PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Risk and prognostic nomograms for hepatocellular carcinoma with newly-diagnosed pulmonary metastasis using SEER data
items: Factors affecting the composition of the gut microbiota, and its modulation
items: Exploring the potential of deep-blue autofluorescence for monitoring amyloid fibril formation and dissociation
items: Experimental removal of introduced slider turtles offers new insight into competition with a native, threatened turtle
items: Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study
items: Assessment of the factors influencing primary care physicians’ approach to vaccination of adult risk groups in Istanbul, Turkey
items: Molecular taxonomy of endemic coastal Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species
items: Modeling tree diversity, stand structure and productivity of northern temperate coniferous forests of Mexico
items: Ontogenetic braincase development in Psittacosaurus lujiatunensis (Dinosauria: Ceratopsia) using micro-computed tomography
items: Variation in denitrifying bacterial communities along a primary succession in the Hailuogou Glacier retreat area, China

Risk and prognostic nomograms for hepatocellular carcinoma with newly-diagnosed pulmonary metastasis using SEER data
type: item
type: AcademicArticle
description: Purpose This research aimed to identify risk factors of pulmonary metastasis (PM) from hepatocellular carcinoma (HCC) and prognostic factors of patients with PM from HCC at initial diagnosis. Methods Patients diagnosed with HCC between 2010 and 2015 were reviewed retrospectively in the Surveillance, Epidemiology, and End Results (SEER) database. Patients with PM from HCC at initial diagnosis were identified from the entire cohort. Predictors for PM from HCC were identified by multivariate logistic regression analysis. Independent prognostic factors for patients with PM were determined by univariate and multivariate Cox regression analysis. Nomograms were also constructed for quantifying risk of metastasis and overall survival estimation visually. Results Our research included 30,641 patients diagnosed with HCC, of whom 1,732 cases were with PM from HCC at initial diagnosis. The risk factors causing PM from HCC were age (P = 0.001), race (P < 0.001), primary tumor size (P < 0.001), T stage (P < 0.001), N stage (P < 0.001), alpha-fetoprotein (P < 0.001), bone metastasis (P < 0.001), brain metastasis (P < 0.001), and intrahepatic metastasis (P < 0.001). The significantly prognostic factors for overall survival were age (P = 0.014), T stage (P = 0.009), surgical approach (P < 0.001), and chemotherapy (P < 0.001). Harrell’s C-index statistics of two nomograms were 0.768 and 0.687 respectively, indicating satisfactory predictive power. Conclusions This research provided evaluation of risk factors and prognosis for patients with PM from HCC. Two nomograms we developed can be convenient individualized tools to facilitate clinical decision-making.
format: application/pdf
format: text/html
creator: Guanzhi Ye
creator: Lin Wang
creator: Zhengyang Hu
creator: Jiaqi Liang
creator: Yunyi Bian
creator: Cheng Zhan
creator: Zongwu Lin
subject: Bioinformatics
subject: Computational Biology
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.7496
publisher: PeerJ Inc.
rights: © 2019 Ye et al.
abstract: Purpose This research aimed to identify risk factors of pulmonary metastasis (PM) from hepatocellular carcinoma (HCC) and prognostic factors of patients with PM from HCC at initial diagnosis. Methods Patients diagnosed with HCC between 2010 and 2015 were reviewed retrospectively in the Surveillance, Epidemiology, and End Results (SEER) database. Patients with PM from HCC at initial diagnosis were identified from the entire cohort. Predictors for PM from HCC were identified by multivariate logistic regression analysis. Independent prognostic factors for patients with PM were determined by univariate and multivariate Cox regression analysis. Nomograms were also constructed for quantifying risk of metastasis and overall survival estimation visually. Results Our research included 30,641 patients diagnosed with HCC, of whom 1,732 cases were with PM from HCC at initial diagnosis. The risk factors causing PM from HCC were age (P = 0.001), race (P < 0.001), primary tumor size (P < 0.001), T stage (P < 0.001), N stage (P < 0.001), alpha-fetoprotein (P < 0.001), bone metastasis (P < 0.001), brain metastasis (P < 0.001), and intrahepatic metastasis (P < 0.001). The significantly prognostic factors for overall survival were age (P = 0.014), T stage (P = 0.009), surgical approach (P < 0.001), and chemotherapy (P < 0.001). Harrell’s C-index statistics of two nomograms were 0.768 and 0.687 respectively, indicating satisfactory predictive power. Conclusions This research provided evaluation of risk factors and prognosis for patients with PM from HCC. Two nomograms we developed can be convenient individualized tools to facilitate clinical decision-making.
bibliographic citation: Ye et al. (2019) Risk and prognostic nomograms for hepatocellular carcinoma with newly-diagnosed pulmonary metastasis using SEER data. PeerJ 7:e7496 https://doi.org/10.7717/peerj.7496
date submitted: 2019-04-01
date accepted: 2019-07-16
issued: 2019-08-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Guanzhi
author list: Agent
  family name: Wang
  given name: Lin
author list: Agent
  family name: Hu
  given name: Zhengyang
author list: Agent
  family name: Liang
  given name: Jiaqi
author list: Agent
  family name: Bian
  given name: Yunyi
author list: Agent
  family name: Zhan
  given name: Cheng
author list: Agent
  family name: Lin
  given name: Zongwu
doi: 10.7717/peerj.7496
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-16
copyright: © 2019 Ye et al.
attribution name: Ye et al.

Factors affecting the composition of the gut microbiota, and its modulation
type: item
type: AcademicArticle
description: Gut microbiota have important functions in the body, and imbalances in the composition and diversity of those microbiota can cause several diseases. The host fosters favorable microbiota by releasing specific factors, such as microRNAs, and nonspecific factors, such as antimicrobial peptides, mucus and immunoglobulin A that encourage the growth of specific types of bacteria and inhibit the growth of others. Diet, antibiotics, and age can change gut microbiota, and many studies have shown the relationship between disorders of the microbiota and several diseases and reported some ways to modulate that balance. In this review, we highlight how the host shapes its gut microbiota via specific and nonspecific factors, how environmental and nutritional factors affect it, and how to modulate it using prebiotics, probiotics, and fecal microbiota transplantation.
format: application/pdf
format: text/html
creator: Nihal Hasan
creator: Hongyi Yang
subject: Microbiology
description: doi:10.7717/peerj.7502
publisher: PeerJ Inc.
rights: © 2019 Hasan and Yang
abstract: Gut microbiota have important functions in the body, and imbalances in the composition and diversity of those microbiota can cause several diseases. The host fosters favorable microbiota by releasing specific factors, such as microRNAs, and nonspecific factors, such as antimicrobial peptides, mucus and immunoglobulin A that encourage the growth of specific types of bacteria and inhibit the growth of others. Diet, antibiotics, and age can change gut microbiota, and many studies have shown the relationship between disorders of the microbiota and several diseases and reported some ways to modulate that balance. In this review, we highlight how the host shapes its gut microbiota via specific and nonspecific factors, how environmental and nutritional factors affect it, and how to modulate it using prebiotics, probiotics, and fecal microbiota transplantation.
bibliographic citation: Hasan et al. (2019) Factors affecting the composition of the gut microbiota, and its modulation. PeerJ 7:e7502 https://doi.org/10.7717/peerj.7502
date submitted: 2019-05-01
date accepted: 2019-07-17
issued: 2019-08-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hasan
  given name: Nihal
author list: Agent
  family name: Yang
  given name: Hongyi
doi: 10.7717/peerj.7502
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-16
copyright: © 2019 Hasan and Yang
attribution name: Hasan and Yang

Exploring the potential of deep-blue autofluorescence for monitoring amyloid fibril formation and dissociation
type: item
type: AcademicArticle
description: Protein aggregation into amyloid fibrils has been linked to multiple neurodegenerative disorders. Determining the kinetics of fibril formation, as well as their structural stability are important for the mechanistic understanding of amyloid aggregation. Tracking both fibril association and dissociation is usually performed by measuring light scattering of the solution or fluorescence of amyloid specific dyes, such as thioflavin-T. A possible addition to these methods is the recently discovered deep-blue autofluorescence (dbAF), which is linked to amyloid formation. In this work we explore the potential of this phenomenon to monitor amyloid fibril formation and dissociation, as well as show its possible relation to fibril size rather than amyloid structure.
format: application/pdf
format: text/html
creator: Mantas Ziaunys
creator: Tomas Sneideris
creator: Vytautas Smirnovas
subject: Biochemistry
subject: Biophysics
description: doi:10.7717/peerj.7554
publisher: PeerJ Inc.
rights: © 2019 Ziaunys et al.
abstract: Protein aggregation into amyloid fibrils has been linked to multiple neurodegenerative disorders. Determining the kinetics of fibril formation, as well as their structural stability are important for the mechanistic understanding of amyloid aggregation. Tracking both fibril association and dissociation is usually performed by measuring light scattering of the solution or fluorescence of amyloid specific dyes, such as thioflavin-T. A possible addition to these methods is the recently discovered deep-blue autofluorescence (dbAF), which is linked to amyloid formation. In this work we explore the potential of this phenomenon to monitor amyloid fibril formation and dissociation, as well as show its possible relation to fibril size rather than amyloid structure.
bibliographic citation: Ziaunys et al. (2019) Exploring the potential of deep-blue autofluorescence for monitoring amyloid fibril formation and dissociation. PeerJ 7:e7554 https://doi.org/10.7717/peerj.7554
date submitted: 2019-06-05
date accepted: 2019-07-25
issued: 2019-08-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ziaunys
  given name: Mantas
author list: Agent
  family name: Sneideris
  given name: Tomas
author list: Agent
  family name: Smirnovas
  given name: Vytautas
doi: 10.7717/peerj.7554
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-16
copyright: ©2019 Ziaunys et al.
attribution name: Ziaunys et al.

Experimental removal of introduced slider turtles offers new insight into competition with a native, threatened turtle
type: item
type: AcademicArticle
description: The red-eared slider turtle (Trachemys scripta elegans; RES) is often considered one of the world’s most invasive species. Results from laboratory and mesocosm experiments suggest that introduced RES outcompete native turtles for key ecological resources, but such experiments can overestimate the strength of competition. We report on the first field experiment with a wild turtle community, involving introduced RES and a declining native species of conservation concern, the western pond turtle (Emys marmorata; WPT). Using a before/after experimental design, we show that after removing most of an introduced RES population, the remaining RES dramatically shifted their spatial basking distribution in a manner consistent with strong intraspecific competition. WPT also altered their spatial basking distribution after the RES removal, but in ways inconsistent with strong interspecific competition. However, we documented reduced levels of WPT basking post-removal, which may reflect a behavioral shift attributable to the lower density of the turtle community. WPT body condition also increased after we removed RES, consistent with either indirect or direct competition between WPT and RES and providing the first evidence that RES can compete with a native turtle in the wild. We conclude that the negative impacts on WPT basking by RES in natural contexts are more limited than suggested by experiments with captive turtles, although wild WPT do appear to compete for food with introduced RES. Our results highlight the importance of manipulative field experiments when studying biological invasions, and the potential value of RES removal as a management strategy for WPT.
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creator: Max R. Lambert
creator: Jennifer M. McKenzie
creator: Robyn M. Screen
creator: Adam G. Clause
creator: Benjamin B. Johnson
creator: Genevieve G. Mount
creator: H Bradley Shaffer
creator: Gregory B. Pauly
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.7444
publisher: PeerJ Inc.
rights: © 2019 Lambert et al.
abstract: The red-eared slider turtle (Trachemys scripta elegans; RES) is often considered one of the world’s most invasive species. Results from laboratory and mesocosm experiments suggest that introduced RES outcompete native turtles for key ecological resources, but such experiments can overestimate the strength of competition. We report on the first field experiment with a wild turtle community, involving introduced RES and a declining native species of conservation concern, the western pond turtle (Emys marmorata; WPT). Using a before/after experimental design, we show that after removing most of an introduced RES population, the remaining RES dramatically shifted their spatial basking distribution in a manner consistent with strong intraspecific competition. WPT also altered their spatial basking distribution after the RES removal, but in ways inconsistent with strong interspecific competition. However, we documented reduced levels of WPT basking post-removal, which may reflect a behavioral shift attributable to the lower density of the turtle community. WPT body condition also increased after we removed RES, consistent with either indirect or direct competition between WPT and RES and providing the first evidence that RES can compete with a native turtle in the wild. We conclude that the negative impacts on WPT basking by RES in natural contexts are more limited than suggested by experiments with captive turtles, although wild WPT do appear to compete for food with introduced RES. Our results highlight the importance of manipulative field experiments when studying biological invasions, and the potential value of RES removal as a management strategy for WPT.
bibliographic citation: Lambert et al. (2019) Experimental removal of introduced slider turtles offers new insight into competition with a native, threatened turtle. PeerJ 7:e7444 https://doi.org/10.7717/peerj.7444
date submitted: 2019-05-13
date accepted: 2019-07-09
issued: 2019-08-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lambert
  given name: Max R.
author list: Agent
  family name: McKenzie
  given name: Jennifer M.
author list: Agent
  family name: Screen
  given name: Robyn M.
author list: Agent
  family name: Clause
  given name: Adam G.
author list: Agent
  family name: Johnson
  given name: Benjamin B.
author list: Agent
  family name: Mount
  given name: Genevieve G.
author list: Agent
  family name: Shaffer
  given name: H Bradley
author list: Agent
  family name: Pauly
  given name: Gregory B.
doi: 10.7717/peerj.7444
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-15
copyright: ©2019 Lambert et al.
attribution name: Lambert et al.

Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study
type: item
type: AcademicArticle
description: Background Lactobacillus spp. are common bacteria in the cervical and vaginal microbiota (CVM) and are thought to represent a “healthy” cervicovaginal state. Several studies have found an independent association between ethnicity/race and cervical and vaginal microbiota (CVM) composition. Women of sub-Saharan African descent appear to be significantly more likely to have non-Lactobacillus-dominated CVM compared to women of European descent. The factors contributing to these differences remain to be fully elucidated. The CVM of Black South African women and factors influencing their CVM remain understudied. In this study, we characterized the cervical microbiota of reproductive-age South African women and assessed the associations of these microbiota with participants’ metadata. Methods The cervical microbiota from cervical DNA of 62 reproductive-age women were profiled by Ion Torrent sequencing the V4 hypervariable region of the bacterial 16S ribosomal RNA (rRNA) gene and analyzed with the Quantitative Insights Into Microbial Ecology (QIIME), UPARSE, and metagenomeSeq tools. Associations between cervical microbiota and participants’ metadata were assessed using GraphPad Prism, R packages and an in-house script. Results The cervical microbiota clustered into three distinct community state types (CSTs): Lactobacillus iners-dominated cervical microbiota (CST I (38.7%, 24/62)), unclassified Lactobacillus-dominated cervical microbiota (CST II (4.8%, 3/62)), and diverse cervical microbiota (CST III (56.5%, 35/62)) with an array of heterogeneous bacteria, predominantly the bacterial vaginosis (BV)-associated Gardnerella, Prevotella, Sneathia, and Shuttleworthia. CST III was associated with BV (p = 0.001). Women in CST I were more likely to be on hormonal contraception, especially progestin-based, compared to women in CST III (odds ratio: 5.2 (95% CI [1.6–17.2]); p = 0.005). Women on hormonal contraception had a significantly lower alpha (Shannon indices: 0.9 (0.2–1.9) vers…
format: application/pdf
format: text/html
creator: Harris Onywera
creator: Anna-Lise Williamson
creator: Zizipho Z.A. Mbulawa
creator: David Coetzee
creator: Tracy L. Meiring
subject: Ecology
subject: Microbiology
subject: Epidemiology
subject: Women’s Health
description: doi:10.7717/peerj.7488
publisher: PeerJ Inc.
rights: © 2019 Onywera et al.
abstract: Background Lactobacillus spp. are common bacteria in the cervical and vaginal microbiota (CVM) and are thought to represent a “healthy” cervicovaginal state. Several studies have found an independent association between ethnicity/race and cervical and vaginal microbiota (CVM) composition. Women of sub-Saharan African descent appear to be significantly more likely to have non-Lactobacillus-dominated CVM compared to women of European descent. The factors contributing to these differences remain to be fully elucidated. The CVM of Black South African women and factors influencing their CVM remain understudied. In this study, we characterized the cervical microbiota of reproductive-age South African women and assessed the associations of these microbiota with participants’ metadata. Methods The cervical microbiota from cervical DNA of 62 reproductive-age women were profiled by Ion Torrent sequencing the V4 hypervariable region of the bacterial 16S ribosomal RNA (rRNA) gene and analyzed with the Quantitative Insights Into Microbial Ecology (QIIME), UPARSE, and metagenomeSeq tools. Associations between cervical microbiota and participants’ metadata were assessed using GraphPad Prism, R packages and an in-house script. Results The cervical microbiota clustered into three distinct community state types (CSTs): Lactobacillus iners-dominated cervical microbiota (CST I (38.7%, 24/62)), unclassified Lactobacillus-dominated cervical microbiota (CST II (4.8%, 3/62)), and diverse cervical microbiota (CST III (56.5%, 35/62)) with an array of heterogeneous bacteria, predominantly the bacterial vaginosis (BV)-associated Gardnerella, Prevotella, Sneathia, and Shuttleworthia. CST III was associated with BV (p = 0.001). Women in CST I were more likely to be on hormonal contraception, especially progestin-based, compared to women in CST III (odds ratio: 5.2 (95% CI [1.6–17.2]); p = 0.005). Women on hormonal contraception had a significantly lower alpha (Shannon indices: 0.9 (0.2–1.9) vers…
bibliographic citation: Onywera et al. (2019) Factors associated with the composition and diversity of the cervical microbiota of reproductive-age Black South African women: a retrospective cross-sectional study. PeerJ 7:e7488 https://doi.org/10.7717/peerj.7488
date submitted: 2019-04-11
date accepted: 2019-07-16
issued: 2019-08-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Onywera
  given name: Harris
author list: Agent
  family name: Williamson
  given name: Anna-Lise
author list: Agent
  family name: Mbulawa
  given name: Zizipho Z.A.
author list: Agent
  family name: Coetzee
  given name: David
author list: Agent
  family name: Meiring
  given name: Tracy L.
doi: 10.7717/peerj.7488
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-15
copyright: ©2019 Onywera et al.
attribution name: Onywera et al.

Assessment of the factors influencing primary care physicians’ approach to vaccination of adult risk groups in Istanbul, Turkey
type: item
type: AcademicArticle
description: Background We aimed to assess the factors influencing primary care physicians’ (PCPs) approach to adult vaccination in specific risk groups and evaluate the compliance to adult immunization guidelines. Methods This cross-sectional study performed between January 2016 and April 2016 in İstanbul, Turkey. A questionnaire designed to obtain physicians’ demographical data, experience, immunization status, and attitude on prescribing or recommending vaccines for adults in the risk group. Healthy individuals older than 65 and patients suffer from chronic diseases or had splenectomy before are considered as a risk group. The questionnaire was sent via email to a randomly selected group of 1,500 PCPs. The data of 221 physicians who responded emails were recorded for statistical analysis. Results Of the 221 participants (123 women, 98 men), the majority were aged 31–40 years. Their vaccination rates were 74.2% for hepatitis B, 54.3% for seasonal influenza, and 47.1% for tetanus. Among participants, the highest recommendation and prescription rate of adult vaccines was recorded in PCPs aged 31–40 years. In addition, PCPs with <10 years occupational experience were found to prescribe adult vaccines more frequently than PCPs with longer occupational experience. Conclusions Primary care physicians with lower age and relatively less experience are more intent to prescribe adult vaccines to patients that are in risk groups. This result may be due to increased awareness of adult immunization among PCPs who had more recent medical training. However, many other factors could have caused this difference, including physicians’ approach to primary medical care.
format: application/pdf
format: text/html
creator: Fatma Yılmaz Karadağ
creator: Zuhal Aydan Sağlam
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.7516
publisher: PeerJ Inc.
rights: © 2019 Yılmaz Karadağ and Sağlam
abstract: Background We aimed to assess the factors influencing primary care physicians’ (PCPs) approach to adult vaccination in specific risk groups and evaluate the compliance to adult immunization guidelines. Methods This cross-sectional study performed between January 2016 and April 2016 in İstanbul, Turkey. A questionnaire designed to obtain physicians’ demographical data, experience, immunization status, and attitude on prescribing or recommending vaccines for adults in the risk group. Healthy individuals older than 65 and patients suffer from chronic diseases or had splenectomy before are considered as a risk group. The questionnaire was sent via email to a randomly selected group of 1,500 PCPs. The data of 221 physicians who responded emails were recorded for statistical analysis. Results Of the 221 participants (123 women, 98 men), the majority were aged 31–40 years. Their vaccination rates were 74.2% for hepatitis B, 54.3% for seasonal influenza, and 47.1% for tetanus. Among participants, the highest recommendation and prescription rate of adult vaccines was recorded in PCPs aged 31–40 years. In addition, PCPs with <10 years occupational experience were found to prescribe adult vaccines more frequently than PCPs with longer occupational experience. Conclusions Primary care physicians with lower age and relatively less experience are more intent to prescribe adult vaccines to patients that are in risk groups. This result may be due to increased awareness of adult immunization among PCPs who had more recent medical training. However, many other factors could have caused this difference, including physicians’ approach to primary medical care.
bibliographic citation: Yılmaz Karadağ et al. (2019) Assessment of the factors influencing primary care physicians’ approach to vaccination of adult risk groups in Istanbul, Turkey. PeerJ 7:e7516 https://doi.org/10.7717/peerj.7516
date submitted: 2018-12-23
date accepted: 2019-07-18
issued: 2019-08-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yılmaz Karadağ
  given name: Fatma
author list: Agent
  family name: Sağlam
  given name: Zuhal Aydan
doi: 10.7717/peerj.7516
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-15
copyright: © 2019 Yılmaz Karadağ and Sağlam
attribution name: Yılmaz Karadağ and Sağlam

Molecular taxonomy of endemic coastal Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species
type: item
type: AcademicArticle
description: Past phylogeographic work has shown Ligia hawaiensis, a coastal isopod species endemic to the Hawaiian Islands, to be a paraphyletic complex of several highly genetically divergent yet morphologically cryptic lineages. Despite the need for a taxonomic revision of this species, the lack of morphological differentiation has proven an impediment to formally describe new Ligia species in the region. Molecular characters and species delimitation approaches have been successfully used to formally describe cryptic species in other crustacean taxa, suggesting they may aid taxonomic revisions of L. hawaiensis. Herein, various distance- and tree-based molecular species delimitation approaches are applied on a concatenated dataset comprised of both mitochondrial and nuclear gene sequences of L. hawaiensis and L. perkinsi, a terrestrial species endemic to the Hawaiian archipelago. Results of these analyses informed a taxonomic revision leading to the redescription of L. hawaiensis and the description of seven new cryptic species on the basis of molecular characters: L. dante, L. eleluensis, L. honu, L. kamehameha, L. mauinuiensis, L. pele, and L. rolliensis. These coastal Ligia species from the Hawaiian archipelago appear to be largely limited to single islands, where they appear largely constrained to volcanic rift zones suggesting allopatric events at local scales may drive diversification for poorly dispersing organisms in the Hawaiian coastlines. Additional work remains needed to fully assess the role of said events; however, the description of these novel species underscore their potential to aid in studies of local diversification of marine organisms in Hawai‘i. Lastly, this represents the first application of molecular taxonomic approaches to formally describe genetic lineages found in Ligia isopods as species, underscoring the promise these methods hold to taxonomic revisions in other species in the genus shown to harbor cryptic genetic lineages.
format: application/pdf
format: text/html
creator: Carlos A. Santamaria
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7531
publisher: PeerJ Inc.
rights: © 2019 Santamaria
abstract: Past phylogeographic work has shown Ligia hawaiensis, a coastal isopod species endemic to the Hawaiian Islands, to be a paraphyletic complex of several highly genetically divergent yet morphologically cryptic lineages. Despite the need for a taxonomic revision of this species, the lack of morphological differentiation has proven an impediment to formally describe new Ligia species in the region. Molecular characters and species delimitation approaches have been successfully used to formally describe cryptic species in other crustacean taxa, suggesting they may aid taxonomic revisions of L. hawaiensis. Herein, various distance- and tree-based molecular species delimitation approaches are applied on a concatenated dataset comprised of both mitochondrial and nuclear gene sequences of L. hawaiensis and L. perkinsi, a terrestrial species endemic to the Hawaiian archipelago. Results of these analyses informed a taxonomic revision leading to the redescription of L. hawaiensis and the description of seven new cryptic species on the basis of molecular characters: L. dante, L. eleluensis, L. honu, L. kamehameha, L. mauinuiensis, L. pele, and L. rolliensis. These coastal Ligia species from the Hawaiian archipelago appear to be largely limited to single islands, where they appear largely constrained to volcanic rift zones suggesting allopatric events at local scales may drive diversification for poorly dispersing organisms in the Hawaiian coastlines. Additional work remains needed to fully assess the role of said events; however, the description of these novel species underscore their potential to aid in studies of local diversification of marine organisms in Hawai‘i. Lastly, this represents the first application of molecular taxonomic approaches to formally describe genetic lineages found in Ligia isopods as species, underscoring the promise these methods hold to taxonomic revisions in other species in the genus shown to harbor cryptic genetic lineages.
bibliographic citation: Santamaria (2019) Molecular taxonomy of endemic coastal Ligia isopods from the Hawaiian Islands: re-description of L. hawaiensis and description of seven novel cryptic species. PeerJ 7:e7531 https://doi.org/10.7717/peerj.7531
date submitted: 2018-12-07
date accepted: 2019-07-22
issued: 2019-08-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santamaria
  given name: Carlos A.
doi: 10.7717/peerj.7531
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-15
copyright: ©2019 Santamaria
attribution name: Santamaria

Modeling tree diversity, stand structure and productivity of northern temperate coniferous forests of Mexico
type: item
type: AcademicArticle
description: There is increasing evidence complex forest structure and tree diversity correlates positively with the productivity of forest ecosystems. However, there is little quantitative information regarding the effect of these factors on stand productivity of northern temperate coniferous forests of Mexico. This study aimed to test the hypothesis tree diversity and canopy structure positively associates with forest productivity. Parameterization of tree diversity, stand structure and productivity were carried out on dasometric data from 36 permanent sampling plots re-measured in 1982, 1993, and 2004. Statistical analysis of stand parameters tested the null hypothesis. Statistical relationships revealed well-balanced canopy strata and imbalanced diameter structures positively correlated with stand productivity. Tree diversity was also positively linked with stand productivity, but the effect appeared to be most important in the early to intermediate stages of succession. Further research is required to understand the long-term effects of tree diversity and canopy structure on stand productivity. These preliminary observations stress the importance of prescribing silvicultural practices that maintain the three-dimensional structure of stands and diversity of forest canopies that aim to preserve ecosystem function, diversity, and productivity.
format: application/pdf
format: text/html
creator: José Návar
subject: Natural Resource Management
subject: Forestry
description: doi:10.7717/peerj.7051
publisher: PeerJ Inc.
rights: © 2019 Návar
abstract: There is increasing evidence complex forest structure and tree diversity correlates positively with the productivity of forest ecosystems. However, there is little quantitative information regarding the effect of these factors on stand productivity of northern temperate coniferous forests of Mexico. This study aimed to test the hypothesis tree diversity and canopy structure positively associates with forest productivity. Parameterization of tree diversity, stand structure and productivity were carried out on dasometric data from 36 permanent sampling plots re-measured in 1982, 1993, and 2004. Statistical analysis of stand parameters tested the null hypothesis. Statistical relationships revealed well-balanced canopy strata and imbalanced diameter structures positively correlated with stand productivity. Tree diversity was also positively linked with stand productivity, but the effect appeared to be most important in the early to intermediate stages of succession. Further research is required to understand the long-term effects of tree diversity and canopy structure on stand productivity. These preliminary observations stress the importance of prescribing silvicultural practices that maintain the three-dimensional structure of stands and diversity of forest canopies that aim to preserve ecosystem function, diversity, and productivity.
bibliographic citation: Návar (2019) Modeling tree diversity, stand structure and productivity of northern temperate coniferous forests of Mexico. PeerJ 7:e7051 https://doi.org/10.7717/peerj.7051
date submitted: 2018-02-27
date accepted: 2019-05-02
issued: 2019-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Návar
  given name: José
doi: 10.7717/peerj.7051
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-14
copyright: ©2019 Návar
attribution name: Návar

Ontogenetic braincase development in Psittacosaurus lujiatunensis (Dinosauria: Ceratopsia) using micro-computed tomography
type: item
type: AcademicArticle
description: Ontogenetic sequences are relatively rare among dinosaurs, with Ceratopsia being one of the better represented clades, and especially among geologically earlier forms, such as Psittacosaurus. Psittacosaurus is a small, bipedal basal ceratopsian abundant in the Lower Cretaceous deposits of Asia, whose cranial and endocranial morphology has been well studied, but only cursory details have been published on the bones surrounding the brain. Using reconstructions created from micro-computed tomography scans of well-preserved skulls from the Barremian–Aptian Yixian Formation, China, we document morphological changes in the braincase of Psittacosaurus lujiatunensis through three growth stages, hatchling, juvenile, and adult, thus providing the first detailed study of ceratopsian braincase morphology through ontogeny. Notable ontogenetic changes in the braincase of P. lujiatunensis include a dramatic relative reduction in size of the supraoccipital, an increase in the lateral expansion of the paroccipital processes and a decrease in the angle between the lateral semicircular canal and the palatal plane. These ontogenetic morphological changes in the braincase relate to expansion of the cranium and brain through growth, as well as reflecting the switch from quadrupedal juveniles to bipedal adults as documented in the changing orientation of the horizontal semicircular canal through ontogeny. Recognition of these patterns in a basal ceratopsian has implications for understanding key events in later ceratopsian evolution, such as the development of the parieto-squamosal frill in derived neoceratopsians.
format: application/pdf
format: text/html
creator: Claire M. Bullar
creator: Qi Zhao
creator: Michael J. Benton
creator: Michael J. Ryan
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.7217
publisher: PeerJ Inc.
rights: © 2019 Bullar et al.
abstract: Ontogenetic sequences are relatively rare among dinosaurs, with Ceratopsia being one of the better represented clades, and especially among geologically earlier forms, such as Psittacosaurus. Psittacosaurus is a small, bipedal basal ceratopsian abundant in the Lower Cretaceous deposits of Asia, whose cranial and endocranial morphology has been well studied, but only cursory details have been published on the bones surrounding the brain. Using reconstructions created from micro-computed tomography scans of well-preserved skulls from the Barremian–Aptian Yixian Formation, China, we document morphological changes in the braincase of Psittacosaurus lujiatunensis through three growth stages, hatchling, juvenile, and adult, thus providing the first detailed study of ceratopsian braincase morphology through ontogeny. Notable ontogenetic changes in the braincase of P. lujiatunensis include a dramatic relative reduction in size of the supraoccipital, an increase in the lateral expansion of the paroccipital processes and a decrease in the angle between the lateral semicircular canal and the palatal plane. These ontogenetic morphological changes in the braincase relate to expansion of the cranium and brain through growth, as well as reflecting the switch from quadrupedal juveniles to bipedal adults as documented in the changing orientation of the horizontal semicircular canal through ontogeny. Recognition of these patterns in a basal ceratopsian has implications for understanding key events in later ceratopsian evolution, such as the development of the parieto-squamosal frill in derived neoceratopsians.
bibliographic citation: Bullar et al. (2019) Ontogenetic braincase development in Psittacosaurus lujiatunensis (Dinosauria: Ceratopsia) using micro-computed tomography. PeerJ 7:e7217 https://doi.org/10.7717/peerj.7217
date submitted: 2018-10-23
date accepted: 2019-05-31
issued: 2019-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bullar
  given name: Claire M.
author list: Agent
  family name: Zhao
  given name: Qi
author list: Agent
  family name: Benton
  given name: Michael J.
author list: Agent
  family name: Ryan
  given name: Michael J.
doi: 10.7717/peerj.7217
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-14
copyright: © 2019 Bullar et al.
attribution name: Bullar et al.

Variation in denitrifying bacterial communities along a primary succession in the Hailuogou Glacier retreat area, China
type: item
type: AcademicArticle
description: Background The Hailuogou Glacier is located at the Gongga Mountain on the southeastern edge of the Tibetan Plateau, and has retreated continuously as a result of global warming. The retreat of the Hailuogou Glacier has left behind a primary succession along soil chronosequences. Hailuogou Glacier’s retreated area provides an excellent living environment for the colonization of microbes and plants, making it an ideal model to explore plant successions, microbial communities, and the interaction of plants and microbes during the colonization process. However, to date, the density of the nitrogen cycling microbial communities remain unknown, especially for denitrifiers in the primary succession of the Hailuogou Glacier. Therefore, we investigated the structural succession and its driving factors for denitrifying bacterial communities during the four successional stages (0, 20, 40, and 60 years). Methods The diversity, community composition, and abundance of nosZ-denitrifiers were determined using molecular tools, including terminal restriction fragment length polymorphism and quantitative polymerase chain reactions (qPCR). Results nosZ-denitrifiers were more abundant and diverse in soils from successional years 20–60 compared to 0–5 years, and was highest in Site3 (40 years). The denitrifying bacterial community composition was more complex in older soils (40–60 years) than in younger soils (≤20 years). The terminal restriction fragments (T-RFs) of Azospirillum (90 bp) and Rubrivivax (95 bp) were dominant in soisl during early successional stages (0–20 years) and in the mature phase (40–60 years), respectively. Specific T-RFs of Bradyrhizobium (100 bp) and Pseudomonas (275 bp) were detected only in Site3 and Site4, respectively. Moreover, the unidentified 175 bp T-RFs was detected only in Site3. Of the abiotic factors that were measured in this study, soil available phosphorus, available potassium and denitrifying enzyme activity (DEA) correlated significantly with the…
format: application/pdf
format: text/html
creator: Yan Bai
creator: Xiying Huang
creator: Xiangrui Zhou
creator: Quanju Xiang
creator: Ke Zhao
creator: Xiumei Yu
creator: Qiang Chen
creator: Hao Jiang
creator: Tashi Nyima
creator: Xue Gao
creator: Yunfu Gu
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Soil Science
subject: Ecotoxicology
description: doi:10.7717/peerj.7356
publisher: PeerJ Inc.
rights: © 2019 Bai et al.
abstract: Background The Hailuogou Glacier is located at the Gongga Mountain on the southeastern edge of the Tibetan Plateau, and has retreated continuously as a result of global warming. The retreat of the Hailuogou Glacier has left behind a primary succession along soil chronosequences. Hailuogou Glacier’s retreated area provides an excellent living environment for the colonization of microbes and plants, making it an ideal model to explore plant successions, microbial communities, and the interaction of plants and microbes during the colonization process. However, to date, the density of the nitrogen cycling microbial communities remain unknown, especially for denitrifiers in the primary succession of the Hailuogou Glacier. Therefore, we investigated the structural succession and its driving factors for denitrifying bacterial communities during the four successional stages (0, 20, 40, and 60 years). Methods The diversity, community composition, and abundance of nosZ-denitrifiers were determined using molecular tools, including terminal restriction fragment length polymorphism and quantitative polymerase chain reactions (qPCR). Results nosZ-denitrifiers were more abundant and diverse in soils from successional years 20–60 compared to 0–5 years, and was highest in Site3 (40 years). The denitrifying bacterial community composition was more complex in older soils (40–60 years) than in younger soils (≤20 years). The terminal restriction fragments (T-RFs) of Azospirillum (90 bp) and Rubrivivax (95 bp) were dominant in soisl during early successional stages (0–20 years) and in the mature phase (40–60 years), respectively. Specific T-RFs of Bradyrhizobium (100 bp) and Pseudomonas (275 bp) were detected only in Site3 and Site4, respectively. Moreover, the unidentified 175 bp T-RFs was detected only in Site3. Of the abiotic factors that were measured in this study, soil available phosphorus, available potassium and denitrifying enzyme activity (DEA) correlated significantly with the…
bibliographic citation: Bai et al. (2019) Variation in denitrifying bacterial communities along a primary succession in the Hailuogou Glacier retreat area, China. PeerJ 7:e7356 https://doi.org/10.7717/peerj.7356
date submitted: 2019-01-08
date accepted: 2019-06-26
issued: 2019-08-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Yan
author list: Agent
  family name: Huang
  given name: Xiying
author list: Agent
  family name: Zhou
  given name: Xiangrui
author list: Agent
  family name: Xiang
  given name: Quanju
author list: Agent
  family name: Zhao
  given name: Ke
author list: Agent
  family name: Yu
  given name: Xiumei
author list: Agent
  family name: Chen
  given name: Qiang
author list: Agent
  family name: Jiang
  given name: Hao
author list: Agent
  family name: Nyima
  given name: Tashi
author list: Agent
  family name: Gao
  given name: Xue
author list: Agent
  family name: Gu
  given name: Yunfu
doi: 10.7717/peerj.7356
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-14
copyright: ©2019 Bai et al.
attribution name: Bai et al.

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