PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Novel epitopes identified from efflux pumps of Mycobacterium tuberculosis could induce cytotoxic T lymphocyte response
items: Improved estimates of age, growth and reproduction for the regionally endemic Galapagos sailfin grouper Mycteroperca olfax (Jenyns, 1840)
items: Moth flies and sand flies (Diptera: Psychodidae) in Cretaceous Burmese amber
items: Detection of Alzheimer’s disease by displacement field and machine learning
items: Diet, exercise and mental-wellbeing of healthcare professionals (doctors, dentists and nurses) in Pakistan
items: Chinese Interpreting Studies: a data-driven analysis of a dynamic field of enquiry
items: The non-avian theropod quadrate I: standardized terminology with an overview of the anatomy and function
items: A practical guide and power analysis for GLMMs: detecting among treatment variation in random effects
items: APOE genotype and age modifies the correlation between cognitive status and metabolites from hippocampus by a 2D 1H-MRS in non-demented elders
items: MaqFACS (Macaque Facial Action Coding System) can be used to document facial movements in Barbary macaques (Macaca sylvanus)

Novel epitopes identified from efflux pumps of Mycobacterium tuberculosis could induce cytotoxic T lymphocyte response
type: item
type: AcademicArticle
description: Overcoming drug-resistance is one of the major challenges to control tuberculosis (TB). The up-regulation of efflux pumps is one common mechanism that leads to drug-resistance. Therefore, immunotherapy targeting these efflux pump antigens could be promising strategy to be combined with current chemotherapy. Considering that CD8+ cytotoxic T lymphocytes (CTLs) induced by antigenic peptides (epitopes) could elicit HLA-restricted anti-TB immune response, efflux pumps from classical ABC family (Mycobacterium tuberculosis, Mtb) were chosen as target antigens to identify CTL epitopes. HLA-A2 restricted candidate peptides from Rv2937, Rv2686c and Rv2687c of Mycobacterium tuberculosis were predicted, synthesized and tested. Five peptides could induce IFN-γ release and cytotoxic activity in PBMCs from HLA-A2+ PPD+ donors. Results from HLA-A2/Kb transgenic mice immunization assay suggested that four peptides Rv2937-p168, Rv2937-p266, Rv2686c-p151, and Rv2686c-p181 could induce significant CTL response in vivo. These results suggested that these novel epitopes could be used as immunotherapy candidates to TB drug-resistance.
format: application/pdf
format: text/html
creator: Ming-xia Zhai
creator: Fei Chen
creator: Yuan-yuan Zhao
creator: Ya-hong Wu
creator: Guo-dong Li
creator: Yan-feng Gao
creator: Yuan-ming Qi
subject: Biochemistry
subject: Microbiology
subject: Immunology
description: doi:10.7717/peerj.1229
publisher: PeerJ Inc.
rights: © 2015 Zhai et al.
abstract: Overcoming drug-resistance is one of the major challenges to control tuberculosis (TB). The up-regulation of efflux pumps is one common mechanism that leads to drug-resistance. Therefore, immunotherapy targeting these efflux pump antigens could be promising strategy to be combined with current chemotherapy. Considering that CD8+ cytotoxic T lymphocytes (CTLs) induced by antigenic peptides (epitopes) could elicit HLA-restricted anti-TB immune response, efflux pumps from classical ABC family (Mycobacterium tuberculosis, Mtb) were chosen as target antigens to identify CTL epitopes. HLA-A2 restricted candidate peptides from Rv2937, Rv2686c and Rv2687c of Mycobacterium tuberculosis were predicted, synthesized and tested. Five peptides could induce IFN-γ release and cytotoxic activity in PBMCs from HLA-A2+ PPD+ donors. Results from HLA-A2/Kb transgenic mice immunization assay suggested that four peptides Rv2937-p168, Rv2937-p266, Rv2686c-p151, and Rv2686c-p181 could induce significant CTL response in vivo. These results suggested that these novel epitopes could be used as immunotherapy candidates to TB drug-resistance.
bibliographic citation: Zhai et al. (2015) Novel epitopes identified from efflux pumps of Mycobacterium tuberculosis could induce cytotoxic T lymphocyte response. PeerJ 3:e1229 https://doi.org/10.7717/peerj.1229
date submitted: 2015-04-15
date accepted: 2015-08-14
issued: 2015-09-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhai
  given name: Ming-xia
author list: Agent
  family name: Chen
  given name: Fei
author list: Agent
  family name: Zhao
  given name: Yuan-yuan
author list: Agent
  family name: Wu
  given name: Ya-hong
author list: Agent
  family name: Li
  given name: Guo-dong
author list: Agent
  family name: Gao
  given name: Yan-feng
author list: Agent
  family name: Qi
  given name: Yuan-ming
doi: 10.7717/peerj.1229
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-22
copyright: © 2015 Zhai et al.
attribution name: Zhai et al.

Improved estimates of age, growth and reproduction for the regionally endemic Galapagos sailfin grouper Mycteroperca olfax (Jenyns, 1840)
type: item
type: AcademicArticle
description: The Galapagos Sailfin grouper, Mycteroperca olfax, locally known as bacalao and listed as vulnerable by the IUCN, is culturally, economically, and ecologically important to the Galapagos archipelago and its people. It is regionally endemic to the Eastern Tropical Pacific, and, while an important fishery resource that has shown substantial declines in recent years, to date no effective management regulations are in place to ensure the sustainability of the Galapagos fishery for this species. Previous estimates of longevity and size at maturity for bacalao are inconsistent with estimates for congeners, which brings into question the accuracy of prior estimates. We set out to assess the age, growth, and reproductive biology of bacalao in order to provide more accurate life history information to inform more effective fisheries management for this species. The oldest fish in our sample was 21 years old, which is 2–3 times greater than previously reported estimates of longevity. Parameter estimates for the von Bertalanffy growth function (k = 0.11, L∞ = 110 cm TL, and to = − 1.7 years) show bacalao to grow much slower and attain substantially larger asymptotic maximum length than previous studies. Mean size at maturity (as female) was estimated at 65.3 cm TL, corresponding to a mean age of 6.5 years. We found that sex ratios were extremely female biased (0.009 M:1F), with a large majority of the individuals in our experimental catch being immature (79%). Our results show that bacalao grow slower, live longer, and mature at a much larger size and greater age than previously thought, with very few mature males in the population. These findings have important implications for the fishery of this valuable species and provide the impetus for a long-overdue species management plan to ensure its long-term sustainability.
format: application/pdf
format: text/html
creator: Paolo Usseglio
creator: Alan M. Friedlander
creator: Edward E. DeMartini
creator: Anna Schuhbauer
creator: Eva Schemmel
creator: Pelayo Salinas de Léon
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.1270
publisher: PeerJ Inc.
rights: © 2015
abstract: The Galapagos Sailfin grouper, Mycteroperca olfax, locally known as bacalao and listed as vulnerable by the IUCN, is culturally, economically, and ecologically important to the Galapagos archipelago and its people. It is regionally endemic to the Eastern Tropical Pacific, and, while an important fishery resource that has shown substantial declines in recent years, to date no effective management regulations are in place to ensure the sustainability of the Galapagos fishery for this species. Previous estimates of longevity and size at maturity for bacalao are inconsistent with estimates for congeners, which brings into question the accuracy of prior estimates. We set out to assess the age, growth, and reproductive biology of bacalao in order to provide more accurate life history information to inform more effective fisheries management for this species. The oldest fish in our sample was 21 years old, which is 2–3 times greater than previously reported estimates of longevity. Parameter estimates for the von Bertalanffy growth function (k = 0.11, L∞ = 110 cm TL, and to = − 1.7 years) show bacalao to grow much slower and attain substantially larger asymptotic maximum length than previous studies. Mean size at maturity (as female) was estimated at 65.3 cm TL, corresponding to a mean age of 6.5 years. We found that sex ratios were extremely female biased (0.009 M:1F), with a large majority of the individuals in our experimental catch being immature (79%). Our results show that bacalao grow slower, live longer, and mature at a much larger size and greater age than previously thought, with very few mature males in the population. These findings have important implications for the fishery of this valuable species and provide the impetus for a long-overdue species management plan to ensure its long-term sustainability.
bibliographic citation: Usseglio et al. (2015) Improved estimates of age, growth and reproduction for the regionally endemic Galapagos sailfin grouper Mycteroperca olfax (Jenyns, 1840). PeerJ 3:e1270 https://doi.org/10.7717/peerj.1270
date submitted: 2015-06-12
date accepted: 2015-09-03
issued: 2015-09-17
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Usseglio
  given name: Paolo
author list: Agent
  family name: Friedlander
  given name: Alan M.
author list: Agent
  family name: DeMartini
  given name: Edward E.
author list: Agent
  family name: Schuhbauer
  given name: Anna
author list: Agent
  family name: Schemmel
  given name: Eva
author list: Agent
  family name: Salinas de Léon
  given name: Pelayo
doi: 10.7717/peerj.1270
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-17

Moth flies and sand flies (Diptera: Psychodidae) in Cretaceous Burmese amber
type: item
type: AcademicArticle
description: One new subfamily, four new genera and 10 new species of Psychodidae are described from Burmese amber which significantly increases our knowledge about this group in the Cretaceous. Protopsychodinae n. subfam. probably represents the oldest known ancestor of modern Psychodinae and includes three species within two genera: Datzia setosa gen. et sp. n., Datzia bispina gen. et sp. n., and Mandalayia beumersorum gen. et sp. n. Sycoracinae and Phlebotominae are represented by two genera each in the studied material, Palaeoparasycorax globosus gen. et sp. n., Palaeoparasycorax suppus gen. et sp. n., Parasycorax simplex sp. n., and Phlebotomites aphoe sp. n. and Phlebotomus vetus sp. n., respectively. Bruchomyiinae is represented by Nemopalpus quadrispiculatus sp. n. Furthermore, one genus of an incertae sedis subfamily, Bamara groehni gen. et sp. n., is described. The systematic positions of the new taxa are discussed.
format: application/pdf
format: text/html
creator: Frauke Stebner
creator: Mónica M. Solórzano Kraemer
creator: Sergio Ibáñez-Bernal
creator: Rüdiger Wagner
subject: Entomology
subject: Paleontology
description: doi:10.7717/peerj.1254
publisher: PeerJ Inc.
rights: © 2015 Stebner et al.
abstract: One new subfamily, four new genera and 10 new species of Psychodidae are described from Burmese amber which significantly increases our knowledge about this group in the Cretaceous. Protopsychodinae n. subfam. probably represents the oldest known ancestor of modern Psychodinae and includes three species within two genera: Datzia setosa gen. et sp. n., Datzia bispina gen. et sp. n., and Mandalayia beumersorum gen. et sp. n. Sycoracinae and Phlebotominae are represented by two genera each in the studied material, Palaeoparasycorax globosus gen. et sp. n., Palaeoparasycorax suppus gen. et sp. n., Parasycorax simplex sp. n., and Phlebotomites aphoe sp. n. and Phlebotomus vetus sp. n., respectively. Bruchomyiinae is represented by Nemopalpus quadrispiculatus sp. n. Furthermore, one genus of an incertae sedis subfamily, Bamara groehni gen. et sp. n., is described. The systematic positions of the new taxa are discussed.
bibliographic citation: Stebner et al. (2015) Moth flies and sand flies (Diptera: Psychodidae) in Cretaceous Burmese amber. PeerJ 3:e1254 https://doi.org/10.7717/peerj.1254
date submitted: 2015-04-14
date accepted: 2015-08-31
issued: 2015-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stebner
  given name: Frauke
author list: Agent
  family name: Solórzano Kraemer
  given name: Mónica M.
author list: Agent
  family name: Ibáñez-Bernal
  given name: Sergio
author list: Agent
  family name: Wagner
  given name: Rüdiger
doi: 10.7717/peerj.1254
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-17
copyright: © 2015 Stebner et al.
attribution name: Stebner et al.

Detection of Alzheimer’s disease by displacement field and machine learning
type: item
type: AcademicArticle
description: Aim. Alzheimer’s disease (AD) is a chronic neurodegenerative disease. Recently, computer scientists have developed various methods for early detection based on computer vision and machine learning techniques. Method. In this study, we proposed a novel AD detection method by displacement field (DF) estimation between a normal brain and an AD brain. The DF was treated as the AD-related features, reduced by principal component analysis (PCA), and finally fed into three classifiers: support vector machine (SVM), generalized eigenvalue proximal SVM (GEPSVM), and twin SVM (TSVM). The 10-fold cross validation repeated 50 times. Results. The results showed the “DF + PCA + TSVM” achieved the accuracy of 92.75 ± 1.77, sensitivity of 90.56 ± 1.15, specificity of 93.37 ± 2.05, and precision of 79.61 ± 2.21. This result is better than or comparable with not only the other proposed two methods, but also ten state-of-the-art methods. Besides, our method discovers the AD is related to following brain regions disclosed in recent publications: Angular Gyrus, Anterior Cingulate, Cingulate Gyrus, Culmen, Cuneus, Fusiform Gyrus, Inferior Frontal Gyrus, Inferior Occipital Gyrus, Inferior Parietal Lobule, Inferior Semi-Lunar Lobule, Inferior Temporal Gyrus, Insula, Lateral Ventricle, Lingual Gyrus, Medial Frontal Gyrus, Middle Frontal Gyrus, Middle Occipital Gyrus, Middle Temporal Gyrus, Paracentral Lobule, Parahippocampal Gyrus, Postcentral Gyrus, Posterior Cingulate, Precentral Gyrus, Precuneus, Sub-Gyral, Superior Parietal Lobule, Superior Temporal Gyrus, Supramarginal Gyrus, and Uncus. Conclusion. The displacement filed is effective in detection of AD and related brain-regions.
format: application/pdf
format: text/html
creator: Yudong Zhang
creator: Shuihua Wang
subject: Neuroscience
subject: Psychiatry and Psychology
subject: Radiology and Medical Imaging
subject: Computational Science
description: doi:10.7717/peerj.1251
publisher: PeerJ Inc.
rights: © 2015 Zhang and Wang
abstract: Aim. Alzheimer’s disease (AD) is a chronic neurodegenerative disease. Recently, computer scientists have developed various methods for early detection based on computer vision and machine learning techniques. Method. In this study, we proposed a novel AD detection method by displacement field (DF) estimation between a normal brain and an AD brain. The DF was treated as the AD-related features, reduced by principal component analysis (PCA), and finally fed into three classifiers: support vector machine (SVM), generalized eigenvalue proximal SVM (GEPSVM), and twin SVM (TSVM). The 10-fold cross validation repeated 50 times. Results. The results showed the “DF + PCA + TSVM” achieved the accuracy of 92.75 ± 1.77, sensitivity of 90.56 ± 1.15, specificity of 93.37 ± 2.05, and precision of 79.61 ± 2.21. This result is better than or comparable with not only the other proposed two methods, but also ten state-of-the-art methods. Besides, our method discovers the AD is related to following brain regions disclosed in recent publications: Angular Gyrus, Anterior Cingulate, Cingulate Gyrus, Culmen, Cuneus, Fusiform Gyrus, Inferior Frontal Gyrus, Inferior Occipital Gyrus, Inferior Parietal Lobule, Inferior Semi-Lunar Lobule, Inferior Temporal Gyrus, Insula, Lateral Ventricle, Lingual Gyrus, Medial Frontal Gyrus, Middle Frontal Gyrus, Middle Occipital Gyrus, Middle Temporal Gyrus, Paracentral Lobule, Parahippocampal Gyrus, Postcentral Gyrus, Posterior Cingulate, Precentral Gyrus, Precuneus, Sub-Gyral, Superior Parietal Lobule, Superior Temporal Gyrus, Supramarginal Gyrus, and Uncus. Conclusion. The displacement filed is effective in detection of AD and related brain-regions.
bibliographic citation: Zhang et al. (2015) Detection of Alzheimer’s disease by displacement field and machine learning. PeerJ 3:e1251 https://doi.org/10.7717/peerj.1251
date submitted: 2015-07-28
date accepted: 2015-08-29
issued: 2015-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yudong
author list: Agent
  family name: Wang
  given name: Shuihua
doi: 10.7717/peerj.1251
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-17
copyright: © 2015 Zhang and Wang
attribution name: Zhang and Wang

Diet, exercise and mental-wellbeing of healthcare professionals (doctors, dentists and nurses) in Pakistan
type: item
type: AcademicArticle
description: Background. “Health is wealth” is a time tested adage. Health becomes more relevant when it comes to professionals whose job is to provide people with services that maintain an optimum state of mental, physical and social well-being. Healthcare professionals (HCP) differ from general population in regards to the nature of their work, stress, burnout etc. which begs the need to have a robust state of health for the ones who provide it to others. We initiated this study to see if healthcare professionals “practice what they preach others.” Methods. We employed a cross-sectional study design with convenience-sampling technique. Questionnaires were administered directly to the three groups of healthcare professionals (Doctors, Dentists and Nurses) across the province Punjab after their consent. 1,319 healthcare professionals took part in the study (response rate of 87.35). Warwick Edinburg Mental Wellbeing Scale (WEMWBS) was used to assess mental wellbeing. USDA Dietary Guidelines-2010 were employed to quantify diet. American Heart Association (AHA) guidelines were employed for the analysis of exercise. Results. A total of 1,190 healthcare professionals formed the final sample with doctors and nurses forming the major proportion. Out of 1,190 participants only one healthcare professional was found to eat according to USDA Dietary Guidelines; others ate more of protein group and less of fruits, dairy and vegetable groups. 76% did not perform any exercise. 71.5% worked >48 h/week. More than 50% of healthcare professionals were sleeping <7 h/day. WEMWBS score of the entire sample was 47.97 ± 9.53 S.D. Conclusion. Our findings suggest that healthcare professionals do not practice what they preach. Their mental wellbeing, diet and exercise habits are not up to the mark and should be improved to foster the whole healthcare system for individual and community benefits.
format: application/pdf
format: text/html
creator: Waqas Ahmad
creator: Frances Taggart
creator: Muhammad Shoaib Shafique
creator: Yumna Muzafar
creator: Shehnam Abidi
creator: Noor Ghani
creator: Zahra Malik
creator: Tehmina Zahid
creator: Ahmed Waqas
creator: Naila Ghaffar
subject: Internal Medicine
subject: Nutrition
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.1250
publisher: PeerJ Inc.
rights: © 2015 Ahmad et al.
abstract: Background. “Health is wealth” is a time tested adage. Health becomes more relevant when it comes to professionals whose job is to provide people with services that maintain an optimum state of mental, physical and social well-being. Healthcare professionals (HCP) differ from general population in regards to the nature of their work, stress, burnout etc. which begs the need to have a robust state of health for the ones who provide it to others. We initiated this study to see if healthcare professionals “practice what they preach others.” Methods. We employed a cross-sectional study design with convenience-sampling technique. Questionnaires were administered directly to the three groups of healthcare professionals (Doctors, Dentists and Nurses) across the province Punjab after their consent. 1,319 healthcare professionals took part in the study (response rate of 87.35). Warwick Edinburg Mental Wellbeing Scale (WEMWBS) was used to assess mental wellbeing. USDA Dietary Guidelines-2010 were employed to quantify diet. American Heart Association (AHA) guidelines were employed for the analysis of exercise. Results. A total of 1,190 healthcare professionals formed the final sample with doctors and nurses forming the major proportion. Out of 1,190 participants only one healthcare professional was found to eat according to USDA Dietary Guidelines; others ate more of protein group and less of fruits, dairy and vegetable groups. 76% did not perform any exercise. 71.5% worked >48 h/week. More than 50% of healthcare professionals were sleeping <7 h/day. WEMWBS score of the entire sample was 47.97 ± 9.53 S.D. Conclusion. Our findings suggest that healthcare professionals do not practice what they preach. Their mental wellbeing, diet and exercise habits are not up to the mark and should be improved to foster the whole healthcare system for individual and community benefits.
bibliographic citation: Ahmad et al. (2015) Diet, exercise and mental-wellbeing of healthcare professionals (doctors, dentists and nurses) in Pakistan. PeerJ 3:e1250 https://doi.org/10.7717/peerj.1250
date submitted: 2015-05-19
date accepted: 2015-08-29
issued: 2015-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahmad
  given name: Waqas
author list: Agent
  family name: Taggart
  given name: Frances
author list: Agent
  family name: Shafique
  given name: Muhammad Shoaib
author list: Agent
  family name: Muzafar
  given name: Yumna
author list: Agent
  family name: Abidi
  given name: Shehnam
author list: Agent
  family name: Ghani
  given name: Noor
author list: Agent
  family name: Malik
  given name: Zahra
author list: Agent
  family name: Zahid
  given name: Tehmina
author list: Agent
  family name: Waqas
  given name: Ahmed
author list: Agent
  family name: Ghaffar
  given name: Naila
doi: 10.7717/peerj.1250
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-17
copyright: © 2015 Ahmad et al.
attribution name: Ahmad et al.

Chinese Interpreting Studies: a data-driven analysis of a dynamic field of enquiry
type: item
type: AcademicArticle
description: Over the five decades since its beginnings, Chinese Interpreting Studies (CIS) has evolved into a dynamic field of academic enquiry with more than 3,500 scholars and 4,200 publications. Using quantitative and qualitative analysis, this scientometric study delves deep into CIS citation data to examine some of the noteworthy trends and patterns of behavior in the field: how can the field’s progress be quantified by means of citation analysis? Do its authors tend repeatedly to cite ‘classic’ papers or are they more drawn to their colleagues’ latest research? What different effects does the choice of empirical vs. theoretical research have on the use of citations in the various research brackets? The findings show that the field is steadily moving forward with new papers continuously being cited, although a number of influential papers stand out, having received a stream of citations in all the years examined. CIS scholars also have a tendency to cite much older English than Chinese publications across all document types, and empirical research has the greatest influence on the citation behavior of doctoral scholars, while theoretical studies have the largest impact on that of article authors. The goal of this study is to demonstrate the merits of blending quantitative and qualitative analyses to uncover hidden trends.
format: application/pdf
format: text/html
creator: Ziyun Xu
creator: Leonid Pekelis
subject: Science and Medical Education
subject: Science Policy
subject: Statistics
subject: Computational Science
description: doi:10.7717/peerj.1249
publisher: PeerJ Inc.
rights: © 2015 Xu and Pekelis
abstract: Over the five decades since its beginnings, Chinese Interpreting Studies (CIS) has evolved into a dynamic field of academic enquiry with more than 3,500 scholars and 4,200 publications. Using quantitative and qualitative analysis, this scientometric study delves deep into CIS citation data to examine some of the noteworthy trends and patterns of behavior in the field: how can the field’s progress be quantified by means of citation analysis? Do its authors tend repeatedly to cite ‘classic’ papers or are they more drawn to their colleagues’ latest research? What different effects does the choice of empirical vs. theoretical research have on the use of citations in the various research brackets? The findings show that the field is steadily moving forward with new papers continuously being cited, although a number of influential papers stand out, having received a stream of citations in all the years examined. CIS scholars also have a tendency to cite much older English than Chinese publications across all document types, and empirical research has the greatest influence on the citation behavior of doctoral scholars, while theoretical studies have the largest impact on that of article authors. The goal of this study is to demonstrate the merits of blending quantitative and qualitative analyses to uncover hidden trends.
bibliographic citation: Xu et al. (2015) Chinese Interpreting Studies: a data-driven analysis of a dynamic field of enquiry. PeerJ 3:e1249 https://doi.org/10.7717/peerj.1249
date submitted: 2015-04-15
date accepted: 2015-08-28
issued: 2015-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Ziyun
author list: Agent
  family name: Pekelis
  given name: Leonid
doi: 10.7717/peerj.1249
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-17
copyright: © 2015 Xu and Pekelis
attribution name: Xu and Pekelis

The non-avian theropod quadrate I: standardized terminology with an overview of the anatomy and function
type: item
type: AcademicArticle
description: The quadrate of reptiles and most other tetrapods plays an important morphofunctional role by allowing the articulation of the mandible with the cranium. In Theropoda, the morphology of the quadrate is particularly complex and varies importantly among different clades of non-avian theropods, therefore conferring a strong taxonomic potential. Inconsistencies in the notation and terminology used in discussions of the theropod quadrate anatomy have been noticed, including at least one instance when no less than eight different terms were given to the same structure. A standardized list of terms and notations for each quadrate anatomical entity is proposed here, with the goal of facilitating future descriptions of this important cranial bone. In addition, an overview of the literature on quadrate function and pneumaticity in non-avian theropods is presented, along with a discussion of the inferences that could be made from this research. Specifically, the quadrate of the large majority of non-avian theropods is akinetic but the diagonally oriented intercondylar sulcus of the mandibular articulation allowed both rami of the mandible to move laterally when opening the mouth in many of theropods. Pneumaticity of the quadrate is also present in most averostran clades and the pneumatic chamber—invaded by the quadrate diverticulum of the mandibular arch pneumatic system—was connected to one or several pneumatic foramina on the medial, lateral, posterior, anterior or ventral sides of the quadrate.
format: application/pdf
format: text/html
creator: Christophe Hendrickx
creator: Ricardo Araújo
creator: Octávio Mateus
subject: Paleontology
description: doi:10.7717/peerj.1245
publisher: PeerJ Inc.
rights: © 2015 Hendrickx et al.
abstract: The quadrate of reptiles and most other tetrapods plays an important morphofunctional role by allowing the articulation of the mandible with the cranium. In Theropoda, the morphology of the quadrate is particularly complex and varies importantly among different clades of non-avian theropods, therefore conferring a strong taxonomic potential. Inconsistencies in the notation and terminology used in discussions of the theropod quadrate anatomy have been noticed, including at least one instance when no less than eight different terms were given to the same structure. A standardized list of terms and notations for each quadrate anatomical entity is proposed here, with the goal of facilitating future descriptions of this important cranial bone. In addition, an overview of the literature on quadrate function and pneumaticity in non-avian theropods is presented, along with a discussion of the inferences that could be made from this research. Specifically, the quadrate of the large majority of non-avian theropods is akinetic but the diagonally oriented intercondylar sulcus of the mandibular articulation allowed both rami of the mandible to move laterally when opening the mouth in many of theropods. Pneumaticity of the quadrate is also present in most averostran clades and the pneumatic chamber—invaded by the quadrate diverticulum of the mandibular arch pneumatic system—was connected to one or several pneumatic foramina on the medial, lateral, posterior, anterior or ventral sides of the quadrate.
bibliographic citation: Hendrickx et al. (2015) The non-avian theropod quadrate I: standardized terminology with an overview of the anatomy and function. PeerJ 3:e1245 https://doi.org/10.7717/peerj.1245
date submitted: 2014-05-04
date accepted: 2015-08-25
issued: 2015-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hendrickx
  given name: Christophe
author list: Agent
  family name: Araújo
  given name: Ricardo
author list: Agent
  family name: Mateus
  given name: Octávio
doi: 10.7717/peerj.1245
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-17
copyright: © 2015 Hendrickx et al.
attribution name: Hendrickx et al.

A practical guide and power analysis for GLMMs: detecting among treatment variation in random effects
type: item
type: AcademicArticle
description: In ecology and evolution generalized linear mixed models (GLMMs) are becoming increasingly used to test for differences in variation by treatment at multiple hierarchical levels. Yet, the specific sampling schemes that optimize the power of an experiment to detect differences in random effects by treatment/group remain unknown. In this paper we develop a blueprint for conducting power analyses for GLMMs focusing on detecting differences in variance by treatment. We present parameterization and power analyses for random-intercepts and random-slopes GLMMs because of their generality as focal parameters for most applications and because of their immediate applicability to emerging questions in the field of behavioral ecology. We focus on the extreme case of hierarchically structured binomial data, though the framework presented here generalizes easily to any error distribution model. First, we determine the optimal ratio of individuals to repeated measures within individuals that maximizes power to detect differences by treatment in among-individual variation in intercept, among-individual variation in slope, and within-individual variation in intercept. Second, we explore how power to detect differences in target variance parameters is affected by total variation. Our results indicate heterogeneity in power across ratios of individuals to repeated measures with an optimal ratio determined by both the target variance parameter and total sample size. Additionally, power to detect each variance parameter was low overall (in most cases >1,000 total observations per treatment needed to achieve 80% power) and decreased with increasing variance in non-target random effects. With growing interest in variance as the parameter of inquiry, these power analyses provide a crucial component for designing experiments focused on detecting differences in variance. We hope to inspire novel experimental designs in ecology and evolution investigating the causes and implications of indivi…
format: application/pdf
format: text/html
creator: Morgan P. Kain
creator: Ben M. Bolker
creator: Michael W. McCoy
subject: Ecology
subject: Mathematical Biology
subject: Statistics
description: doi:10.7717/peerj.1226
publisher: PeerJ Inc.
rights: © 2015 Kain et al.
abstract: In ecology and evolution generalized linear mixed models (GLMMs) are becoming increasingly used to test for differences in variation by treatment at multiple hierarchical levels. Yet, the specific sampling schemes that optimize the power of an experiment to detect differences in random effects by treatment/group remain unknown. In this paper we develop a blueprint for conducting power analyses for GLMMs focusing on detecting differences in variance by treatment. We present parameterization and power analyses for random-intercepts and random-slopes GLMMs because of their generality as focal parameters for most applications and because of their immediate applicability to emerging questions in the field of behavioral ecology. We focus on the extreme case of hierarchically structured binomial data, though the framework presented here generalizes easily to any error distribution model. First, we determine the optimal ratio of individuals to repeated measures within individuals that maximizes power to detect differences by treatment in among-individual variation in intercept, among-individual variation in slope, and within-individual variation in intercept. Second, we explore how power to detect differences in target variance parameters is affected by total variation. Our results indicate heterogeneity in power across ratios of individuals to repeated measures with an optimal ratio determined by both the target variance parameter and total sample size. Additionally, power to detect each variance parameter was low overall (in most cases >1,000 total observations per treatment needed to achieve 80% power) and decreased with increasing variance in non-target random effects. With growing interest in variance as the parameter of inquiry, these power analyses provide a crucial component for designing experiments focused on detecting differences in variance. We hope to inspire novel experimental designs in ecology and evolution investigating the causes and implications of indivi…
bibliographic citation: Kain et al. (2015) A practical guide and power analysis for GLMMs: detecting among treatment variation in random effects. PeerJ 3:e1226 https://doi.org/10.7717/peerj.1226
date submitted: 2015-06-16
date accepted: 2015-08-11
issued: 2015-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kain
  given name: Morgan P.
author list: Agent
  family name: Bolker
  given name: Ben M.
author list: Agent
  family name: McCoy
  given name: Michael W.
doi: 10.7717/peerj.1226
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-17
copyright: © 2015 Kain et al.
attribution name: Kain et al.

APOE genotype and age modifies the correlation between cognitive status and metabolites from hippocampus by a 2D 1H-MRS in non-demented elders
type: item
type: AcademicArticle
description: Purpose. To examine the associations among age, Apolipoprotein E (APOE) genotype, metabolic changes in the hippocampus detected by 2D 1H magnetic resonance spectroscopy (MRS), and neuropsychological measures of cognition in non-demented elders. Materials and Methods. We studied a cohort of 16 cognitively normal controls (CN) and 11 amnestic mild cognitive impairment (aMCI) patients between 66 and 88 years old who were genotyped for APOE genetic polymorphism. Measurements of 2D1H-MRS metabolites were obtained in the hippocampus region. Adjusting by age among all subjects, the association between metabolic changes and cognitive function was measured by Spearman partial rank-order correlation. The effect of APOE status was measured by separating the subjects into APOE genotype subgroups, including the APOEε4 carriers and APOEε4 non-carriers. Results. In contrast to the CN group matched with age, gender, and education, aMCI patients showed increased myo-inositol (mI)/Creatine (Cr) ratio only in the right hippocampus. No differences were noted on N-acetylaspartate (NAA)/Cr and mI/NAA from bilateral hippocampus, and so was mI/Cr ratio in left hippocampus between aMCI and CN. The mI/Cr ratio from the right hippocampus in non-demented elders was negatively correlated with Montreal Cognitive Assessment (MoCA) scores. Whether ε4 genotype or age was added as a covariate, none of the correlation effects remained significant. Additionally, adjusting for age and APOE genotype together, there was no significant correlation between them. Conclusion. Since the higher mI/Cr from the right hippocampus of the patients with aMCI than those from CN, the mI/Cr could be a more specific predictor of general cognitive function in aMCI patients. There is an association between higher mI/Cr in right hippocampus and worse cognitive function for the non-demented older adults, and the correlation could be modified by APOE status and age. That provided a window on objectively understanding the mec…
format: application/pdf
format: text/html
creator: Zhenyu Yin
creator: Wenbo Wu
creator: Renyuan Liu
creator: Xue Liang
creator: Tingting Yu
creator: Xiaoling Chen
creator: Jie Feng
creator: Aibin Guo
creator: Yu Xie
creator: Haiyan Yang
creator: Mingmin Huang
creator: Chuanshuai Tian
creator: Bing Zhang
creator: Yun Xu
subject: Neuroscience
subject: Diabetes and Endocrinology
subject: Geriatrics
subject: Metabolic Sciences
description: doi:10.7717/peerj.1202
publisher: PeerJ Inc.
rights: © 2015 Yin et al.
abstract: Purpose. To examine the associations among age, Apolipoprotein E (APOE) genotype, metabolic changes in the hippocampus detected by 2D 1H magnetic resonance spectroscopy (MRS), and neuropsychological measures of cognition in non-demented elders. Materials and Methods. We studied a cohort of 16 cognitively normal controls (CN) and 11 amnestic mild cognitive impairment (aMCI) patients between 66 and 88 years old who were genotyped for APOE genetic polymorphism. Measurements of 2D1H-MRS metabolites were obtained in the hippocampus region. Adjusting by age among all subjects, the association between metabolic changes and cognitive function was measured by Spearman partial rank-order correlation. The effect of APOE status was measured by separating the subjects into APOE genotype subgroups, including the APOEε4 carriers and APOEε4 non-carriers. Results. In contrast to the CN group matched with age, gender, and education, aMCI patients showed increased myo-inositol (mI)/Creatine (Cr) ratio only in the right hippocampus. No differences were noted on N-acetylaspartate (NAA)/Cr and mI/NAA from bilateral hippocampus, and so was mI/Cr ratio in left hippocampus between aMCI and CN. The mI/Cr ratio from the right hippocampus in non-demented elders was negatively correlated with Montreal Cognitive Assessment (MoCA) scores. Whether ε4 genotype or age was added as a covariate, none of the correlation effects remained significant. Additionally, adjusting for age and APOE genotype together, there was no significant correlation between them. Conclusion. Since the higher mI/Cr from the right hippocampus of the patients with aMCI than those from CN, the mI/Cr could be a more specific predictor of general cognitive function in aMCI patients. There is an association between higher mI/Cr in right hippocampus and worse cognitive function for the non-demented older adults, and the correlation could be modified by APOE status and age. That provided a window on objectively understanding the mec…
bibliographic citation: Yin et al. (2015) APOE genotype and age modifies the correlation between cognitive status and metabolites from hippocampus by a 2D 1H-MRS in non-demented elders. PeerJ 3:e1202 https://doi.org/10.7717/peerj.1202
date submitted: 2015-04-30
date accepted: 2015-07-30
issued: 2015-09-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Zhenyu
author list: Agent
  family name: Wu
  given name: Wenbo
author list: Agent
  family name: Liu
  given name: Renyuan
author list: Agent
  family name: Liang
  given name: Xue
author list: Agent
  family name: Yu
  given name: Tingting
author list: Agent
  family name: Chen
  given name: Xiaoling
author list: Agent
  family name: Feng
  given name: Jie
author list: Agent
  family name: Guo
  given name: Aibin
author list: Agent
  family name: Xie
  given name: Yu
author list: Agent
  family name: Yang
  given name: Haiyan
author list: Agent
  family name: Huang
  given name: Mingmin
author list: Agent
  family name: Tian
  given name: Chuanshuai
author list: Agent
  family name: Zhang
  given name: Bing
author list: Agent
  family name: Xu
  given name: Yun
doi: 10.7717/peerj.1202
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-17
copyright: © 2015 Yin et al.
attribution name: Yin et al.

MaqFACS (Macaque Facial Action Coding System) can be used to document facial movements in Barbary macaques (Macaca sylvanus)
type: item
type: AcademicArticle
description: Human and non-human primates exhibit facial movements or displays to communicate with one another. The evolution of form and function of those displays could be better understood through multispecies comparisons. Anatomically based coding systems (Facial Action Coding Systems: FACS) are developed to enable such comparisons because they are standardized and systematic and aid identification of homologous expressions underpinned by similar muscle contractions. To date, FACS has been developed for humans, and subsequently modified for chimpanzees, rhesus macaques, orangutans, hylobatids, dogs, and cats. Here, we wanted to test whether the MaqFACS system developed in rhesus macaques (Macaca mulatta) could be used to code facial movements in Barbary macaques (M. sylvanus), a species phylogenetically close to the rhesus macaques. The findings show that the facial movement capacity of Barbary macaques can be reliably coded using the MaqFACS. We found differences in use and form of some movements, most likely due to specializations in the communicative repertoire of each species, rather than morphological differences.
format: application/pdf
format: text/html
creator: Églantine Julle-Danière
creator: Jérôme Micheletta
creator: Jamie Whitehouse
creator: Marine Joly
creator: Carolin Gass
creator: Anne M. Burrows
creator: Bridget M. Waller
subject: Animal Behavior
description: doi:10.7717/peerj.1248
publisher: PeerJ Inc.
rights: © 2015 Julle-Danière et al.
abstract: Human and non-human primates exhibit facial movements or displays to communicate with one another. The evolution of form and function of those displays could be better understood through multispecies comparisons. Anatomically based coding systems (Facial Action Coding Systems: FACS) are developed to enable such comparisons because they are standardized and systematic and aid identification of homologous expressions underpinned by similar muscle contractions. To date, FACS has been developed for humans, and subsequently modified for chimpanzees, rhesus macaques, orangutans, hylobatids, dogs, and cats. Here, we wanted to test whether the MaqFACS system developed in rhesus macaques (Macaca mulatta) could be used to code facial movements in Barbary macaques (M. sylvanus), a species phylogenetically close to the rhesus macaques. The findings show that the facial movement capacity of Barbary macaques can be reliably coded using the MaqFACS. We found differences in use and form of some movements, most likely due to specializations in the communicative repertoire of each species, rather than morphological differences.
bibliographic citation: Julle-Danière et al. (2015) MaqFACS (Macaque Facial Action Coding System) can be used to document facial movements in Barbary macaques (Macaca sylvanus). PeerJ 3:e1248 https://doi.org/10.7717/peerj.1248
date submitted: 2015-06-15
date accepted: 2015-08-27
issued: 2015-09-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Julle-Danière
  given name: Églantine
author list: Agent
  family name: Micheletta
  given name: Jérôme
author list: Agent
  family name: Whitehouse
  given name: Jamie
author list: Agent
  family name: Joly
  given name: Marine
author list: Agent
  family name: Gass
  given name: Carolin
author list: Agent
  family name: Burrows
  given name: Anne M.
author list: Agent
  family name: Waller
  given name: Bridget M.
doi: 10.7717/peerj.1248
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-09-15
copyright: © 2015 Julle-Danière et al.
attribution name: Julle-Danière et al.

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