PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effect of changes in the fractal structure of a littoral zone in the course of lake succession on the abundance, body size sequence and biomass of beetles
items: Human dimensions of wildfires in NW Spain: causes, value of the burned vegetation and administrative measures
items: In silico study of medical decision-making for rare diseases: heterogeneity of decision-makers in a population improves overall benefit
items: High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia
items: https://peerj.com/articles/5626
items: Effectiveness of winter temperatures for satisfying chilling requirements for reproductive budburst of red alder (Alnus rubra)
items: Using bioinformatics tools for the discovery of Dengue RNA-dependent RNA polymerase inhibitors
items: Plurality in multi-disciplinary research: multiple institutional affiliations are associated with increased citations
items: Variation of soil bacterial communities along a chronosequence of Eucalyptus plantation
items: Successful transplantation of guinea pig gut microbiota in mice and its effect on pneumonic plague sensitivity

Effect of changes in the fractal structure of a littoral zone in the course of lake succession on the abundance, body size sequence and biomass of beetles
type: item
type: AcademicArticle
description: Dystrophic lakes undergo natural disharmonic succession, in the course of which an increasingly complex and diverse, mosaic-like pattern of habitats evolves. In the final seral stage, the most important role is played by a spreading Sphagnum mat, which gradually reduces the lake’s open water surface area. Long-term transformations in the primary structure of lakes cause changes in the structure of lake-dwelling fauna assemblages. Knowledge of the succession mechanisms in lake fauna is essential for proper lake management. The use of fractal concepts helps to explain the character of fauna in relation to other aspects of the changing complexity of habitats. Our 12-year-long study into the succession of water beetles has covered habitats of 40 selected lakes which are diverse in terms of the fractal dimension. The taxonomic diversity and density of lake beetles increase parallel to an increase in the fractal dimension. An in-depth analysis of the fractal structure proved to be helpful in explaining the directional changes in fauna induced by the natural succession of lakes. Negative correlations appear between the body size and abundance. An increase in the density of beetles within the higher dimension fractals is counterbalanced by a change in the size of individual organisms. As a result, the biomass is constant, regardless of the fractal dimension.
format: application/pdf
format: text/html
creator: Joanna Pakulnicka
creator: Andrzej Zawal
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Freshwater Biology
description: doi:10.7717/peerj.5662
publisher: PeerJ Inc.
rights: © 2018 Pakulnicka and Zawal
abstract: Dystrophic lakes undergo natural disharmonic succession, in the course of which an increasingly complex and diverse, mosaic-like pattern of habitats evolves. In the final seral stage, the most important role is played by a spreading Sphagnum mat, which gradually reduces the lake’s open water surface area. Long-term transformations in the primary structure of lakes cause changes in the structure of lake-dwelling fauna assemblages. Knowledge of the succession mechanisms in lake fauna is essential for proper lake management. The use of fractal concepts helps to explain the character of fauna in relation to other aspects of the changing complexity of habitats. Our 12-year-long study into the succession of water beetles has covered habitats of 40 selected lakes which are diverse in terms of the fractal dimension. The taxonomic diversity and density of lake beetles increase parallel to an increase in the fractal dimension. An in-depth analysis of the fractal structure proved to be helpful in explaining the directional changes in fauna induced by the natural succession of lakes. Negative correlations appear between the body size and abundance. An increase in the density of beetles within the higher dimension fractals is counterbalanced by a change in the size of individual organisms. As a result, the biomass is constant, regardless of the fractal dimension.
bibliographic citation: Pakulnicka et al. (2018) Effect of changes in the fractal structure of a littoral zone in the course of lake succession on the abundance, body size sequence and biomass of beetles. PeerJ 6:e5662 https://doi.org/10.7717/peerj.5662
date submitted: 2018-05-24
date accepted: 2018-08-29
issued: 2018-09-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pakulnicka
  given name: Joanna
author list: Agent
  family name: Zawal
  given name: Andrzej
doi: 10.7717/peerj.5662
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-26
copyright: ©2018 Pakulnicka and Zawal
attribution name: Pakulnicka and Zawal

Human dimensions of wildfires in NW Spain: causes, value of the burned vegetation and administrative measures
type: item
type: AcademicArticle
description: Exploring the human dimensions of forest fires is a crucial, although often overlooked, aspect of wildfire research, since wildfires often have important socio-economic impacts and humans are nowadays the main cause of wildfires in many areas of the world. We carried out a telephone survey (N = 345 interviews) in one of the most fire-prone areas in Europe (NW Spain) in order to assess citizens’ awareness about wildfire causes and risks, their perception of the value of the vegetation and of administrative measures to fight against fires. Perceptions of respondents about fire causes were in general realistic although fires caused by pyromaniacs and for profit were overestimated, while vegetation management was comparatively underestimated. Citizens were broadly aware of the fire risk associated with different vegetation types, rightly considering native oak forests and agricultural fields as less risky than shrublands and pine and eucalypt plantations. Tree-dominated vegetation was more valued than treeless formations, and native forests more than tree plantations, which seems related to a preference for ecological value over utilitarian considerations. In addition, the value of eucalypt plantations was clearly affected by the education level of respondents, being less valued as the education level increased. Most citizens considered that the administration was not doing enough to fight against fires. The law that compels landowners to reduce fuels in wildland-urban interfaces was considered effective by most respondents (72%), but 50% considered it difficult to implement by landowners. This may explain the poor degree of compliance of this law.
format: application/pdf
format: text/html
creator: María Calviño-Cancela
creator: Nuria Cañizo-Novelle
subject: Natural Resource Management
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.5657
publisher: PeerJ Inc.
rights: © 2018 Calviño-Cancela and Cañizo-Novelle
abstract: Exploring the human dimensions of forest fires is a crucial, although often overlooked, aspect of wildfire research, since wildfires often have important socio-economic impacts and humans are nowadays the main cause of wildfires in many areas of the world. We carried out a telephone survey (N = 345 interviews) in one of the most fire-prone areas in Europe (NW Spain) in order to assess citizens’ awareness about wildfire causes and risks, their perception of the value of the vegetation and of administrative measures to fight against fires. Perceptions of respondents about fire causes were in general realistic although fires caused by pyromaniacs and for profit were overestimated, while vegetation management was comparatively underestimated. Citizens were broadly aware of the fire risk associated with different vegetation types, rightly considering native oak forests and agricultural fields as less risky than shrublands and pine and eucalypt plantations. Tree-dominated vegetation was more valued than treeless formations, and native forests more than tree plantations, which seems related to a preference for ecological value over utilitarian considerations. In addition, the value of eucalypt plantations was clearly affected by the education level of respondents, being less valued as the education level increased. Most citizens considered that the administration was not doing enough to fight against fires. The law that compels landowners to reduce fuels in wildland-urban interfaces was considered effective by most respondents (72%), but 50% considered it difficult to implement by landowners. This may explain the poor degree of compliance of this law.
bibliographic citation: Calviño-Cancela et al. (2018) Human dimensions of wildfires in NW Spain: causes, value of the burned vegetation and administrative measures. PeerJ 6:e5657 https://doi.org/10.7717/peerj.5657
date submitted: 2018-03-29
date accepted: 2018-08-28
issued: 2018-09-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Calviño-Cancela
  given name: María
author list: Agent
  family name: Cañizo-Novelle
  given name: Nuria
doi: 10.7717/peerj.5657
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-26
copyright: ©2018 Calviño-Cancela and Cañizo-Novelle
attribution name: Calviño-Cancela and Cañizo-Novelle

In silico study of medical decision-making for rare diseases: heterogeneity of decision-makers in a population improves overall benefit
type: item
type: AcademicArticle
description: Background Medical decision-making is difficult when information is limited due to its rareness. For example, there are two treatment options for patients affected by a rare disease with high lethality. The information about both treatment effects is unavailable or very limited. Patients are inclined to accept one of the interventions rather than waiting for death, but they are reluctant to be assigned the inferior one. While a single patient selects one treatment that seems better based on the limited information, he or she loses the chance to select the other treatment, which may be the better option. This is the so-called dilemma between exploitation (enjoying the benefits of using current knowledge) and exploration (taking the risk to obtain new knowledge). In clinical settings, the statistical advice for individual patients seems to be the maximum expected success rate or something equivalent and patients’ selections tend to be homogeneous, which does not solve the dilemma. In this study, our aim is to investigate the effects of the heterogeneity of decision-makers in the decision process. Methods Here, we proposed a decision strategy that introduced the heterogeneity of decision-makers by considering patients’ self-decisions where the patients’ heterogeneous attitudes towards the treatment are integrated into the probabilistic utility function based on the Beta Bayesian posterior. Based on the context of two-armed bandit treatment options with limited information, we compared the overall success rate of treatment between our heterogeneous decision strategy and a homogeneous decision strategy that is defined to select the treatment with the largest posterior mean. Results The heterogeneity of decision-makers in a population improved the overall benefit of treatment under some conditions. Discussion In clinical settings, there exists heterogeneity of decision-making among patients. Our study investigated a targeting strategy by respecting the self-decision of al…
format: application/pdf
format: text/html
creator: Juan Wang
creator: Ryo Yamada
subject: Bioinformatics
subject: Clinical Trials
subject: Public Health
subject: Ethical Issues
subject: Statistics
description: doi:10.7717/peerj.5677
publisher: PeerJ Inc.
rights: © 2018 Wang and Yamada
abstract: Background Medical decision-making is difficult when information is limited due to its rareness. For example, there are two treatment options for patients affected by a rare disease with high lethality. The information about both treatment effects is unavailable or very limited. Patients are inclined to accept one of the interventions rather than waiting for death, but they are reluctant to be assigned the inferior one. While a single patient selects one treatment that seems better based on the limited information, he or she loses the chance to select the other treatment, which may be the better option. This is the so-called dilemma between exploitation (enjoying the benefits of using current knowledge) and exploration (taking the risk to obtain new knowledge). In clinical settings, the statistical advice for individual patients seems to be the maximum expected success rate or something equivalent and patients’ selections tend to be homogeneous, which does not solve the dilemma. In this study, our aim is to investigate the effects of the heterogeneity of decision-makers in the decision process. Methods Here, we proposed a decision strategy that introduced the heterogeneity of decision-makers by considering patients’ self-decisions where the patients’ heterogeneous attitudes towards the treatment are integrated into the probabilistic utility function based on the Beta Bayesian posterior. Based on the context of two-armed bandit treatment options with limited information, we compared the overall success rate of treatment between our heterogeneous decision strategy and a homogeneous decision strategy that is defined to select the treatment with the largest posterior mean. Results The heterogeneity of decision-makers in a population improved the overall benefit of treatment under some conditions. Discussion In clinical settings, there exists heterogeneity of decision-making among patients. Our study investigated a targeting strategy by respecting the self-decision of al…
bibliographic citation: Wang et al. (2018) In silico study of medical decision-making for rare diseases: heterogeneity of decision-makers in a population improves overall benefit. PeerJ 6:e5677 https://doi.org/10.7717/peerj.5677
date submitted: 2018-04-11
date accepted: 2018-08-29
issued: 2018-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Juan
author list: Agent
  family name: Yamada
  given name: Ryo
doi: 10.7717/peerj.5677
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-25
copyright: ©2018 Wang and Yamada
attribution name: Wang and Yamada

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia
type: item
type: AcademicArticle
description: Background Knowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-organisms constitute the overwhelming majority of life forms in any given location, in terms of both diversity and abundance. Here we address how the diversity and community turnover of operational taxonomic units (OTU) of organisms in soil and litter respond to soil physicochemical properties; whether OTU diversities and community composition in soil and litter are correlated with each other; and whether they respond in a similar way to soil properties. Methods We used recently inferred OTUs from high-throughput metabarcoding of the 16S (prokaryotes) and 18S (eukaryotes) genes to estimate OTU diversity (OTU richness and effective number of OTUs) and community composition for prokaryotes and eukaryotes in soil and litter across four localities in Brazilian Amazonia. All analyses were run separately for prokaryote and eukaryote OTUs, and for each group using both presence-absence and abundance data. Combining these with novel data on soil chemical and physical properties, we identify abiotic correlates of soil and litter organism diversity and community structure using regression, ordination, and variance partitioning analysis. Results Soil organic carbon content was the strongest factor explaining OTU diversity (negative correlation) and pH was the strongest factor explaining community turnover for prokaryotes and eukaryotes in both soil and litter. We found significant effects also for other soil variables, including both chemical and physical properties. The correlation between OTU diversity in litter and in soil was non-significant for eukaryotes and weak for prokaryotes. The community compositions of both prokaryotes and …
format: application/pdf
format: text/html
creator: Camila D. Ritter
creator: Alexander Zizka
creator: Fabian Roger
creator: Hanna Tuomisto
creator: Christopher Barnes
creator: R. Henrik Nilsson
creator: Alexandre Antonelli
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.5661
publisher: PeerJ Inc.
rights: © 2018 Ritter et al.
abstract: Background Knowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-organisms constitute the overwhelming majority of life forms in any given location, in terms of both diversity and abundance. Here we address how the diversity and community turnover of operational taxonomic units (OTU) of organisms in soil and litter respond to soil physicochemical properties; whether OTU diversities and community composition in soil and litter are correlated with each other; and whether they respond in a similar way to soil properties. Methods We used recently inferred OTUs from high-throughput metabarcoding of the 16S (prokaryotes) and 18S (eukaryotes) genes to estimate OTU diversity (OTU richness and effective number of OTUs) and community composition for prokaryotes and eukaryotes in soil and litter across four localities in Brazilian Amazonia. All analyses were run separately for prokaryote and eukaryote OTUs, and for each group using both presence-absence and abundance data. Combining these with novel data on soil chemical and physical properties, we identify abiotic correlates of soil and litter organism diversity and community structure using regression, ordination, and variance partitioning analysis. Results Soil organic carbon content was the strongest factor explaining OTU diversity (negative correlation) and pH was the strongest factor explaining community turnover for prokaryotes and eukaryotes in both soil and litter. We found significant effects also for other soil variables, including both chemical and physical properties. The correlation between OTU diversity in litter and in soil was non-significant for eukaryotes and weak for prokaryotes. The community compositions of both prokaryotes and …
bibliographic citation: Ritter et al. (2018) High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia. PeerJ 6:e5661 https://doi.org/10.7717/peerj.5661
date submitted: 2018-03-13
date accepted: 2018-08-29
issued: 2018-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ritter
  given name: Camila D.
author list: Agent
  family name: Zizka
  given name: Alexander
author list: Agent
  family name: Roger
  given name: Fabian
author list: Agent
  family name: Tuomisto
  given name: Hanna
author list: Agent
  family name: Barnes
  given name: Christopher
author list: Agent
  family name: Nilsson
  given name: R. Henrik
author list: Agent
  family name: Antonelli
  given name: Alexandre
doi: 10.7717/peerj.5661
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-25
copyright: ©2018 Ritter et al.
attribution name: Ritter et al.

https://peerj.com/articles/5626
type: item
type: AcademicArticle
title: An adaptive scale Gaussian filter to explain White’s illusion from the viewpoint of lightness assimilation for a large range of variation in spatial frequency of the grating and aspect ratio of the targets
description: The variation between the actual and perceived lightness of a stimulus has strong dependency on its background, a phenomena commonly known as lightness induction in the literature of visual neuroscience and psychology. For instance, a gray patch may perceptually appear to be darker in a background while it looks brighter when the background is reversed. In the literature it is further reported that such variation can take place in two possible ways. In case of stimulus like the Simultaneous Brightness Contrast (SBC), the apparent lightness changes in the direction opposite to that of the background lightness, a phenomenon often referred to as lightness contrast, while in the others like neon colour spreading or checkerboard illusion it occurs opposite to that, and known as lightness assimilation. The White’s illusion is a typical one which according to many, does not completely conform to any of these two processes. This paper presents the result of quantification of the perceptual strength of the White’s illusion as a function of the width of the background square grating as well as the length of the gray patch. A linear filter model is further proposed to simulate the possible neurophysiological phenomena responsible for this particular visual experience. The model assumes that for the White’s illusion, where the edges are strong and quite a few, i.e., the spectrum is rich in high frequency components, the inhibitory surround in the classical Difference-of-Gaussians (DoG) filter gets suppressed, and the filter essentially reduces to an adaptive scale Gaussian kernel that brings about lightness assimilation. The linear filter model with a Gaussian kernel is used to simulate the White’s illusion phenomena with wide variation of spatial frequency of the background grating as well as the length of the gray patch. The appropriateness of the model is presented through simulation results, which are highly tuned to the present as well as earlier psychometric results.
format: application/pdf
format: text/html
creator: Soma Mitra
creator: Debasis Mazumdar
creator: Kuntal Ghosh
creator: Kamales Bhaumik
subject: Computational Biology
subject: Neuroscience
description: doi:10.7717/peerj.5626
publisher: PeerJ Inc.
rights: © 2018 Mitra et al.
abstract: The variation between the actual and perceived lightness of a stimulus has strong dependency on its background, a phenomena commonly known as lightness induction in the literature of visual neuroscience and psychology. For instance, a gray patch may perceptually appear to be darker in a background while it looks brighter when the background is reversed. In the literature it is further reported that such variation can take place in two possible ways. In case of stimulus like the Simultaneous Brightness Contrast (SBC), the apparent lightness changes in the direction opposite to that of the background lightness, a phenomenon often referred to as lightness contrast, while in the others like neon colour spreading or checkerboard illusion it occurs opposite to that, and known as lightness assimilation. The White’s illusion is a typical one which according to many, does not completely conform to any of these two processes. This paper presents the result of quantification of the perceptual strength of the White’s illusion as a function of the width of the background square grating as well as the length of the gray patch. A linear filter model is further proposed to simulate the possible neurophysiological phenomena responsible for this particular visual experience. The model assumes that for the White’s illusion, where the edges are strong and quite a few, i.e., the spectrum is rich in high frequency components, the inhibitory surround in the classical Difference-of-Gaussians (DoG) filter gets suppressed, and the filter essentially reduces to an adaptive scale Gaussian kernel that brings about lightness assimilation. The linear filter model with a Gaussian kernel is used to simulate the White’s illusion phenomena with wide variation of spatial frequency of the background grating as well as the length of the gray patch. The appropriateness of the model is presented through simulation results, which are highly tuned to the present as well as earlier psychometric results.
bibliographic citation: Mitra et al. (2018) An adaptive scale Gaussian filter to explain White’s illusion from the viewpoint of lightness assimilation for a large range of variation in spatial frequency of the grating and aspect ratio of the targets. PeerJ 6:e5626 https://doi.org/10.7717/peerj.5626
date submitted: 2018-04-02
date accepted: 2018-08-22
issued: 2018-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mitra
  given name: Soma
author list: Agent
  family name: Mazumdar
  given name: Debasis
author list: Agent
  family name: Ghosh
  given name: Kuntal
author list: Agent
  family name: Bhaumik
  given name: Kamales
doi: 10.7717/peerj.5626
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-25
copyright: ©2018 Mitra et al.
attribution name: Mitra et al.

Effectiveness of winter temperatures for satisfying chilling requirements for reproductive budburst of red alder (Alnus rubra)
type: item
type: AcademicArticle
description: Background Experiencing an adequate amount of cold temperatures over winter is necessary for many temperate tree species to break dormancy and flower in spring. Thus, changes in winter and spring temperatures associated with climate change may influence when trees break dormancy and flower in the future. There have been several experimental studies that have quantified the effectiveness of cold temperatures for chilling requirements for vegetative budburst of temperate trees; however, there are few experimental studies addressing the chilling requirements for reproductive budburst of trees, as it is difficult to place reproductively mature trees in temperature-controlled environments. Methods To identify how changing temperatures associated with climate change may impact reproductive phenology, we completed a temperature-controlled growth chamber experiment using cuttings of reproductive branches of red alder (Alnus rubra), one of the most widespread hardwood tree species of the Pacific Northwest, USA. The purpose of this study was to examine how colder (4 °C) and warmer (9 °C) winter temperature regimes influenced the timing of reproductive budburst of red alder cuttings in spring. We also compared the date of budburst of cuttings to that of branches from intact trees. Results We found that cuttings flowered earlier after pretreatment with a 4 °C winter temperature regime than after a 9 °C winter temperature regime. We found no significant differences between the timing of male budburst of cuttings exposed to ambient conditions compared to male budburst of branches from intact trees. We used our experimental data to estimate a “possibility-line” that shows the accumulated chilling and forcing temperatures necessary prior to reproductive budburst of red alder. Discussion This study provides a preliminary indication that warmer winters with climate change may not be as effective as colder winters for satisfying chilling temperature requirements of a Northwest hardwoo…
format: application/pdf
format: text/html
creator: Janet S. Prevéy
creator: Constance A. Harrington
subject: Climate Change Biology
subject: Forestry
description: doi:10.7717/peerj.5221
publisher: PeerJ Inc.
rights: © 2018
abstract: Background Experiencing an adequate amount of cold temperatures over winter is necessary for many temperate tree species to break dormancy and flower in spring. Thus, changes in winter and spring temperatures associated with climate change may influence when trees break dormancy and flower in the future. There have been several experimental studies that have quantified the effectiveness of cold temperatures for chilling requirements for vegetative budburst of temperate trees; however, there are few experimental studies addressing the chilling requirements for reproductive budburst of trees, as it is difficult to place reproductively mature trees in temperature-controlled environments. Methods To identify how changing temperatures associated with climate change may impact reproductive phenology, we completed a temperature-controlled growth chamber experiment using cuttings of reproductive branches of red alder (Alnus rubra), one of the most widespread hardwood tree species of the Pacific Northwest, USA. The purpose of this study was to examine how colder (4 °C) and warmer (9 °C) winter temperature regimes influenced the timing of reproductive budburst of red alder cuttings in spring. We also compared the date of budburst of cuttings to that of branches from intact trees. Results We found that cuttings flowered earlier after pretreatment with a 4 °C winter temperature regime than after a 9 °C winter temperature regime. We found no significant differences between the timing of male budburst of cuttings exposed to ambient conditions compared to male budburst of branches from intact trees. We used our experimental data to estimate a “possibility-line” that shows the accumulated chilling and forcing temperatures necessary prior to reproductive budburst of red alder. Discussion This study provides a preliminary indication that warmer winters with climate change may not be as effective as colder winters for satisfying chilling temperature requirements of a Northwest hardwoo…
bibliographic citation: Prevéy et al. (2018) Effectiveness of winter temperatures for satisfying chilling requirements for reproductive budburst of red alder (Alnus rubra). PeerJ 6:e5221 https://doi.org/10.7717/peerj.5221
date submitted: 2018-06-18
date accepted: 2018-06-21
issued: 2018-09-25
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Prevéy
  given name: Janet S.
author list: Agent
  family name: Harrington
  given name: Constance A.
doi: 10.7717/peerj.5221
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-25

Using bioinformatics tools for the discovery of Dengue RNA-dependent RNA polymerase inhibitors
type: item
type: AcademicArticle
description: Background Dengue fever has rapidly manifested into a serious global health concern. The emergence of various viral serotypes has prompted the urgent need for innovative drug design techniques. Of the viral non-structural enzymes, the NS5 RNA-dependent RNA polymerase has been established as a promising target due to its lack of an enzymatic counterpart in mammalian cells and its conserved structure amongst all serotypes. The onus is now on scientists to probe further into understanding this enzyme and its mechanism of action. The field of bioinformatics has evolved greatly over recent decades, with updated drug design tools now being publically available. Methods In this study, bioinformatics tools were used to provide a comprehensive sequence and structural analysis of the two most prominent serotypes of Dengue RNA-dependent RNA polymerase. A list of popular flavivirus inhibitors were also chosen to dock to the active site of the enzyme. The best docked compound was then used as a template to generate a pharmacophore model that may assist in the design of target-specific Dengue virus inhibitors. Results Comparative sequence alignment exhibited similarity between all three domains of serotype 2 and 3.Sequence analysis revealed highly conserved regions at residues Meth530, Thr543 Asp597, Glu616, Arg659 and Pro671. Mapping of the active site demonstrated two highly conserved residues: Ser710 and Arg729. Of the active site interacting residues, Ser796 was common amongst all ten docked compounds, indicating its importance in the drug design process. Of the ten docked flavivirus inhibitors, NITD-203 showed the best binding affinity to the active site. Further pharmacophore modeling of NITD-203 depicted significant pharmacophoric elements that are necessary for stable binding to the active site. Discussion This study utilized publically available bioinformatics tools to provide a comprehensive framework on Dengue RNA-dependent RNA polymerase. Based on docking studies, a p…
format: application/pdf
format: text/html
creator: Nomagugu B. Nncube
creator: Pritika Ramharack
creator: Mahmoud E.S. Soliman
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Infectious Diseases
description: doi:10.7717/peerj.5068
publisher: PeerJ Inc.
rights: © 2018 Nncube et al.
abstract: Background Dengue fever has rapidly manifested into a serious global health concern. The emergence of various viral serotypes has prompted the urgent need for innovative drug design techniques. Of the viral non-structural enzymes, the NS5 RNA-dependent RNA polymerase has been established as a promising target due to its lack of an enzymatic counterpart in mammalian cells and its conserved structure amongst all serotypes. The onus is now on scientists to probe further into understanding this enzyme and its mechanism of action. The field of bioinformatics has evolved greatly over recent decades, with updated drug design tools now being publically available. Methods In this study, bioinformatics tools were used to provide a comprehensive sequence and structural analysis of the two most prominent serotypes of Dengue RNA-dependent RNA polymerase. A list of popular flavivirus inhibitors were also chosen to dock to the active site of the enzyme. The best docked compound was then used as a template to generate a pharmacophore model that may assist in the design of target-specific Dengue virus inhibitors. Results Comparative sequence alignment exhibited similarity between all three domains of serotype 2 and 3.Sequence analysis revealed highly conserved regions at residues Meth530, Thr543 Asp597, Glu616, Arg659 and Pro671. Mapping of the active site demonstrated two highly conserved residues: Ser710 and Arg729. Of the active site interacting residues, Ser796 was common amongst all ten docked compounds, indicating its importance in the drug design process. Of the ten docked flavivirus inhibitors, NITD-203 showed the best binding affinity to the active site. Further pharmacophore modeling of NITD-203 depicted significant pharmacophoric elements that are necessary for stable binding to the active site. Discussion This study utilized publically available bioinformatics tools to provide a comprehensive framework on Dengue RNA-dependent RNA polymerase. Based on docking studies, a p…
bibliographic citation: Nncube et al. (2018) Using bioinformatics tools for the discovery of Dengue RNA-dependent RNA polymerase inhibitors. PeerJ 6:e5068 https://doi.org/10.7717/peerj.5068
date submitted: 2018-01-24
date accepted: 2018-06-04
issued: 2018-09-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nncube
  given name: Nomagugu B.
author list: Agent
  family name: Ramharack
  given name: Pritika
author list: Agent
  family name: Soliman
  given name: Mahmoud E.S.
doi: 10.7717/peerj.5068
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-25
copyright: ©2018 Nncube et al.
attribution name: Nncube et al.

Plurality in multi-disciplinary research: multiple institutional affiliations are associated with increased citations
type: item
type: AcademicArticle
description: Background The institutional affiliations and associated collaborative networks that scientists foster during their research careers are salient in the production of high-quality science. The phenomenon of multiple institutional affiliations and its relationship to research output remains relatively unexplored in the literature. Methods We examined 27,612 scientific articles, modelling the normalized citation counts received against the number of authors and affiliations held. Results In agreement with previous research, we found that teamwork is an important factor in high impact papers, with average citations received increasing concordant with the number of co-authors listed. For articles with more than five co-authors, we noted an increase in average citations received when authors with more than one institutional affiliation contributed to the research. Discussion Multiple author affiliations may play a positive role in the production of high-impact science. This increased researcher mobility should be viewed by institutional boards as meritorious in the pursuit of scientific discovery.
format: application/pdf
format: text/html
creator: Paul Sanfilippo
creator: Alex W. Hewitt
creator: David A. Mackey
subject: Science and Medical Education
subject: Science Policy
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.5664
publisher: PeerJ Inc.
rights: © 2018 Sanfilippo et al.
abstract: Background The institutional affiliations and associated collaborative networks that scientists foster during their research careers are salient in the production of high-quality science. The phenomenon of multiple institutional affiliations and its relationship to research output remains relatively unexplored in the literature. Methods We examined 27,612 scientific articles, modelling the normalized citation counts received against the number of authors and affiliations held. Results In agreement with previous research, we found that teamwork is an important factor in high impact papers, with average citations received increasing concordant with the number of co-authors listed. For articles with more than five co-authors, we noted an increase in average citations received when authors with more than one institutional affiliation contributed to the research. Discussion Multiple author affiliations may play a positive role in the production of high-impact science. This increased researcher mobility should be viewed by institutional boards as meritorious in the pursuit of scientific discovery.
bibliographic citation: Sanfilippo et al. (2018) Plurality in multi-disciplinary research: multiple institutional affiliations are associated with increased citations. PeerJ 6:e5664 https://doi.org/10.7717/peerj.5664
date submitted: 2018-03-08
date accepted: 2018-08-29
issued: 2018-09-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sanfilippo
  given name: Paul
author list: Agent
  family name: Hewitt
  given name: Alex W.
author list: Agent
  family name: Mackey
  given name: David A.
doi: 10.7717/peerj.5664
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-24
copyright: ©2018 Sanfilippo et al.
attribution name: Sanfilippo et al.

Variation of soil bacterial communities along a chronosequence of Eucalyptus plantation
type: item
type: AcademicArticle
description: Eucalyptus is harvested for wood and fiber production in many tropical and sub-tropical habitats globally. Plantation has been controversial because of its influence on the surrounding environment, however, the influence of massive Eucalyptus planting on soil microbial communities is unclear. Here we applied high-throughput sequencing of the 16S rRNA gene to assess the microbial community composition and diversity of planting chronosequences, involving two, five and ten years of Eucalyptus plantation, comparing to that of secondary-forest in South China. We found that significant changes in the composition of soil bacteria occurred when the forests were converted from secondary-forest to Eucalyptus. The bacterial community structure was clearly distinct from control and five year samples after Eucalyptus was grown for 2 and 10 years, highlighting the influence of this plantation on local soil microbial communities. These groupings indicated a cycle of impact (2 and 10 year plantations) and low impact (5-year plantations) in this chronosequence of Eucalyptus plantation. Community patterns were underpinned by shifts in soil properties such as pH and phosphorus concentration. Concurrently, key soil taxonomic groups such as Actinobacteria showed abundance shifts, increasing in impacted plantations and decreasing in low impacted samples. Shifts in taxonomy were reflected in a shift in metabolic potential, including pathways for nutrient cycles such as carbon fixation, which changed in abundance over time following Eucalyptus plantation. Combined these results confirm that Eucalyptus plantation can change the community structure and diversity of soil microorganisms with strong implications for land-management and maintaining the health of these ecosystems.
format: application/pdf
format: text/html
creator: Jiayu Li
creator: Jiayi Lin
creator: Chenyu Pei
creator: Kaitao Lai
creator: Thomas C. Jeffries
creator: Guangda Tang
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.5648
publisher: PeerJ Inc.
rights: © 2018 Li et al.
abstract: Eucalyptus is harvested for wood and fiber production in many tropical and sub-tropical habitats globally. Plantation has been controversial because of its influence on the surrounding environment, however, the influence of massive Eucalyptus planting on soil microbial communities is unclear. Here we applied high-throughput sequencing of the 16S rRNA gene to assess the microbial community composition and diversity of planting chronosequences, involving two, five and ten years of Eucalyptus plantation, comparing to that of secondary-forest in South China. We found that significant changes in the composition of soil bacteria occurred when the forests were converted from secondary-forest to Eucalyptus. The bacterial community structure was clearly distinct from control and five year samples after Eucalyptus was grown for 2 and 10 years, highlighting the influence of this plantation on local soil microbial communities. These groupings indicated a cycle of impact (2 and 10 year plantations) and low impact (5-year plantations) in this chronosequence of Eucalyptus plantation. Community patterns were underpinned by shifts in soil properties such as pH and phosphorus concentration. Concurrently, key soil taxonomic groups such as Actinobacteria showed abundance shifts, increasing in impacted plantations and decreasing in low impacted samples. Shifts in taxonomy were reflected in a shift in metabolic potential, including pathways for nutrient cycles such as carbon fixation, which changed in abundance over time following Eucalyptus plantation. Combined these results confirm that Eucalyptus plantation can change the community structure and diversity of soil microorganisms with strong implications for land-management and maintaining the health of these ecosystems.
bibliographic citation: Li et al. (2018) Variation of soil bacterial communities along a chronosequence of Eucalyptus plantation. PeerJ 6:e5648 https://doi.org/10.7717/peerj.5648
date submitted: 2018-05-28
date accepted: 2018-08-25
issued: 2018-09-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jiayu
author list: Agent
  family name: Lin
  given name: Jiayi
author list: Agent
  family name: Pei
  given name: Chenyu
author list: Agent
  family name: Lai
  given name: Kaitao
author list: Agent
  family name: Jeffries
  given name: Thomas C.
author list: Agent
  family name: Tang
  given name: Guangda
doi: 10.7717/peerj.5648
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-24
copyright: ©2018 Li et al.
attribution name: Li et al.

Successful transplantation of guinea pig gut microbiota in mice and its effect on pneumonic plague sensitivity
type: item
type: AcademicArticle
description: Microbiota-driven variations in the inflammatory response are predicted to regulate host responses to infection. Increasing evidence indicates that the gastrointestinal and respiratory tracts have an intimate relationship with each other. Gut microbiota can influence lung immunity whereby gut-derived injurious factors can reach the lungs and systemic circulation via the intestinal lymphatics. The intestinal microbiota’s ability to resist colonization can be extended to systemic infections or to pathogens infecting distant sites such as the lungs. Unlike the situation with large mammals, the microtus Yersinia pestis 201 strain exhibits strong virulence in mice, but nearly no virulence to large mammals (such as guinea pigs). Hence, to assess whether the intestinal microbiota from guinea pigs was able to affect the sensitivity of mice to challenge infection with the Y. pestis 201 strain, we fed mice with guinea pig diets for two months, after which they were administered 0.5 ml of guinea pig fecal suspension for 30 days by oral gavage. The stools from each mouse were collected on days 0, 15, and 30, DNA was extracted from them, and 16S rRNA sequencing was performed to assess the diversity and composition of the gut microbiota. We found that the intestinal microbiota transplants from the guinea pigs were able to colonize the mouse intestines. The mice were then infected with Yersinia pestis 201 by lung invasion, but no statistical difference was found in the survival rates of the mice that were colonized with the guinea pig’s gut microbiota and the control mice. This indicates that the intestinal microbiota transplantation from the guinea pigs did not affect the sensitivity of the mice to pneumonic plague.
format: application/pdf
format: text/html
creator: Xiang Li
creator: Zhengchao Li
creator: Yuxiao Chang
creator: Fengyi Hou
creator: Zongyu Huang
creator: Han Ni
creator: Ruifu Yang
creator: Yujing Bi
subject: Biodiversity
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.5637
publisher: PeerJ Inc.
rights: © 2018 Li et al.
abstract: Microbiota-driven variations in the inflammatory response are predicted to regulate host responses to infection. Increasing evidence indicates that the gastrointestinal and respiratory tracts have an intimate relationship with each other. Gut microbiota can influence lung immunity whereby gut-derived injurious factors can reach the lungs and systemic circulation via the intestinal lymphatics. The intestinal microbiota’s ability to resist colonization can be extended to systemic infections or to pathogens infecting distant sites such as the lungs. Unlike the situation with large mammals, the microtus Yersinia pestis 201 strain exhibits strong virulence in mice, but nearly no virulence to large mammals (such as guinea pigs). Hence, to assess whether the intestinal microbiota from guinea pigs was able to affect the sensitivity of mice to challenge infection with the Y. pestis 201 strain, we fed mice with guinea pig diets for two months, after which they were administered 0.5 ml of guinea pig fecal suspension for 30 days by oral gavage. The stools from each mouse were collected on days 0, 15, and 30, DNA was extracted from them, and 16S rRNA sequencing was performed to assess the diversity and composition of the gut microbiota. We found that the intestinal microbiota transplants from the guinea pigs were able to colonize the mouse intestines. The mice were then infected with Yersinia pestis 201 by lung invasion, but no statistical difference was found in the survival rates of the mice that were colonized with the guinea pig’s gut microbiota and the control mice. This indicates that the intestinal microbiota transplantation from the guinea pigs did not affect the sensitivity of the mice to pneumonic plague.
bibliographic citation: Li et al. (2018) Successful transplantation of guinea pig gut microbiota in mice and its effect on pneumonic plague sensitivity. PeerJ 6:e5637 https://doi.org/10.7717/peerj.5637
date submitted: 2018-03-20
date accepted: 2018-08-25
issued: 2018-09-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xiang
author list: Agent
  family name: Li
  given name: Zhengchao
author list: Agent
  family name: Chang
  given name: Yuxiao
author list: Agent
  family name: Hou
  given name: Fengyi
author list: Agent
  family name: Huang
  given name: Zongyu
author list: Agent
  family name: Ni
  given name: Han
author list: Agent
  family name: Yang
  given name: Ruifu
author list: Agent
  family name: Bi
  given name: Yujing
doi: 10.7717/peerj.5637
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-24
copyright: ©2018 Li et al.
attribution name: Li et al.

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