PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Article processing charges for open access publication—the situation for research intensive universities in the USA and Canada
items: Non-invasive assessment of phosphate metabolism and oxidative capacity in working skeletal muscle in healthy young Chinese volunteers using 31P Magnetic Resonance Spectroscopy
items: Impact of agricultural management on bacterial laccase-encoding genes with possible implications for soil carbon storage in semi-arid Mediterranean olive farming
items: Detection of methylation, acetylation and glycosylation of protein residues by monitoring 13C chemical-shift changes: A quantum-chemical study
items: Simultaneous bilateral laser therapy accelerates recovery after noise-induced hearing loss in a rat model
items: Neural and endocranial anatomy of Triassic phytosaurian reptiles and convergence with fossil and modern crocodylians
items: Percentile curves for skinfold thickness for Canadian children and youth
items: Emotional intelligence and depressive symptoms in Spanish institutionalized elders: does emotional self-efficacy act as a mediator?
items: Fast men slow more than fast women in a 10 kilometer road race
items: Computer-assisted initial diagnosis of rare diseases

Article processing charges for open access publication—the situation for research intensive universities in the USA and Canada
type: item
type: AcademicArticle
description: Background. Open access (OA) publishing via article processing charges (APCs) is growing as an alternative to subscription publishing. The Pay It Forward (PIF) Project is exploring the feasibility of transitioning from paying subscriptions to funding APCs for faculty at research intensive universities. Estimating of the cost of APCs for the journals authors at research intensive universities tend to publish is essential for the PIF project and similar initiatives. This paper presents our research into this question. Methods. We identified APC prices for publications by authors at the 4 research intensive United States (US) and Canadian universities involved in the study. We also obtained APC payment records from several Western European universities and funding agencies. Both data sets were merged with Web of Science (WoS) metadata. We calculated the average APCs for articles and proceedings in 13 discipline categories published by researchers at research intensive universities. We also identified 41 journals published by traditionally subscription publishers which have recently converted to APC funded OA and recorded the APCs they charge. Results. We identified 7,629 payment records from the 4 European APC payment databases and 14,356 OA articles authored by PIF partner university faculty for which we had listed APC prices. APCs for full OA journals published by PIF authors averaged 1,775 USD; full OA journal APCs paid by Western European funders averaged 1,865 USD; hybrid APCs paid by Western European funders averaged 2,887 USD. The APC for converted journals published by major subscription publishers averaged 1,825 USD. APC funded OA is concentrated in the life and basic sciences. APCs funded articles in the social sciences and humanities are often multidisciplinary and published in journals such as PLOS ONE that largely publish in the life sciences. Conclusions. Full OA journal APCs average a little under 2,000 USD while hybrid articles average about 3,000 USD f…
format: application/pdf
format: text/html
creator: David Solomon
creator: Bo-Christer Björk
subject: Science and Medical Education
subject: Science Policy
description: doi:10.7717/peerj.2264
publisher: PeerJ Inc.
rights: © 2016 Solomon and Björk
abstract: Background. Open access (OA) publishing via article processing charges (APCs) is growing as an alternative to subscription publishing. The Pay It Forward (PIF) Project is exploring the feasibility of transitioning from paying subscriptions to funding APCs for faculty at research intensive universities. Estimating of the cost of APCs for the journals authors at research intensive universities tend to publish is essential for the PIF project and similar initiatives. This paper presents our research into this question. Methods. We identified APC prices for publications by authors at the 4 research intensive United States (US) and Canadian universities involved in the study. We also obtained APC payment records from several Western European universities and funding agencies. Both data sets were merged with Web of Science (WoS) metadata. We calculated the average APCs for articles and proceedings in 13 discipline categories published by researchers at research intensive universities. We also identified 41 journals published by traditionally subscription publishers which have recently converted to APC funded OA and recorded the APCs they charge. Results. We identified 7,629 payment records from the 4 European APC payment databases and 14,356 OA articles authored by PIF partner university faculty for which we had listed APC prices. APCs for full OA journals published by PIF authors averaged 1,775 USD; full OA journal APCs paid by Western European funders averaged 1,865 USD; hybrid APCs paid by Western European funders averaged 2,887 USD. The APC for converted journals published by major subscription publishers averaged 1,825 USD. APC funded OA is concentrated in the life and basic sciences. APCs funded articles in the social sciences and humanities are often multidisciplinary and published in journals such as PLOS ONE that largely publish in the life sciences. Conclusions. Full OA journal APCs average a little under 2,000 USD while hybrid articles average about 3,000 USD f…
bibliographic citation: Solomon et al. (2016) Article processing charges for open access publication—the situation for research intensive universities in the USA and Canada. PeerJ 4:e2264 https://doi.org/10.7717/peerj.2264
date submitted: 2016-04-28
date accepted: 2016-06-27
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Solomon
  given name: David
author list: Agent
  family name: Björk
  given name: Bo-Christer
doi: 10.7717/peerj.2264
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Solomon and Björk
attribution name: Solomon and Björk

Non-invasive assessment of phosphate metabolism and oxidative capacity in working skeletal muscle in healthy young Chinese volunteers using 31P Magnetic Resonance Spectroscopy
type: item
type: AcademicArticle
description: Background. Generally, males display greater strength and muscle capacity than females while performing a task. Muscle biopsy is regarded as the reference method of evaluating muscle functions; however, it is invasive and has sampling errors, and is not practical for longitudinal studies and dynamic measurement during excise. In this study, we built an in-house force control and gauge system for quantitatively applying force to quadriceps while the subjects underwent 31P Magnetic Resonance Spectroscopy (31P-MRS); our aim was to investigate if there is a sex difference of phosphate metabolite change in working muscles in young heathy Chinese volunteers. Methods. Volunteers performed knee-extending excises using a force control and gauge system while lying prone in a Philips 3T Magnetic Resonance (MR) scanner. The 31P-MRS coil was firmly placed under the middle of the quadriceps . 31P-MRS measurements of inorganic phosphate (Pi), phosphocreatine (PCr) and adenosine triphosphate (ATP) were acquired from quadriceps while subjects were in a state of pre-, during- and post-exercise. The PCr, Pi, PCr/Pi, PCr/ATP, pH, work/energy cost ratio (WE), kPCr and oxidative capacity were compared between males and females. Results. A total of 17 volunteers underwent the study. Males: N = 10, age = 23.30 ± 1.25years; females: N = 7, age = 23.57 ± 0.79 years. In this study, males had significantly greater WE (16.33 ± 6.46 vs. 7.82 ± 2.16, p = 0.002) than females. Among PCr, Pi, PCr/Pi, PCr/ATP, pH, kPCr and oxidative capacity at different exercise status, only PCr/Pi (during-exercise, males = 5.630 ± 1.647, females = 4.014 ± 1.298, p = 0.047), PCr/ATP (during-exercise, males =1.273 ± 0.219, females = 1.523 ± 0.167, p = 0.025), and ATP (post-exercise, males = 24.469 ± 3.911 mmol/kg, females = 18.353 ± 4.818 mmol/kg, p = 0.035) had significant sex differences. Males had significantly greater PCr/Pi, but less PCr/ATP than females during exercise, suggesting males had higher energy transf…
format: application/pdf
format: text/html
creator: Ming Li
creator: Fei Chen
creator: Huiting Wang
creator: Wenbo Wu
creator: Xin Zhang
creator: Chuanshuai Tian
creator: Haiping Yu
creator: Renyuan Liu
creator: Bin Zhu
creator: Bing Zhang
creator: Zhenyu Dai
subject: Neurology
subject: Radiology and Medical Imaging
subject: Metabolic Sciences
description: doi:10.7717/peerj.2259
publisher: PeerJ Inc.
rights: © 2016 Li et al.
abstract: Background. Generally, males display greater strength and muscle capacity than females while performing a task. Muscle biopsy is regarded as the reference method of evaluating muscle functions; however, it is invasive and has sampling errors, and is not practical for longitudinal studies and dynamic measurement during excise. In this study, we built an in-house force control and gauge system for quantitatively applying force to quadriceps while the subjects underwent 31P Magnetic Resonance Spectroscopy (31P-MRS); our aim was to investigate if there is a sex difference of phosphate metabolite change in working muscles in young heathy Chinese volunteers. Methods. Volunteers performed knee-extending excises using a force control and gauge system while lying prone in a Philips 3T Magnetic Resonance (MR) scanner. The 31P-MRS coil was firmly placed under the middle of the quadriceps . 31P-MRS measurements of inorganic phosphate (Pi), phosphocreatine (PCr) and adenosine triphosphate (ATP) were acquired from quadriceps while subjects were in a state of pre-, during- and post-exercise. The PCr, Pi, PCr/Pi, PCr/ATP, pH, work/energy cost ratio (WE), kPCr and oxidative capacity were compared between males and females. Results. A total of 17 volunteers underwent the study. Males: N = 10, age = 23.30 ± 1.25years; females: N = 7, age = 23.57 ± 0.79 years. In this study, males had significantly greater WE (16.33 ± 6.46 vs. 7.82 ± 2.16, p = 0.002) than females. Among PCr, Pi, PCr/Pi, PCr/ATP, pH, kPCr and oxidative capacity at different exercise status, only PCr/Pi (during-exercise, males = 5.630 ± 1.647, females = 4.014 ± 1.298, p = 0.047), PCr/ATP (during-exercise, males =1.273 ± 0.219, females = 1.523 ± 0.167, p = 0.025), and ATP (post-exercise, males = 24.469 ± 3.911 mmol/kg, females = 18.353 ± 4.818 mmol/kg, p = 0.035) had significant sex differences. Males had significantly greater PCr/Pi, but less PCr/ATP than females during exercise, suggesting males had higher energy transf…
bibliographic citation: Li et al. (2016) Non-invasive assessment of phosphate metabolism and oxidative capacity in working skeletal muscle in healthy young Chinese volunteers using 31P Magnetic Resonance Spectroscopy. PeerJ 4:e2259 https://doi.org/10.7717/peerj.2259
date submitted: 2016-04-22
date accepted: 2016-06-24
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Ming
author list: Agent
  family name: Chen
  given name: Fei
author list: Agent
  family name: Wang
  given name: Huiting
author list: Agent
  family name: Wu
  given name: Wenbo
author list: Agent
  family name: Zhang
  given name: Xin
author list: Agent
  family name: Tian
  given name: Chuanshuai
author list: Agent
  family name: Yu
  given name: Haiping
author list: Agent
  family name: Liu
  given name: Renyuan
author list: Agent
  family name: Zhu
  given name: Bin
author list: Agent
  family name: Zhang
  given name: Bing
author list: Agent
  family name: Dai
  given name: Zhenyu
doi: 10.7717/peerj.2259
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Li et al.
attribution name: Li et al.

Impact of agricultural management on bacterial laccase-encoding genes with possible implications for soil carbon storage in semi-arid Mediterranean olive farming
type: item
type: AcademicArticle
description: Background: In this work, we aimed to gain insights into the contribution of soil bacteria to carbon sequestration in Mediterranean habitats. In particular, we aimed to use bacterial laccase-encoding genes as molecular markers for soil organic C cycling. Using rainfed olive farming as an experimental model, we determined the stability and accumulation levels of humic substances and applied these data to bacterial laccase-encoding gene expression and diversity in soils under four different agricultural management systems (bare soils under tillage/no tillage and vegetation cover under chemical/mechanical management). Materials and Methods: Humic C (> 104 Da) was subjected to isoelectric focusing. The GC-MS method was used to analyze aromatic hydrocarbons. Real-Time PCR quantification and denaturing gradient gel electrophoresis (DGGE) for functional bacterial laccase-like multicopper oxidase (LMCO)-encoding genes and transcripts were also carried out. Results: Soils under spontaneous vegetation, eliminated in springtime using mechanical methods for more than 30 years, showed the highest humic acid levels as well as the largest bacterial population rich in laccase genes and transcripts. The structure of the bacterial community based on LMCO genes also pointed to phylogenetic differences between these soils due to the impact of different management systems. Soils where herbicides were used to eliminate spontaneous vegetation once a year and those where pre-emergence herbicides resulted in bare soils clustered together for DNA-based DGGE analysis, which indicated a certain amount of microbial selection due to the application of herbicides. When LMCO-encoding gene expression was studied, soils where cover vegetation was managed either with herbicides or with mechanical methods showed less than 10% similarity, suggesting that the type of weed management strategy used can impact weed community composition and consequently laccase substrates derived from vegetation decay. Con…
format: application/pdf
format: text/html
creator: Beatriz Moreno
creator: Emilio Benitez
subject: Agricultural Science
subject: Environmental Sciences
subject: Microbiology
subject: Natural Resource Management
subject: Soil Science
description: doi:10.7717/peerj.2257
publisher: PeerJ Inc.
rights: © 2016 Moreno & Benitez
abstract: Background: In this work, we aimed to gain insights into the contribution of soil bacteria to carbon sequestration in Mediterranean habitats. In particular, we aimed to use bacterial laccase-encoding genes as molecular markers for soil organic C cycling. Using rainfed olive farming as an experimental model, we determined the stability and accumulation levels of humic substances and applied these data to bacterial laccase-encoding gene expression and diversity in soils under four different agricultural management systems (bare soils under tillage/no tillage and vegetation cover under chemical/mechanical management). Materials and Methods: Humic C (> 104 Da) was subjected to isoelectric focusing. The GC-MS method was used to analyze aromatic hydrocarbons. Real-Time PCR quantification and denaturing gradient gel electrophoresis (DGGE) for functional bacterial laccase-like multicopper oxidase (LMCO)-encoding genes and transcripts were also carried out. Results: Soils under spontaneous vegetation, eliminated in springtime using mechanical methods for more than 30 years, showed the highest humic acid levels as well as the largest bacterial population rich in laccase genes and transcripts. The structure of the bacterial community based on LMCO genes also pointed to phylogenetic differences between these soils due to the impact of different management systems. Soils where herbicides were used to eliminate spontaneous vegetation once a year and those where pre-emergence herbicides resulted in bare soils clustered together for DNA-based DGGE analysis, which indicated a certain amount of microbial selection due to the application of herbicides. When LMCO-encoding gene expression was studied, soils where cover vegetation was managed either with herbicides or with mechanical methods showed less than 10% similarity, suggesting that the type of weed management strategy used can impact weed community composition and consequently laccase substrates derived from vegetation decay. Con…
bibliographic citation: Moreno et al. (2016) Impact of agricultural management on bacterial laccase-encoding genes with possible implications for soil carbon storage in semi-arid Mediterranean olive farming. PeerJ 4:e2257 https://doi.org/10.7717/peerj.2257
date submitted: 2016-03-16
date accepted: 2016-06-24
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreno
  given name: Beatriz
author list: Agent
  family name: Benitez
  given name: Emilio
doi: 10.7717/peerj.2257
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: © 2016 Moreno & Benitez
attribution name: Moreno & Benitez

Detection of methylation, acetylation and glycosylation of protein residues by monitoring 13C chemical-shift changes: A quantum-chemical study
type: item
type: AcademicArticle
description: Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here the feasibility of using 13C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the 13C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a proof-of-concept, we used 13C chemical shifts, computed at the DFT-level of theory, to test this hypothesis. Moreover, as a validation test of this approach, we compare our theoretical computations of the 13Cε chemical-shift values against existing experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ∼1 ppm. Then, further use of this approach to select the most suitable 13C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.
format: application/pdf
format: text/html
creator: Pablo G. Garay
creator: Osvaldo A. Martin
creator: Harold A. Scheraga
creator: Jorge A. Vila
subject: Biochemistry
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.2253
publisher: PeerJ Inc.
rights: © 2016 Garay et al.
abstract: Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here the feasibility of using 13C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the 13C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a proof-of-concept, we used 13C chemical shifts, computed at the DFT-level of theory, to test this hypothesis. Moreover, as a validation test of this approach, we compare our theoretical computations of the 13Cε chemical-shift values against existing experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ∼1 ppm. Then, further use of this approach to select the most suitable 13C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.
bibliographic citation: Garay et al. (2016) Detection of methylation, acetylation and glycosylation of protein residues by monitoring 13C chemical-shift changes: A quantum-chemical study. PeerJ 4:e2253 https://doi.org/10.7717/peerj.2253
date submitted: 2016-04-20
date accepted: 2016-06-23
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garay
  given name: Pablo G.
author list: Agent
  family name: Martin
  given name: Osvaldo A.
author list: Agent
  family name: Scheraga
  given name: Harold A.
author list: Agent
  family name: Vila
  given name: Jorge A.
doi: 10.7717/peerj.2253
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Garay et al.
attribution name: Garay et al.

Simultaneous bilateral laser therapy accelerates recovery after noise-induced hearing loss in a rat model
type: item
type: AcademicArticle
description: Noise-induced hearing loss is a common type of hearing loss. The effects of laser therapy have been investigated from various perspectives, including in wound healing, inflammation reduction, and nerve regeneration, as well as in hearing research. A promising feature of the laser is its capability to penetrate soft tissue; depending on the wavelength, laser energy can penetrate into the deepest part of the body without damaging non-target soft tissues. Based on this idea, we developed bilateral transtympanic laser therapy, which uses simultaneous laser irradiation in both ears, and evaluated the effects of bilateral laser therapy on cochlear damage caused by noise overexposure. Thus, the purpose of this research was to assess the benefits of simultaneous bilateral laser therapy compared with unilateral laser therapy and a control. Eighteen Sprague-Dawley rats were exposed to narrow-band noise at 115 dB SPL for 6 h. Multiple auditory brainstem responses were measured after each laser irradiation, and cochlear hair cells were counted after the 15th such irradiation. The penetration depth of the 808 nm laser was also measured after sacrifice. Approximately 5% of the laser energy reached the contralateral cochlea. Both bilateral and unilateral laser therapy decreased the hearing threshold after noise overstimulation in the rat model. The bilateral laser therapy group showed faster functional recovery at all tested frequencies compared with the unilateral laser therapy group. However, there was no difference in the endpoint ABR results or final hair cell survival, which was analyzed histologically.
format: application/pdf
format: text/html
creator: Jae-Hun Lee
creator: So-Young Chang
creator: Wesley J. Moy
creator: Connie Oh
creator: Se-Hyung Kim
creator: Chung-Ku Rhee
creator: Jin-Chul Ahn
creator: Phil-Sang Chung
creator: Jae Yun Jung
creator: Min Young Lee
subject: Neuroscience
subject: Otorhinolaryngology
description: doi:10.7717/peerj.2252
publisher: PeerJ Inc.
rights: © 2016 Lee et al.
abstract: Noise-induced hearing loss is a common type of hearing loss. The effects of laser therapy have been investigated from various perspectives, including in wound healing, inflammation reduction, and nerve regeneration, as well as in hearing research. A promising feature of the laser is its capability to penetrate soft tissue; depending on the wavelength, laser energy can penetrate into the deepest part of the body without damaging non-target soft tissues. Based on this idea, we developed bilateral transtympanic laser therapy, which uses simultaneous laser irradiation in both ears, and evaluated the effects of bilateral laser therapy on cochlear damage caused by noise overexposure. Thus, the purpose of this research was to assess the benefits of simultaneous bilateral laser therapy compared with unilateral laser therapy and a control. Eighteen Sprague-Dawley rats were exposed to narrow-band noise at 115 dB SPL for 6 h. Multiple auditory brainstem responses were measured after each laser irradiation, and cochlear hair cells were counted after the 15th such irradiation. The penetration depth of the 808 nm laser was also measured after sacrifice. Approximately 5% of the laser energy reached the contralateral cochlea. Both bilateral and unilateral laser therapy decreased the hearing threshold after noise overstimulation in the rat model. The bilateral laser therapy group showed faster functional recovery at all tested frequencies compared with the unilateral laser therapy group. However, there was no difference in the endpoint ABR results or final hair cell survival, which was analyzed histologically.
bibliographic citation: Lee et al. (2016) Simultaneous bilateral laser therapy accelerates recovery after noise-induced hearing loss in a rat model. PeerJ 4:e2252 https://doi.org/10.7717/peerj.2252
date submitted: 2016-05-10
date accepted: 2016-06-23
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Jae-Hun
author list: Agent
  family name: Chang
  given name: So-Young
author list: Agent
  family name: Moy
  given name: Wesley J.
author list: Agent
  family name: Oh
  given name: Connie
author list: Agent
  family name: Kim
  given name: Se-Hyung
author list: Agent
  family name: Rhee
  given name: Chung-Ku
author list: Agent
  family name: Ahn
  given name: Jin-Chul
author list: Agent
  family name: Chung
  given name: Phil-Sang
author list: Agent
  family name: Jung
  given name: Jae Yun
author list: Agent
  family name: Lee
  given name: Min Young
doi: 10.7717/peerj.2252
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Lee et al.
attribution name: Lee et al.

Neural and endocranial anatomy of Triassic phytosaurian reptiles and convergence with fossil and modern crocodylians
type: item
type: AcademicArticle
description: Phytosaurs are a clade of large, carnivorous pseudosuchian archosaurs from the Late Triassic with a near cosmopolitan distribution. Their superficial resemblance to longirostrine (long-snouted) crocodylians, such as gharials, has often been used in the past to infer ecological and behavioural convergence between the two groups. Although more than thirty species of phytosaur are currently recognised, little is known about the endocranial anatomy of this clade. Here, we describe the endocranial anatomy (including the brain, inner ear, neurovascular structures and sinus systems) of the two non-mystriosuchine phytosaurs Parasuchus angustifrons (=“Paleorhinus angustifrons”) and Ebrachosuchus neukami from the Late Triassic of Germany based on digital reconstructions. Results show that the endocasts of both taxa are very similar to each other in their rostrocaudally elongate morphology, with long olfactory tracts, weakly demarcated cerebral regions and dorsoventrally short endosseous labyrinths. In addition, several sinuses, including large antorbital sinuses and prominent dural venous sinuses, were reconstructed. Comparisons with the endocranial anatomy of derived phytosaurs indicate that Phytosauria is united by the presence of elongate olfactory tracts and longitudinally arranged brain architecture—characters which are also shared with Crocodyliformes. However, a substantial morphological variability is observed in the cephalic and pontine flexure and the presence of a pineal organ across the different phytosaur species. These results suggest that the endocranial anatomy in Phytosauria generally follows a plesiomorphic pattern, with moderate variation within the clade likely resulting from divergent sensory and behavioural adaptations.
format: application/pdf
format: text/html
creator: Stephan Lautenschlager
creator: Richard J. Butler
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.2251
publisher: PeerJ Inc.
rights: © 2016 Lautenschlager and Butler
abstract: Phytosaurs are a clade of large, carnivorous pseudosuchian archosaurs from the Late Triassic with a near cosmopolitan distribution. Their superficial resemblance to longirostrine (long-snouted) crocodylians, such as gharials, has often been used in the past to infer ecological and behavioural convergence between the two groups. Although more than thirty species of phytosaur are currently recognised, little is known about the endocranial anatomy of this clade. Here, we describe the endocranial anatomy (including the brain, inner ear, neurovascular structures and sinus systems) of the two non-mystriosuchine phytosaurs Parasuchus angustifrons (=“Paleorhinus angustifrons”) and Ebrachosuchus neukami from the Late Triassic of Germany based on digital reconstructions. Results show that the endocasts of both taxa are very similar to each other in their rostrocaudally elongate morphology, with long olfactory tracts, weakly demarcated cerebral regions and dorsoventrally short endosseous labyrinths. In addition, several sinuses, including large antorbital sinuses and prominent dural venous sinuses, were reconstructed. Comparisons with the endocranial anatomy of derived phytosaurs indicate that Phytosauria is united by the presence of elongate olfactory tracts and longitudinally arranged brain architecture—characters which are also shared with Crocodyliformes. However, a substantial morphological variability is observed in the cephalic and pontine flexure and the presence of a pineal organ across the different phytosaur species. These results suggest that the endocranial anatomy in Phytosauria generally follows a plesiomorphic pattern, with moderate variation within the clade likely resulting from divergent sensory and behavioural adaptations.
bibliographic citation: Lautenschlager et al. (2016) Neural and endocranial anatomy of Triassic phytosaurian reptiles and convergence with fossil and modern crocodylians. PeerJ 4:e2251 https://doi.org/10.7717/peerj.2251
date submitted: 2016-04-30
date accepted: 2016-06-22
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lautenschlager
  given name: Stephan
author list: Agent
  family name: Butler
  given name: Richard J.
doi: 10.7717/peerj.2251
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Lautenschlager and Butler
attribution name: Lautenschlager and Butler

Percentile curves for skinfold thickness for Canadian children and youth
type: item
type: AcademicArticle
description: Background. Skinfold thickness (SFT) measurements are a reliable and feasible method for assessing body fat in children but their use and interpretation is hindered by the scarcity of reference values in representative populations of children. The objective of the present study was to develop age- and sex-specific percentile curves for five SFT measures (biceps, triceps, subscapular, suprailiac, medial calf) in a representative population of Canadian children and youth. Methods. We analyzed data from 3,938 children and adolescents between 6 and 19 years of age who participated in the Canadian Health Measures Survey cycles 1 (2007/2009) and 2 (2009/2011). Standardized procedures were used to measure SFT. Age- and sex-specific centiles for SFT were calculated using the GAMLSS method. Results. Percentile curves were materially different in absolute value and shape for boys and girls. Percentile girls in girls steadily increased with age whereas percentile curves in boys were characterized by a pubertal centered peak. Conclusions. The current study has presented for the first time percentile curves for five SFT measures in a representative sample of Canadian children and youth.
format: application/pdf
format: text/html
creator: Stefan Kuhle
creator: Jillian Ashley-Martin
creator: Bryan Maguire
creator: David C. Hamilton
subject: Epidemiology
subject: Nutrition
subject: Pediatrics
subject: Public Health
subject: Statistics
description: doi:10.7717/peerj.2247
publisher: PeerJ Inc.
rights: © 2016 Kuhle et al.
abstract: Background. Skinfold thickness (SFT) measurements are a reliable and feasible method for assessing body fat in children but their use and interpretation is hindered by the scarcity of reference values in representative populations of children. The objective of the present study was to develop age- and sex-specific percentile curves for five SFT measures (biceps, triceps, subscapular, suprailiac, medial calf) in a representative population of Canadian children and youth. Methods. We analyzed data from 3,938 children and adolescents between 6 and 19 years of age who participated in the Canadian Health Measures Survey cycles 1 (2007/2009) and 2 (2009/2011). Standardized procedures were used to measure SFT. Age- and sex-specific centiles for SFT were calculated using the GAMLSS method. Results. Percentile curves were materially different in absolute value and shape for boys and girls. Percentile girls in girls steadily increased with age whereas percentile curves in boys were characterized by a pubertal centered peak. Conclusions. The current study has presented for the first time percentile curves for five SFT measures in a representative sample of Canadian children and youth.
bibliographic citation: Kuhle et al. (2016) Percentile curves for skinfold thickness for Canadian children and youth. PeerJ 4:e2247 https://doi.org/10.7717/peerj.2247
date submitted: 2016-05-17
date accepted: 2016-06-22
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kuhle
  given name: Stefan
author list: Agent
  family name: Ashley-Martin
  given name: Jillian
author list: Agent
  family name: Maguire
  given name: Bryan
author list: Agent
  family name: Hamilton
  given name: David C.
doi: 10.7717/peerj.2247
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Kuhle et al.
attribution name: Kuhle et al.

Emotional intelligence and depressive symptoms in Spanish institutionalized elders: does emotional self-efficacy act as a mediator?
type: item
type: AcademicArticle
description: Background. This work examines the relationship between emotional intelligence (EI) and depressive symptomatology in institutionalized older adults, delving into the mechanisms underlying this relationship. Considering that previous evidence of the variation of the EI-depression relationship depending on whether the emotional ability or the perception of that ability is evaluated, a model of multiple mediation was tested in which the dimensions of emotional self-efficacy (ESE) act as mediators in the relationship between ability EI and depressive symptomatology. Methods. The sample consisted of 115 institutionalized older adults (47.82% women; 80.3 ± 7.9 years of age) from the province of Jaén (Spain) who completed a test of ESE, a measure of ability EI, and a self-administered questionnaire of depressive symptoms. Results. The results showed a positive association between older adults’ emotional performance and depressive symptomatology, finding stronger associations with ESE than with EI abilities. In addition, multiple mediation analyses showed that two of the four dimensions of ESE fully mediated the relationship between ability EI and depressive symptoms. Discussion. These findings suggest that older adults’ high levels of emotional competence generate a feeling of ESE which can protect them against depressive symptoms. This work supports the predictive validity of emotional abilities and ESE for the mental health of a group that is particularly vulnerable to depression, institutionalized older adults. The limitations of the work are discussed, and future lines of research were considered.
format: application/pdf
format: text/html
creator: Octavio Luque-Reca
creator: José María Augusto-Landa
creator: Manuel Pulido-Martos
subject: Geriatrics
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2246
publisher: PeerJ Inc.
rights: © 2016 Luque-Reca et al.
abstract: Background. This work examines the relationship between emotional intelligence (EI) and depressive symptomatology in institutionalized older adults, delving into the mechanisms underlying this relationship. Considering that previous evidence of the variation of the EI-depression relationship depending on whether the emotional ability or the perception of that ability is evaluated, a model of multiple mediation was tested in which the dimensions of emotional self-efficacy (ESE) act as mediators in the relationship between ability EI and depressive symptomatology. Methods. The sample consisted of 115 institutionalized older adults (47.82% women; 80.3 ± 7.9 years of age) from the province of Jaén (Spain) who completed a test of ESE, a measure of ability EI, and a self-administered questionnaire of depressive symptoms. Results. The results showed a positive association between older adults’ emotional performance and depressive symptomatology, finding stronger associations with ESE than with EI abilities. In addition, multiple mediation analyses showed that two of the four dimensions of ESE fully mediated the relationship between ability EI and depressive symptoms. Discussion. These findings suggest that older adults’ high levels of emotional competence generate a feeling of ESE which can protect them against depressive symptoms. This work supports the predictive validity of emotional abilities and ESE for the mental health of a group that is particularly vulnerable to depression, institutionalized older adults. The limitations of the work are discussed, and future lines of research were considered.
bibliographic citation: Luque-Reca et al. (2016) Emotional intelligence and depressive symptoms in Spanish institutionalized elders: does emotional self-efficacy act as a mediator?. PeerJ 4:e2246 https://doi.org/10.7717/peerj.2246
date submitted: 2016-03-04
date accepted: 2016-06-22
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luque-Reca
  given name: Octavio
author list: Agent
  family name: Augusto-Landa
  given name: José María
author list: Agent
  family name: Pulido-Martos
  given name: Manuel
doi: 10.7717/peerj.2246
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Luque-Reca et al.
attribution name: Luque-Reca et al.

Fast men slow more than fast women in a 10 kilometer road race
type: item
type: AcademicArticle
description: Background. Previous studies have demonstrated that men are more likely than women to slow in the marathon (footrace). This study investigated whether the sex difference in pacing occurs for a shorter race distance. Materials & Methods. Data were acquired from the Bolder Boulder 10 km road race for the years 2008–2013, which encompassed 191,693 performances. There were two pacing measures, percentage change in pace of the first 3 miles relative to the final 3.2 miles and percentage change in pace of the first mile relative to the final 5.2 miles. Pacing was analyzed as a continuous variable and as two categorical variables, as follows: “maintain the pace,” defined as slowing <5% and “marked slowing,” defined as slowing ≥10%. Results. Among the fastest (men < 48:40; women < 55:27) and second fastest (men < 53:54; women < 60:28) sex-specific finishing time sextiles, men slowed significantly more than women with both pacing measures, but there were no consistently significant sex differences in pacing among the slower four sextiles. For the fastest sextile, the odds for women were 1.96 (first pacing measure) and 1.36 (second measure) times greater than men to maintain the pace. For the fastest sextile, the odds for women were 0.46 (first measure) and 0.65 (second measure) times that of men to exhibit marked slowing. Multiple regression indicated that being older was associated with lesser slowing, but the sex difference among faster runners persisted when age was controlled. Conclusions. There was a sex difference in pacing during a 10 km race where glycogen depletion is not typically relevant. These results support the hypothesis that the sex difference in pacing partly reflects a sex difference in decision making.
format: application/pdf
format: text/html
creator: Robert O. Deaner
creator: Vittorio Addona
creator: Rickey E. Carter
creator: Michael J. Joyner
creator: Sandra K. Hunter
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2235
publisher: PeerJ Inc.
rights: © 2016 Deaner et al.
abstract: Background. Previous studies have demonstrated that men are more likely than women to slow in the marathon (footrace). This study investigated whether the sex difference in pacing occurs for a shorter race distance. Materials & Methods. Data were acquired from the Bolder Boulder 10 km road race for the years 2008–2013, which encompassed 191,693 performances. There were two pacing measures, percentage change in pace of the first 3 miles relative to the final 3.2 miles and percentage change in pace of the first mile relative to the final 5.2 miles. Pacing was analyzed as a continuous variable and as two categorical variables, as follows: “maintain the pace,” defined as slowing <5% and “marked slowing,” defined as slowing ≥10%. Results. Among the fastest (men < 48:40; women < 55:27) and second fastest (men < 53:54; women < 60:28) sex-specific finishing time sextiles, men slowed significantly more than women with both pacing measures, but there were no consistently significant sex differences in pacing among the slower four sextiles. For the fastest sextile, the odds for women were 1.96 (first pacing measure) and 1.36 (second measure) times greater than men to maintain the pace. For the fastest sextile, the odds for women were 0.46 (first measure) and 0.65 (second measure) times that of men to exhibit marked slowing. Multiple regression indicated that being older was associated with lesser slowing, but the sex difference among faster runners persisted when age was controlled. Conclusions. There was a sex difference in pacing during a 10 km race where glycogen depletion is not typically relevant. These results support the hypothesis that the sex difference in pacing partly reflects a sex difference in decision making.
bibliographic citation: Deaner et al. (2016) Fast men slow more than fast women in a 10 kilometer road race. PeerJ 4:e2235 https://doi.org/10.7717/peerj.2235
date submitted: 2016-05-13
date accepted: 2016-06-20
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deaner
  given name: Robert O.
author list: Agent
  family name: Addona
  given name: Vittorio
author list: Agent
  family name: Carter
  given name: Rickey E.
author list: Agent
  family name: Joyner
  given name: Michael J.
author list: Agent
  family name: Hunter
  given name: Sandra K.
doi: 10.7717/peerj.2235
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Deaner et al.
attribution name: Deaner et al.

Computer-assisted initial diagnosis of rare diseases
type: item
type: AcademicArticle
description: Introduction. Most documented rare diseases have genetic origin. Because of their low individual frequency, an initial diagnosis based on phenotypic symptoms is not always easy, as practitioners might never have been exposed to patients suffering from the relevant disease. It is thus important to develop tools that facilitate symptom-based initial diagnosis of rare diseases by clinicians. In this work we aimed at developing a computational approach to aid in that initial diagnosis. We also aimed at implementing this approach in a user friendly web prototype. We call this tool Rare Disease Discovery. Finally, we also aimed at testing the performance of the prototype. Methods. Rare Disease Discovery uses the publicly available ORPHANET data set of association between rare diseases and their symptoms to automatically predict the most likely rare diseases based on a patient’s symptoms. We apply the method to retrospectively diagnose a cohort of 187 rare disease patients with confirmed diagnosis. Subsequently we test the precision, sensitivity, and global performance of the system under different scenarios by running large scale Monte Carlo simulations. All settings account for situations where absent and/or unrelated symptoms are considered in the diagnosis. Results. We find that this expert system has high diagnostic precision (≥80%) and sensitivity (≥99%), and is robust to both absent and unrelated symptoms. Discussion. The Rare Disease Discovery prediction engine appears to provide a fast and robust method for initial assisted differential diagnosis of rare diseases. We coupled this engine with a user-friendly web interface and it can be freely accessed at http://disease-discovery.udl.cat/. The code and most current database for the whole project can be downloaded from https://github.com/Wrrzag/DiseaseDiscovery/tree/no_classifiers.
format: application/pdf
format: text/html
creator: Rui Alves
creator: Marc Piñol
creator: Jordi Vilaplana
creator: Ivan Teixidó
creator: Joaquim Cruz
creator: Jorge Comas
creator: Ester Vilaprinyo
creator: Albert Sorribas
creator: Francesc Solsona
subject: Bioinformatics
subject: Evidence Based Medicine
subject: Translational Medicine
subject: Science and Medical Education
subject: Computational Science
description: doi:10.7717/peerj.2211
publisher: PeerJ Inc.
rights: © 2016 Alves et al.
abstract: Introduction. Most documented rare diseases have genetic origin. Because of their low individual frequency, an initial diagnosis based on phenotypic symptoms is not always easy, as practitioners might never have been exposed to patients suffering from the relevant disease. It is thus important to develop tools that facilitate symptom-based initial diagnosis of rare diseases by clinicians. In this work we aimed at developing a computational approach to aid in that initial diagnosis. We also aimed at implementing this approach in a user friendly web prototype. We call this tool Rare Disease Discovery. Finally, we also aimed at testing the performance of the prototype. Methods. Rare Disease Discovery uses the publicly available ORPHANET data set of association between rare diseases and their symptoms to automatically predict the most likely rare diseases based on a patient’s symptoms. We apply the method to retrospectively diagnose a cohort of 187 rare disease patients with confirmed diagnosis. Subsequently we test the precision, sensitivity, and global performance of the system under different scenarios by running large scale Monte Carlo simulations. All settings account for situations where absent and/or unrelated symptoms are considered in the diagnosis. Results. We find that this expert system has high diagnostic precision (≥80%) and sensitivity (≥99%), and is robust to both absent and unrelated symptoms. Discussion. The Rare Disease Discovery prediction engine appears to provide a fast and robust method for initial assisted differential diagnosis of rare diseases. We coupled this engine with a user-friendly web interface and it can be freely accessed at http://disease-discovery.udl.cat/. The code and most current database for the whole project can be downloaded from https://github.com/Wrrzag/DiseaseDiscovery/tree/no_classifiers.
bibliographic citation: Alves et al. (2016) Computer-assisted initial diagnosis of rare diseases. PeerJ 4:e2211 https://doi.org/10.7717/peerj.2211
date submitted: 2016-02-06
date accepted: 2016-06-13
issued: 2016-07-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alves
  given name: Rui
author list: Agent
  family name: Piñol
  given name: Marc
author list: Agent
  family name: Vilaplana
  given name: Jordi
author list: Agent
  family name: Teixidó
  given name: Ivan
author list: Agent
  family name: Cruz
  given name: Joaquim
author list: Agent
  family name: Comas
  given name: Jorge
author list: Agent
  family name: Vilaprinyo
  given name: Ester
author list: Agent
  family name: Sorribas
  given name: Albert
author list: Agent
  family name: Solsona
  given name: Francesc
doi: 10.7717/peerj.2211
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-07-21
copyright: ©2016 Alves et al.
attribution name: Alves et al.

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