second recovery data, which were collected two months apart. Our results indicated that social interactions in online communities such as PLM were significantly associated with the current and future recoveries of patients with mental disorders.
format: application/pdf
format: text/html
creator: Xinpei Ma
creator: Hiroki Sayama
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.1163
publisher: PeerJ Inc.
rights: © 2015 Ma and Sayama
abstract: Recent research has established both a theoretical basis and strong empirical evidence that effective social behavior plays a beneficial role in the maintenance of physical and psychological well-being of people. To test whether social behavior and well-being are also associated in online communities, we studied the correlations between the recovery of patients with mental disorders and their behaviors in online social media. As the source of the data related to the social behavior and progress of mental recovery, we used PatientsLikeMe (PLM), the world’s first open-participation research platform for the development of patient-centered health outcome measures. We first constructed an online social network structure based on patient-to-patient ties among 200 patients obtained from PLM. We then characterized patients’ online social activities by measuring the numbers of “posts and views” and “helpful marks” each patient obtained. The patients’ recovery data were obtained from their self-reported status information that was also available on PLM. We found that some node properties (in-degree, eigenvector centrality and PageRank) and the two online social activity measures were significantly correlated with patients’ recovery. Furthermore, we re-collected the patients’ recovery data two months after the first data collection. We found significant correlations between the patients’ social behaviors and the second recovery data, which were collected two months apart. Our results indicated that social interactions in online communities such as PLM were significantly associated with the current and future recoveries of patients with mental disorders.
bibliographic citation: Ma et al. (2015) Mental disorder recovery correlated with centralities and interactions on an online social network. PeerJ 3:e1163 https://doi.org/10.7717/peerj.1163
date submitted: 2015-04-06
date accepted: 2015-07-17
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Xinpei
author list: Agent
  family name: Sayama
  given name: Hiroki
doi: 10.7717/peerj.1163
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 Ma and Sayama
attribution name: Ma and Sayama

Environmental influences on the Indo–Pacific octocoral Isis hippuris Linnaeus 1758 (Alcyonacea: Isididae): genetic fixation or phenotypic plasticity?
type: item
type: AcademicArticle
description: As conspicuous modular components of benthic marine habitats, gorgonian (sea fan) octocorals have perplexed taxonomists for centuries through their shear diversity, particularly throughout the Indo–Pacific. Phenotypic incongruence within and between seemingly unitary lineages across contrasting environments can provide the raw material to investigate processes of disruptive selection. Two distinct phenotypes of the Isidid Isis hippuris Linnaeus, 1758 partition between differing reef environments: long-branched bushy colonies on degraded reefs, and short-branched multi/planar colonies on healthy reefs within the Wakatobi Marine National Park (WMNP), Indonesia. Multivariate analyses reveal phenotypic traits between morphotypes were likely integrated primarily at the colony level with increased polyp density and consistently smaller sclerite dimensions at the degraded site. Sediment load and turbidity, hence light availability, primarily influenced phenotypic differences between the two sites. This distinct morphological dissimilarity between the two sites is a reliable indicator of reef health; selection primarily acting on colony morphology, porosity through branching structure, as well as sclerite diversity and size. ITS2 sequence and predicted RNA secondary structure further revealed intraspecific variation between I. hippuris morphotypes relative to such environments (ΦST = 0.7683, P < 0.001). This evidence suggests—but does not confirm—that I. hippuris morphotypes within the WMNP are two separate species; however, to what extent and taxonomic assignment requires further investigation across its full geographic distribution. Incongruence between colonies present in the WMNP with tenuously described Isis alternatives (Isis reticulata Nutting, 1910, Isis minorbrachyblasta Zou, Huang & Wang, 1991), questions the validity of such assignments. Furthermore, phylogenetic analyses confirm early taxonomic suggestion that the characteristic jointed axis of the Isididae is i…
format: application/pdf
format: text/html
creator: Sonia J. Rowley
creator: Xavier Pochon
creator: Les Watling
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.1128
publisher: PeerJ Inc.
rights: © 2015 Rowley et al.
abstract: As conspicuous modular components of benthic marine habitats, gorgonian (sea fan) octocorals have perplexed taxonomists for centuries through their shear diversity, particularly throughout the Indo–Pacific. Phenotypic incongruence within and between seemingly unitary lineages across contrasting environments can provide the raw material to investigate processes of disruptive selection. Two distinct phenotypes of the Isidid Isis hippuris Linnaeus, 1758 partition between differing reef environments: long-branched bushy colonies on degraded reefs, and short-branched multi/planar colonies on healthy reefs within the Wakatobi Marine National Park (WMNP), Indonesia. Multivariate analyses reveal phenotypic traits between morphotypes were likely integrated primarily at the colony level with increased polyp density and consistently smaller sclerite dimensions at the degraded site. Sediment load and turbidity, hence light availability, primarily influenced phenotypic differences between the two sites. This distinct morphological dissimilarity between the two sites is a reliable indicator of reef health; selection primarily acting on colony morphology, porosity through branching structure, as well as sclerite diversity and size. ITS2 sequence and predicted RNA secondary structure further revealed intraspecific variation between I. hippuris morphotypes relative to such environments (ΦST = 0.7683, P < 0.001). This evidence suggests—but does not confirm—that I. hippuris morphotypes within the WMNP are two separate species; however, to what extent and taxonomic assignment requires further investigation across its full geographic distribution. Incongruence between colonies present in the WMNP with tenuously described Isis alternatives (Isis reticulata Nutting, 1910, Isis minorbrachyblasta Zou, Huang & Wang, 1991), questions the validity of such assignments. Furthermore, phylogenetic analyses confirm early taxonomic suggestion that the characteristic jointed axis of the Isididae is i…
bibliographic citation: Rowley et al. (2015) Environmental influences on the Indo–Pacific octocoral Isis hippuris Linnaeus 1758 (Alcyonacea: Isididae): genetic fixation or phenotypic plasticity?. PeerJ 3:e1128 https://doi.org/10.7717/peerj.1128
date submitted: 2015-04-28
date accepted: 2015-07-05
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rowley
  given name: Sonia J.
author list: Agent
  family name: Pochon
  given name: Xavier
author list: Agent
  family name: Watling
  given name: Les
doi: 10.7717/peerj.1128
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 Rowley et al.
attribution name: Rowley et al.

In vitro biomechanical evaluation of internal fixation techniques on the canine lumbosacral junction
type: item
type: AcademicArticle
description: Few biomechanical studies have evaluated the effect of internal stabilization techniques after decompressive surgery on the stability of the canine lumbosacral junction. The purpose of this canine cadaver study is to evaluate the stability of the canine lumbosacral (LS) spine in flexion and extension following laminectomy and discectomy and then stabilization with each of the three techniques: pins and polymethylmethacrylate (P/PMMA), two dorsal locking plates (SOP) or bilateral transarticular facet screws (FACET).Using a cantilever biomechanical system, bending moments were applied to the LS and range of motion (ROM) was recorded via a rotational potentiometer. With 3 Nm, the ROM (n = 4 in each group) for P/PMMA, SOP and FACET were 1.92 ± 0.96°, 2.56 ± 0.55°and 3.18 ± 1.14°, respectively. With moments up to 35 Nm, the P/PMMA specimens appeared stable. Sacroiliac motion in the SOP and FACET groups invalidated further comparisons. Each of the stabilization techniques (P/PMMA, SOP, and FACET) significantly decreased the range of motion in flexion and extension for low bending moments.
format: application/pdf
format: text/html
creator: Peter Early
creator: Peter Mente
creator: Stacy Dillard
creator: Simon Roe
subject: Veterinary Medicine
description: doi:10.7717/peerj.1094
publisher: PeerJ Inc.
rights: © 2015 Early et al.
abstract: Few biomechanical studies have evaluated the effect of internal stabilization techniques after decompressive surgery on the stability of the canine lumbosacral junction. The purpose of this canine cadaver study is to evaluate the stability of the canine lumbosacral (LS) spine in flexion and extension following laminectomy and discectomy and then stabilization with each of the three techniques: pins and polymethylmethacrylate (P/PMMA), two dorsal locking plates (SOP) or bilateral transarticular facet screws (FACET).Using a cantilever biomechanical system, bending moments were applied to the LS and range of motion (ROM) was recorded via a rotational potentiometer. With 3 Nm, the ROM (n = 4 in each group) for P/PMMA, SOP and FACET were 1.92 ± 0.96°, 2.56 ± 0.55°and 3.18 ± 1.14°, respectively. With moments up to 35 Nm, the P/PMMA specimens appeared stable. Sacroiliac motion in the SOP and FACET groups invalidated further comparisons. Each of the stabilization techniques (P/PMMA, SOP, and FACET) significantly decreased the range of motion in flexion and extension for low bending moments.
bibliographic citation: Early et al. (2015) In vitro biomechanical evaluation of internal fixation techniques on the canine lumbosacral junction. PeerJ 3:e1094 https://doi.org/10.7717/peerj.1094
date submitted: 2015-03-17
date accepted: 2015-06-18
issued: 2015-08-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Early
  given name: Peter
author list: Agent
  family name: Mente
  given name: Peter
author list: Agent
  family name: Dillard
  given name: Stacy
author list: Agent
  family name: Roe
  given name: Simon
doi: 10.7717/peerj.1094
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-20
copyright: © 2015 Early et al.
attribution name: Early et al.

Coalescent: an open-science framework for importance sampling in coalescent theory
type: item
type: AcademicArticle
description: Background. In coalescent theory, computer programs often use importance sampling to calculate likelihoods and other statistical quantities. An importance sampling scheme can exploit human intuition to improve statistical efficiency of computations, but unfortunately, in the absence of general computer frameworks on importance sampling, researchers often struggle to translate new sampling schemes computationally or benchmark against different schemes, in a manner that is reliable and maintainable. Moreover, most studies use computer programs lacking a convenient user interface or the flexibility to meet the current demands of open science. In particular, current computer frameworks can only evaluate the efficiency of a single importance sampling scheme or compare the efficiencies of different schemes in an ad hoc manner. Results. We have designed a general framework (http://coalescent.sourceforge.net; language: Java; License: GPLv3) for importance sampling that computes likelihoods under the standard neutral coalescent model of a single, well-mixed population of constant size over time following infinite sites model of mutation. The framework models the necessary core concepts, comes integrated with several data sets of varying size, implements the standard competing proposals, and integrates tightly with our previous framework for calculating exact probabilities. For a given dataset, it computes the likelihood and provides the maximum likelihood estimate of the mutation parameter. Well-known benchmarks in the coalescent literature validate the accuracy of the framework. The framework provides an intuitive user interface with minimal clutter. For performance, the framework switches automatically to modern multicore hardware, if available. It runs on three major platforms (Windows, Mac and Linux). Extensive tests and coverage make the framework reliable and maintainable. Conclusions. In coalescent theory, many studies of computational efficiency consider only effecti…
format: application/pdf
format: text/html
creator: Susanta Tewari
creator: John L. Spouge
subject: Computational Biology
subject: Genetics
subject: Mathematical Biology
subject: Science Policy
subject: Statistics
description: doi:10.7717/peerj.1203
publisher: PeerJ Inc.
rights: © 2015
abstract: Background. In coalescent theory, computer programs often use importance sampling to calculate likelihoods and other statistical quantities. An importance sampling scheme can exploit human intuition to improve statistical efficiency of computations, but unfortunately, in the absence of general computer frameworks on importance sampling, researchers often struggle to translate new sampling schemes computationally or benchmark against different schemes, in a manner that is reliable and maintainable. Moreover, most studies use computer programs lacking a convenient user interface or the flexibility to meet the current demands of open science. In particular, current computer frameworks can only evaluate the efficiency of a single importance sampling scheme or compare the efficiencies of different schemes in an ad hoc manner. Results. We have designed a general framework (http://coalescent.sourceforge.net; language: Java; License: GPLv3) for importance sampling that computes likelihoods under the standard neutral coalescent model of a single, well-mixed population of constant size over time following infinite sites model of mutation. The framework models the necessary core concepts, comes integrated with several data sets of varying size, implements the standard competing proposals, and integrates tightly with our previous framework for calculating exact probabilities. For a given dataset, it computes the likelihood and provides the maximum likelihood estimate of the mutation parameter. Well-known benchmarks in the coalescent literature validate the accuracy of the framework. The framework provides an intuitive user interface with minimal clutter. For performance, the framework switches automatically to modern multicore hardware, if available. It runs on three major platforms (Windows, Mac and Linux). Extensive tests and coverage make the framework reliable and maintainable. Conclusions. In coalescent theory, many studies of computational efficiency consider only effecti…
bibliographic citation: Tewari et al. (2015) Coalescent: an open-science framework for importance sampling in coalescent theory. PeerJ 3:e1203 https://doi.org/10.7717/peerj.1203
date submitted: 2014-05-25
date accepted: 2015-07-30
issued: 2015-08-18
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Tewari
  given name: Susanta
author list: Agent
  family name: Spouge
  given name: John L.
doi: 10.7717/peerj.1203
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-18

Biological and ecological traits of marine species
type: item
type: AcademicArticle
description: This paper reviews the utility and availability of biological and ecological traits for marine species so as to prioritise the development of a world database on marine species traits. In addition, the ‘status’ of species for conservation, that is, whether they are introduced or invasive, of fishery or aquaculture interest, harmful, or used as an ecological indicator, were reviewed because these attributes are of particular interest to society. Whereas traits are an enduring characteristic of a species and/or population, a species status may vary geographically and over time. Criteria for selecting traits were that they could be applied to most taxa, were easily available, and their inclusion would result in new research and/or management applications. Numerical traits were favoured over categorical. Habitat was excluded as it can be derived from a selection of these traits. Ten traits were prioritized for inclusion in the most comprehensive open access database on marine species (World Register of Marine Species), namely taxonomic classification, environment, geography, depth, substratum, mobility, skeleton, diet, body size and reproduction. These traits and statuses are being added to the database and new use cases may further subdivide and expand upon them.
format: application/pdf
format: text/html
creator: Mark John Costello
creator: Simon Claus
creator: Stefanie Dekeyzer
creator: Leen Vandepitte
creator: Éamonn Ó Tuama
creator: Dan Lear
creator: Harvey Tyler-Walters
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Taxonomy
description: doi:10.7717/peerj.1201
publisher: PeerJ Inc.
rights: © 2015 Costello et al.
abstract: This paper reviews the utility and availability of biological and ecological traits for marine species so as to prioritise the development of a world database on marine species traits. In addition, the ‘status’ of species for conservation, that is, whether they are introduced or invasive, of fishery or aquaculture interest, harmful, or used as an ecological indicator, were reviewed because these attributes are of particular interest to society. Whereas traits are an enduring characteristic of a species and/or population, a species status may vary geographically and over time. Criteria for selecting traits were that they could be applied to most taxa, were easily available, and their inclusion would result in new research and/or management applications. Numerical traits were favoured over categorical. Habitat was excluded as it can be derived from a selection of these traits. Ten traits were prioritized for inclusion in the most comprehensive open access database on marine species (World Register of Marine Species), namely taxonomic classification, environment, geography, depth, substratum, mobility, skeleton, diet, body size and reproduction. These traits and statuses are being added to the database and new use cases may further subdivide and expand upon them.
bibliographic citation: Costello et al. (2015) Biological and ecological traits of marine species. PeerJ 3:e1201 https://doi.org/10.7717/peerj.1201
date submitted: 2015-03-09
date accepted: 2015-07-29
issued: 2015-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Costello
  given name: Mark John
author list: Agent
  family name: Claus
  given name: Simon
author list: Agent
  family name: Dekeyzer
  given name: Stefanie
author list: Agent
  family name: Vandepitte
  given name: Leen
author list: Agent
  family name: Tuama
  given name: Éamonn Ó
author list: Agent
  family name: Lear
  given name: Dan
author list: Agent
  family name: Tyler-Walters
  given name: Harvey
doi: 10.7717/peerj.1201
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-18
copyright: © 2015 Costello et al.
attribution name: Costello et al.

The application of fractional Mel cepstral coefficient in deceptive speech detection
type: item
type: AcademicArticle
description: The inconvenience operation of EEG P300 or functional magnetic resonance imaging (FMRI) will be overcome, when the deceptive information can be effectively detected from speech signal analysis. In this paper, the fractional Mel cepstral coefficient (FrCC) is proposed as the speech character for deception detection. The different fractional order can reveal various personalities of the speakers. The linear discriminant analysis (LDA) model (which has the ability of global optimal vector mapping) is introduced, and the performance of FrCC and MFCC in deceptive detection is compared when all the data are mapped to low dimensional. Then, the hidden Markov model (HMM) is introduced as a long-term signal analysis tool. Twenty-five male and 25 female participants are involved in the experiment. The results show that the clustering effect of optimal fractional order FrCC is better than that of MFCC. The average accuracy for male and female speaker is 59.9% and 56.2%, respectively, by using the FrCC under the LDA model. When MFCC is used, the accuracy is reduced by 3.2% and 5.9%, respectively, for male and female. The accuracy can be increased to 71.0% and 70.2% for male and female speakers when HMM is used. Moreover, some individual accuracy is increased over 20%, or even more than 85%, when FrCC is introduced. The results show that the deceptive information is indeed hidden in the speech signals. Therefore, speech-based psychophysiology calculating may be a valuable research field.
format: application/pdf
format: text/html
creator: Xinyu Pan
creator: Heming Zhao
creator: Yan Zhou
subject: Bioinformatics
subject: Computational Biology
subject: Psychiatry and Psychology
subject: Computational Science
description: doi:10.7717/peerj.1194
publisher: PeerJ Inc.
rights: © 2015 Pan et al.
abstract: The inconvenience operation of EEG P300 or functional magnetic resonance imaging (FMRI) will be overcome, when the deceptive information can be effectively detected from speech signal analysis. In this paper, the fractional Mel cepstral coefficient (FrCC) is proposed as the speech character for deception detection. The different fractional order can reveal various personalities of the speakers. The linear discriminant analysis (LDA) model (which has the ability of global optimal vector mapping) is introduced, and the performance of FrCC and MFCC in deceptive detection is compared when all the data are mapped to low dimensional. Then, the hidden Markov model (HMM) is introduced as a long-term signal analysis tool. Twenty-five male and 25 female participants are involved in the experiment. The results show that the clustering effect of optimal fractional order FrCC is better than that of MFCC. The average accuracy for male and female speaker is 59.9% and 56.2%, respectively, by using the FrCC under the LDA model. When MFCC is used, the accuracy is reduced by 3.2% and 5.9%, respectively, for male and female. The accuracy can be increased to 71.0% and 70.2% for male and female speakers when HMM is used. Moreover, some individual accuracy is increased over 20%, or even more than 85%, when FrCC is introduced. The results show that the deceptive information is indeed hidden in the speech signals. Therefore, speech-based psychophysiology calculating may be a valuable research field.
bibliographic citation: Pan et al. (2015) The application of fractional Mel cepstral coefficient in deceptive speech detection. PeerJ 3:e1194 https://doi.org/10.7717/peerj.1194
date submitted: 2015-05-13
date accepted: 2015-07-27
issued: 2015-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Xinyu
author list: Agent
  family name: Zhao
  given name: Heming
author list: Agent
  family name: Zhou
  given name: Yan
doi: 10.7717/peerj.1194
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-18
copyright: © 2015 Pan et al.
attribution name: Pan et al.

Perivascular mast cells regulate vein graft neointimal formation and remodeling
type: item
type: AcademicArticle
description: Objective. Emerging evidence suggests an important role for mast cells in vein graft failure. This study addressed the hypothesis that perivascular mast cells regulate in situ vascular inflammatory and proliferative responses and subsequent vein graft neointimal lesion formation, using an optimized local mast cell reconstitution method. Methods and Results. Neointimal hyperplasia was induced by insertion of a vein graft into the right carotid artery in wild type and mast cell deficient KitW−sh/W−sh mice. In some experiments, mast cells were reconstituted systemically (tail vein injection of bone marrow-derived mast cells) or locally (directly into the right neck area) prior to vein grafting. Vein graft neointimal lesion formation was significantly (P < 0.05) reduced in KitW−sh/W−sh mice. Mast cell deficiency reduced the number of proliferating cells, and inhibited L-selectin, CCL2, M-CSF and MIP-3α expression in the vein grafts. Local but not systemic mast cell reconstitution restored a perivascular mast cell population that subsequently promoted neointimal formation in mast cell deficient mice. Conclusion. Our data demonstrate that perivascular mast cells play a key role in promoting neointima formation by inducing local acute inflammatory and proliferative responses. These results suggest that ex vivo intraoperative targeting of mast cells may have therapeutic potential for the prevention of pathological vein graft remodeling.
format: application/pdf
format: text/html
creator: Junxi Wu
creator: Gianluca Grassia
creator: Helen Cambrook
creator: Armando Ialenti
creator: Neil MacRitchie
creator: Jaclyn Carberry
creator: Roger M. Wadsworth
creator: Catherine Lawrence
creator: Simon Kennedy
creator: Pasquale Maffia
subject: Cardiology
subject: Immunology
subject: Pharmacology
description: doi:10.7717/peerj.1192
publisher: PeerJ Inc.
rights: © 2015 Wu et al.
abstract: Objective. Emerging evidence suggests an important role for mast cells in vein graft failure. This study addressed the hypothesis that perivascular mast cells regulate in situ vascular inflammatory and proliferative responses and subsequent vein graft neointimal lesion formation, using an optimized local mast cell reconstitution method. Methods and Results. Neointimal hyperplasia was induced by insertion of a vein graft into the right carotid artery in wild type and mast cell deficient KitW−sh/W−sh mice. In some experiments, mast cells were reconstituted systemically (tail vein injection of bone marrow-derived mast cells) or locally (directly into the right neck area) prior to vein grafting. Vein graft neointimal lesion formation was significantly (P < 0.05) reduced in KitW−sh/W−sh mice. Mast cell deficiency reduced the number of proliferating cells, and inhibited L-selectin, CCL2, M-CSF and MIP-3α expression in the vein grafts. Local but not systemic mast cell reconstitution restored a perivascular mast cell population that subsequently promoted neointimal formation in mast cell deficient mice. Conclusion. Our data demonstrate that perivascular mast cells play a key role in promoting neointima formation by inducing local acute inflammatory and proliferative responses. These results suggest that ex vivo intraoperative targeting of mast cells may have therapeutic potential for the prevention of pathological vein graft remodeling.
bibliographic citation: Wu et al. (2015) Perivascular mast cells regulate vein graft neointimal formation and remodeling. PeerJ 3:e1192 https://doi.org/10.7717/peerj.1192
date submitted: 2015-03-16
date accepted: 2015-07-26
issued: 2015-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Junxi
author list: Agent
  family name: Grassia
  given name: Gianluca
author list: Agent
  family name: Cambrook
  given name: Helen
author list: Agent
  family name: Ialenti
  given name: Armando
author list: Agent
  family name: MacRitchie
  given name: Neil
author list: Agent
  family name: Carberry
  given name: Jaclyn
author list: Agent
  family name: Wadsworth
  given name: Roger M.
author list: Agent
  family name: Lawrence
  given name: Catherine
author list: Agent
  family name: Kennedy
  given name: Simon
author list: Agent
  family name: Maffia
  given name: Pasquale
doi: 10.7717/peerj.1192
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-18
copyright: © 2015 Wu et al.
attribution name: Wu et al.

Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota
type: item
type: AcademicArticle
description: Research on insect microbiota has greatly expanded over the past decade, along with a growing appreciation of the microbial contributions to insect ecology and evolution. Many of these studies use DNA sequencing to characterize the diversity and composition of insect-associated microbial communities. The choice of strategies used for specimen collection, storage, and handling could introduce biases in molecular assessments of insect microbiota, but such potential influences have not been systematically evaluated. Likewise, although it is common practice to surface sterilize insects prior to DNA extraction, it is not known if this time-consuming step has any effect on microbial community analyses. To resolve these methodological unknowns, we conducted an experiment wherein replicate individual insects of four species were stored intact for two months using five different methods—freezing, ethanol, dimethyl sulfoxide (DMSO), cetrimonium bromide (CTAB), and room-temperature storage without preservative—and then subjected to whole-specimen 16S rRNA gene sequencing to assess whether the structure of the insect-associated bacterial communities was impacted by these different storage strategies. Overall, different insect species harbored markedly distinct bacterial communities, a pattern that was highly robust to the method used to store samples. Storage method had little to no effect on assessments of microbiota composition, and the magnitude of the effect differed among the insect species examined. No single method emerged as “best,” i.e., one consistently having the highest similarity in community structure to control specimens, which were not stored prior to homogenization and DNA sequencing. We also found that surface sterilization did not change bacterial community structure as compared to unsterilized insects, presumably due to the vastly greater microbial biomass inside the insect body relative to its surface. We therefore recommend that researchers can use any of …
format: application/pdf
format: text/html
creator: Tobin J. Hammer
creator: Jacob C. Dickerson
creator: Noah Fierer
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Microbiology
description: doi:10.7717/peerj.1190
publisher: PeerJ Inc.
rights: © 2015 Hammer et al.
abstract: Research on insect microbiota has greatly expanded over the past decade, along with a growing appreciation of the microbial contributions to insect ecology and evolution. Many of these studies use DNA sequencing to characterize the diversity and composition of insect-associated microbial communities. The choice of strategies used for specimen collection, storage, and handling could introduce biases in molecular assessments of insect microbiota, but such potential influences have not been systematically evaluated. Likewise, although it is common practice to surface sterilize insects prior to DNA extraction, it is not known if this time-consuming step has any effect on microbial community analyses. To resolve these methodological unknowns, we conducted an experiment wherein replicate individual insects of four species were stored intact for two months using five different methods—freezing, ethanol, dimethyl sulfoxide (DMSO), cetrimonium bromide (CTAB), and room-temperature storage without preservative—and then subjected to whole-specimen 16S rRNA gene sequencing to assess whether the structure of the insect-associated bacterial communities was impacted by these different storage strategies. Overall, different insect species harbored markedly distinct bacterial communities, a pattern that was highly robust to the method used to store samples. Storage method had little to no effect on assessments of microbiota composition, and the magnitude of the effect differed among the insect species examined. No single method emerged as “best,” i.e., one consistently having the highest similarity in community structure to control specimens, which were not stored prior to homogenization and DNA sequencing. We also found that surface sterilization did not change bacterial community structure as compared to unsterilized insects, presumably due to the vastly greater microbial biomass inside the insect body relative to its surface. We therefore recommend that researchers can use any of …
bibliographic citation: Hammer et al. (2015) Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota. PeerJ 3:e1190 https://doi.org/10.7717/peerj.1190
date submitted: 2015-04-28
date accepted: 2015-07-24
issued: 2015-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hammer
  given name: Tobin J.
author list: Agent
  family name: Dickerson
  given name: Jacob C.
author list: Agent
  family name: Fierer
  given name: Noah
doi: 10.7717/peerj.1190
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-18
copyright: © 2015 Hammer et al.
attribution name: Hammer et al.

Ichthyoplankton assemblage structure of springs in the Yangtze Estuary revealed by biological and environmental visions
type: item
type: AcademicArticle
description: The ichthyoplankton assemblage structure in the Yangtze Estuary was analyzed based on four springs in 1999, 2001, 2004 and 2007 in order to provide detailed characterizations of the ichthyoplankton assemblage in springs, examine the long-term dynamics of spring ichthyoplankton assemblages, and evaluate the influence of environmental factors on the spatial distribution and inter-annual variations of ichthyoplankton assemblages associated with the Yangtze Estuary. Forty-two ichthyoplankton species belonging to 23 families were collected. Engraulidae was the most abundant family, including six species and comprising 67.91% of the total catch. Only four species (Coilia mystus, Engraulis japonicus, Trachidermis fasciatus and Allanetta bleekeri) could be considered dominant, accounting for 88.70% of total abundance. The structure of the ichthyoplankton spring assemblage persisted on an annual basis, with the dominant species reappearing consistently even though their abundance fluctuated from year to year. This inter-annual variation probably reflects variable environmental conditions influenced by jellyfish blooms, declining river flow, and overfishing. Canonical correspondence analysis indicated aspatial structure of the ichthyoplankton assemblage in three areas: (1) an inner assemblage dominated by C. mystus; (2) a central assemblage dominated by A. bleekeri and T. fasciatus; and (3) a shelf assemblage featuring E. japonicus. The observed ichthyoplankton assemblage structure appears to be strongly influenced by depth, salinity and suspended particulate matter gradients.
format: application/pdf
format: text/html
creator: Hui Zhang
creator: Weiwei Xian
creator: Shude Liu
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
subject: Marine Biology
description: doi:10.7717/peerj.1186
publisher: PeerJ Inc.
rights: © 2015 Zhang et al.
abstract: The ichthyoplankton assemblage structure in the Yangtze Estuary was analyzed based on four springs in 1999, 2001, 2004 and 2007 in order to provide detailed characterizations of the ichthyoplankton assemblage in springs, examine the long-term dynamics of spring ichthyoplankton assemblages, and evaluate the influence of environmental factors on the spatial distribution and inter-annual variations of ichthyoplankton assemblages associated with the Yangtze Estuary. Forty-two ichthyoplankton species belonging to 23 families were collected. Engraulidae was the most abundant family, including six species and comprising 67.91% of the total catch. Only four species (Coilia mystus, Engraulis japonicus, Trachidermis fasciatus and Allanetta bleekeri) could be considered dominant, accounting for 88.70% of total abundance. The structure of the ichthyoplankton spring assemblage persisted on an annual basis, with the dominant species reappearing consistently even though their abundance fluctuated from year to year. This inter-annual variation probably reflects variable environmental conditions influenced by jellyfish blooms, declining river flow, and overfishing. Canonical correspondence analysis indicated aspatial structure of the ichthyoplankton assemblage in three areas: (1) an inner assemblage dominated by C. mystus; (2) a central assemblage dominated by A. bleekeri and T. fasciatus; and (3) a shelf assemblage featuring E. japonicus. The observed ichthyoplankton assemblage structure appears to be strongly influenced by depth, salinity and suspended particulate matter gradients.
bibliographic citation: Zhang et al. (2015) Ichthyoplankton assemblage structure of springs in the Yangtze Estuary revealed by biological and environmental visions. PeerJ 3:e1186 https://doi.org/10.7717/peerj.1186
date submitted: 2015-06-19
date accepted: 2015-07-24
issued: 2015-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Hui
author list: Agent
  family name: Xian
  given name: Weiwei
author list: Agent
  family name: Liu
  given name: Shude
doi: 10.7717/peerj.1186
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-18
copyright: © 2015 Zhang et al.
attribution name: Zhang et al.

Face matching in a long task: enforced rest and desk-switching cannot maintain identification accuracy
type: item
type: AcademicArticle
description: In face matching, observers have to decide whether two photographs depict the same person or different people. This task is not only remarkably difficult but accuracy declines further during prolonged testing. The current study investigated whether this decline in long tasks can be eliminated with regular rest-breaks (Experiment 1) or room-switching (Experiment 2). Both experiments replicated the accuracy decline for long face-matching tasks and showed that this could not be eliminated with rest or room-switching. These findings suggest that person identification in applied settings, such as passport control, might be particularly error-prone due to the long and repetitive nature of the task. The experiments also show that it is difficult to counteract these problems.
format: application/pdf
format: text/html
creator: Hamood M. Alenezi
creator: Markus Bindemann
creator: Matthew C. Fysh
creator: Robert A. Johnston
subject: Neuroscience
subject: Neurology
subject: Ophthalmology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.1184
publisher: PeerJ Inc.
rights: © 2015 Alenezi et al.
abstract: In face matching, observers have to decide whether two photographs depict the same person or different people. This task is not only remarkably difficult but accuracy declines further during prolonged testing. The current study investigated whether this decline in long tasks can be eliminated with regular rest-breaks (Experiment 1) or room-switching (Experiment 2). Both experiments replicated the accuracy decline for long face-matching tasks and showed that this could not be eliminated with rest or room-switching. These findings suggest that person identification in applied settings, such as passport control, might be particularly error-prone due to the long and repetitive nature of the task. The experiments also show that it is difficult to counteract these problems.
bibliographic citation: Alenezi et al. (2015) Face matching in a long task: enforced rest and desk-switching cannot maintain identification accuracy. PeerJ 3:e1184 https://doi.org/10.7717/peerj.1184
date submitted: 2014-12-04
date accepted: 2015-07-23
issued: 2015-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alenezi
  given name: Hamood M.
author list: Agent
  family name: Bindemann
  given name: Markus
author list: Agent
  family name: Fysh
  given name: Matthew C.
author list: Agent
  family name: Johnston
  given name: Robert A.
doi: 10.7717/peerj.1184
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-08-18
copyright: © 2015 Alenezi et al.
attribution name: Alenezi et al.

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