PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Functional, size and taxonomic diversity of fish along a depth gradient in the deep sea
items: The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets
items: Emotion recognition using Kinect motion capture data of human gaits
items: A juvenile subfossil crocodylian from Anjohibe Cave, Northwestern Madagascar
items: Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline
items: Gua Sha, a press-stroke treatment of the skin, boosts the immune response to intradermal vaccination
items: Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls
items: Resilience does not explain the dissociation between chronic pain and physical activity in South Africans living with HIV
items: Lowland tapir distribution and habitat loss in South America
items: An association between feather damaging behavior and corticosterone metabolite excretion in captive African grey parrots (Psittacus erithacus)

Functional, size and taxonomic diversity of fish along a depth gradient in the deep sea
type: item
type: AcademicArticle
description: Biodiversity is well studied in ecology and the concept has been developed to include traits of species, rather than solely taxonomy, to better reflect the functional diversity of a system. The deep sea provides a natural environmental gradient within which to study changes in different diversity metrics, but traits of deep-sea fish are not widely known, hampering the application of functional diversity to this globally important system. We used morphological traits to determine the functional richness and functional divergence of demersal fish assemblages along the continental slope in the Northeast Atlantic, at depths of 300–2,000 m. We compared these metrics to size diversity based on individual body size and species richness. Functional richness and size diversity showed similar patterns, with the highest diversity at intermediate depths; functional divergence showed the opposite pattern, with the highest values at the shallowest and deepest parts of the study site. Species richness increased with depth. The functional implications of these patterns were deduced by examining depth-related changes in morphological traits and the dominance of feeding guilds as illustrated by stable isotope analyses. The patterns in diversity and the variation in certain morphological traits can potentially be explained by changes in the relative dominance of pelagic and benthic feeding guilds. All measures of diversity examined here suggest that the deep areas of the continental slope may be equally or more diverse than assemblages just beyond the continental shelf.
format: application/pdf
format: text/html
creator: Beth L. Mindel
creator: Francis C. Neat
creator: Clive N. Trueman
creator: Thomas J. Webb
creator: Julia L. Blanchard
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.2387
publisher: PeerJ Inc.
rights: © 2016 Mindel et al.
abstract: Biodiversity is well studied in ecology and the concept has been developed to include traits of species, rather than solely taxonomy, to better reflect the functional diversity of a system. The deep sea provides a natural environmental gradient within which to study changes in different diversity metrics, but traits of deep-sea fish are not widely known, hampering the application of functional diversity to this globally important system. We used morphological traits to determine the functional richness and functional divergence of demersal fish assemblages along the continental slope in the Northeast Atlantic, at depths of 300–2,000 m. We compared these metrics to size diversity based on individual body size and species richness. Functional richness and size diversity showed similar patterns, with the highest diversity at intermediate depths; functional divergence showed the opposite pattern, with the highest values at the shallowest and deepest parts of the study site. Species richness increased with depth. The functional implications of these patterns were deduced by examining depth-related changes in morphological traits and the dominance of feeding guilds as illustrated by stable isotope analyses. The patterns in diversity and the variation in certain morphological traits can potentially be explained by changes in the relative dominance of pelagic and benthic feeding guilds. All measures of diversity examined here suggest that the deep areas of the continental slope may be equally or more diverse than assemblages just beyond the continental shelf.
bibliographic citation: Mindel et al. (2016) Functional, size and taxonomic diversity of fish along a depth gradient in the deep sea. PeerJ 4:e2387 https://doi.org/10.7717/peerj.2387
date submitted: 2015-06-23
date accepted: 2016-07-31
issued: 2016-09-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mindel
  given name: Beth L.
author list: Agent
  family name: Neat
  given name: Francis C.
author list: Agent
  family name: Trueman
  given name: Clive N.
author list: Agent
  family name: Webb
  given name: Thomas J.
author list: Agent
  family name: Blanchard
  given name: Julia L.
doi: 10.7717/peerj.2387
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-15
copyright: © 2016 Mindel et al.
attribution name: Mindel et al.

The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets
type: item
type: AcademicArticle
description: An acute outbreak of porcine hemagglutinating encephalomyelitis virus (PHEV) infection in piglets, characterized with neurological symptoms, vomiting, diarrhea, and wasting, occurred in China. Coronavirus-like particles were observed in the homogenized tissue suspensions of the brain of dead piglets by electron microscopy, and a wild PHEV strain was isolated, characterized, and designated as PHEV-CC14. Histopathologic examinations of the dead piglets showed characteristics of non-suppurative encephalitis, and some neurons in the cerebral cortex were degenerated and necrotic, and neuronophagia. Similarly, mice inoculated with PHEV-CC14 were found to have central nervous system (CNS) dysfunction, with symptoms of depression, arched waists, standing and vellicating front claws. Furthmore, PHEV-positive labeling of neurons in cortices of dead piglets and infected mice supported the viral infections of the nervous system. Then, the major structural genes of PHEV-CC14 were sequenced and phylogenetically analyzed, and the strain shared 95%–99.2% nt identity with the other PHEV strains available in GenBank. Phylogenetic analysis clearly proved that the wild strain clustered into a subclass with a HEV-JT06 strain. These findings suggested that the virus had a strong tropism for CNS, in this way, inducing nonsuppurative encephalitis as the cause of death in piglets. Simultaneously, the predicted risk of widespread transmission showed a certain variation among the PHEV strains currently circulating around the world. Above all, the information presented in this study can not only provide good reference for the experimental diagnosis of PHEV infection for pig breeding, but also promote its new effective vaccine development.
format: application/pdf
format: text/html
creator: Zi Li
creator: Wenqi He
creator: Yungang Lan
creator: Kui Zhao
creator: Xiaoling Lv
creator: Huijun Lu
creator: Ning Ding
creator: Jing Zhang
creator: Junchao Shi
creator: Changjian Shan
creator: Feng Gao
subject: Veterinary Medicine
subject: Virology
description: doi:10.7717/peerj.2443
publisher: PeerJ Inc.
rights: © 2016 Li et al.
abstract: An acute outbreak of porcine hemagglutinating encephalomyelitis virus (PHEV) infection in piglets, characterized with neurological symptoms, vomiting, diarrhea, and wasting, occurred in China. Coronavirus-like particles were observed in the homogenized tissue suspensions of the brain of dead piglets by electron microscopy, and a wild PHEV strain was isolated, characterized, and designated as PHEV-CC14. Histopathologic examinations of the dead piglets showed characteristics of non-suppurative encephalitis, and some neurons in the cerebral cortex were degenerated and necrotic, and neuronophagia. Similarly, mice inoculated with PHEV-CC14 were found to have central nervous system (CNS) dysfunction, with symptoms of depression, arched waists, standing and vellicating front claws. Furthmore, PHEV-positive labeling of neurons in cortices of dead piglets and infected mice supported the viral infections of the nervous system. Then, the major structural genes of PHEV-CC14 were sequenced and phylogenetically analyzed, and the strain shared 95%–99.2% nt identity with the other PHEV strains available in GenBank. Phylogenetic analysis clearly proved that the wild strain clustered into a subclass with a HEV-JT06 strain. These findings suggested that the virus had a strong tropism for CNS, in this way, inducing nonsuppurative encephalitis as the cause of death in piglets. Simultaneously, the predicted risk of widespread transmission showed a certain variation among the PHEV strains currently circulating around the world. Above all, the information presented in this study can not only provide good reference for the experimental diagnosis of PHEV infection for pig breeding, but also promote its new effective vaccine development.
bibliographic citation: Li et al. (2016) The evidence of porcine hemagglutinating encephalomyelitis virus induced nonsuppurative encephalitis as the cause of death in piglets. PeerJ 4:e2443 https://doi.org/10.7717/peerj.2443
date submitted: 2016-06-14
date accepted: 2016-08-13
issued: 2016-09-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zi
author list: Agent
  family name: He
  given name: Wenqi
author list: Agent
  family name: Lan
  given name: Yungang
author list: Agent
  family name: Zhao
  given name: Kui
author list: Agent
  family name: Lv
  given name: Xiaoling
author list: Agent
  family name: Lu
  given name: Huijun
author list: Agent
  family name: Ding
  given name: Ning
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Shi
  given name: Junchao
author list: Agent
  family name: Shan
  given name: Changjian
author list: Agent
  family name: Gao
  given name: Feng
doi: 10.7717/peerj.2443
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-15
copyright: ©2016 Li et al.
attribution name: Li et al.

Emotion recognition using Kinect motion capture data of human gaits
type: item
type: AcademicArticle
description: Automatic emotion recognition is of great value in many applications, however, to fully display the application value of emotion recognition, more portable, non-intrusive, inexpensive technologies need to be developed. Human gaits could reflect the walker’s emotional state, and could be an information source for emotion recognition. This paper proposed a novel method to recognize emotional state through human gaits by using Microsoft Kinect, a low-cost, portable, camera-based sensor. Fifty-nine participants’ gaits under neutral state, induced anger and induced happiness were recorded by two Kinect cameras, and the original data were processed through joint selection, coordinate system transformation, sliding window gauss filtering, differential operation, and data segmentation. Features of gait patterns were extracted from 3-dimentional coordinates of 14 main body joints by Fourier transformation and Principal Component Analysis (PCA). The classifiers NaiveBayes, RandomForests, LibSVM and SMO (Sequential Minimal Optimization) were trained and evaluated, and the accuracy of recognizing anger and happiness from neutral state achieved 80.5% and 75.4%. Although the results of distinguishing angry and happiness states were not ideal in current study, it showed the feasibility of automatically recognizing emotional states from gaits, with the characteristics meeting the application requirements.
format: application/pdf
format: text/html
creator: Shun Li
creator: Liqing Cui
creator: Changye Zhu
creator: Baobin Li
creator: Nan Zhao
creator: Tingshao Zhu
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2364
publisher: PeerJ Inc.
rights: © 2016 Li et al.
abstract: Automatic emotion recognition is of great value in many applications, however, to fully display the application value of emotion recognition, more portable, non-intrusive, inexpensive technologies need to be developed. Human gaits could reflect the walker’s emotional state, and could be an information source for emotion recognition. This paper proposed a novel method to recognize emotional state through human gaits by using Microsoft Kinect, a low-cost, portable, camera-based sensor. Fifty-nine participants’ gaits under neutral state, induced anger and induced happiness were recorded by two Kinect cameras, and the original data were processed through joint selection, coordinate system transformation, sliding window gauss filtering, differential operation, and data segmentation. Features of gait patterns were extracted from 3-dimentional coordinates of 14 main body joints by Fourier transformation and Principal Component Analysis (PCA). The classifiers NaiveBayes, RandomForests, LibSVM and SMO (Sequential Minimal Optimization) were trained and evaluated, and the accuracy of recognizing anger and happiness from neutral state achieved 80.5% and 75.4%. Although the results of distinguishing angry and happiness states were not ideal in current study, it showed the feasibility of automatically recognizing emotional states from gaits, with the characteristics meeting the application requirements.
bibliographic citation: Li et al. (2016) Emotion recognition using Kinect motion capture data of human gaits. PeerJ 4:e2364 https://doi.org/10.7717/peerj.2364
date submitted: 2015-10-28
date accepted: 2016-07-24
issued: 2016-09-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Shun
author list: Agent
  family name: Cui
  given name: Liqing
author list: Agent
  family name: Zhu
  given name: Changye
author list: Agent
  family name: Li
  given name: Baobin
author list: Agent
  family name: Zhao
  given name: Nan
author list: Agent
  family name: Zhu
  given name: Tingshao
doi: 10.7717/peerj.2364
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-15
copyright: ©2016 Li et al.
attribution name: Li et al.

A juvenile subfossil crocodylian from Anjohibe Cave, Northwestern Madagascar
type: item
type: AcademicArticle
description: Madagascar’s subfossil record preserves a diverse community of animals including elephant birds, pygmy hippopotamus, giant lemurs, turtles, crocodiles, bats, rodents, and carnivorans. These fossil accumulations give us a window into the island’s past from 80,000 years ago to a mere few hundred years ago, recording the extinction of some groups and the persistence of others. The crocodylian subfossil record is limited to two taxa, Voay robustus and Crocodylus niloticus, found at sites distributed throughout the island. V. robustus is extinct while C. niloticus is still found on the island today, but whether these two species overlapped temporally, or if Voay was driven to extinction by competing with Crocodylus remains unknown. While their size and presumed behavior was similar to each other, nearly nothing is known about the growth and development of Voay, as the overwhelming majority of fossil specimens represent mature adult individuals. Here we describe a nearly complete juvenile crocodylian specimen from Anjohibe Cave, northwestern Madagascar. The specimen is referred to Crocodylus based on the presence of caviconchal recesses on the medial wall of the maxillae, and to C. niloticus based on the presence of an oval shaped internal choana, lack of rostral ornamentation and a long narrow snout. However, as there are currently no described juvenile specimens of Voay robustus, it is important to recognize that some of the defining characteristics of that genus may have changed through ontogeny. Elements include a nearly complete skull and many postcranial elements (cervical, thoracic, sacral, and caudal vertebrae, pectoral elements, pelvic elements, forelimb and hindlimb elements, osteoderms). Crocodylus niloticus currently inhabits Madagascar but is locally extinct from this particular region; radiometric dating indicates an age of ∼460–310 years before present (BP). This specimen clearly represents a juvenile based on the extremely small size and open sutures/detac…
format: application/pdf
format: text/html
creator: Joshua C. Mathews
creator: Karen E. Samonds
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.2296
publisher: PeerJ Inc.
rights: © 2016 Mathews and Samonds
abstract: Madagascar’s subfossil record preserves a diverse community of animals including elephant birds, pygmy hippopotamus, giant lemurs, turtles, crocodiles, bats, rodents, and carnivorans. These fossil accumulations give us a window into the island’s past from 80,000 years ago to a mere few hundred years ago, recording the extinction of some groups and the persistence of others. The crocodylian subfossil record is limited to two taxa, Voay robustus and Crocodylus niloticus, found at sites distributed throughout the island. V. robustus is extinct while C. niloticus is still found on the island today, but whether these two species overlapped temporally, or if Voay was driven to extinction by competing with Crocodylus remains unknown. While their size and presumed behavior was similar to each other, nearly nothing is known about the growth and development of Voay, as the overwhelming majority of fossil specimens represent mature adult individuals. Here we describe a nearly complete juvenile crocodylian specimen from Anjohibe Cave, northwestern Madagascar. The specimen is referred to Crocodylus based on the presence of caviconchal recesses on the medial wall of the maxillae, and to C. niloticus based on the presence of an oval shaped internal choana, lack of rostral ornamentation and a long narrow snout. However, as there are currently no described juvenile specimens of Voay robustus, it is important to recognize that some of the defining characteristics of that genus may have changed through ontogeny. Elements include a nearly complete skull and many postcranial elements (cervical, thoracic, sacral, and caudal vertebrae, pectoral elements, pelvic elements, forelimb and hindlimb elements, osteoderms). Crocodylus niloticus currently inhabits Madagascar but is locally extinct from this particular region; radiometric dating indicates an age of ∼460–310 years before present (BP). This specimen clearly represents a juvenile based on the extremely small size and open sutures/detac…
bibliographic citation: Mathews et al. (2016) A juvenile subfossil crocodylian from Anjohibe Cave, Northwestern Madagascar. PeerJ 4:e2296 https://doi.org/10.7717/peerj.2296
date submitted: 2016-01-28
date accepted: 2016-07-06
issued: 2016-09-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mathews
  given name: Joshua C.
author list: Agent
  family name: Samonds
  given name: Karen E.
doi: 10.7717/peerj.2296
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-15
copyright: ©2016 Mathews and Samonds
attribution name: Mathews and Samonds

Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline
type: item
type: AcademicArticle
description: Streptococcus pneumoniae typically express one of 92 serologically distinct capsule polysaccharide (cps) types (serotypes). Some of these serotypes are closely related to each other; using the commercially available typing antisera, these are assigned to common serogroups containing types that show cross-reactivity. In this serotyping scheme, factor antisera are used to allocate serotypes within a serogroup, based on patterns of reactions. This serotyping method is technically demanding, requires considerable experience and the reading of the results can be subjective. This study describes the analysis of the S. pneumoniae capsular operon genetic sequence to determine serotype distinguishing features and the development, evaluation and verification of an automated whole genome sequence (WGS)-based serotyping bioinformatics tool, PneumoCaT (Pneumococcal Capsule Typing). Initially, WGS data from 871 S. pneumoniae isolates were mapped to reference cps locus sequences for the 92 serotypes. Thirty-two of 92 serotypes could be unambiguously identified based on sequence similarities within the cps operon. The remaining 60 were allocated to one of 20 ‘genogroups’ that broadly correspond to the immunologically defined serogroups. By comparing the cps reference sequences for each genogroup, unique molecular differences were determined for serotypes within 18 of the 20 genogroups and verified using the set of 871 isolates. This information was used to design a decision-tree style algorithm within the PneumoCaT bioinformatics tool to predict to serotype level for 89/94 (92 + 2 molecular types/subtypes) from WGS data and to serogroup level for serogroups 24 and 32, which currently comprise 2.1% of UK referred, invasive isolates submitted to the National Reference Laboratory (NRL), Public Health England (June 2014–July 2015). PneumoCaT was evaluated with an internal validation set of 2065 UK isolates covering 72/92 serotypes, including 19 non-typeable isolates and an external val…
format: application/pdf
format: text/html
creator: Georgia Kapatai
creator: Carmen L. Sheppard
creator: Ali Al-Shahib
creator: David J. Litt
creator: Anthony P. Underwood
creator: Timothy G. Harrison
creator: Norman K. Fry
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.2477
publisher: PeerJ Inc.
rights: © 2016 Kapatai et al.
abstract: Streptococcus pneumoniae typically express one of 92 serologically distinct capsule polysaccharide (cps) types (serotypes). Some of these serotypes are closely related to each other; using the commercially available typing antisera, these are assigned to common serogroups containing types that show cross-reactivity. In this serotyping scheme, factor antisera are used to allocate serotypes within a serogroup, based on patterns of reactions. This serotyping method is technically demanding, requires considerable experience and the reading of the results can be subjective. This study describes the analysis of the S. pneumoniae capsular operon genetic sequence to determine serotype distinguishing features and the development, evaluation and verification of an automated whole genome sequence (WGS)-based serotyping bioinformatics tool, PneumoCaT (Pneumococcal Capsule Typing). Initially, WGS data from 871 S. pneumoniae isolates were mapped to reference cps locus sequences for the 92 serotypes. Thirty-two of 92 serotypes could be unambiguously identified based on sequence similarities within the cps operon. The remaining 60 were allocated to one of 20 ‘genogroups’ that broadly correspond to the immunologically defined serogroups. By comparing the cps reference sequences for each genogroup, unique molecular differences were determined for serotypes within 18 of the 20 genogroups and verified using the set of 871 isolates. This information was used to design a decision-tree style algorithm within the PneumoCaT bioinformatics tool to predict to serotype level for 89/94 (92 + 2 molecular types/subtypes) from WGS data and to serogroup level for serogroups 24 and 32, which currently comprise 2.1% of UK referred, invasive isolates submitted to the National Reference Laboratory (NRL), Public Health England (June 2014–July 2015). PneumoCaT was evaluated with an internal validation set of 2065 UK isolates covering 72/92 serotypes, including 19 non-typeable isolates and an external val…
bibliographic citation: Kapatai et al. (2016) Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline. PeerJ 4:e2477 https://doi.org/10.7717/peerj.2477
date submitted: 2016-06-14
date accepted: 2016-08-23
issued: 2016-09-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kapatai
  given name: Georgia
author list: Agent
  family name: Sheppard
  given name: Carmen L.
author list: Agent
  family name: Al-Shahib
  given name: Ali
author list: Agent
  family name: Litt
  given name: David J.
author list: Agent
  family name: Underwood
  given name: Anthony P.
author list: Agent
  family name: Harrison
  given name: Timothy G.
author list: Agent
  family name: Fry
  given name: Norman K.
doi: 10.7717/peerj.2477
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-14
copyright: ©2016 Kapatai et al.
attribution name: Kapatai et al.

Gua Sha, a press-stroke treatment of the skin, boosts the immune response to intradermal vaccination
type: item
type: AcademicArticle
description: Objective The skin is an important immunological barrier of the body as well as an optimal route for vaccine administration. Gua Sha, which involves press-stroke treatment of the skin, is an effective folk therapy, widely accepted in East Asia, for various symptoms; however, the mechanisms underlying its therapeutic effects have not been clarified. We investigated the influence of Gua Sha on the immunological features of the skin. Methods Gua Sha was performed on BALB/c mice and the effects were evaluated using anatomical, histological, and cytometric methods as well as cytokine determination locally and systemically. The effect on intradermal vaccination was assessed with antigen-specific subtype antibody responses. Results Blood vessel expansion, erythrocyte extravasation, and increased ratios of immune active cells were observed in the skin tissue following the treatment. Pro-inflammatory cytokines were up-regulated, and immunosuppressive cytokines, down-regulated, in the treated and untreated skin and systemic circulation; no obvious variations were detected in case of anti-inflammatory cytokines. Interestingly, intradermal delivery of a model vaccine following Gua Sha induced about three-fold higher IgG titers with a more Th1-biased antibody subtype profile. Conclusion Gua Sha treatment can up-regulate the innate and adaptive immune functions of the skin and boost the response against intradermal antigens. Thus, Gua Sha may serve as a safe, inexpensive, and independent physical adjuvant for intradermal vaccination.
format: application/pdf
format: text/html
creator: Tingting Chen
creator: Ninghua Liu
creator: Jinxuan Liu
creator: Xiaoying Zhang
creator: Zhen Huang
creator: Yuhui Zang
creator: Jiangning Chen
creator: Lei Dong
creator: Junfeng Zhang
creator: Zhi Ding
subject: Dermatology
subject: Immunology
description: doi:10.7717/peerj.2451
publisher: PeerJ Inc.
rights: © 2016 Chen et al.
abstract: Objective The skin is an important immunological barrier of the body as well as an optimal route for vaccine administration. Gua Sha, which involves press-stroke treatment of the skin, is an effective folk therapy, widely accepted in East Asia, for various symptoms; however, the mechanisms underlying its therapeutic effects have not been clarified. We investigated the influence of Gua Sha on the immunological features of the skin. Methods Gua Sha was performed on BALB/c mice and the effects were evaluated using anatomical, histological, and cytometric methods as well as cytokine determination locally and systemically. The effect on intradermal vaccination was assessed with antigen-specific subtype antibody responses. Results Blood vessel expansion, erythrocyte extravasation, and increased ratios of immune active cells were observed in the skin tissue following the treatment. Pro-inflammatory cytokines were up-regulated, and immunosuppressive cytokines, down-regulated, in the treated and untreated skin and systemic circulation; no obvious variations were detected in case of anti-inflammatory cytokines. Interestingly, intradermal delivery of a model vaccine following Gua Sha induced about three-fold higher IgG titers with a more Th1-biased antibody subtype profile. Conclusion Gua Sha treatment can up-regulate the innate and adaptive immune functions of the skin and boost the response against intradermal antigens. Thus, Gua Sha may serve as a safe, inexpensive, and independent physical adjuvant for intradermal vaccination.
bibliographic citation: Chen et al. (2016) Gua Sha, a press-stroke treatment of the skin, boosts the immune response to intradermal vaccination. PeerJ 4:e2451 https://doi.org/10.7717/peerj.2451
date submitted: 2016-04-19
date accepted: 2016-08-16
issued: 2016-09-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Tingting
author list: Agent
  family name: Liu
  given name: Ninghua
author list: Agent
  family name: Liu
  given name: Jinxuan
author list: Agent
  family name: Zhang
  given name: Xiaoying
author list: Agent
  family name: Huang
  given name: Zhen
author list: Agent
  family name: Zang
  given name: Yuhui
author list: Agent
  family name: Chen
  given name: Jiangning
author list: Agent
  family name: Dong
  given name: Lei
author list: Agent
  family name: Zhang
  given name: Junfeng
author list: Agent
  family name: Ding
  given name: Zhi
doi: 10.7717/peerj.2451
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-14
copyright: ©2016 Chen et al.
attribution name: Chen et al.

Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls
type: item
type: AcademicArticle
description: Background The composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. To identify characteristics of diseased and healthy saliva we thus wanted to compare saliva metaproteomes from patients with periodontitis and dental caries to healthy individuals. Methods Stimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. The proteins in the saliva samples were subjected to denaturing buffer and digested enzymatically with LysC and trypsin. The resulting peptide mixtures were cleaned up by solid-phase extraction and separated online with 2 h gradients by nano-scale C18 reversed-phase chromatography connected to a mass spectrometer through an electrospray source. The eluting peptides were analyzed on a tandem mass spectrometer operated in data-dependent acquisition mode. Results We identified a total of 35,664 unique peptides from 4,161 different proteins, of which 1,946 and 2,090 were of bacterial and human origin, respectively. The human protein profiles displayed significant overexpression of the complement system and inflammatory markers in periodontitis and dental caries compared to healthy controls. Bacterial proteome profiles and functional annotation were very similar in health and disease. Conclusions Overexpression of proteins related to the complement system and inflammation seems to correlate with oral disease status. Similar bacterial proteomes in healthy and diseased individuals suggests that the salivary microbiota predominantly thrives in a planktonic state expressing no disease-associated characteristics of metabolic activity.
format: application/pdf
format: text/html
creator: Daniel Belstrøm
creator: Rosa R. Jersie-Christensen
creator: David Lyon
creator: Christian Damgaard
creator: Lars J. Jensen
creator: Palle Holmstrup
creator: Jesper V. Olsen
subject: Microbiology
subject: Dentistry
subject: Immunology
description: doi:10.7717/peerj.2433
publisher: PeerJ Inc.
rights: © 2016 Belstrøm et al.
abstract: Background The composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. To identify characteristics of diseased and healthy saliva we thus wanted to compare saliva metaproteomes from patients with periodontitis and dental caries to healthy individuals. Methods Stimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. The proteins in the saliva samples were subjected to denaturing buffer and digested enzymatically with LysC and trypsin. The resulting peptide mixtures were cleaned up by solid-phase extraction and separated online with 2 h gradients by nano-scale C18 reversed-phase chromatography connected to a mass spectrometer through an electrospray source. The eluting peptides were analyzed on a tandem mass spectrometer operated in data-dependent acquisition mode. Results We identified a total of 35,664 unique peptides from 4,161 different proteins, of which 1,946 and 2,090 were of bacterial and human origin, respectively. The human protein profiles displayed significant overexpression of the complement system and inflammatory markers in periodontitis and dental caries compared to healthy controls. Bacterial proteome profiles and functional annotation were very similar in health and disease. Conclusions Overexpression of proteins related to the complement system and inflammation seems to correlate with oral disease status. Similar bacterial proteomes in healthy and diseased individuals suggests that the salivary microbiota predominantly thrives in a planktonic state expressing no disease-associated characteristics of metabolic activity.
bibliographic citation: Belstrøm et al. (2016) Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls. PeerJ 4:e2433 https://doi.org/10.7717/peerj.2433
date submitted: 2016-06-29
date accepted: 2016-08-12
issued: 2016-09-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Belstrøm
  given name: Daniel
author list: Agent
  family name: Jersie-Christensen
  given name: Rosa R.
author list: Agent
  family name: Lyon
  given name: David
author list: Agent
  family name: Damgaard
  given name: Christian
author list: Agent
  family name: Jensen
  given name: Lars J.
author list: Agent
  family name: Holmstrup
  given name: Palle
author list: Agent
  family name: Olsen
  given name: Jesper V.
doi: 10.7717/peerj.2433
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-14
copyright: © 2016 Belstrøm et al.
attribution name: Belstrøm et al.

Resilience does not explain the dissociation between chronic pain and physical activity in South Africans living with HIV
type: item
type: AcademicArticle
description: Pain burden is high in people living with HIV (PLWH), but the effect of this pain on functionality is equivocal. Resilience, the ability to cope with adversity, may promote adaptation to pain, so we hypothesised that higher resilience would correlate with less pain-related impairment of activity. We recruited 197 black South African PLWH, 99 with chronic pain (CP) and 98 patients without. We measured pain intensity and interference using the Brief Pain Inventory, and resilience using the Resilience Scale. Participants were generally highly resilient. Greater resilience correlated with better health-related quality of life, but not with pain intensity or interference. We also measured physical activity objectively, by actigraphy, in a subset of patients (37 with chronic pain and 31 without chronic pain), who wore accelerometers for two weeks. There was no difference in duration or intensity of activity between those with and without pain, and activity was not associated with resilience. In this sample, pain was not associated with altered physical activity. Resilience did not explain differences in pain intensity or pain interference but was associated with improved quality of life. Financial stresses and the fear of HIV stigma may have driven patients to conceal pain and to suppress its expected impairment of activity.
format: application/pdf
format: text/html
creator: Antonia L. Wadley
creator: Duncan Mitchell
creator: Peter R. Kamerman
subject: Anesthesiology and Pain Management
subject: HIV
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2464
publisher: PeerJ Inc.
rights: © 2016 Wadley et al.
abstract: Pain burden is high in people living with HIV (PLWH), but the effect of this pain on functionality is equivocal. Resilience, the ability to cope with adversity, may promote adaptation to pain, so we hypothesised that higher resilience would correlate with less pain-related impairment of activity. We recruited 197 black South African PLWH, 99 with chronic pain (CP) and 98 patients without. We measured pain intensity and interference using the Brief Pain Inventory, and resilience using the Resilience Scale. Participants were generally highly resilient. Greater resilience correlated with better health-related quality of life, but not with pain intensity or interference. We also measured physical activity objectively, by actigraphy, in a subset of patients (37 with chronic pain and 31 without chronic pain), who wore accelerometers for two weeks. There was no difference in duration or intensity of activity between those with and without pain, and activity was not associated with resilience. In this sample, pain was not associated with altered physical activity. Resilience did not explain differences in pain intensity or pain interference but was associated with improved quality of life. Financial stresses and the fear of HIV stigma may have driven patients to conceal pain and to suppress its expected impairment of activity.
bibliographic citation: Wadley et al. (2016) Resilience does not explain the dissociation between chronic pain and physical activity in South Africans living with HIV. PeerJ 4:e2464 https://doi.org/10.7717/peerj.2464
date submitted: 2016-05-06
date accepted: 2016-08-19
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wadley
  given name: Antonia L.
author list: Agent
  family name: Mitchell
  given name: Duncan
author list: Agent
  family name: Kamerman
  given name: Peter R.
doi: 10.7717/peerj.2464
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: © 2016 Wadley et al.
attribution name: Wadley et al.

Lowland tapir distribution and habitat loss in South America
type: item
type: AcademicArticle
description: The development of species distribution models (SDMs) can help conservation efforts by generating potential distributions and identifying areas of high environmental suitability for protection. Our study presents a distribution and habitat map for lowland tapir in South America. We also describe the potential habitat suitability of various geographical regions and habitat loss, inside and outside of protected areas network. Two different SDM approaches, MAXENT and ENFA, produced relative different Habitat Suitability Maps for the lowland tapir. While MAXENT was efficient at identifying areas as suitable or unsuitable, it was less efficient (when compared to the results by ENFA) at identifying the gradient of habitat suitability. MAXENT is a more multifaceted technique that establishes more complex relationships between dependent and independent variables. Our results demonstrate that for at least one species, the lowland tapir, the use of a simple consensual approach (average of ENFA and MAXENT models outputs) better reflected its current distribution patterns. The Brazilian ecoregions have the highest habitat loss for the tapir. Cerrado and Atlantic Forest account for nearly half (48.19%) of the total area lost. The Amazon region contains the largest area under protection, and the most extensive remaining habitat for the tapir, but also showed high levels of habitat loss outside protected areas, which increases the importance of support for proper management.
format: application/pdf
format: text/html
creator: Jose Luis Passos Cordeiro
creator: José M.V. Fragoso
creator: Danielle Crawshaw
creator: Luiz Flamarion B. Oliveira
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.2456
publisher: PeerJ Inc.
rights: © 2016 Cordeiro et al.
abstract: The development of species distribution models (SDMs) can help conservation efforts by generating potential distributions and identifying areas of high environmental suitability for protection. Our study presents a distribution and habitat map for lowland tapir in South America. We also describe the potential habitat suitability of various geographical regions and habitat loss, inside and outside of protected areas network. Two different SDM approaches, MAXENT and ENFA, produced relative different Habitat Suitability Maps for the lowland tapir. While MAXENT was efficient at identifying areas as suitable or unsuitable, it was less efficient (when compared to the results by ENFA) at identifying the gradient of habitat suitability. MAXENT is a more multifaceted technique that establishes more complex relationships between dependent and independent variables. Our results demonstrate that for at least one species, the lowland tapir, the use of a simple consensual approach (average of ENFA and MAXENT models outputs) better reflected its current distribution patterns. The Brazilian ecoregions have the highest habitat loss for the tapir. Cerrado and Atlantic Forest account for nearly half (48.19%) of the total area lost. The Amazon region contains the largest area under protection, and the most extensive remaining habitat for the tapir, but also showed high levels of habitat loss outside protected areas, which increases the importance of support for proper management.
bibliographic citation: Cordeiro et al. (2016) Lowland tapir distribution and habitat loss in South America. PeerJ 4:e2456 https://doi.org/10.7717/peerj.2456
date submitted: 2015-12-09
date accepted: 2016-08-17
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cordeiro
  given name: Jose Luis Passos
author list: Agent
  family name: Fragoso
  given name: José M.V.
author list: Agent
  family name: Crawshaw
  given name: Danielle
author list: Agent
  family name: Oliveira
  given name: Luiz Flamarion B.
doi: 10.7717/peerj.2456
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: ©2016 Cordeiro et al.
attribution name: Cordeiro et al.

An association between feather damaging behavior and corticosterone metabolite excretion in captive African grey parrots (Psittacus erithacus)
type: item
type: AcademicArticle
description: Background African grey parrots (Psittacus erithacus) are kept as pets and are frequently hand-reared. It has been observed that hand-reared African grey parrots may develop behavioral disorders such as feather damaging behavior (FDB). It is well known that chronic stress is involved in behavioral disorders in captive parrots. The main glucocorticoid in birds is corticosterone; its quantification provides information about adrenocortical activity and is considered to be a reliable indicator of stress levels in birds. We analyzed the differences in the excretion of corticosterone metabolites (CM) in the droppings of African grey parrots characterized by: 1. different rearing histories (parent rearing vs. hand rearing); and 2. the presence or absence of FDB in hand-reared parrots. Methods A total of 82 African grey parrots that were kept in captivity were considered. According to breeding methods, three groups of birds were defined: 1. The parent-reared (PR) parrots included birds kept in pairs (n = 30 pairs) with a conspecific partner of the opposite sex. All of these birds were healthy and never showed FDB signs; 2. The healthy hand-reared parrots (H-HR) included pet parrots individually kept, that were hand-reared and did not display any sign of FDB (n = 11, 7 males and 4 females); 3. The FDB hand-reared parrot (FDB-HR) included pet parrots individually kept, that were hand-reared and displayed FDB (n = 11, 7 males and 4 females). Droppings were collected in the morning over three alternating days in autumn 2014 and spring 2015. The CM were determined using a multi-species corticosterone enzyme immunoassay kit. Split-plot repeated-measure ANOVA was used to examine any differences using group, season and group × season as the main factors. Results Different quantities of CM in droppings were found for the three groups. The mean CM value was 587 ng/g in the PR parrots, 494 ng/g in the H-HR parrots and 1,744 ng/g in the FDB-HR parrots, irrespective of the season. The …
format: application/pdf
format: text/html
creator: Pierluca Costa
creator: Elisabetta Macchi
creator: Emanuela Valle
creator: Michele De Marco
creator: Daniele M. Nucera
creator: Laura Gasco
creator: Achille Schiavone
subject: Animal Behavior
subject: Veterinary Medicine
description: doi:10.7717/peerj.2462
publisher: PeerJ Inc.
rights: © 2016 Costa et al.
abstract: Background African grey parrots (Psittacus erithacus) are kept as pets and are frequently hand-reared. It has been observed that hand-reared African grey parrots may develop behavioral disorders such as feather damaging behavior (FDB). It is well known that chronic stress is involved in behavioral disorders in captive parrots. The main glucocorticoid in birds is corticosterone; its quantification provides information about adrenocortical activity and is considered to be a reliable indicator of stress levels in birds. We analyzed the differences in the excretion of corticosterone metabolites (CM) in the droppings of African grey parrots characterized by: 1. different rearing histories (parent rearing vs. hand rearing); and 2. the presence or absence of FDB in hand-reared parrots. Methods A total of 82 African grey parrots that were kept in captivity were considered. According to breeding methods, three groups of birds were defined: 1. The parent-reared (PR) parrots included birds kept in pairs (n = 30 pairs) with a conspecific partner of the opposite sex. All of these birds were healthy and never showed FDB signs; 2. The healthy hand-reared parrots (H-HR) included pet parrots individually kept, that were hand-reared and did not display any sign of FDB (n = 11, 7 males and 4 females); 3. The FDB hand-reared parrot (FDB-HR) included pet parrots individually kept, that were hand-reared and displayed FDB (n = 11, 7 males and 4 females). Droppings were collected in the morning over three alternating days in autumn 2014 and spring 2015. The CM were determined using a multi-species corticosterone enzyme immunoassay kit. Split-plot repeated-measure ANOVA was used to examine any differences using group, season and group × season as the main factors. Results Different quantities of CM in droppings were found for the three groups. The mean CM value was 587 ng/g in the PR parrots, 494 ng/g in the H-HR parrots and 1,744 ng/g in the FDB-HR parrots, irrespective of the season. The …
bibliographic citation: Costa et al. (2016) An association between feather damaging behavior and corticosterone metabolite excretion in captive African grey parrots (Psittacus erithacus). PeerJ 4:e2462 https://doi.org/10.7717/peerj.2462
date submitted: 2016-04-20
date accepted: 2016-08-18
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Costa
  given name: Pierluca
author list: Agent
  family name: Macchi
  given name: Elisabetta
author list: Agent
  family name: Valle
  given name: Emanuela
author list: Agent
  family name: De Marco
  given name: Michele
author list: Agent
  family name: Nucera
  given name: Daniele M.
author list: Agent
  family name: Gasco
  given name: Laura
author list: Agent
  family name: Schiavone
  given name: Achille
doi: 10.7717/peerj.2462
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: ©2016 Costa et al.
attribution name: Costa et al.

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