PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: How to normalize metatranscriptomic count data for differential expression analysis
items: Exploring the psychological health of emergency dispatch centre operatives: a systematic review and narrative synthesis
items: Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI
items: Tolerance: the forgotten child of plant resistance
items: L1 and L2 reading skills in Dutch adolescents with a familial risk of dyslexia
items: Investigating the level of agreement of two positioning protocols when using dual energy X-ray absorptiometry in the assessment of body composition
items: Tumor-infiltrating CD8+ lymphocytes predict different clinical outcomes in organ- and non-organ-confined urothelial carcinoma of the bladder following radical cystectomy
items: A retrospective study: does upper airway morphology differ between non-positional and positional obstructive sleep apnea?
items: Neurodynamic mobilization and foam rolling improved delayed-onset muscle soreness in a healthy adult population: a randomized controlled clinical trial
items: Multigene phylogeny of the scyphozoan jellyfish family Pelagiidae reveals that the common U.S. Atlantic sea nettle comprises two distinct species (Chrysaora quinquecirrha and C. chesapeakei)

How to normalize metatranscriptomic count data for differential expression analysis
type: item
type: AcademicArticle
description: Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. Methods We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count data. For taxon-specific scaling and recombination of scaled counts we provide a simple R script. Results When applying transcriptomic tools for differential expression analysis directly to metatranscriptomic data with an organism-independent (global) scaling of counts the resulting differences may be difficult to interpret. The differences may correspond to changing functional profiles of the contributing organisms but may also result from a variation of taxonomic abundances. Taxon-specific scaling eliminates this variation and therefore the resulting differences actually reflect a different behavior of organisms under changing conditions. In simulation studies we show that the divergence between results from global and taxon-specific scaling can be drastic. In particular, the variation of organism abundances can imply a considerable increase of significant differences with global scaling. Also, on real metatranscriptomic data, the predictions from taxon-specific and…
format: application/pdf
format: text/html
creator: Heiner Klingenberg
creator: Peter Meinicke
subject: Bioinformatics
subject: Statistics
description: doi:10.7717/peerj.3859
publisher: PeerJ Inc.
rights: © 2017 Klingenberg and Meinicke
abstract: Background Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression analysis in metatranscriptomics. Methods We propose a model for differential expression in metatranscriptomics that explicitly accounts for variations in the taxonomic composition of transcripts across different samples. As a main consequence the correct normalization of metatranscriptomic count data under this model requires the taxonomic separation of the data into organism-specific bins. Then the taxon-specific scaling of organism profiles yields a valid normalization and allows us to recombine the scaled profiles into a metatranscriptomic count matrix. This matrix can then be analyzed with statistical tools for transcriptomic count data. For taxon-specific scaling and recombination of scaled counts we provide a simple R script. Results When applying transcriptomic tools for differential expression analysis directly to metatranscriptomic data with an organism-independent (global) scaling of counts the resulting differences may be difficult to interpret. The differences may correspond to changing functional profiles of the contributing organisms but may also result from a variation of taxonomic abundances. Taxon-specific scaling eliminates this variation and therefore the resulting differences actually reflect a different behavior of organisms under changing conditions. In simulation studies we show that the divergence between results from global and taxon-specific scaling can be drastic. In particular, the variation of organism abundances can imply a considerable increase of significant differences with global scaling. Also, on real metatranscriptomic data, the predictions from taxon-specific and…
bibliographic citation: Klingenberg et al. (2017) How to normalize metatranscriptomic count data for differential expression analysis. PeerJ 5:e3859 https://doi.org/10.7717/peerj.3859
date submitted: 2017-05-10
date accepted: 2017-09-06
issued: 2017-10-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klingenberg
  given name: Heiner
author list: Agent
  family name: Meinicke
  given name: Peter
doi: 10.7717/peerj.3859
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-17
copyright: ©2017 Klingenberg and Meinicke
attribution name: Klingenberg and Meinicke

Exploring the psychological health of emergency dispatch centre operatives: a systematic review and narrative synthesis
type: item
type: AcademicArticle
description: Background The study objective was to investigate and synthesize available evidence relating to the psychological health of Emergency Dispatch Centre (EDC) operatives, and to identify key stressors experienced by EDC operatives. Methods Eight electronic databases (Embase, PubMed, Medline, CINAHL, PsycInfo, PsycArticles, The Psychology and Behavioural Sciences Collection, and Google Scholar) were searched. All study designs were included, and no date limits were set. Studies were included if they were published in English, and explored the psychological health of any EDC operatives, across fire, police, and emergency medical services. Studies were excluded if they related solely to other emergency workers, such as police officers or paramedics. Methodological quality of included studies was assessed using checklists adapted from the Critical Appraisal Skills Programme. A narrative synthesis was conducted, using thematic analysis. Results A total of 16 articles were included in the review. Two overarching themes were identified during the narrative synthesis: ‘Organisational and Operational Factors’ and ‘Interactions with Others’. Stressors identified included being exposed to traumatic calls, lacking control over high workload, and working in under-resourced and pressured environments. Lack of support from management and providing an emotionally demanding service were additional sources of stress. Peer support and social support from friends and family were helpful in managing work-related stress. Discussion EDC operatives experience stress as a result of their work, which appears to be related to negative psychological health outcomes. Future research should explore the long-term effects of this stress, and the potential for workplace interventions to alleviate the negative impacts on psychological health. PROSPERO Registration Number CRD42014010806.
format: application/pdf
format: text/html
creator: Sarah E. Golding
creator: Claire Horsfield
creator: Annette Davies
creator: Bernadette Egan
creator: Martyn Jones
creator: Mary Raleigh
creator: Patricia Schofield
creator: Allison Squires
creator: Kath Start
creator: Tom Quinn
creator: Mark Cropley
subject: Emergency and Critical Care
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3735
publisher: PeerJ Inc.
rights: © 2017 Golding et al.
abstract: Background The study objective was to investigate and synthesize available evidence relating to the psychological health of Emergency Dispatch Centre (EDC) operatives, and to identify key stressors experienced by EDC operatives. Methods Eight electronic databases (Embase, PubMed, Medline, CINAHL, PsycInfo, PsycArticles, The Psychology and Behavioural Sciences Collection, and Google Scholar) were searched. All study designs were included, and no date limits were set. Studies were included if they were published in English, and explored the psychological health of any EDC operatives, across fire, police, and emergency medical services. Studies were excluded if they related solely to other emergency workers, such as police officers or paramedics. Methodological quality of included studies was assessed using checklists adapted from the Critical Appraisal Skills Programme. A narrative synthesis was conducted, using thematic analysis. Results A total of 16 articles were included in the review. Two overarching themes were identified during the narrative synthesis: ‘Organisational and Operational Factors’ and ‘Interactions with Others’. Stressors identified included being exposed to traumatic calls, lacking control over high workload, and working in under-resourced and pressured environments. Lack of support from management and providing an emotionally demanding service were additional sources of stress. Peer support and social support from friends and family were helpful in managing work-related stress. Discussion EDC operatives experience stress as a result of their work, which appears to be related to negative psychological health outcomes. Future research should explore the long-term effects of this stress, and the potential for workplace interventions to alleviate the negative impacts on psychological health. PROSPERO Registration Number CRD42014010806.
bibliographic citation: Golding et al. (2017) Exploring the psychological health of emergency dispatch centre operatives: a systematic review and narrative synthesis. PeerJ 5:e3735 https://doi.org/10.7717/peerj.3735
date submitted: 2017-04-08
date accepted: 2017-08-04
issued: 2017-10-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Golding
  given name: Sarah E.
author list: Agent
  family name: Horsfield
  given name: Claire
author list: Agent
  family name: Davies
  given name: Annette
author list: Agent
  family name: Egan
  given name: Bernadette
author list: Agent
  family name: Jones
  given name: Martyn
author list: Agent
  family name: Raleigh
  given name: Mary
author list: Agent
  family name: Schofield
  given name: Patricia
author list: Agent
  family name: Squires
  given name: Allison
author list: Agent
  family name: Start
  given name: Kath
author list: Agent
  family name: Quinn
  given name: Tom
author list: Agent
  family name: Cropley
  given name: Mark
doi: 10.7717/peerj.3735
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-17
copyright: ©2017 Golding et al.
attribution name: Golding et al.

Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI
type: item
type: AcademicArticle
description: Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island.
format: application/pdf
format: text/html
creator: Miranda H. Hengy
creator: Dean J. Horton
creator: Donald G. Uzarski
creator: Deric R. Learman
subject: Biodiversity
subject: Ecology
subject: Environmental Sciences
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.3937
publisher: PeerJ Inc.
rights: © 2017 Hengy et al.
abstract: Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island.
bibliographic citation: Hengy et al. (2017) Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI. PeerJ 5:e3937 https://doi.org/10.7717/peerj.3937
date submitted: 2017-06-13
date accepted: 2017-09-26
issued: 2017-10-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hengy
  given name: Miranda H.
author list: Agent
  family name: Horton
  given name: Dean J.
author list: Agent
  family name: Uzarski
  given name: Donald G.
author list: Agent
  family name: Learman
  given name: Deric R.
doi: 10.7717/peerj.3937
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-16
copyright: ©2017 Hengy et al.
attribution name: Hengy et al.

Tolerance: the forgotten child of plant resistance
type: item
type: AcademicArticle
description: Plant resistance against insect herbivory has greatly focused on antibiosis, whereby the plant has a deleterious effect on the herbivore, and antixenosis, whereby the plant is able to direct the herbivore away from it. Although these two types of resistance may reduce injury and yield loss, they can produce selection pressures on insect herbivores that lead to pest resistance. Tolerance, on the other hand, is a more sustainable pest management strategy because it involves only a plant response and therefore does not cause evolution of resistance in target pest populations. Despite its attractive attributes, tolerance has been poorly studied and understood. In this critical, interpretive review, we discuss tolerance to insect herbivory and the biological and socioeconomic factors that have limited its use in plant resistance and integrated pest management. First, tolerance is difficult to identify, and the mechanisms conferring it are poorly understood. Second, the genetics of tolerance are mostly unknown. Third, several obstacles hinder the establishment of high-throughput phenotyping methods for large-scale screening of tolerance. Fourth, tolerance has received little attention from entomologists because, for most, their primary interest, research training, and funding opportunities are in mechanisms which affect pest biology, not plant biology. Fifth, the efforts of plant resistance are directed at controlling pest populations rather than managing plant stress. We conclude this paper by discussing future research and development activities.
format: application/pdf
format: text/html
creator: Robert K.D. Peterson
creator: Andrea C. Varella
creator: Leon G. Higley
subject: Agricultural Science
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.3934
publisher: PeerJ Inc.
rights: © 2017 Peterson et al.
abstract: Plant resistance against insect herbivory has greatly focused on antibiosis, whereby the plant has a deleterious effect on the herbivore, and antixenosis, whereby the plant is able to direct the herbivore away from it. Although these two types of resistance may reduce injury and yield loss, they can produce selection pressures on insect herbivores that lead to pest resistance. Tolerance, on the other hand, is a more sustainable pest management strategy because it involves only a plant response and therefore does not cause evolution of resistance in target pest populations. Despite its attractive attributes, tolerance has been poorly studied and understood. In this critical, interpretive review, we discuss tolerance to insect herbivory and the biological and socioeconomic factors that have limited its use in plant resistance and integrated pest management. First, tolerance is difficult to identify, and the mechanisms conferring it are poorly understood. Second, the genetics of tolerance are mostly unknown. Third, several obstacles hinder the establishment of high-throughput phenotyping methods for large-scale screening of tolerance. Fourth, tolerance has received little attention from entomologists because, for most, their primary interest, research training, and funding opportunities are in mechanisms which affect pest biology, not plant biology. Fifth, the efforts of plant resistance are directed at controlling pest populations rather than managing plant stress. We conclude this paper by discussing future research and development activities.
bibliographic citation: Peterson et al. (2017) Tolerance: the forgotten child of plant resistance. PeerJ 5:e3934 https://doi.org/10.7717/peerj.3934
date submitted: 2017-07-20
date accepted: 2017-09-26
issued: 2017-10-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Peterson
  given name: Robert K.D.
author list: Agent
  family name: Varella
  given name: Andrea C.
author list: Agent
  family name: Higley
  given name: Leon G.
doi: 10.7717/peerj.3934
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-16
copyright: ©2017 Peterson et al.
attribution name: Peterson et al.

L1 and L2 reading skills in Dutch adolescents with a familial risk of dyslexia
type: item
type: AcademicArticle
description: Background The present study investigated differences in reading and spelling outcomes in Dutch and English as a second language (ESL) in adolescents with a high familial risk of dyslexia, of whom some have developed dyslexia (HRDys) while others have not (HRnonDys), in comparison to a low familial risk control group without dyslexia (LRnonDys). This allowed us to investigate the persistence of dyslexia in the first language (L1) and the effect of dyslexia on the second language (L2), which has, in this case, a lower orthographic transparency. Furthermore, the inclusion of the HRnonDys group allowed us to investigate the continuity of the familial risk of dyslexia, as previous studies observed that the HRnonDys group often scores in between the HRDys and LRnonDys group, and whether these readers without reading deficits in Dutch, have more reading difficulties in ESL. Methods The data of three groups of adolescents were analyzed; 27 LRnonDys, 25 HRdys 25 HRnonDys. The mean age was 14;1 years; months, and 37 were male. All were native speakers of Dutch, attended regular secondary education (grade 7–10), and were non-native speakers of English. Using MANOVA the groups were compared on Dutch and English word reading fluency (WRF), spelling and vocabulary, Dutch pseudoword and loanword reading fluency, phonological awareness (PA), rapid automatized naming (RAN), and verbal short term and working memory. A repeated measures ANOVA was used to compare English and Dutch WRF, spelling and vocabulary directly within the three groups. Results The analyses revealed that the HRDys group had a deficit in both reading and spelling in Dutch and ESL. They also performed poorer than the LRnonDys group on all other measures. Effect sizes were especially large for pseudoword reading and the reaction times during the PA task. The HRnonDys group scored generally poorer than the LRnonDys group but this difference was only significant for Dutch pseudoword reading, PA reaction times and ver…
format: application/pdf
format: text/html
creator: Ellie R.H. van Setten
creator: Wim Tops
creator: Britt E. Hakvoort
creator: Aryan van der Leij
creator: Natasha M. Maurits
creator: Ben A.M. Maassen
subject: Cognitive Disorders
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.3895
publisher: PeerJ Inc.
rights: © 2017 van Setten et al.
abstract: Background The present study investigated differences in reading and spelling outcomes in Dutch and English as a second language (ESL) in adolescents with a high familial risk of dyslexia, of whom some have developed dyslexia (HRDys) while others have not (HRnonDys), in comparison to a low familial risk control group without dyslexia (LRnonDys). This allowed us to investigate the persistence of dyslexia in the first language (L1) and the effect of dyslexia on the second language (L2), which has, in this case, a lower orthographic transparency. Furthermore, the inclusion of the HRnonDys group allowed us to investigate the continuity of the familial risk of dyslexia, as previous studies observed that the HRnonDys group often scores in between the HRDys and LRnonDys group, and whether these readers without reading deficits in Dutch, have more reading difficulties in ESL. Methods The data of three groups of adolescents were analyzed; 27 LRnonDys, 25 HRdys 25 HRnonDys. The mean age was 14;1 years; months, and 37 were male. All were native speakers of Dutch, attended regular secondary education (grade 7–10), and were non-native speakers of English. Using MANOVA the groups were compared on Dutch and English word reading fluency (WRF), spelling and vocabulary, Dutch pseudoword and loanword reading fluency, phonological awareness (PA), rapid automatized naming (RAN), and verbal short term and working memory. A repeated measures ANOVA was used to compare English and Dutch WRF, spelling and vocabulary directly within the three groups. Results The analyses revealed that the HRDys group had a deficit in both reading and spelling in Dutch and ESL. They also performed poorer than the LRnonDys group on all other measures. Effect sizes were especially large for pseudoword reading and the reaction times during the PA task. The HRnonDys group scored generally poorer than the LRnonDys group but this difference was only significant for Dutch pseudoword reading, PA reaction times and ver…
bibliographic citation: van Setten et al. (2017) L1 and L2 reading skills in Dutch adolescents with a familial risk of dyslexia. PeerJ 5:e3895 https://doi.org/10.7717/peerj.3895
date submitted: 2017-04-25
date accepted: 2017-09-15
issued: 2017-10-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: van Setten
  given name: Ellie R.H.
author list: Agent
  family name: Tops
  given name: Wim
author list: Agent
  family name: Hakvoort
  given name: Britt E.
author list: Agent
  family name: van der Leij
  given name: Aryan
author list: Agent
  family name: Maurits
  given name: Natasha M.
author list: Agent
  family name: Maassen
  given name: Ben A.M.
doi: 10.7717/peerj.3895
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-16
copyright: ©2017 van Setten et al.
attribution name: van Setten et al.

Investigating the level of agreement of two positioning protocols when using dual energy X-ray absorptiometry in the assessment of body composition
type: item
type: AcademicArticle
description: Background Dual energy X-ray absorptiometry (DXA) is a commonly used instrument for analysing segmental body composition (BC). The information from the scan guides the clinician in the treatment of conditions such as obesity and can be used to monitor recovery of lean mass following injury. Two commonly used DXA positioning protocols have been identified—the Nana positioning protocol and the National Health and Nutrition Examination Survey (NHANES). Both protocols have been shown to be reliable. However, only one study has assessed the level of agreement between the protocols and ascertained the participants’ preference of protocol based upon comfort. Given the paucity of research in the field and the growing use of DXA in both healthy and pathological populations further research determining the most appropriate positioning protocol is warranted. Therefore, the aims of this study were to assess the level of agreement between results from the NHANES protocol and Nana protocol, and the participants’ preference of protocol based on comfort. Methods Thirty healthy participants (15 males, 15 females, aged 23–59 years) volunteered to participate in this study. These participants underwent two whole body DXA scans in a single morning (Nana positioning protocol and NHANES positioning protocol), in a randomised order. Each participant attended for scanning wearing minimal clothing and having fasted overnight, refrained from exercise in the past 24 h and voided their bladders. Level of agreement, comparing NAHNES to Nana protocol was assessed using an intra-class correlation coefficient (ICC), concordance correlation coefficient (CCC) and percentage change in mean. Limit of agreement comparing the two protocols were assessed using plots, mean difference and confidence limits. Participants were asked to indicate the protocol they found most comfortable. Results When assessing level of agreement between protocols both the ICC and CCC scores were very high and ranged from 0.987…
format: application/pdf
format: text/html
creator: Flinn Shiel
creator: Carl Persson
creator: Vini Simas
creator: James Furness
creator: Mike Climstein
creator: Ben Schram
subject: Drugs and Devices
subject: Epidemiology
subject: Kinesiology
subject: Nutrition
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.3880
publisher: PeerJ Inc.
rights: © 2017 Shiel et al.
abstract: Background Dual energy X-ray absorptiometry (DXA) is a commonly used instrument for analysing segmental body composition (BC). The information from the scan guides the clinician in the treatment of conditions such as obesity and can be used to monitor recovery of lean mass following injury. Two commonly used DXA positioning protocols have been identified—the Nana positioning protocol and the National Health and Nutrition Examination Survey (NHANES). Both protocols have been shown to be reliable. However, only one study has assessed the level of agreement between the protocols and ascertained the participants’ preference of protocol based upon comfort. Given the paucity of research in the field and the growing use of DXA in both healthy and pathological populations further research determining the most appropriate positioning protocol is warranted. Therefore, the aims of this study were to assess the level of agreement between results from the NHANES protocol and Nana protocol, and the participants’ preference of protocol based on comfort. Methods Thirty healthy participants (15 males, 15 females, aged 23–59 years) volunteered to participate in this study. These participants underwent two whole body DXA scans in a single morning (Nana positioning protocol and NHANES positioning protocol), in a randomised order. Each participant attended for scanning wearing minimal clothing and having fasted overnight, refrained from exercise in the past 24 h and voided their bladders. Level of agreement, comparing NAHNES to Nana protocol was assessed using an intra-class correlation coefficient (ICC), concordance correlation coefficient (CCC) and percentage change in mean. Limit of agreement comparing the two protocols were assessed using plots, mean difference and confidence limits. Participants were asked to indicate the protocol they found most comfortable. Results When assessing level of agreement between protocols both the ICC and CCC scores were very high and ranged from 0.987…
bibliographic citation: Shiel et al. (2017) Investigating the level of agreement of two positioning protocols when using dual energy X-ray absorptiometry in the assessment of body composition. PeerJ 5:e3880 https://doi.org/10.7717/peerj.3880
date submitted: 2017-05-16
date accepted: 2017-09-12
issued: 2017-10-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shiel
  given name: Flinn
author list: Agent
  family name: Persson
  given name: Carl
author list: Agent
  family name: Simas
  given name: Vini
author list: Agent
  family name: Furness
  given name: James
author list: Agent
  family name: Climstein
  given name: Mike
author list: Agent
  family name: Schram
  given name: Ben
doi: 10.7717/peerj.3880
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-16
copyright: ©2017 Shiel et al.
attribution name: Shiel et al.

Tumor-infiltrating CD8+ lymphocytes predict different clinical outcomes in organ- and non-organ-confined urothelial carcinoma of the bladder following radical cystectomy
type: item
type: AcademicArticle
description: Tumor-infiltrating lymphocytes (TILs) are associated with better clinical outcomes in many tumors. TILs represent a cell-mediated immune response against the carcinoma. CD8+ TILs are a crucial component of cell-mediated immunity. The significance of CD8+ TILs has not been reported respectively in organ- and non-organ-confined urothelial carcinoma (UC) of the bladder. We explored the prognostic value of CD8+ TILs in the two groups. The presence of CD8+ TILs was assessed by immunohistochemical staining of whole tissue sections from 75 organ and 51 non-organ-confined disease patients with long-term follow-up, and its correlation with clinicopathological features and overall survival (OS) was determined. The CD8+ TIL immunohistochemical staining score was 0 (<1%), 1 (≥1%), 2 (≥5%), or 3 (≥10%) based on the percentage of positively stained cells out of total cells. A patient was considered CD8 negative if the score was 0. There were no associations between CD8+ TILs and age, sex, nuclear grade, and adjuvant or neoadjuvant chemotherapy in organ- and non-organ-confined disease. The presence of CD8+ TILs was seen more frequently in pTa-1 than pT2 stage (p = 0.033) in organ-confined disease. No associations between CD8+ TILs and pT stage, pN stage were found in non-organ-confined disease. CD8+ TILs were associated with better OS (log-rank test, P = 0.036) in non-organ-confined disease, but with poorer OS (log-rank test, P = 0.040) in organ-confined disease by the Kaplan–Meier method. In multivariate analysis, CD8+ TILs were an independent favorable prognostic factor in non-organ-confined disease, but were an independent unfavorable prognostic factor in organ-confined disease. These results suggest that CD8+ TILs have clinically significant anti-tumor activity in non-organ-confined disease, but may have pro-tumor activity in organ-confined disease. Therefore, we should be cautious if CD8+ TILs are aimed to be exploited in the treatment of bladder cancer.
format: application/pdf
format: text/html
creator: Shiqiang Zhang
creator: Jun Wang
creator: Xinyu Zhang
creator: Fangjian Zhou
subject: Immunology
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.3921
publisher: PeerJ Inc.
rights: © 2017 Zhang et al.
abstract: Tumor-infiltrating lymphocytes (TILs) are associated with better clinical outcomes in many tumors. TILs represent a cell-mediated immune response against the carcinoma. CD8+ TILs are a crucial component of cell-mediated immunity. The significance of CD8+ TILs has not been reported respectively in organ- and non-organ-confined urothelial carcinoma (UC) of the bladder. We explored the prognostic value of CD8+ TILs in the two groups. The presence of CD8+ TILs was assessed by immunohistochemical staining of whole tissue sections from 75 organ and 51 non-organ-confined disease patients with long-term follow-up, and its correlation with clinicopathological features and overall survival (OS) was determined. The CD8+ TIL immunohistochemical staining score was 0 (<1%), 1 (≥1%), 2 (≥5%), or 3 (≥10%) based on the percentage of positively stained cells out of total cells. A patient was considered CD8 negative if the score was 0. There were no associations between CD8+ TILs and age, sex, nuclear grade, and adjuvant or neoadjuvant chemotherapy in organ- and non-organ-confined disease. The presence of CD8+ TILs was seen more frequently in pTa-1 than pT2 stage (p = 0.033) in organ-confined disease. No associations between CD8+ TILs and pT stage, pN stage were found in non-organ-confined disease. CD8+ TILs were associated with better OS (log-rank test, P = 0.036) in non-organ-confined disease, but with poorer OS (log-rank test, P = 0.040) in organ-confined disease by the Kaplan–Meier method. In multivariate analysis, CD8+ TILs were an independent favorable prognostic factor in non-organ-confined disease, but were an independent unfavorable prognostic factor in organ-confined disease. These results suggest that CD8+ TILs have clinically significant anti-tumor activity in non-organ-confined disease, but may have pro-tumor activity in organ-confined disease. Therefore, we should be cautious if CD8+ TILs are aimed to be exploited in the treatment of bladder cancer.
bibliographic citation: Zhang et al. (2017) Tumor-infiltrating CD8+ lymphocytes predict different clinical outcomes in organ- and non-organ-confined urothelial carcinoma of the bladder following radical cystectomy. PeerJ 5:e3921 https://doi.org/10.7717/peerj.3921
date submitted: 2017-07-26
date accepted: 2017-09-22
issued: 2017-10-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Shiqiang
author list: Agent
  family name: Wang
  given name: Jun
author list: Agent
  family name: Zhang
  given name: Xinyu
author list: Agent
  family name: Zhou
  given name: Fangjian
doi: 10.7717/peerj.3921
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-13
copyright: ©2017 Zhang et al.
attribution name: Zhang et al.

A retrospective study: does upper airway morphology differ between non-positional and positional obstructive sleep apnea?
type: item
type: AcademicArticle
description: Objective The objective of this study was to explore the differences in upper airway morphology between positional (POSA) and non-positional (NPOSA) obstructive sleep apnea. Methods This retrospective study enrolled 75 patients (45 NPOSA and 30 POSA) who underwent polysomnography (PSG) and computed tomography (CT). The differences in, and relationships of, the PSG values and CT data between POSA and NPOSA were analyzed. Results Significant (p < 0.05) differences between the two groups were found in the apnea/hypopnea index (AHI), lateral-AHI (L-AHI), soft palate length (SPL), cross-sectional palatopharyngeal area, and the coronal diameter (CD) of the palatopharyngeal area at the narrowest part of the glossopharynx, which were all higher in POSA, except for SPL, AHI, and L-AHI. L-AHI was correlated with the cross-sectional area (r = − 0.306, p = 0.008) and CD (r = − 0.398, p < 0.001) of the palatopharyngeal area, the cross-sectional area (r = − 0.241, p = 0.038) and CD (r = − 0.297, p = 0.010) of the narrowest level of the glossopharynx, the CD of the glossopharynx (r = 0.284, p = 0.013), body mass index (BMI, r = 0.273, p = 0.018), SPL (r = 0.284, p = 0.014), and vallecula-tip of tongue (r = 0.250, p = 0.030). The SPL and CD at the narrowest part of the glossopharynx were included in the simplified screening model. Conclusions In NPOSA, the CD of the upper airway was smaller, and the soft palate was longer, than in POSA. These differences may play significant roles in explaining the main differences between NPOSA and POSA.
format: application/pdf
format: text/html
creator: Xiao Jiao
creator: Jianyin Zou
creator: Suru Liu
creator: Jian Guan
creator: Hongliang Yi
creator: Shankai Yin
subject: Otorhinolaryngology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.3918
publisher: PeerJ Inc.
rights: © 2017 Jiao et al.
abstract: Objective The objective of this study was to explore the differences in upper airway morphology between positional (POSA) and non-positional (NPOSA) obstructive sleep apnea. Methods This retrospective study enrolled 75 patients (45 NPOSA and 30 POSA) who underwent polysomnography (PSG) and computed tomography (CT). The differences in, and relationships of, the PSG values and CT data between POSA and NPOSA were analyzed. Results Significant (p < 0.05) differences between the two groups were found in the apnea/hypopnea index (AHI), lateral-AHI (L-AHI), soft palate length (SPL), cross-sectional palatopharyngeal area, and the coronal diameter (CD) of the palatopharyngeal area at the narrowest part of the glossopharynx, which were all higher in POSA, except for SPL, AHI, and L-AHI. L-AHI was correlated with the cross-sectional area (r = − 0.306, p = 0.008) and CD (r = − 0.398, p < 0.001) of the palatopharyngeal area, the cross-sectional area (r = − 0.241, p = 0.038) and CD (r = − 0.297, p = 0.010) of the narrowest level of the glossopharynx, the CD of the glossopharynx (r = 0.284, p = 0.013), body mass index (BMI, r = 0.273, p = 0.018), SPL (r = 0.284, p = 0.014), and vallecula-tip of tongue (r = 0.250, p = 0.030). The SPL and CD at the narrowest part of the glossopharynx were included in the simplified screening model. Conclusions In NPOSA, the CD of the upper airway was smaller, and the soft palate was longer, than in POSA. These differences may play significant roles in explaining the main differences between NPOSA and POSA.
bibliographic citation: Jiao et al. (2017) A retrospective study: does upper airway morphology differ between non-positional and positional obstructive sleep apnea?. PeerJ 5:e3918 https://doi.org/10.7717/peerj.3918
date submitted: 2017-05-22
date accepted: 2017-09-22
issued: 2017-10-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiao
  given name: Xiao
author list: Agent
  family name: Zou
  given name: Jianyin
author list: Agent
  family name: Liu
  given name: Suru
author list: Agent
  family name: Guan
  given name: Jian
author list: Agent
  family name: Yi
  given name: Hongliang
author list: Agent
  family name: Yin
  given name: Shankai
doi: 10.7717/peerj.3918
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-13
copyright: ©2017 Jiao et al.
attribution name: Jiao et al.

Neurodynamic mobilization and foam rolling improved delayed-onset muscle soreness in a healthy adult population: a randomized controlled clinical trial
type: item
type: AcademicArticle
description: Objectives Compare the immediate effects of a Neurodynamic Mobilization (NM) treatment or foam roller (FR) treatment after DOMS. Design Double blind randomised clinical trial. Setting The participants performed 100 drop jumps (5 sets of 20 repetitions, separated by 2 min rests) from a 0.5-m high box in a University biomechanics laboratory to induce muscle soreness. The participants were randomly assigned in a counter-balanced fashion to either a FR or NM treatment group. Participants Thirty-two healthy subjects (21 males and 11 females, mean age 22.6 ± 2.2 years) were randomly assigned into the NM group (n = 16) or the FR group (n = 16). Main Outcome Measures The numeric pain rating scale (NPRS; 0–10), isometric leg strength with dynamometry, surface electromyography at maximum voluntary isometric contraction (MVIC) and muscle peak activation (MPA) upon landing after a test jump were measured at baseline, 48 h after baseline before treatment, and immediately after treatment. Results Both groups showed significant reduction in NPRS scores after treatment (NM: 59%, p < .01; FR: 45%, p < .01), but no difference was found between them (p > .05). The percentage change improvement in the MVIC for the rectus femoris was the only significant difference between the groups (p < 0.05) at post-treatment. After treatment, only the FR group had a statistically significant improvement (p < 0.01) in strength compared to pre-treatment. Conclusion Our results illustrate that both treatments are effective in reducing pain perception after DOMS whereas only FR application showed differences for the MVIC in the rectus femoris and strength.
format: application/pdf
format: text/html
creator: Blanca Romero-Moraleda
creator: Roy La Touche
creator: Sergio Lerma-Lara
creator: Raúl Ferrer-Peña
creator: Víctor Paredes
creator: Ana Belén Peinado
creator: Daniel Muñoz-García
subject: Clinical Trials
subject: Evidence Based Medicine
subject: Geriatrics
subject: Nursing
subject: Rheumatology
description: doi:10.7717/peerj.3908
publisher: PeerJ Inc.
rights: © 2017 Romero-Moraleda et al.
abstract: Objectives Compare the immediate effects of a Neurodynamic Mobilization (NM) treatment or foam roller (FR) treatment after DOMS. Design Double blind randomised clinical trial. Setting The participants performed 100 drop jumps (5 sets of 20 repetitions, separated by 2 min rests) from a 0.5-m high box in a University biomechanics laboratory to induce muscle soreness. The participants were randomly assigned in a counter-balanced fashion to either a FR or NM treatment group. Participants Thirty-two healthy subjects (21 males and 11 females, mean age 22.6 ± 2.2 years) were randomly assigned into the NM group (n = 16) or the FR group (n = 16). Main Outcome Measures The numeric pain rating scale (NPRS; 0–10), isometric leg strength with dynamometry, surface electromyography at maximum voluntary isometric contraction (MVIC) and muscle peak activation (MPA) upon landing after a test jump were measured at baseline, 48 h after baseline before treatment, and immediately after treatment. Results Both groups showed significant reduction in NPRS scores after treatment (NM: 59%, p < .01; FR: 45%, p < .01), but no difference was found between them (p > .05). The percentage change improvement in the MVIC for the rectus femoris was the only significant difference between the groups (p < 0.05) at post-treatment. After treatment, only the FR group had a statistically significant improvement (p < 0.01) in strength compared to pre-treatment. Conclusion Our results illustrate that both treatments are effective in reducing pain perception after DOMS whereas only FR application showed differences for the MVIC in the rectus femoris and strength.
bibliographic citation: Romero-Moraleda et al. (2017) Neurodynamic mobilization and foam rolling improved delayed-onset muscle soreness in a healthy adult population: a randomized controlled clinical trial. PeerJ 5:e3908 https://doi.org/10.7717/peerj.3908
date submitted: 2017-05-26
date accepted: 2017-09-19
issued: 2017-10-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Romero-Moraleda
  given name: Blanca
author list: Agent
  family name: La Touche
  given name: Roy
author list: Agent
  family name: Lerma-Lara
  given name: Sergio
author list: Agent
  family name: Ferrer-Peña
  given name: Raúl
author list: Agent
  family name: Paredes
  given name: Víctor
author list: Agent
  family name: Peinado
  given name: Ana Belén
author list: Agent
  family name: Muñoz-García
  given name: Daniel
doi: 10.7717/peerj.3908
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-13
copyright: ©2017 Romero-Moraleda et al.
attribution name: Romero-Moraleda et al.

Multigene phylogeny of the scyphozoan jellyfish family Pelagiidae reveals that the common U.S. Atlantic sea nettle comprises two distinct species (Chrysaora quinquecirrha and C. chesapeakei)
type: item
type: AcademicArticle
description: Background Species of the scyphozoan family Pelagiidae (e.g., Pelagia noctiluca, Chrysaora quinquecirrha) are well-known for impacting fisheries, aquaculture, and tourism, especially for the painful sting they can inflict on swimmers. However, historical taxonomic uncertainty at the genus (e.g., new genus Mawia) and species levels hinders progress in studying their biology and evolutionary adaptations that make them nuisance species, as well as ability to understand and/or mitigate their ecological and economic impacts. Methods We collected nuclear (28S rDNA) and mitochondrial (cytochrome c oxidase I and 16S rDNA) sequence data from individuals of all four pelagiid genera, including 11 of 13 currently recognized species of Chrysaora. To examine species boundaries in the U.S. Atlantic sea nettle Chrysaora quinquecirrha, specimens were included from its entire range along the U.S. Atlantic and Gulf of Mexico coasts, with representatives also examined morphologically (macromorphology and cnidome). Results Phylogenetic analyses show that the genus Chrysaora is paraphyletic with respect to other pelagiid genera. In combined analyses, Mawia, sampled from the coast of Senegal, is most closely related to Sanderia malayensis, and Pelagia forms a close relationship to a clade of Pacific Chrysaora species (Chrysaora achlyos, Chrysaora colorata, Chrysaora fuscescens, and Chrysaora melanaster). Chrysaora quinquecirrha is polyphyletic, with one clade from the U.S. coastal Atlantic and another in U.S. Atlantic estuaries and Gulf of Mexico. These genetic differences are reflected in morphology, e.g., tentacle and lappet number, oral arm length, and nematocyst dimensions. Caribbean sea nettles (Jamaica and Panama) are genetically similar to the U.S. Atlantic estuaries and Gulf of Mexico clade of Chrysaora quinquecirrha. Discussion Our phylogenetic hypothesis for Pelagiidae contradicts current generic definitions, revealing major disagreements between DNA-based and morphology-based p…
format: application/pdf
format: text/html
creator: Keith M. Bayha
creator: Allen G. Collins
creator: Patrick M. Gaffney
subject: Biodiversity
subject: Evolutionary Studies
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.3863
publisher: PeerJ Inc.
rights: © 2017 Bayha et al.
abstract: Background Species of the scyphozoan family Pelagiidae (e.g., Pelagia noctiluca, Chrysaora quinquecirrha) are well-known for impacting fisheries, aquaculture, and tourism, especially for the painful sting they can inflict on swimmers. However, historical taxonomic uncertainty at the genus (e.g., new genus Mawia) and species levels hinders progress in studying their biology and evolutionary adaptations that make them nuisance species, as well as ability to understand and/or mitigate their ecological and economic impacts. Methods We collected nuclear (28S rDNA) and mitochondrial (cytochrome c oxidase I and 16S rDNA) sequence data from individuals of all four pelagiid genera, including 11 of 13 currently recognized species of Chrysaora. To examine species boundaries in the U.S. Atlantic sea nettle Chrysaora quinquecirrha, specimens were included from its entire range along the U.S. Atlantic and Gulf of Mexico coasts, with representatives also examined morphologically (macromorphology and cnidome). Results Phylogenetic analyses show that the genus Chrysaora is paraphyletic with respect to other pelagiid genera. In combined analyses, Mawia, sampled from the coast of Senegal, is most closely related to Sanderia malayensis, and Pelagia forms a close relationship to a clade of Pacific Chrysaora species (Chrysaora achlyos, Chrysaora colorata, Chrysaora fuscescens, and Chrysaora melanaster). Chrysaora quinquecirrha is polyphyletic, with one clade from the U.S. coastal Atlantic and another in U.S. Atlantic estuaries and Gulf of Mexico. These genetic differences are reflected in morphology, e.g., tentacle and lappet number, oral arm length, and nematocyst dimensions. Caribbean sea nettles (Jamaica and Panama) are genetically similar to the U.S. Atlantic estuaries and Gulf of Mexico clade of Chrysaora quinquecirrha. Discussion Our phylogenetic hypothesis for Pelagiidae contradicts current generic definitions, revealing major disagreements between DNA-based and morphology-based p…
bibliographic citation: Bayha et al. (2017) Multigene phylogeny of the scyphozoan jellyfish family Pelagiidae reveals that the common U.S. Atlantic sea nettle comprises two distinct species (Chrysaora quinquecirrha and C. chesapeakei). PeerJ 5:e3863 https://doi.org/10.7717/peerj.3863
date submitted: 2017-06-12
date accepted: 2017-09-08
issued: 2017-10-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bayha
  given name: Keith M.
author list: Agent
  family name: Collins
  given name: Allen G.
author list: Agent
  family name: Gaffney
  given name: Patrick M.
doi: 10.7717/peerj.3863
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-13
copyright: © 2017 Bayha et al.
attribution name: Bayha et al.

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