PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Exoskeletons of Bougainvilliidae and other Hydroidolina (Cnidaria, Hydrozoa): structure and composition
items: Small-scale spatial variation in population- and individual-level reproductive parameters of the blue-legged hermit crab Clibanarius tricolor
items: Risk analysis of colorectal cancer incidence by gene expression analysis
items: Effect of interleukin (IL)-35 on IL-17 expression and production by human CD4+ T cells
items: ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium
items: Opportunities drive the global distribution of protected areas
items: The preventive effect of dexmedetomidine on paroxysmal sympathetic hyperactivity in severe traumatic brain injury patients who have undergone surgery: a retrospective study
items: Is there a relation between dental anxiety, fear and general psychological status?
items: Spawning aggregation of white-streaked grouper Epinephelus ongus: spatial distribution and annual variation in the fish density within a spawning ground
items: Modafinil decreases anxiety-like behaviour in zebrafish

Exoskeletons of Bougainvilliidae and other Hydroidolina (Cnidaria, Hydrozoa): structure and composition
type: item
type: AcademicArticle
description: The exoskeleton is an important source of characters for the taxonomy of Hydroidolina. It originates as epidermal secretions and, among other functions, protects the coenosarc of the polypoid stage. However, comparative studies on the exoskeletal tissue origin, development, chemical, and structural characteristics, as well as its evolution and homology, are few and fragmented. This study compares the structure and composition of the exoskeleton and underlying coenosarc in members of “Anthoathecata” and some Leptothecata, but does so mainly in bougainvilliid polyps histological analyses. We also studied the development of the exoskeleton under experimental conditions. We identified three types of glandular epidermal cells related to the origin of the exoskeleton and the secretion of its polysaccharides component. The exoskeleton of the species studied is either bilayered (perisarc and exosarc, especially in bougainvilliids) or corneous (perisarc). The exoskeleton varies in chemical composition, structural rigidity, thickness, extension, and coverage in the different regions of the colony. In bilayered exoskeletons, the exosarc is produced first and appears to be a key step in the formation of the rigid exoskeleton. The exoskeleton contains anchoring structures such as desmocytes and “perisarc extensions.”
format: application/pdf
format: text/html
creator: María A. Mendoza-Becerril
creator: José Eduardo A.R. Marian
creator: Alvaro Esteves Migotto
creator: Antonio Carlos Marques
subject: Cell Biology
subject: Marine Biology
subject: Taxonomy
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.2964
publisher: PeerJ Inc.
rights: © 2017 Mendoza-Becerril et al.
abstract: The exoskeleton is an important source of characters for the taxonomy of Hydroidolina. It originates as epidermal secretions and, among other functions, protects the coenosarc of the polypoid stage. However, comparative studies on the exoskeletal tissue origin, development, chemical, and structural characteristics, as well as its evolution and homology, are few and fragmented. This study compares the structure and composition of the exoskeleton and underlying coenosarc in members of “Anthoathecata” and some Leptothecata, but does so mainly in bougainvilliid polyps histological analyses. We also studied the development of the exoskeleton under experimental conditions. We identified three types of glandular epidermal cells related to the origin of the exoskeleton and the secretion of its polysaccharides component. The exoskeleton of the species studied is either bilayered (perisarc and exosarc, especially in bougainvilliids) or corneous (perisarc). The exoskeleton varies in chemical composition, structural rigidity, thickness, extension, and coverage in the different regions of the colony. In bilayered exoskeletons, the exosarc is produced first and appears to be a key step in the formation of the rigid exoskeleton. The exoskeleton contains anchoring structures such as desmocytes and “perisarc extensions.”
bibliographic citation: Mendoza-Becerril et al. (2017) Exoskeletons of Bougainvilliidae and other Hydroidolina (Cnidaria, Hydrozoa): structure and composition. PeerJ 5:e2964 https://doi.org/10.7717/peerj.2964
date submitted: 2016-09-26
date accepted: 2017-01-06
issued: 2017-02-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mendoza-Becerril
  given name: María A.
author list: Agent
  family name: Marian
  given name: José Eduardo A.R.
author list: Agent
  family name: Migotto
  given name: Alvaro Esteves
author list: Agent
  family name: Marques
  given name: Antonio Carlos
doi: 10.7717/peerj.2964
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-16
copyright: ©2017 Mendoza-Becerril et al.
attribution name: Mendoza-Becerril et al.

Small-scale spatial variation in population- and individual-level reproductive parameters of the blue-legged hermit crab Clibanarius tricolor
type: item
type: AcademicArticle
description: Management of the few regulated ornamental fisheries relies on inadequate information about the life history of the target species. Herein, we investigated the reproductive biology of the most heavily traded marine invertebrate in the western Atlantic; the blue-legged hermit crab Clibanarius tricolor. We report on density, individual-level, and population-level reproductive parameters in 14 populations spanning the Florida Keys. In C. tricolor, abundance, population-level, and individual-level reproductive parameters exhibited substantial small-scale spatial variation in the Florida Keys. For instance, the proportion of brooding females varied between 10–94% across localities. In females, average (±SD) fecundity varied between 184 (±54) and 614 (±301) embryos crab-1 across populations. Fecundity usually increases with female body size in hermit crabs. However, we found no effect of female body size on fecundity in three of the populations. Altogether, our observations suggest that C. tricolor may fit a source-sink metapopulation dynamic in the Florida Keys with low reproductive intensity and absence of a parental body size—fecundity relationship resulting in net reproductive loses at some localities. We argue in favor of additional studies describing population dynamics and other aspects of the natural history of C. tricolor (e.g., development type, larval duration) to reveal ‘source’ populations, capable of exporting larvae to nearby populations. Our observations imply that future studies aimed at assessing standing stocks or describing other aspects of the life history of this hermit crab need to focus on multiple localities simultaneously. This and future studies on the reproductive biology of this species will form the baseline for models aimed at assessing the stock condition and sustainability of this heavily harvested crustacean.
format: application/pdf
format: text/html
creator: J. Antonio Baeza
creator: Donald C. Behringer
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.3004
publisher: PeerJ Inc.
rights: © 2017 Baeza and Behringer
abstract: Management of the few regulated ornamental fisheries relies on inadequate information about the life history of the target species. Herein, we investigated the reproductive biology of the most heavily traded marine invertebrate in the western Atlantic; the blue-legged hermit crab Clibanarius tricolor. We report on density, individual-level, and population-level reproductive parameters in 14 populations spanning the Florida Keys. In C. tricolor, abundance, population-level, and individual-level reproductive parameters exhibited substantial small-scale spatial variation in the Florida Keys. For instance, the proportion of brooding females varied between 10–94% across localities. In females, average (±SD) fecundity varied between 184 (±54) and 614 (±301) embryos crab-1 across populations. Fecundity usually increases with female body size in hermit crabs. However, we found no effect of female body size on fecundity in three of the populations. Altogether, our observations suggest that C. tricolor may fit a source-sink metapopulation dynamic in the Florida Keys with low reproductive intensity and absence of a parental body size—fecundity relationship resulting in net reproductive loses at some localities. We argue in favor of additional studies describing population dynamics and other aspects of the natural history of C. tricolor (e.g., development type, larval duration) to reveal ‘source’ populations, capable of exporting larvae to nearby populations. Our observations imply that future studies aimed at assessing standing stocks or describing other aspects of the life history of this hermit crab need to focus on multiple localities simultaneously. This and future studies on the reproductive biology of this species will form the baseline for models aimed at assessing the stock condition and sustainability of this heavily harvested crustacean.
bibliographic citation: Baeza et al. (2017) Small-scale spatial variation in population- and individual-level reproductive parameters of the blue-legged hermit crab Clibanarius tricolor. PeerJ 5:e3004 https://doi.org/10.7717/peerj.3004
date submitted: 2016-10-25
date accepted: 2017-01-19
issued: 2017-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baeza
  given name: J. Antonio
author list: Agent
  family name: Behringer
  given name: Donald C.
doi: 10.7717/peerj.3004
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-15
copyright: ©2017 Baeza and Behringer
attribution name: Baeza and Behringer

Risk analysis of colorectal cancer incidence by gene expression analysis
type: item
type: AcademicArticle
description: Background Colorectal cancer (CRC) is one of the leading cancers worldwide. Several studies have performed microarray data analyses for cancer classification and prognostic analyses. Microarray assays also enable the identification of gene signatures for molecular characterization and treatment prediction. Objective Microarray gene expression data from the online Gene Expression Omnibus (GEO) database were used to to distinguish colorectal cancer from normal colon tissue samples. Methods We collected microarray data from the GEO database to establish colorectal cancer microarray gene expression datasets for a combined analysis. Using the Prediction Analysis for Microarrays (PAM) method and the GSEA MSigDB resource, we analyzed the 14,698 genes that were identified through an examination of their expression values between normal and tumor tissues. Results Ten genes (ABCG2, AQP8, SPIB, CA7, CLDN8, SCNN1B, SLC30A10, CD177, PADI2, and TGFBI) were found to be good indicators of the candidate genes that correlate with CRC. From these selected genes, an average of six significant genes were obtained using the PAM method, with an accuracy rate of 95%. The results demonstrate the potential of utilizing a model with the PAM method for data mining. After a detailed review of the published reports, the results confirmed that the screened candidate genes are good indicators for cancer risk analysis using the PAM method. Conclusions Six genes were selected with 95% accuracy to effectively classify normal and colorectal cancer tissues. We hope that these results will provide the basis for new research projects in clinical practice that aim to rapidly assess colorectal cancer risk using microarray gene expression analysis.
format: application/pdf
format: text/html
creator: Wei-Chuan Shangkuan
creator: Hung-Che Lin
creator: Yu-Tien Chang
creator: Chen-En Jian
creator: Hueng-Chuen Fan
creator: Kang-Hua Chen
creator: Ya-Fang Liu
creator: Huan-Ming Hsu
creator: Hsiu-Ling Chou
creator: Chung-Tay Yao
creator: Chi-Ming Chu
creator: Sui-Lung Su
creator: Chi-Wen Chang
subject: Bioinformatics
subject: Mathematical Biology
subject: Molecular Biology
subject: Oncology
subject: Statistics
description: doi:10.7717/peerj.3003
publisher: PeerJ Inc.
rights: © 2017 Shangkuan et al.
abstract: Background Colorectal cancer (CRC) is one of the leading cancers worldwide. Several studies have performed microarray data analyses for cancer classification and prognostic analyses. Microarray assays also enable the identification of gene signatures for molecular characterization and treatment prediction. Objective Microarray gene expression data from the online Gene Expression Omnibus (GEO) database were used to to distinguish colorectal cancer from normal colon tissue samples. Methods We collected microarray data from the GEO database to establish colorectal cancer microarray gene expression datasets for a combined analysis. Using the Prediction Analysis for Microarrays (PAM) method and the GSEA MSigDB resource, we analyzed the 14,698 genes that were identified through an examination of their expression values between normal and tumor tissues. Results Ten genes (ABCG2, AQP8, SPIB, CA7, CLDN8, SCNN1B, SLC30A10, CD177, PADI2, and TGFBI) were found to be good indicators of the candidate genes that correlate with CRC. From these selected genes, an average of six significant genes were obtained using the PAM method, with an accuracy rate of 95%. The results demonstrate the potential of utilizing a model with the PAM method for data mining. After a detailed review of the published reports, the results confirmed that the screened candidate genes are good indicators for cancer risk analysis using the PAM method. Conclusions Six genes were selected with 95% accuracy to effectively classify normal and colorectal cancer tissues. We hope that these results will provide the basis for new research projects in clinical practice that aim to rapidly assess colorectal cancer risk using microarray gene expression analysis.
bibliographic citation: Shangkuan et al. (2017) Risk analysis of colorectal cancer incidence by gene expression analysis. PeerJ 5:e3003 https://doi.org/10.7717/peerj.3003
date submitted: 2016-09-28
date accepted: 2017-01-19
issued: 2017-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shangkuan
  given name: Wei-Chuan
author list: Agent
  family name: Lin
  given name: Hung-Che
author list: Agent
  family name: Chang
  given name: Yu-Tien
author list: Agent
  family name: Jian
  given name: Chen-En
author list: Agent
  family name: Fan
  given name: Hueng-Chuen
author list: Agent
  family name: Chen
  given name: Kang-Hua
author list: Agent
  family name: Liu
  given name: Ya-Fang
author list: Agent
  family name: Hsu
  given name: Huan-Ming
author list: Agent
  family name: Chou
  given name: Hsiu-Ling
author list: Agent
  family name: Yao
  given name: Chung-Tay
author list: Agent
  family name: Chu
  given name: Chi-Ming
author list: Agent
  family name: Su
  given name: Sui-Lung
author list: Agent
  family name: Chang
  given name: Chi-Wen
doi: 10.7717/peerj.3003
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-15
copyright: ©2017 Shangkuan et al.
attribution name: Shangkuan et al.

Effect of interleukin (IL)-35 on IL-17 expression and production by human CD4+ T cells
type: item
type: AcademicArticle
description: Background Interleukin (IL)-17 produced by mainly T helper 17 (Th17) cells may play an important destructive role in chronic periodontitis (CP). Thus, anti-inflammatory cytokines, such as IL-35, might have a beneficial effect in periodontitis by inhibiting differentiation of Th17 cells. Th17 differentiation is regulated by the retinoic acid receptor-related orphan receptor (ROR) α (encoded by RORA) and RORγt (encoded by RORC). However, the role of IL-35 in periodontitis is not clear and the effect of IL-35 on the function of Th17 cells is still incompletely understood. Therefore, we investigated the effects of IL-35 on Th17 cells. Methods Peripheral blood mononuclear cells (PBMCs) were sampled from three healthy volunteers and three CP patients and were analyzed by flow cytometry for T cell population. Th17 cells differentiated by a cytokine cocktail (recombinant transforming growth factor-β, rIL-6, rIL-1β, anti-interferon (IFN)-γ, anti-IL-2 and anti-IL-4) from PBMCs were cultured with or without rIL-35. IL17A (which usually refers to IL-17), RORA and RORCmRNA expression was analyzed by quantitative polymerase chain reaction, and IL-17A production was determined by enzyme-linked immunosorbent assay. Results The proportion of IL-17A+CD4+ slightly increased in CP patients compared with healthy controls, however, there were no significant differences in the percentage of IL-17A+CD4+ as well as IFN-γ+CD4+ and Foxp3+CD4+ T cells between healthy controls and CP patients. IL17A, RORA and RORC mRNA expression was significantly increased in Th17 cells induced by the cytokine cocktail, and the induction was significantly inhibited by addition of rIL-35 (1 ng/mL). IL-17A production in Th17 cells was significantly inhibited by rIL-35 addition (1 ng/mL). Discussion The present study suggests that IL-35 could directly suppress IL-17 expression via RORα and RORγt inhibition and might play an important role in inflammatory diseases such as periodontitis.
format: application/pdf
format: text/html
creator: Kosuke Okada
creator: Takeki Fujimura
creator: Takeshi Kikuchi
creator: Makoto Aino
creator: Yosuke Kamiya
creator: Ario Izawa
creator: Yuki Iwamura
creator: Hisashi Goto
creator: Iichiro Okabe
creator: Eriko Miyake
creator: Yoshiaki Hasegawa
creator: Makio Mogi
creator: Akio Mitani
subject: Dentistry
subject: Immunology
description: doi:10.7717/peerj.2999
publisher: PeerJ Inc.
rights: © 2017 Okada et al.
abstract: Background Interleukin (IL)-17 produced by mainly T helper 17 (Th17) cells may play an important destructive role in chronic periodontitis (CP). Thus, anti-inflammatory cytokines, such as IL-35, might have a beneficial effect in periodontitis by inhibiting differentiation of Th17 cells. Th17 differentiation is regulated by the retinoic acid receptor-related orphan receptor (ROR) α (encoded by RORA) and RORγt (encoded by RORC). However, the role of IL-35 in periodontitis is not clear and the effect of IL-35 on the function of Th17 cells is still incompletely understood. Therefore, we investigated the effects of IL-35 on Th17 cells. Methods Peripheral blood mononuclear cells (PBMCs) were sampled from three healthy volunteers and three CP patients and were analyzed by flow cytometry for T cell population. Th17 cells differentiated by a cytokine cocktail (recombinant transforming growth factor-β, rIL-6, rIL-1β, anti-interferon (IFN)-γ, anti-IL-2 and anti-IL-4) from PBMCs were cultured with or without rIL-35. IL17A (which usually refers to IL-17), RORA and RORCmRNA expression was analyzed by quantitative polymerase chain reaction, and IL-17A production was determined by enzyme-linked immunosorbent assay. Results The proportion of IL-17A+CD4+ slightly increased in CP patients compared with healthy controls, however, there were no significant differences in the percentage of IL-17A+CD4+ as well as IFN-γ+CD4+ and Foxp3+CD4+ T cells between healthy controls and CP patients. IL17A, RORA and RORC mRNA expression was significantly increased in Th17 cells induced by the cytokine cocktail, and the induction was significantly inhibited by addition of rIL-35 (1 ng/mL). IL-17A production in Th17 cells was significantly inhibited by rIL-35 addition (1 ng/mL). Discussion The present study suggests that IL-35 could directly suppress IL-17 expression via RORα and RORγt inhibition and might play an important role in inflammatory diseases such as periodontitis.
bibliographic citation: Okada et al. (2017) Effect of interleukin (IL)-35 on IL-17 expression and production by human CD4+ T cells. PeerJ 5:e2999 https://doi.org/10.7717/peerj.2999
date submitted: 2016-09-09
date accepted: 2017-01-17
issued: 2017-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Okada
  given name: Kosuke
author list: Agent
  family name: Fujimura
  given name: Takeki
author list: Agent
  family name: Kikuchi
  given name: Takeshi
author list: Agent
  family name: Aino
  given name: Makoto
author list: Agent
  family name: Kamiya
  given name: Yosuke
author list: Agent
  family name: Izawa
  given name: Ario
author list: Agent
  family name: Iwamura
  given name: Yuki
author list: Agent
  family name: Goto
  given name: Hisashi
author list: Agent
  family name: Okabe
  given name: Iichiro
author list: Agent
  family name: Miyake
  given name: Eriko
author list: Agent
  family name: Hasegawa
  given name: Yoshiaki
author list: Agent
  family name: Mogi
  given name: Makio
author list: Agent
  family name: Mitani
  given name: Akio
doi: 10.7717/peerj.2999
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-15
copyright: ©2017 Okada et al.
attribution name: Okada et al.

ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium
type: item
type: AcademicArticle
description: Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype’s determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22 Fusarium species were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and mycotoxicology to join the fr…
format: application/pdf
format: text/html
creator: Tomasz Kulik
creator: Kessy Abarenkov
creator: Maciej Buśko
creator: Katarzyna Bilska
creator: Anne D. van Diepeningen
creator: Anna Ostrowska-Kołodziejczak
creator: Katarzyna Krawczyk
creator: Balázs Brankovics
creator: Sebastian Stenglein
creator: Jakub Sawicki
creator: Juliusz Perkowski
subject: Bioinformatics
subject: Mycology
description: doi:10.7717/peerj.2992
publisher: PeerJ Inc.
rights: © 2017 Kulik et al.
abstract: Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype’s determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22 Fusarium species were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and mycotoxicology to join the fr…
bibliographic citation: Kulik et al. (2017) ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium. PeerJ 5:e2992 https://doi.org/10.7717/peerj.2992
date submitted: 2016-09-12
date accepted: 2017-01-15
issued: 2017-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kulik
  given name: Tomasz
author list: Agent
  family name: Abarenkov
  given name: Kessy
author list: Agent
  family name: Buśko
  given name: Maciej
author list: Agent
  family name: Bilska
  given name: Katarzyna
author list: Agent
  family name: van Diepeningen
  given name: Anne D.
author list: Agent
  family name: Ostrowska-Kołodziejczak
  given name: Anna
author list: Agent
  family name: Krawczyk
  given name: Katarzyna
author list: Agent
  family name: Brankovics
  given name: Balázs
author list: Agent
  family name: Stenglein
  given name: Sebastian
author list: Agent
  family name: Sawicki
  given name: Jakub
author list: Agent
  family name: Perkowski
  given name: Juliusz
doi: 10.7717/peerj.2992
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-15
copyright: ©2017 Kulik et al.
attribution name: Kulik et al.

Opportunities drive the global distribution of protected areas
type: item
type: AcademicArticle
description: Background Protected areas, regarded today as a cornerstone of nature conservation, result from an array of multiple motivations and opportunities. We explored at global and regional levels the current distribution of protected areas along biophysical, human, and biological gradients, and assessed to what extent protection has pursued (i) a balanced representation of biophysical environments, (ii) a set of preferred conditions (biological, spiritual, economic, or geopolitical), or (iii) existing opportunities for conservation regardless of any representation or preference criteria. Methods We used histograms to describe the distribution of terrestrial protected areas along biophysical, human, and biological independent gradients and linear and non-linear regression and correlation analyses to describe the sign, shape, and strength of the relationships. We used a random forest analysis to rank the importance of different variables related to conservation preferences and opportunity drivers, and an evenness metric to quantify representativeness. Results We find that protection at a global level is primarily driven by the opportunities provided by isolation and a low population density (variable importance = 34.6 and 19.9, respectively). Preferences play a secondary role, with a bias towards tourism attractiveness and proximity to international borders (variable importance = 12.7 and 3.4, respectively). Opportunities shape protection strongly in “North America & Australia–NZ” and “Latin America & Caribbean,” while the importance of the representativeness of biophysical environments is higher in “Sub-Saharan Africa” (1.3 times the average of other regions). Discussion Environmental representativeness and biodiversity protection are top priorities in land conservation agendas. However, our results suggest that they have been minor players driving current protection at both global and regional levels. Attempts to increase their relevance will necessarily have to recognize…
format: application/pdf
format: text/html
creator: Germán Baldi
creator: Marcos Texeira
creator: Osvaldo A. Martin
creator: H. Ricardo Grau
creator: Esteban G. Jobbágy
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Natural Resource Management
description: doi:10.7717/peerj.2989
publisher: PeerJ Inc.
rights: © 2017 Baldi et al.
abstract: Background Protected areas, regarded today as a cornerstone of nature conservation, result from an array of multiple motivations and opportunities. We explored at global and regional levels the current distribution of protected areas along biophysical, human, and biological gradients, and assessed to what extent protection has pursued (i) a balanced representation of biophysical environments, (ii) a set of preferred conditions (biological, spiritual, economic, or geopolitical), or (iii) existing opportunities for conservation regardless of any representation or preference criteria. Methods We used histograms to describe the distribution of terrestrial protected areas along biophysical, human, and biological independent gradients and linear and non-linear regression and correlation analyses to describe the sign, shape, and strength of the relationships. We used a random forest analysis to rank the importance of different variables related to conservation preferences and opportunity drivers, and an evenness metric to quantify representativeness. Results We find that protection at a global level is primarily driven by the opportunities provided by isolation and a low population density (variable importance = 34.6 and 19.9, respectively). Preferences play a secondary role, with a bias towards tourism attractiveness and proximity to international borders (variable importance = 12.7 and 3.4, respectively). Opportunities shape protection strongly in “North America & Australia–NZ” and “Latin America & Caribbean,” while the importance of the representativeness of biophysical environments is higher in “Sub-Saharan Africa” (1.3 times the average of other regions). Discussion Environmental representativeness and biodiversity protection are top priorities in land conservation agendas. However, our results suggest that they have been minor players driving current protection at both global and regional levels. Attempts to increase their relevance will necessarily have to recognize…
bibliographic citation: Baldi et al. (2017) Opportunities drive the global distribution of protected areas. PeerJ 5:e2989 https://doi.org/10.7717/peerj.2989
date submitted: 2016-09-20
date accepted: 2017-01-13
issued: 2017-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baldi
  given name: Germán
author list: Agent
  family name: Texeira
  given name: Marcos
author list: Agent
  family name: Martin
  given name: Osvaldo A.
author list: Agent
  family name: Grau
  given name: H. Ricardo
author list: Agent
  family name: Jobbágy
  given name: Esteban G.
doi: 10.7717/peerj.2989
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-15
copyright: ©2017 Baldi et al.
attribution name: Baldi et al.

The preventive effect of dexmedetomidine on paroxysmal sympathetic hyperactivity in severe traumatic brain injury patients who have undergone surgery: a retrospective study
type: item
type: AcademicArticle
description: Background Paroxysmal sympathetic hyperactivity (PSH) results and aggravates in secondary brain injury, which seriously affects the prognosis of severe traumatic brain injury patients. Although several studies have focused on the treatment of PSH, few have concentrated on its prevention. Methods Ninety post-operation (post-op) severe traumatic brain injury (sTBI) patients admitted from October 2014 to April 2016 were chosen to participate in this study. Fifty of the post-op sTBI patients were sedated with dexmedetomidine and were referred as the “dexmedetomidine group” (admitted from May 2015 to April 2016). The other 40 patients (admitted from October 2014 to May 2015) received other sedations and were referred as the “control group.” The two groups were then compared based on their PSH scores and the scores and ratios of those patients who met the criteria of “probable,” “possible” and “unlikely” using the PSH assessment measure (PSH-AM) designed by Baguley et al. (2014). The durations of the neurosurgery intensive care unit (NICU) and hospital stays and the Glasgow outcome scale (GOS) values for the two groups were also compared to evaluate the therapeutic effects and the patients’ prognosis. Results The overall PSH score for the dexmedetomidine group was 5.26 ± 4.66, compared with 8.58 ± 8.09 for the control group. The difference between the two groups’ PSH scores was significant (P = 0.017). The score of the patients who met the criterion of “probable” was 18.33 ± 1.53 in the dexmedetomidine group and 22.63 ± 2.97 in the control group, and the difference was statistically significant (P = 0.045). The ratio of patients who were classified as “unlikely” between the two groups was statistically significant (P = 0.028); that is, 42 (84%) in the dexmedetomidine group and 25 (62.5%) in the control group. The differences in NICU, hospital stays and GOS values between the two groups were not significant. Conclusion Dexmedetomidine has a preventive effect on PSH in sTBI…
format: application/pdf
format: text/html
creator: Qilin Tang
creator: Xiang Wu
creator: Weiji Weng
creator: Hongpeng Li
creator: Junfeng Feng
creator: Qing Mao
creator: Guoyi Gao
creator: Jiyao Jiang
subject: Drugs and Devices
subject: Emergency and Critical Care
subject: Neurology
description: doi:10.7717/peerj.2986
publisher: PeerJ Inc.
rights: © 2017 Tang et al.
abstract: Background Paroxysmal sympathetic hyperactivity (PSH) results and aggravates in secondary brain injury, which seriously affects the prognosis of severe traumatic brain injury patients. Although several studies have focused on the treatment of PSH, few have concentrated on its prevention. Methods Ninety post-operation (post-op) severe traumatic brain injury (sTBI) patients admitted from October 2014 to April 2016 were chosen to participate in this study. Fifty of the post-op sTBI patients were sedated with dexmedetomidine and were referred as the “dexmedetomidine group” (admitted from May 2015 to April 2016). The other 40 patients (admitted from October 2014 to May 2015) received other sedations and were referred as the “control group.” The two groups were then compared based on their PSH scores and the scores and ratios of those patients who met the criteria of “probable,” “possible” and “unlikely” using the PSH assessment measure (PSH-AM) designed by Baguley et al. (2014). The durations of the neurosurgery intensive care unit (NICU) and hospital stays and the Glasgow outcome scale (GOS) values for the two groups were also compared to evaluate the therapeutic effects and the patients’ prognosis. Results The overall PSH score for the dexmedetomidine group was 5.26 ± 4.66, compared with 8.58 ± 8.09 for the control group. The difference between the two groups’ PSH scores was significant (P = 0.017). The score of the patients who met the criterion of “probable” was 18.33 ± 1.53 in the dexmedetomidine group and 22.63 ± 2.97 in the control group, and the difference was statistically significant (P = 0.045). The ratio of patients who were classified as “unlikely” between the two groups was statistically significant (P = 0.028); that is, 42 (84%) in the dexmedetomidine group and 25 (62.5%) in the control group. The differences in NICU, hospital stays and GOS values between the two groups were not significant. Conclusion Dexmedetomidine has a preventive effect on PSH in sTBI…
bibliographic citation: Tang et al. (2017) The preventive effect of dexmedetomidine on paroxysmal sympathetic hyperactivity in severe traumatic brain injury patients who have undergone surgery: a retrospective study. PeerJ 5:e2986 https://doi.org/10.7717/peerj.2986
date submitted: 2016-10-16
date accepted: 2017-01-12
issued: 2017-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Qilin
author list: Agent
  family name: Wu
  given name: Xiang
author list: Agent
  family name: Weng
  given name: Weiji
author list: Agent
  family name: Li
  given name: Hongpeng
author list: Agent
  family name: Feng
  given name: Junfeng
author list: Agent
  family name: Mao
  given name: Qing
author list: Agent
  family name: Gao
  given name: Guoyi
author list: Agent
  family name: Jiang
  given name: Jiyao
doi: 10.7717/peerj.2986
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-15
copyright: ©2017 Tang et al.
attribution name: Tang et al.

Is there a relation between dental anxiety, fear and general psychological status?
type: item
type: AcademicArticle
description: Background Dental anxiety is a widespread problem in many populations. This problem can be a barrier to dental care and may lead to poor oral health. Dental anxiety may be related to psychological status. Aims The aim of the present study was to assess the levels of dental anxiety, dental fear, Beck Depression, and state-trait anxiety according to age, gender and education level in patients at the periodontology clinic in the Diyarbakır Mouth and Dental Health Center. Study Design A total of 231 patients (115 males, 116 females) filled out dental fear scale (DFS), dental anxiety scale (DAS), Beck Depression Inventory (BDI), state-trait anxiety inventory-state (STAI-S), and state-trait anxiety inventory–trait (STAI-T) questionnaires, and evaluations of DFS, DAS, BDI, STAI-S, and STAI-T were conducted according to age, gender, and education level. Results The mean DFS, DAS, BDI, STAI-T, and STAI –S were 45.64, 9.15, 13.16, 38.90, and 40.18, respectively. There was a significant association among DFS, DAS, BDI, STAI-S, and STAI-T (p < 0.05). These surveys scores were significantly higher in females than males (p < 0.05). The results of this study indicated that gender age and education level have important effects on DFS, DAS, BDI, STAI-S, and STAI-T (p < 0.05). Conclusion Dental anxiety and dental fear were found to be related to psychological status (BDI, STAI-S, and STAI-T) over time. There are some patients with unaddressed psychological distress.
format: application/pdf
format: text/html
creator: Tuba Talo Yildirim
creator: Serkan Dundar
creator: Alihan Bozoglan
creator: Tahir Karaman
creator: Neval Dildes
creator: Filiz Acun Kaya
creator: Eyyup Altintas
creator: Faruk Oztekin
creator: Osman Atas
creator: Hilal Alan
subject: Dentistry
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.2978
publisher: PeerJ Inc.
rights: © 2017 Talo Yildirim et al.
abstract: Background Dental anxiety is a widespread problem in many populations. This problem can be a barrier to dental care and may lead to poor oral health. Dental anxiety may be related to psychological status. Aims The aim of the present study was to assess the levels of dental anxiety, dental fear, Beck Depression, and state-trait anxiety according to age, gender and education level in patients at the periodontology clinic in the Diyarbakır Mouth and Dental Health Center. Study Design A total of 231 patients (115 males, 116 females) filled out dental fear scale (DFS), dental anxiety scale (DAS), Beck Depression Inventory (BDI), state-trait anxiety inventory-state (STAI-S), and state-trait anxiety inventory–trait (STAI-T) questionnaires, and evaluations of DFS, DAS, BDI, STAI-S, and STAI-T were conducted according to age, gender, and education level. Results The mean DFS, DAS, BDI, STAI-T, and STAI –S were 45.64, 9.15, 13.16, 38.90, and 40.18, respectively. There was a significant association among DFS, DAS, BDI, STAI-S, and STAI-T (p < 0.05). These surveys scores were significantly higher in females than males (p < 0.05). The results of this study indicated that gender age and education level have important effects on DFS, DAS, BDI, STAI-S, and STAI-T (p < 0.05). Conclusion Dental anxiety and dental fear were found to be related to psychological status (BDI, STAI-S, and STAI-T) over time. There are some patients with unaddressed psychological distress.
bibliographic citation: Talo Yildirim et al. (2017) Is there a relation between dental anxiety, fear and general psychological status?. PeerJ 5:e2978 https://doi.org/10.7717/peerj.2978
date submitted: 2016-11-08
date accepted: 2017-01-10
issued: 2017-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Talo Yildirim
  given name: Tuba
author list: Agent
  family name: Dundar
  given name: Serkan
author list: Agent
  family name: Bozoglan
  given name: Alihan
author list: Agent
  family name: Karaman
  given name: Tahir
author list: Agent
  family name: Dildes
  given name: Neval
author list: Agent
  family name: Acun Kaya
  given name: Filiz
author list: Agent
  family name: Altintas
  given name: Eyyup
author list: Agent
  family name: Oztekin
  given name: Faruk
author list: Agent
  family name: Atas
  given name: Osman
author list: Agent
  family name: Alan
  given name: Hilal
doi: 10.7717/peerj.2978
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-15
copyright: ©2017 Talo Yildirim et al.
attribution name: Talo Yildirim et al.

Spawning aggregation of white-streaked grouper Epinephelus ongus: spatial distribution and annual variation in the fish density within a spawning ground
type: item
type: AcademicArticle
description: White-streaked grouper (Epinephelus ongus) is an important fisheries target and forms spawning aggregations at particular spawning grounds. The aims of the present study were to investigate the ecological characteristics of annual spawning aggregations such as (1) spatial variations in the density of E. ongus at the spawning ground, (2) the relationship between fish density and environmental variables, (3) inter-annual variations in the spawning aggregation, (4) the proportion of males to females at the spawning ground for several days pre—and post-spawning and (5) the relationship between male density and female density at the protected spawning ground, based on observations over five years at an Okinawan coral reef. Although the protected spawning ground area was large (ca. 2,500 m × 700 m), high density of E. ongus (over 25 individuals per 100 m2) was found in a limited area (within c.a. 750 m × 50 m). Current velocity and coverage of rocks had significant positive effects on the spatial distribution of E. ongus at the spawning ground. Inter-annual variation in the degree of aggregation was found and this variation was explained by the annual variation of mean seawater temperature during 40 days before the spawning day. The male–female ratio (male:female) at the spawning ground was ca. 3:1 for three years (May 2012, May 2014 and May 2015) whereas >13:1 for one year (May 2013). Significant positive relationships between male density and female density were found at the aggregation sites. It is suggested that E. ongus use aggregation sites with greater current velocity to reduce the risk of egg predation and seawater temperature is one of the main factors that is responsible for determining the degree of aggregation. It is also suggested that females possibly select sites with a greater density of males and this selection behavior might be the reason why females arrived at the spawning ground after the arrival of the males. For effective management of spawning grou…
format: application/pdf
format: text/html
creator: Atsushi Nanami
creator: Taku Sato
creator: Yuuki Kawabata
creator: Junichi Okuyama
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.3000
publisher: PeerJ Inc.
rights: © 2017 Nanami et al.
abstract: White-streaked grouper (Epinephelus ongus) is an important fisheries target and forms spawning aggregations at particular spawning grounds. The aims of the present study were to investigate the ecological characteristics of annual spawning aggregations such as (1) spatial variations in the density of E. ongus at the spawning ground, (2) the relationship between fish density and environmental variables, (3) inter-annual variations in the spawning aggregation, (4) the proportion of males to females at the spawning ground for several days pre—and post-spawning and (5) the relationship between male density and female density at the protected spawning ground, based on observations over five years at an Okinawan coral reef. Although the protected spawning ground area was large (ca. 2,500 m × 700 m), high density of E. ongus (over 25 individuals per 100 m2) was found in a limited area (within c.a. 750 m × 50 m). Current velocity and coverage of rocks had significant positive effects on the spatial distribution of E. ongus at the spawning ground. Inter-annual variation in the degree of aggregation was found and this variation was explained by the annual variation of mean seawater temperature during 40 days before the spawning day. The male–female ratio (male:female) at the spawning ground was ca. 3:1 for three years (May 2012, May 2014 and May 2015) whereas >13:1 for one year (May 2013). Significant positive relationships between male density and female density were found at the aggregation sites. It is suggested that E. ongus use aggregation sites with greater current velocity to reduce the risk of egg predation and seawater temperature is one of the main factors that is responsible for determining the degree of aggregation. It is also suggested that females possibly select sites with a greater density of males and this selection behavior might be the reason why females arrived at the spawning ground after the arrival of the males. For effective management of spawning grou…
bibliographic citation: Nanami et al. (2017) Spawning aggregation of white-streaked grouper Epinephelus ongus: spatial distribution and annual variation in the fish density within a spawning ground. PeerJ 5:e3000 https://doi.org/10.7717/peerj.3000
date submitted: 2016-10-05
date accepted: 2017-01-18
issued: 2017-02-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nanami
  given name: Atsushi
author list: Agent
  family name: Sato
  given name: Taku
author list: Agent
  family name: Kawabata
  given name: Yuuki
author list: Agent
  family name: Okuyama
  given name: Junichi
doi: 10.7717/peerj.3000
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-14
copyright: ©2017 Nanami et al.
attribution name: Nanami et al.

Modafinil decreases anxiety-like behaviour in zebrafish
type: item
type: AcademicArticle
description: Modafinil (2-((diphenylmethyl)sulfinyl)acetamide), a selective dopamine and norepinephrine transporter inhibitor, is most commonly prescribed for narcolepsy but has gained recent interest for treating a variety of disorders. Zebrafish (Danio rerio) are becoming a model of choice for pharmacological and behavioural research. To investigate the behavioural effects of modafinil on anxiety, we administered doses of 0, 2, 20, and 200 mg/L for 30 minutes then tested zebrafish in the novel approach test. In this test, the fish was placed into a circular arena with a novel object in the center and motion-tracking software was used to quantify the time the fish spent in the outer area of the arena (thigmotaxis zone), middle third of the arena (transition zone) and center of the arena, as well as total distance traveled, immobility and meandering. Modafinil caused a decrease in time spent in the thigmotaxis zone and increased time spent in the transition zone across all doses. Modafinil did not significantly alter the time spent in the center zone (near the novel object), the distance moved, meandering, or the duration of time spent immobile. We also validated this test as a measure of anxiety with the administration of ethanol (1%) which decreased time spent in the thigmotaxis zone and increased time spent in the transition zone. These results suggest that modafinil decreases anxiety-like behaviour in zebrafish.
format: application/pdf
format: text/html
creator: Adrian Johnson
creator: Trevor James Hamilton
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Neuroscience
subject: Pharmacology
description: doi:10.7717/peerj.2994
publisher: PeerJ Inc.
rights: © 2017 Johnson and Hamilton
abstract: Modafinil (2-((diphenylmethyl)sulfinyl)acetamide), a selective dopamine and norepinephrine transporter inhibitor, is most commonly prescribed for narcolepsy but has gained recent interest for treating a variety of disorders. Zebrafish (Danio rerio) are becoming a model of choice for pharmacological and behavioural research. To investigate the behavioural effects of modafinil on anxiety, we administered doses of 0, 2, 20, and 200 mg/L for 30 minutes then tested zebrafish in the novel approach test. In this test, the fish was placed into a circular arena with a novel object in the center and motion-tracking software was used to quantify the time the fish spent in the outer area of the arena (thigmotaxis zone), middle third of the arena (transition zone) and center of the arena, as well as total distance traveled, immobility and meandering. Modafinil caused a decrease in time spent in the thigmotaxis zone and increased time spent in the transition zone across all doses. Modafinil did not significantly alter the time spent in the center zone (near the novel object), the distance moved, meandering, or the duration of time spent immobile. We also validated this test as a measure of anxiety with the administration of ethanol (1%) which decreased time spent in the thigmotaxis zone and increased time spent in the transition zone. These results suggest that modafinil decreases anxiety-like behaviour in zebrafish.
bibliographic citation: Johnson et al. (2017) Modafinil decreases anxiety-like behaviour in zebrafish. PeerJ 5:e2994 https://doi.org/10.7717/peerj.2994
date submitted: 2016-11-01
date accepted: 2017-01-16
issued: 2017-02-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Johnson
  given name: Adrian
author list: Agent
  family name: Hamilton
  given name: Trevor James
doi: 10.7717/peerj.2994
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-14
copyright: ©2017 Johnson and and Hamilton
attribution name: Johnson and Hamilton

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