PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis
items: Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific
items: Tumor-preventing activity of aspirin in multiple cancers based on bioinformatic analyses
items: Wind-driven spume droplet production and the transport of Pseudomonas syringae from aquatic environments
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)

De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis
type: item
type: AcademicArticle
description: Soil salinity is one of the major environmental stresses affecting plant growth, development, and reproduction. Salt stress also affects the accumulation of some secondary metabolites in plants. Glehnia littoralis is an endangered medicinal halophyte that grows in coastal habitats. Peeled and dried Glehnia littoralis roots, named Radix Glehniae, have been used traditionally as a Chinese herbal medicine. Although Glehnia littoralis has great ecological and commercial value, salt-related mechanisms in Glehnia littoralis remain largely unknown. In this study, we analysed the transcriptome of Glehnia littoralis in response to salt stress by RNA-sequencing to identify potential salt tolerance gene networks. After de novo assembly, we obtained 105,875 unigenes, of which 75,559 were annotated in public databases. We identified 10,335 differentially expressed genes (DEGs; false discovery rate <0.05 and |log2 fold-change| ≥ 1) between NaCl treatment (GL2) and control (GL1), with 5,018 upregulated and 5,317 downregulated DEGs. To further this investigation, we performed Gene Ontology (GO) analysis and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. DEGs involved in secondary metabolite biosynthetic pathways, plant signal transduction pathways, and transcription factors in response to salt stress were analysed. In addition, we tested the gene expression of 15 unigenes by quantitative real-time PCR (qRT-PCR) to confirm the RNA-sequencing results. Our findings represent a large-scale assessment of the Glehnia littoralis gene resource, and provide useful information for exploring its molecular mechanisms of salt tolerance. Moreover, genes enriched in metabolic pathways could be used to investigate potential biosynthetic pathways of active compounds by Glehnia littoralis.
format: application/pdf
format: text/html
creator: Li Li
creator: Mimi Li
creator: Xiwu Qi
creator: Xingli Tang
creator: Yifeng Zhou
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.5681
publisher: PeerJ Inc.
rights: © 2018 Li et al.
abstract: Soil salinity is one of the major environmental stresses affecting plant growth, development, and reproduction. Salt stress also affects the accumulation of some secondary metabolites in plants. Glehnia littoralis is an endangered medicinal halophyte that grows in coastal habitats. Peeled and dried Glehnia littoralis roots, named Radix Glehniae, have been used traditionally as a Chinese herbal medicine. Although Glehnia littoralis has great ecological and commercial value, salt-related mechanisms in Glehnia littoralis remain largely unknown. In this study, we analysed the transcriptome of Glehnia littoralis in response to salt stress by RNA-sequencing to identify potential salt tolerance gene networks. After de novo assembly, we obtained 105,875 unigenes, of which 75,559 were annotated in public databases. We identified 10,335 differentially expressed genes (DEGs; false discovery rate <0.05 and |log2 fold-change| ≥ 1) between NaCl treatment (GL2) and control (GL1), with 5,018 upregulated and 5,317 downregulated DEGs. To further this investigation, we performed Gene Ontology (GO) analysis and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. DEGs involved in secondary metabolite biosynthetic pathways, plant signal transduction pathways, and transcription factors in response to salt stress were analysed. In addition, we tested the gene expression of 15 unigenes by quantitative real-time PCR (qRT-PCR) to confirm the RNA-sequencing results. Our findings represent a large-scale assessment of the Glehnia littoralis gene resource, and provide useful information for exploring its molecular mechanisms of salt tolerance. Moreover, genes enriched in metabolic pathways could be used to investigate potential biosynthetic pathways of active compounds by Glehnia littoralis.
bibliographic citation: Li et al. (2018) De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis. PeerJ 6:e5681 https://doi.org/10.7717/peerj.5681
date submitted: 2018-05-17
date accepted: 2018-08-30
issued: 2018-09-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Li
author list: Agent
  family name: Li
  given name: Mimi
author list: Agent
  family name: Qi
  given name: Xiwu
author list: Agent
  family name: Tang
  given name: Xingli
author list: Agent
  family name: Zhou
  given name: Yifeng
doi: 10.7717/peerj.5681
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-26
copyright: ©2018 Li et al.
attribution name: Li et al.

Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific
type: item
type: AcademicArticle
description: Background Gastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific. Methods We investigated the population history and connectivity of five Provanna species in the northwestern Pacific through population genetic analyses using partial sequences of the cytochrome c oxidase subunit I gene. Results We found that P. subglabra, the most abundant and genetically diverse species, is genetically segregated by depth. Among the five species, the three comparatively shallower species (P. lucida, P. kuroshimensis, P. glabra) had a more constant demographic history compared to the deeper species (P. subglabra, P. clathrata). Discussion Environmental differences, especially depth, appears to have a role in the segregation of Provanna snails. The population of P. clathrata in the Irabu Knoll appears to have expanded after P. subglabra population. The remaining three species, P. lucida, P. kuroshimensis, and P. glabra, are only known from a single site each, all of which were shallower than 1,000 m. These data indicate that Provanna gastropods are vertically segregated, and that their population characteristics likely depend on hydrothermal activities.
format: application/pdf
format: text/html
creator: Tomomi Ogura
creator: Hiromi Kayama Watanabe
creator: Chong Chen
creator: Takenori Sasaki
creator: Shigeaki Kojima
creator: Jun-ichiro Ishibashi
creator: Katsunori Fujikura
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Biological Oceanography
description: doi:10.7717/peerj.5673
publisher: PeerJ Inc.
rights: © 2018 Ogura et al.
abstract: Background Gastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific. Methods We investigated the population history and connectivity of five Provanna species in the northwestern Pacific through population genetic analyses using partial sequences of the cytochrome c oxidase subunit I gene. Results We found that P. subglabra, the most abundant and genetically diverse species, is genetically segregated by depth. Among the five species, the three comparatively shallower species (P. lucida, P. kuroshimensis, P. glabra) had a more constant demographic history compared to the deeper species (P. subglabra, P. clathrata). Discussion Environmental differences, especially depth, appears to have a role in the segregation of Provanna snails. The population of P. clathrata in the Irabu Knoll appears to have expanded after P. subglabra population. The remaining three species, P. lucida, P. kuroshimensis, and P. glabra, are only known from a single site each, all of which were shallower than 1,000 m. These data indicate that Provanna gastropods are vertically segregated, and that their population characteristics likely depend on hydrothermal activities.
bibliographic citation: Ogura et al. (2018) Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific. PeerJ 6:e5673 https://doi.org/10.7717/peerj.5673
date submitted: 2018-03-13
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: Ogura
  given name: Tomomi
author list: Agent
  family name: Watanabe
  given name: Hiromi Kayama
author list: Agent
  family name: Chen
  given name: Chong
author list: Agent
  family name: Sasaki
  given name: Takenori
author list: Agent
  family name: Kojima
  given name: Shigeaki
author list: Agent
  family name: Ishibashi
  given name: Jun-ichiro
author list: Agent
  family name: Fujikura
  given name: Katsunori
doi: 10.7717/peerj.5673
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-26
copyright: ©2018 Ogura et al.
attribution name: Ogura et al.

Tumor-preventing activity of aspirin in multiple cancers based on bioinformatic analyses
type: item
type: AcademicArticle
description: Background Acetylsalicylic acid was renamed aspirin in 1899, and it has been widely used for its multiple biological actions. Because of the diversity of the cellular processes and diseases that aspirin reportedly affects and benefits, uncertainty remains regarding its mechanism in different biological systems. Methods The Drugbank and STITCH databases were used to find direct protein targets (DPTs) of aspirin. The Mentha database was used to analyze protein–protein interactions (PPIs) to find DPT-associated genes. DAVID was used for the GO and KEGG enrichment analyses. The cBio Cancer Genomics Portal database was used to mine genetic alterations and networks of aspirin-associated genes in cancer. Results Eighteen direct protein targets (DPT) and 961 DPT-associated genes were identified for aspirin. This enrichment analysis resulted in eight identified KEGG pathways that were associated with cancers. Analysis using the cBio portal indicated that aspirin might have effects on multiple tumor suppressors, such as TP53, PTEN, and RB1 and that TP53 might play a central role in aspirin-associated genes. Discussion The results not only suggest that aspirin might have anti-tumor actions against multiple cancers but could also provide new directions for further research on aspirin using a bioinformatics analysis approach.
format: application/pdf
format: text/html
creator: Diangeng Li
creator: Peng Wang
creator: Yi Yu
creator: Bing Huang
creator: Xuelin Zhang
creator: Chou Xu
creator: Xian Zhao
creator: Zhiwei Yin
creator: Zheng He
creator: Meiling Jin
creator: Changting Liu
subject: Bioinformatics
subject: Drugs and Devices
subject: Oncology
description: doi:10.7717/peerj.5667
publisher: PeerJ Inc.
rights: © 2018 Li et al.
abstract: Background Acetylsalicylic acid was renamed aspirin in 1899, and it has been widely used for its multiple biological actions. Because of the diversity of the cellular processes and diseases that aspirin reportedly affects and benefits, uncertainty remains regarding its mechanism in different biological systems. Methods The Drugbank and STITCH databases were used to find direct protein targets (DPTs) of aspirin. The Mentha database was used to analyze protein–protein interactions (PPIs) to find DPT-associated genes. DAVID was used for the GO and KEGG enrichment analyses. The cBio Cancer Genomics Portal database was used to mine genetic alterations and networks of aspirin-associated genes in cancer. Results Eighteen direct protein targets (DPT) and 961 DPT-associated genes were identified for aspirin. This enrichment analysis resulted in eight identified KEGG pathways that were associated with cancers. Analysis using the cBio portal indicated that aspirin might have effects on multiple tumor suppressors, such as TP53, PTEN, and RB1 and that TP53 might play a central role in aspirin-associated genes. Discussion The results not only suggest that aspirin might have anti-tumor actions against multiple cancers but could also provide new directions for further research on aspirin using a bioinformatics analysis approach.
bibliographic citation: Li et al. (2018) Tumor-preventing activity of aspirin in multiple cancers based on bioinformatic analyses. PeerJ 6:e5667 https://doi.org/10.7717/peerj.5667
date submitted: 2018-04-27
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: Li
  given name: Diangeng
author list: Agent
  family name: Wang
  given name: Peng
author list: Agent
  family name: Yu
  given name: Yi
author list: Agent
  family name: Huang
  given name: Bing
author list: Agent
  family name: Zhang
  given name: Xuelin
author list: Agent
  family name: Xu
  given name: Chou
author list: Agent
  family name: Zhao
  given name: Xian
author list: Agent
  family name: Yin
  given name: Zhiwei
author list: Agent
  family name: He
  given name: Zheng
author list: Agent
  family name: Jin
  given name: Meiling
author list: Agent
  family name: Liu
  given name: Changting
doi: 10.7717/peerj.5667
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-26
copyright: ©2018 Li et al.
attribution name: Li et al.

Wind-driven spume droplet production and the transport of Pseudomonas syringae from aquatic environments
type: item
type: AcademicArticle
description: Natural aquatic environments such as oceans, lakes, and rivers are home to a tremendous diversity of microorganisms. Some may cross the air-water interface within droplets and become airborne, with the potential to impact the Earth’s radiation budget, precipitation processes, and spread of disease. Larger droplets are likely to return to the water or adjacent land, but smaller droplets may be suspended in the atmosphere for transport over long distances. Here, we report on a series of controlled laboratory experiments to quantify wind-driven droplet production from a freshwater source for low wind speeds. The rate of droplet production increased quadratically with wind speed above a critical value (10-m equivalent 5.7 m/s) where droplet production initiated. Droplet diameter and ejection speeds were fit by a gamma distribution. The droplet mass flux and momentum flux increased with wind speed. Two mechanisms of droplet production, bubble bursting and fragmentation, yielded different distributions for diameter, speed, and angle. At a wind speed of about 3.5 m/s, aqueous suspensions of the ice-nucleating bacterium Pseudomonas syringae were collected at rates of 283 cells m−2 s−1 at 5 cm above the water surface, and at 14 cells m−2 s−1 at 10 cm above the water surface. At a wind speed of about 4.0 m/s, aqueous suspensions of P. syringae were collected at rates of 509 cells m−2 s−1 at 5 cm above the water surface, and at 81 cells m−2 s−1 at 10 cm above the water surface. The potential for microbial flux into the atmosphere from aquatic environments was calculated using known concentrations of bacteria in natural freshwater systems. Up to 3.1 × 104 cells m−2 s−1 of water surface were estimated to leave the water in potentially suspended droplets (diameters <100 µm). Understanding the sources and mechanisms for bacteria to aerosolize from freshwater aquatic sources may aid in designing management strategies for pathogenic bacteria, and could shed light on how bacteria are…
format: application/pdf
format: text/html
creator: Renee B. Pietsch
creator: Hinrich Grothe
creator: Regina Hanlon
creator: Craig W. Powers
creator: Sunghwan Jung
creator: Shane D. Ross
creator: David G. Schmale III
subject: Biophysics
subject: Microbiology
subject: Freshwater Biology
subject: Ecohydrology
description: doi:10.7717/peerj.5663
publisher: PeerJ Inc.
rights: © 2018 Pietsch et al.
abstract: Natural aquatic environments such as oceans, lakes, and rivers are home to a tremendous diversity of microorganisms. Some may cross the air-water interface within droplets and become airborne, with the potential to impact the Earth’s radiation budget, precipitation processes, and spread of disease. Larger droplets are likely to return to the water or adjacent land, but smaller droplets may be suspended in the atmosphere for transport over long distances. Here, we report on a series of controlled laboratory experiments to quantify wind-driven droplet production from a freshwater source for low wind speeds. The rate of droplet production increased quadratically with wind speed above a critical value (10-m equivalent 5.7 m/s) where droplet production initiated. Droplet diameter and ejection speeds were fit by a gamma distribution. The droplet mass flux and momentum flux increased with wind speed. Two mechanisms of droplet production, bubble bursting and fragmentation, yielded different distributions for diameter, speed, and angle. At a wind speed of about 3.5 m/s, aqueous suspensions of the ice-nucleating bacterium Pseudomonas syringae were collected at rates of 283 cells m−2 s−1 at 5 cm above the water surface, and at 14 cells m−2 s−1 at 10 cm above the water surface. At a wind speed of about 4.0 m/s, aqueous suspensions of P. syringae were collected at rates of 509 cells m−2 s−1 at 5 cm above the water surface, and at 81 cells m−2 s−1 at 10 cm above the water surface. The potential for microbial flux into the atmosphere from aquatic environments was calculated using known concentrations of bacteria in natural freshwater systems. Up to 3.1 × 104 cells m−2 s−1 of water surface were estimated to leave the water in potentially suspended droplets (diameters <100 µm). Understanding the sources and mechanisms for bacteria to aerosolize from freshwater aquatic sources may aid in designing management strategies for pathogenic bacteria, and could shed light on how bacteria are…
bibliographic citation: Pietsch et al. (2018) Wind-driven spume droplet production and the transport of Pseudomonas syringae from aquatic environments. PeerJ 6:e5663 https://doi.org/10.7717/peerj.5663
date submitted: 2018-02-01
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: Pietsch
  given name: Renee B.
author list: Agent
  family name: Grothe
  given name: Hinrich
author list: Agent
  family name: Hanlon
  given name: Regina
author list: Agent
  family name: Powers
  given name: Craig W.
author list: Agent
  family name: Jung
  given name: Sunghwan
author list: Agent
  family name: Ross
  given name: Shane D.
author list: Agent
  family name: Schmale III
  given name: David G.
doi: 10.7717/peerj.5663
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-09-26
copyright: ©2018 Pietsch et al.
attribution name: Pietsch et al.

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

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