PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of 14-day oral low dose selenium nanoparticles and selenite in rat—as determined by metabolite pattern determination
items: Ecological solutions to reef degradation: optimizing coral reef restoration in the Caribbean and Western Atlantic
items: A revision of Sanpasaurus yaoi Young, 1944 from the Early Jurassic of China, and its relevance to the early evolution of Sauropoda (Dinosauria)
items: Predictions of potential geographical distribution and quality of Schisandra sphenanthera under climate change
items: Single-agent maintenance therapy for advanced non-small cell lung cancer (NSCLC): a systematic review and Bayesian network meta-analysis of 26 randomized controlled trials
items: Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer
items: The cranial endocast of Dipnorhynchus sussmilchi (Sarcopterygii: Dipnoi) and the interrelationships of stem-group lungfishes
items: Climate-related environmental stress in intertidal grazers: scaling-up biochemical responses to assemblage-level processes
items: The influence of flight style on the aerodynamic properties of avian wings as fixed lifting surfaces
items: Intranodal signal suppression in pelvic MR lymphography of prostate cancer patients: a quantitative comparison of ferumoxtran-10 and ferumoxytol

Effects of 14-day oral low dose selenium nanoparticles and selenite in rat—as determined by metabolite pattern determination
type: item
type: AcademicArticle
description: Selenium (Se) is an essential element with a small difference between physiological and toxic doses. To provide more effective and safe Se dosing regimens, as compared to dosing with ionic selenium, nanoparticle formulations have been developed. However, due to the nano-formulation, unexpected toxic effects may occur. We used metabolite pattern determination in urine to investigate biological and/or toxic effects in rats administered nanoparticles and for comparison included ionic selenium at an equimolar dose in the form of sodium selenite. Low doses of 10 and 100 fold the recommended human high level were employed to study the effects at borderline toxicity. Evaluations of all significantly changed putative metabolites, showed that Se nanoparticles and sodium selenite induced similar dose dependent changes of the metabolite pattern. Putative identified metabolites included increased decenedioic acid and hydroxydecanedioic acid for both Se formulations whereas dipeptides were only increased for selenite. These effects could reflect altered fatty acid and protein metabolism, respectively.
format: application/pdf
format: text/html
creator: Niels Hadrup
creator: Katrin Loeschner
creator: Kasper Skov
creator: Gitte Ravn-Haren
creator: Erik H. Larsen
creator: Alicja Mortensen
creator: Henrik R. Lam
creator: Henrik L. Frandsen
subject: Food Science and Technology
subject: Toxicology
subject: Pharmacology
subject: Metabolic Sciences
description: doi:10.7717/peerj.2601
publisher: PeerJ Inc.
rights: © 2016 Hadrup et al.
abstract: Selenium (Se) is an essential element with a small difference between physiological and toxic doses. To provide more effective and safe Se dosing regimens, as compared to dosing with ionic selenium, nanoparticle formulations have been developed. However, due to the nano-formulation, unexpected toxic effects may occur. We used metabolite pattern determination in urine to investigate biological and/or toxic effects in rats administered nanoparticles and for comparison included ionic selenium at an equimolar dose in the form of sodium selenite. Low doses of 10 and 100 fold the recommended human high level were employed to study the effects at borderline toxicity. Evaluations of all significantly changed putative metabolites, showed that Se nanoparticles and sodium selenite induced similar dose dependent changes of the metabolite pattern. Putative identified metabolites included increased decenedioic acid and hydroxydecanedioic acid for both Se formulations whereas dipeptides were only increased for selenite. These effects could reflect altered fatty acid and protein metabolism, respectively.
bibliographic citation: Hadrup et al. (2016) Effects of 14-day oral low dose selenium nanoparticles and selenite in rat—as determined by metabolite pattern determination. PeerJ 4:e2601 https://doi.org/10.7717/peerj.2601
date submitted: 2016-06-21
date accepted: 2016-09-23
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Hadrup
  given name: Niels
author list: Agent
  family name: Loeschner
  given name: Katrin
author list: Agent
  family name: Skov
  given name: Kasper
author list: Agent
  family name: Ravn-Haren
  given name: Gitte
author list: Agent
  family name: Larsen
  given name: Erik H.
author list: Agent
  family name: Mortensen
  given name: Alicja
author list: Agent
  family name: Lam
  given name: Henrik R.
author list: Agent
  family name: Frandsen
  given name: Henrik L.
doi: 10.7717/peerj.2601
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: ©2016 Hadrup et al.
attribution name: Hadrup et al.

Ecological solutions to reef degradation: optimizing coral reef restoration in the Caribbean and Western Atlantic
type: item
type: AcademicArticle
description: Reef restoration activities have proliferated in response to the need to mitigate coral declines and recover lost reef structure, function, and ecosystem services. Here, we describe the recent shift from costly and complex engineering solutions to recover degraded reef structure to more economical and efficient ecological approaches that focus on recovering the living components of reef communities. We review the adoption and expansion of the coral gardening framework in the Caribbean and Western Atlantic where practitioners now grow and outplant 10,000’s of corals onto degraded reefs each year. We detail the steps for establishing a gardening program as well as long-term goals and direct and indirect benefits of this approach in our region. With a strong scientific basis, coral gardening activities now contribute significantly to reef and species recovery, provide important scientific, education, and outreach opportunities, and offer alternate livelihoods to local stakeholders. While challenges still remain, the transition from engineering to ecological solutions for reef degradation has opened the field of coral reef restoration to a wider audience poised to contribute to reef conservation and recovery in regions where coral losses and recruitment bottlenecks hinder natural recovery.
format: application/pdf
format: text/html
creator: Diego Lirman
creator: Stephanie Schopmeyer
subject: Conservation Biology
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.2597
publisher: PeerJ Inc.
rights: © 2016 Lirman and Schopmeyer
abstract: Reef restoration activities have proliferated in response to the need to mitigate coral declines and recover lost reef structure, function, and ecosystem services. Here, we describe the recent shift from costly and complex engineering solutions to recover degraded reef structure to more economical and efficient ecological approaches that focus on recovering the living components of reef communities. We review the adoption and expansion of the coral gardening framework in the Caribbean and Western Atlantic where practitioners now grow and outplant 10,000’s of corals onto degraded reefs each year. We detail the steps for establishing a gardening program as well as long-term goals and direct and indirect benefits of this approach in our region. With a strong scientific basis, coral gardening activities now contribute significantly to reef and species recovery, provide important scientific, education, and outreach opportunities, and offer alternate livelihoods to local stakeholders. While challenges still remain, the transition from engineering to ecological solutions for reef degradation has opened the field of coral reef restoration to a wider audience poised to contribute to reef conservation and recovery in regions where coral losses and recruitment bottlenecks hinder natural recovery.
bibliographic citation: Lirman et al. (2016) Ecological solutions to reef degradation: optimizing coral reef restoration in the Caribbean and Western Atlantic. PeerJ 4:e2597 https://doi.org/10.7717/peerj.2597
date submitted: 2016-08-15
date accepted: 2016-09-16
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lirman
  given name: Diego
author list: Agent
  family name: Schopmeyer
  given name: Stephanie
doi: 10.7717/peerj.2597
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: © 2016 Lirman and Schopmeyer
attribution name: Lirman and Schopmeyer

A revision of Sanpasaurus yaoi Young, 1944 from the Early Jurassic of China, and its relevance to the early evolution of Sauropoda (Dinosauria)
type: item
type: AcademicArticle
description: The Early Jurassic of China has long been recognized for its diverse array of sauropodomorph dinosaurs. However, the contribution of this record to our understanding of early sauropod evolution is complicated by a dearth of information on important transitional taxa. We present a revision of the poorly known taxon Sanpasaurus yaoi Young, 1944 from the late Early Jurassic Ziliujing Formation of Sichuan Province, southwest China. Initially described as the remains of an ornithopod ornithischian, we demonstrate that the material catalogued as IVPP V156 is unambiguously referable to Sauropoda. Although represented by multiple individuals of equivocal association, Sanpasaurus is nonetheless diagnosable with respect to an autapomorphic feature of the holotypic dorsal vertebral series. Additional material thought to be collected from the type locality is tentatively referred to Sanpasaurus. If correctly attributed, a second autapomorphy is present in a referred humerus. The presence of a dorsoventrally compressed pedal ungual in Sanpasaurus is of particular interest, with taxa possessing this typically ‘vulcanodontid’ character exhibiting a much broader geographic distribution than previously thought. Furthermore, the association of this trait with other features of Sanpasaurus that are broadly characteristic of basal eusauropods underscores the mosaic nature of the early sauropod–eusauropod transition. Our revision of Sanpasaurus has palaeobiogeographic implications for Early Jurassic sauropods, with evidence that the group maintained a cosmopolitan Pangaean distribution.
format: application/pdf
format: text/html
creator: Blair W. McPhee
creator: Paul Upchurch
creator: Philip D. Mannion
creator: Corwin Sullivan
creator: Richard J. Butler
creator: Paul M. Barrett
subject: Biogeography
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.2578
publisher: PeerJ Inc.
rights: © 2016 McPhee et al.
abstract: The Early Jurassic of China has long been recognized for its diverse array of sauropodomorph dinosaurs. However, the contribution of this record to our understanding of early sauropod evolution is complicated by a dearth of information on important transitional taxa. We present a revision of the poorly known taxon Sanpasaurus yaoi Young, 1944 from the late Early Jurassic Ziliujing Formation of Sichuan Province, southwest China. Initially described as the remains of an ornithopod ornithischian, we demonstrate that the material catalogued as IVPP V156 is unambiguously referable to Sauropoda. Although represented by multiple individuals of equivocal association, Sanpasaurus is nonetheless diagnosable with respect to an autapomorphic feature of the holotypic dorsal vertebral series. Additional material thought to be collected from the type locality is tentatively referred to Sanpasaurus. If correctly attributed, a second autapomorphy is present in a referred humerus. The presence of a dorsoventrally compressed pedal ungual in Sanpasaurus is of particular interest, with taxa possessing this typically ‘vulcanodontid’ character exhibiting a much broader geographic distribution than previously thought. Furthermore, the association of this trait with other features of Sanpasaurus that are broadly characteristic of basal eusauropods underscores the mosaic nature of the early sauropod–eusauropod transition. Our revision of Sanpasaurus has palaeobiogeographic implications for Early Jurassic sauropods, with evidence that the group maintained a cosmopolitan Pangaean distribution.
bibliographic citation: McPhee et al. (2016) A revision of Sanpasaurus yaoi Young, 1944 from the Early Jurassic of China, and its relevance to the early evolution of Sauropoda (Dinosauria). PeerJ 4:e2578 https://doi.org/10.7717/peerj.2578
date submitted: 2016-08-02
date accepted: 2016-09-16
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McPhee
  given name: Blair W.
author list: Agent
  family name: Upchurch
  given name: Paul
author list: Agent
  family name: Mannion
  given name: Philip D.
author list: Agent
  family name: Sullivan
  given name: Corwin
author list: Agent
  family name: Butler
  given name: Richard J.
author list: Agent
  family name: Barrett
  given name: Paul M.
doi: 10.7717/peerj.2578
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: © 2016 McPhee et al.
attribution name: McPhee et al.

Predictions of potential geographical distribution and quality of Schisandra sphenanthera under climate change
type: item
type: AcademicArticle
description: Climate change will significantly affect plant distribution as well as the quality of medicinal plants. Although numerous studies have analyzed the effect of climate change on future habitats of plants through species distribution models (SDMs), few of them have incorporated the change of effective content of medicinal plants. Schisandra sphenanthera Rehd. et Wils. is an endangered traditional Chinese medical plant which is mainly located in the Qinling Mountains. Combining fuzzy theory and a maximum entropy model, we obtained current spatial distribution of quality assessment for S. spenanthera. Moreover, the future quality and distribution of S. spenanthera were also projected for the periods 2020s, 2050s and 2080s under three different climate change scenarios (SRES-A1B, SRES-A2 and SRES-B1 emission scenarios) described in the Special Report on Emissions Scenarios (SRES) of IPCC (Intergovernmental Panel on Climate Change). The results showed that the moderately suitable habitat of S. sphenanthera under all climate change scenarios remained relatively stable in the study area. The highly suitable habitat of S. sphenanthera would gradually decrease in the future and a higher decline rate of the highly suitable habitat area would occur under climate change scenarios SRES-A1B and SRES-A2. The result suggested that in the study area, there would be no more highly suitable habitat areas for S. sphenanthera when the annual mean temperature exceeds 20 °C or its annual precipitation exceeds 1,200 mm. Our results will be influential in the future ecological conservation and management of S. sphenanthera and can be taken as a reference for habitat suitability assessment research for other medicinal plants.
format: application/pdf
format: text/html
creator: Yanlong Guo
creator: Haiyan Wei
creator: Chunyan Lu
creator: Bei Gao
creator: Wei Gu
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Environmental Sciences
subject: Plant Science
description: doi:10.7717/peerj.2554
publisher: PeerJ Inc.
rights: © 2016 Guo et al.
abstract: Climate change will significantly affect plant distribution as well as the quality of medicinal plants. Although numerous studies have analyzed the effect of climate change on future habitats of plants through species distribution models (SDMs), few of them have incorporated the change of effective content of medicinal plants. Schisandra sphenanthera Rehd. et Wils. is an endangered traditional Chinese medical plant which is mainly located in the Qinling Mountains. Combining fuzzy theory and a maximum entropy model, we obtained current spatial distribution of quality assessment for S. spenanthera. Moreover, the future quality and distribution of S. spenanthera were also projected for the periods 2020s, 2050s and 2080s under three different climate change scenarios (SRES-A1B, SRES-A2 and SRES-B1 emission scenarios) described in the Special Report on Emissions Scenarios (SRES) of IPCC (Intergovernmental Panel on Climate Change). The results showed that the moderately suitable habitat of S. sphenanthera under all climate change scenarios remained relatively stable in the study area. The highly suitable habitat of S. sphenanthera would gradually decrease in the future and a higher decline rate of the highly suitable habitat area would occur under climate change scenarios SRES-A1B and SRES-A2. The result suggested that in the study area, there would be no more highly suitable habitat areas for S. sphenanthera when the annual mean temperature exceeds 20 °C or its annual precipitation exceeds 1,200 mm. Our results will be influential in the future ecological conservation and management of S. sphenanthera and can be taken as a reference for habitat suitability assessment research for other medicinal plants.
bibliographic citation: Guo et al. (2016) Predictions of potential geographical distribution and quality of Schisandra sphenanthera under climate change. PeerJ 4:e2554 https://doi.org/10.7717/peerj.2554
date submitted: 2016-03-18
date accepted: 2016-09-12
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Yanlong
author list: Agent
  family name: Wei
  given name: Haiyan
author list: Agent
  family name: Lu
  given name: Chunyan
author list: Agent
  family name: Gao
  given name: Bei
author list: Agent
  family name: Gu
  given name: Wei
doi: 10.7717/peerj.2554
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: ©2016 Guo et al.
attribution name: Guo et al.

Single-agent maintenance therapy for advanced non-small cell lung cancer (NSCLC): a systematic review and Bayesian network meta-analysis of 26 randomized controlled trials
type: item
type: AcademicArticle
description: Background The benefit of maintenance therapy has been confirmed in patients with non-progressing non-small cell lung cancer (NSCLC) after first-line therapy by many trials and meta-analyses. However, since few head-to-head trials between different regimens have been reported, clinicians still have little guidance on how to select the most efficacious single-agent regimen. Hence, we present a network meta-analysis to assess the comparative treatment efficacy of several single-agent maintenance therapy regimens for stage III/IV NSCLC. Methods A comprehensive literature search of public databases and conference proceedings was performed. Randomized clinical trials (RCTs) meeting the eligible criteria were integrated into a Bayesian network meta-analysis. The primary outcome was overall survival (OS) and the secondary outcome was progression free survival (PFS). Results A total of 26 trials covering 7,839 patients were identified, of which 24 trials were included in the OS analysis, while 23 trials were included in the PFS analysis. Switch-racotumomab-alum vaccine and switch-pemetrexed were identified as the most efficacious regimens based on OS (HR, 0.64; 95% CrI, 0.45–0.92) and PFS (HR, 0.54; 95% CrI, 0.26–1.04) separately. According to the rank order based on OS, switch-racotumomab-alum vaccine had the highest probability as the most effective regimen (52%), while switch-pemetrexed ranked first (34%) based on PFS. Conclusions Several single-agent maintenance therapy regimens can prolong OS and PFS for stage III/IV NSCLC. Switch-racotumomab-alum vaccine maintenance therapy may be the most optimal regimen, but should be confirmed by additional evidence.
format: application/pdf
format: text/html
creator: Qinxue Wang
creator: Haobin Huang
creator: Xiaoning Zeng
creator: Yuan Ma
creator: Xin Zhao
creator: Mao Huang
subject: Evidence Based Medicine
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.2550
publisher: PeerJ Inc.
rights: © 2016 Wang et al.
abstract: Background The benefit of maintenance therapy has been confirmed in patients with non-progressing non-small cell lung cancer (NSCLC) after first-line therapy by many trials and meta-analyses. However, since few head-to-head trials between different regimens have been reported, clinicians still have little guidance on how to select the most efficacious single-agent regimen. Hence, we present a network meta-analysis to assess the comparative treatment efficacy of several single-agent maintenance therapy regimens for stage III/IV NSCLC. Methods A comprehensive literature search of public databases and conference proceedings was performed. Randomized clinical trials (RCTs) meeting the eligible criteria were integrated into a Bayesian network meta-analysis. The primary outcome was overall survival (OS) and the secondary outcome was progression free survival (PFS). Results A total of 26 trials covering 7,839 patients were identified, of which 24 trials were included in the OS analysis, while 23 trials were included in the PFS analysis. Switch-racotumomab-alum vaccine and switch-pemetrexed were identified as the most efficacious regimens based on OS (HR, 0.64; 95% CrI, 0.45–0.92) and PFS (HR, 0.54; 95% CrI, 0.26–1.04) separately. According to the rank order based on OS, switch-racotumomab-alum vaccine had the highest probability as the most effective regimen (52%), while switch-pemetrexed ranked first (34%) based on PFS. Conclusions Several single-agent maintenance therapy regimens can prolong OS and PFS for stage III/IV NSCLC. Switch-racotumomab-alum vaccine maintenance therapy may be the most optimal regimen, but should be confirmed by additional evidence.
bibliographic citation: Wang et al. (2016) Single-agent maintenance therapy for advanced non-small cell lung cancer (NSCLC): a systematic review and Bayesian network meta-analysis of 26 randomized controlled trials. PeerJ 4:e2550 https://doi.org/10.7717/peerj.2550
date submitted: 2016-02-25
date accepted: 2016-09-12
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Qinxue
author list: Agent
  family name: Huang
  given name: Haobin
author list: Agent
  family name: Zeng
  given name: Xiaoning
author list: Agent
  family name: Ma
  given name: Yuan
author list: Agent
  family name: Zhao
  given name: Xin
author list: Agent
  family name: Huang
  given name: Mao
doi: 10.7717/peerj.2550
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: ©2016 Wang et al.
attribution name: Wang et al.

Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer
type: item
type: AcademicArticle
description: Background Breast cancer (BC) is one of the leading cause of death among females worldwide. The increasing incidence of BC is due to various genetic and environmental changes which lead to the disruption of cellular signaling network(s). It is a complex disease in which several interlinking signaling cascades play a crucial role in establishing a complex regulatory network. The logical modeling approach of René Thomas has been applied to analyze the behavior of estrogen receptor-alpha (ER-α) associated Biological Regulatory Network (BRN) for a small part of complex events that leads to BC metastasis. Methods A discrete model was constructed using the kinetic logic formalism and its set of logical parameters were obtained using the model checking technique implemented in the SMBioNet software which is consistent with biological observations. The discrete model was further enriched with continuous dynamics by converting it into an equivalent Petri Net (PN) to analyze the logical parameters of the involved entities. Results In-silico based discrete and continuous modeling of ER-α associated signaling network involved in BC provides information about behaviors and gene-gene interaction in detail. The dynamics of discrete model revealed, imperative behaviors represented as cyclic paths and trajectories leading to pathogenic states such as metastasis. Results suggest that the increased expressions of receptors ER-α, IGF-1R and EGFR slow down the activity of tumor suppressor genes (TSGs) such as BRCA1, p53 and Mdm2 which can lead to metastasis. Therefore, IGF-1R and EGFR are considered as important inhibitory targets to control the metastasis in BC. Conclusion The in-silico approaches allow us to increase our understanding of the functional properties of living organisms. It opens new avenues of investigations of multiple inhibitory targets (ER-α, IGF-1R and EGFR) for wet lab experiments as well as provided valuable insights in the treatment of cancers such as BC.
format: application/pdf
format: text/html
creator: Samra Khalid
creator: Rumeza Hanif
creator: Samar H.K. Tareen
creator: Amnah Siddiqa
creator: Zurah Bibi
creator: Jamil Ahmad
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.2542
publisher: PeerJ Inc.
rights: © 2016 Khalid et al.
abstract: Background Breast cancer (BC) is one of the leading cause of death among females worldwide. The increasing incidence of BC is due to various genetic and environmental changes which lead to the disruption of cellular signaling network(s). It is a complex disease in which several interlinking signaling cascades play a crucial role in establishing a complex regulatory network. The logical modeling approach of René Thomas has been applied to analyze the behavior of estrogen receptor-alpha (ER-α) associated Biological Regulatory Network (BRN) for a small part of complex events that leads to BC metastasis. Methods A discrete model was constructed using the kinetic logic formalism and its set of logical parameters were obtained using the model checking technique implemented in the SMBioNet software which is consistent with biological observations. The discrete model was further enriched with continuous dynamics by converting it into an equivalent Petri Net (PN) to analyze the logical parameters of the involved entities. Results In-silico based discrete and continuous modeling of ER-α associated signaling network involved in BC provides information about behaviors and gene-gene interaction in detail. The dynamics of discrete model revealed, imperative behaviors represented as cyclic paths and trajectories leading to pathogenic states such as metastasis. Results suggest that the increased expressions of receptors ER-α, IGF-1R and EGFR slow down the activity of tumor suppressor genes (TSGs) such as BRCA1, p53 and Mdm2 which can lead to metastasis. Therefore, IGF-1R and EGFR are considered as important inhibitory targets to control the metastasis in BC. Conclusion The in-silico approaches allow us to increase our understanding of the functional properties of living organisms. It opens new avenues of investigations of multiple inhibitory targets (ER-α, IGF-1R and EGFR) for wet lab experiments as well as provided valuable insights in the treatment of cancers such as BC.
bibliographic citation: Khalid et al. (2016) Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer. PeerJ 4:e2542 https://doi.org/10.7717/peerj.2542
date submitted: 2016-06-07
date accepted: 2016-09-07
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khalid
  given name: Samra
author list: Agent
  family name: Hanif
  given name: Rumeza
author list: Agent
  family name: Tareen
  given name: Samar H.K.
author list: Agent
  family name: Siddiqa
  given name: Amnah
author list: Agent
  family name: Bibi
  given name: Zurah
author list: Agent
  family name: Ahmad
  given name: Jamil
doi: 10.7717/peerj.2542
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: ©2016 Khalid et al.
attribution name: Khalid et al.

The cranial endocast of Dipnorhynchus sussmilchi (Sarcopterygii: Dipnoi) and the interrelationships of stem-group lungfishes
type: item
type: AcademicArticle
description: The first virtual cranial endocast of a lungfish from the Early Devonian, Dipnorhynchus sussmilchi, is described. Dipnorhynchus, only the fourth Devonian lungfish for which a near complete cranial endocast is known, is a key taxon for clarifying primitive character states within the group. A ventrally-expanded telencephalic cavity is present in the endocast of Dipnorhynchus demonstrating that this is the primitive state for “true” Dipnoi. Dipnorhynchus also possesses a utricular recess differentiated from the sacculolagenar pouch like that seen in stratigraphically younger lungfish (Dipterus, Chirodipterus, Rhinodipterus), but absent from the dipnomorph Youngolepis. We do not find separate pineal and para-pineal canals in contrast to a reconstruction from previous authors. We conduct the first phylogenetic analysis of Dipnoi based purely on endocast characters, which supports a basal placement of Dipnorhynchus within the dipnoan stem group, in agreement with recent analyses. Our analysis demonstrates the value of endocast characters for inferring phylogenetic relationships.
format: application/pdf
format: text/html
creator: Alice M. Clement
creator: Tom J. Challands
creator: John A. Long
creator: Per E. Ahlberg
subject: Evolutionary Studies
subject: Neuroscience
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.2539
publisher: PeerJ Inc.
rights: © 2016 Clement et al.
abstract: The first virtual cranial endocast of a lungfish from the Early Devonian, Dipnorhynchus sussmilchi, is described. Dipnorhynchus, only the fourth Devonian lungfish for which a near complete cranial endocast is known, is a key taxon for clarifying primitive character states within the group. A ventrally-expanded telencephalic cavity is present in the endocast of Dipnorhynchus demonstrating that this is the primitive state for “true” Dipnoi. Dipnorhynchus also possesses a utricular recess differentiated from the sacculolagenar pouch like that seen in stratigraphically younger lungfish (Dipterus, Chirodipterus, Rhinodipterus), but absent from the dipnomorph Youngolepis. We do not find separate pineal and para-pineal canals in contrast to a reconstruction from previous authors. We conduct the first phylogenetic analysis of Dipnoi based purely on endocast characters, which supports a basal placement of Dipnorhynchus within the dipnoan stem group, in agreement with recent analyses. Our analysis demonstrates the value of endocast characters for inferring phylogenetic relationships.
bibliographic citation: Clement et al. (2016) The cranial endocast of Dipnorhynchus sussmilchi (Sarcopterygii: Dipnoi) and the interrelationships of stem-group lungfishes. PeerJ 4:e2539 https://doi.org/10.7717/peerj.2539
date submitted: 2016-08-11
date accepted: 2016-09-07
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clement
  given name: Alice M.
author list: Agent
  family name: Challands
  given name: Tom J.
author list: Agent
  family name: Long
  given name: John A.
author list: Agent
  family name: Ahlberg
  given name: Per E.
doi: 10.7717/peerj.2539
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: ©2016 Clement et al.
attribution name: Clement et al.

Climate-related environmental stress in intertidal grazers: scaling-up biochemical responses to assemblage-level processes
type: item
type: AcademicArticle
description: Background Organisms are facing increasing levels of environmental stress under climate change that may severely affect the functioning of biological systems at different levels of organization. Growing evidence suggests that reduction in body size is a universal response of organisms to global warming. However, a clear understanding of whether extreme climate events will impose selection directly on phenotypic plastic responses and how these responses affect ecological interactions has remained elusive. Methods We experimentally investigated the effects of extreme desiccation events on antioxidant defense mechanisms of a rocky intertidal gastropod (Patella ulyssiponensis), and evaluated how these effects scaled-up at the population and assemblage levels. Results With increasing levels of desiccation stress, limpets showed significant lower levels of total glutathione, tended to grow less and had reduced per capita interaction strength on their resources. Discussion Results suggested that phenotypic plasticity (i.e., reduction in adults’ body size) allowed buffering biochemical responses to stress to scale-up at the assemblage level. Unveiling the linkages among different levels of biological organization is key to develop indicators that can anticipate large-scale ecological impacts of climate change.
format: application/pdf
format: text/html
creator: Elena Maggi
creator: Mario Cappiello
creator: Antonella Del Corso
creator: Francesca Lenzarini
creator: Eleonora Peroni
creator: Lisandro Benedetti-Cecchi
subject: Biochemistry
subject: Climate Change Biology
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.2533
publisher: PeerJ Inc.
rights: © 2016 Maggi et al.
abstract: Background Organisms are facing increasing levels of environmental stress under climate change that may severely affect the functioning of biological systems at different levels of organization. Growing evidence suggests that reduction in body size is a universal response of organisms to global warming. However, a clear understanding of whether extreme climate events will impose selection directly on phenotypic plastic responses and how these responses affect ecological interactions has remained elusive. Methods We experimentally investigated the effects of extreme desiccation events on antioxidant defense mechanisms of a rocky intertidal gastropod (Patella ulyssiponensis), and evaluated how these effects scaled-up at the population and assemblage levels. Results With increasing levels of desiccation stress, limpets showed significant lower levels of total glutathione, tended to grow less and had reduced per capita interaction strength on their resources. Discussion Results suggested that phenotypic plasticity (i.e., reduction in adults’ body size) allowed buffering biochemical responses to stress to scale-up at the assemblage level. Unveiling the linkages among different levels of biological organization is key to develop indicators that can anticipate large-scale ecological impacts of climate change.
bibliographic citation: Maggi et al. (2016) Climate-related environmental stress in intertidal grazers: scaling-up biochemical responses to assemblage-level processes. PeerJ 4:e2533 https://doi.org/10.7717/peerj.2533
date submitted: 2016-07-13
date accepted: 2016-09-06
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maggi
  given name: Elena
author list: Agent
  family name: Cappiello
  given name: Mario
author list: Agent
  family name: Del Corso
  given name: Antonella
author list: Agent
  family name: Lenzarini
  given name: Francesca
author list: Agent
  family name: Peroni
  given name: Eleonora
author list: Agent
  family name: Benedetti-Cecchi
  given name: Lisandro
doi: 10.7717/peerj.2533
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: ©2016 Maggi et al.
attribution name: Maggi et al.

The influence of flight style on the aerodynamic properties of avian wings as fixed lifting surfaces
type: item
type: AcademicArticle
description: The diversity of wing morphologies in birds reflects their variety of flight styles and the associated aerodynamic and inertial requirements. Although the aerodynamics underlying wing morphology can be informed by aeronautical research, important differences exist between planes and birds. In particular, birds operate at lower, transitional Reynolds numbers than do most aircraft. To date, few quantitative studies have investigated the aerodynamic performance of avian wings as fixed lifting surfaces and none have focused upon the differences between wings from different flight style groups. Dried wings from 10 bird species representing three distinct flight style groups were mounted on a force/torque sensor within a wind tunnel in order to test the hypothesis that wing morphologies associated with different flight styles exhibit different aerodynamic properties. Morphological differences manifested primarily as differences in drag rather than lift. Maximum lift coefficients did not differ between groups, whereas minimum drag coefficients were lowest in undulating flyers (Corvids). The lift to drag ratios were lower than in conventional aerofoils and data from free-flying soaring species; particularly in high frequency, flapping flyers (Anseriformes), which do not rely heavily on glide performance. The results illustrate important aerodynamic differences between the wings of different flight style groups that cannot be explained solely by simple wing-shape measures. Taken at face value, the results also suggest that wing-shape is linked principally to changes in aerodynamic drag, but, of course, it is aerodynamics during flapping and not gliding that is likely to be the primary driver.
format: application/pdf
format: text/html
creator: John J. Lees
creator: Grigorios Dimitriadis
creator: Robert L. Nudds
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.2495
publisher: PeerJ Inc.
rights: © 2016 Lees et al.
abstract: The diversity of wing morphologies in birds reflects their variety of flight styles and the associated aerodynamic and inertial requirements. Although the aerodynamics underlying wing morphology can be informed by aeronautical research, important differences exist between planes and birds. In particular, birds operate at lower, transitional Reynolds numbers than do most aircraft. To date, few quantitative studies have investigated the aerodynamic performance of avian wings as fixed lifting surfaces and none have focused upon the differences between wings from different flight style groups. Dried wings from 10 bird species representing three distinct flight style groups were mounted on a force/torque sensor within a wind tunnel in order to test the hypothesis that wing morphologies associated with different flight styles exhibit different aerodynamic properties. Morphological differences manifested primarily as differences in drag rather than lift. Maximum lift coefficients did not differ between groups, whereas minimum drag coefficients were lowest in undulating flyers (Corvids). The lift to drag ratios were lower than in conventional aerofoils and data from free-flying soaring species; particularly in high frequency, flapping flyers (Anseriformes), which do not rely heavily on glide performance. The results illustrate important aerodynamic differences between the wings of different flight style groups that cannot be explained solely by simple wing-shape measures. Taken at face value, the results also suggest that wing-shape is linked principally to changes in aerodynamic drag, but, of course, it is aerodynamics during flapping and not gliding that is likely to be the primary driver.
bibliographic citation: Lees et al. (2016) The influence of flight style on the aerodynamic properties of avian wings as fixed lifting surfaces. PeerJ 4:e2495 https://doi.org/10.7717/peerj.2495
date submitted: 2016-03-07
date accepted: 2016-08-26
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lees
  given name: John J.
author list: Agent
  family name: Dimitriadis
  given name: Grigorios
author list: Agent
  family name: Nudds
  given name: Robert L.
doi: 10.7717/peerj.2495
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: ©2016 Lees et al.
attribution name: Lees et al.

Intranodal signal suppression in pelvic MR lymphography of prostate cancer patients: a quantitative comparison of ferumoxtran-10 and ferumoxytol
type: item
type: AcademicArticle
description: Objectives The key to MR lymphography is suppression of T2* MR signal in normal lymph nodes, while retaining high signal in metastatic nodes. Our objective is to quantitatively compare the ability of ferumoxtran-10 and ferumoxytol to suppress the MR signal in normal pelvic lymph nodes. Methods In 2010, a set of consecutive patients who underwent intravenous MR Lymphography (MRL) were included. Signal suppression in normal lymph nodes in T2*-weighted images due to uptake of USPIO (Ultra-Small Superparamagnetic Particles of Iron Oxide) was quantified. Signal suppression by two USPIO contrast agents, ferumoxtran-10 and ferumoxytol was compared using Wilcoxon’s signed rank test. Results Forty-four patients were included, of which all 44 had a ferumoxtran-10 MRL and 4 had additionally a ferumoxytol MRL. A total of 684 lymph nodes were identified in the images, of which 174 had been diagnosed as metastatic. USPIO-induced signal suppression in normal lymph nodes was significantly stronger in ferumoxtran-10 MRL than in ferumoxytol MRL (p < 0.005). Conclusions T2* signal suppression in normal pelvic lymph nodes is significantly stronger with ferumoxtran-10 than with ferumoxytol, which may affect diagnostic accuracy.
format: application/pdf
format: text/html
creator: Oscar A. Debats
creator: Ansje S. Fortuin
creator: Hanneke J.M. Meijer
creator: Thomas Hambrock
creator: Geert J.S. Litjens
creator: Jelle O. Barentsz
creator: Henkjan J. Huisman
subject: Oncology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.2471
publisher: PeerJ Inc.
rights: © 2016 Debats et al.
abstract: Objectives The key to MR lymphography is suppression of T2* MR signal in normal lymph nodes, while retaining high signal in metastatic nodes. Our objective is to quantitatively compare the ability of ferumoxtran-10 and ferumoxytol to suppress the MR signal in normal pelvic lymph nodes. Methods In 2010, a set of consecutive patients who underwent intravenous MR Lymphography (MRL) were included. Signal suppression in normal lymph nodes in T2*-weighted images due to uptake of USPIO (Ultra-Small Superparamagnetic Particles of Iron Oxide) was quantified. Signal suppression by two USPIO contrast agents, ferumoxtran-10 and ferumoxytol was compared using Wilcoxon’s signed rank test. Results Forty-four patients were included, of which all 44 had a ferumoxtran-10 MRL and 4 had additionally a ferumoxytol MRL. A total of 684 lymph nodes were identified in the images, of which 174 had been diagnosed as metastatic. USPIO-induced signal suppression in normal lymph nodes was significantly stronger in ferumoxtran-10 MRL than in ferumoxytol MRL (p < 0.005). Conclusions T2* signal suppression in normal pelvic lymph nodes is significantly stronger with ferumoxtran-10 than with ferumoxytol, which may affect diagnostic accuracy.
bibliographic citation: Debats et al. (2016) Intranodal signal suppression in pelvic MR lymphography of prostate cancer patients: a quantitative comparison of ferumoxtran-10 and ferumoxytol. PeerJ 4:e2471 https://doi.org/10.7717/peerj.2471
date submitted: 2016-04-07
date accepted: 2016-08-22
issued: 2016-10-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Debats
  given name: Oscar A.
author list: Agent
  family name: Fortuin
  given name: Ansje S.
author list: Agent
  family name: Meijer
  given name: Hanneke J.M.
author list: Agent
  family name: Hambrock
  given name: Thomas
author list: Agent
  family name: Litjens
  given name: Geert J.S.
author list: Agent
  family name: Barentsz
  given name: Jelle O.
author list: Agent
  family name: Huisman
  given name: Henkjan J.
doi: 10.7717/peerj.2471
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-20
copyright: ©2016 Debats et al.
attribution name: Debats et al.

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