PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of Trichoderma seedling treatment with System of Rice Intensification management and with conventional management of transplanted rice
items: A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses
items: Diverse and variable virus communities in wild plant populations revealed by metagenomic tools
items: Life history responses of two ephemeral plant species to increased precipitation and nitrogen in the Gurbantunggut Desert
items: Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles
items: Artificial liver research output and citations from 2004 to 2017: a bibliometric analysis
items: Non-H3 CDR template selection in antibody modeling through machine learning
items: Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia
items: Local fishermen’s perceptions of the usefulness of artificial reef ecosystem services in Portugal
items: Anuran diversity indicates that Caatinga relictual Neotropical forests are more related to the Atlantic Forest than to the Amazon

Effects of Trichoderma seedling treatment with System of Rice Intensification management and with conventional management of transplanted rice
type: item
type: AcademicArticle
description: Many benefits of Trichoderma inoculation for improving crop production have been documented, including growth and yield enhancement and the alleviation of biotic and abiotic stresses. However, because rice is usually cultivated under continuous flooding that creates anaerobic soil conditions, this limits the benefits of these beneficial fungi. Cultivating rice with the methods of the System of Rice Intensification (SRI) provides rice plants with a more favorable environment for their colonization by beneficial microbes in the soil because the soil is more aerobic under SRI management and contains more organic matter. This study evaluated the effects of Trichoderma inoculation of rice plants under SRI management compared with transplanted and flooded rice plants, considering also the effects of different means of fertilization and different varieties in rice. Experiments were conducted in 2015 and 2016 under the tropical climate of Nepal’s western terai (plains) during both the rainy season (July to November) and the dry season (March to July). The results indicated significantly better performance (P = 0.01) associated with Trichoderma inoculation for both seasons and for both systems of crop management in terms of grain yield and other growth-contributing factors, compared to non-inoculated rice cropping. Relatively higher effects on grain yield were recorded also with organic compared to inorganic fertilization; for unimproved (heirloom) varieties compared with improved varieties; and from SRI vs. conventional flooded crop management. The yield increase with Trichoderma treatments across all trials was 31% higher than in untreated plots (4.9 vs 4.5 mt ha−1). With Trichoderma treatment, yields compared with non-treated plots were 24% higher with organic SRI (6.38 vs 5.13 mt ha−1) and 52% higher with non-organic SRI (6.38 vs 3.53 mt ha−1). With regard to varietal differences, under SRI management Trichoderma inoculation of the improved variety Sukhadhan-3 led to 26%…
format: application/pdf
format: text/html
creator: Ram B. Khadka
creator: Norman Uphoff
subject: Agricultural Science
subject: Microbiology
subject: Mycology
subject: Soil Science
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.5877
publisher: PeerJ Inc.
rights: © 2019 Khadka and Uphoff
abstract: Many benefits of Trichoderma inoculation for improving crop production have been documented, including growth and yield enhancement and the alleviation of biotic and abiotic stresses. However, because rice is usually cultivated under continuous flooding that creates anaerobic soil conditions, this limits the benefits of these beneficial fungi. Cultivating rice with the methods of the System of Rice Intensification (SRI) provides rice plants with a more favorable environment for their colonization by beneficial microbes in the soil because the soil is more aerobic under SRI management and contains more organic matter. This study evaluated the effects of Trichoderma inoculation of rice plants under SRI management compared with transplanted and flooded rice plants, considering also the effects of different means of fertilization and different varieties in rice. Experiments were conducted in 2015 and 2016 under the tropical climate of Nepal’s western terai (plains) during both the rainy season (July to November) and the dry season (March to July). The results indicated significantly better performance (P = 0.01) associated with Trichoderma inoculation for both seasons and for both systems of crop management in terms of grain yield and other growth-contributing factors, compared to non-inoculated rice cropping. Relatively higher effects on grain yield were recorded also with organic compared to inorganic fertilization; for unimproved (heirloom) varieties compared with improved varieties; and from SRI vs. conventional flooded crop management. The yield increase with Trichoderma treatments across all trials was 31% higher than in untreated plots (4.9 vs 4.5 mt ha−1). With Trichoderma treatment, yields compared with non-treated plots were 24% higher with organic SRI (6.38 vs 5.13 mt ha−1) and 52% higher with non-organic SRI (6.38 vs 3.53 mt ha−1). With regard to varietal differences, under SRI management Trichoderma inoculation of the improved variety Sukhadhan-3 led to 26%…
bibliographic citation: Khadka et al. (2019) Effects of Trichoderma seedling treatment with System of Rice Intensification management and with conventional management of transplanted rice. PeerJ 7:e5877 https://doi.org/10.7717/peerj.5877
date submitted: 2018-06-07
date accepted: 2018-10-05
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khadka
  given name: Ram B.
author list: Agent
  family name: Uphoff
  given name: Norman
doi: 10.7717/peerj.5877
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Khadka and Uphoff
attribution name: Khadka and Uphoff

A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses
type: item
type: AcademicArticle
description: Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.
format: application/pdf
format: text/html
creator: Clicia Grativol
creator: Flavia Thiebaut
creator: Sara Sangi
creator: Patricia Montessoro
creator: Walaci da Silva Santos
creator: Adriana S. Hemerly
creator: Paulo C.G. Ferreira
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.6080
publisher: PeerJ Inc.
rights: © 2019 Grativol et al.
abstract: Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.
bibliographic citation: Grativol et al. (2019) A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses. PeerJ 7:e6080 https://doi.org/10.7717/peerj.6080
date submitted: 2018-03-15
date accepted: 2018-11-07
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grativol
  given name: Clicia
author list: Agent
  family name: Thiebaut
  given name: Flavia
author list: Agent
  family name: Sangi
  given name: Sara
author list: Agent
  family name: Montessoro
  given name: Patricia
author list: Agent
  family name: Santos
  given name: Walaci da Silva
author list: Agent
  family name: Hemerly
  given name: Adriana S.
author list: Agent
  family name: Ferreira
  given name: Paulo C.G.
doi: 10.7717/peerj.6080
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Grativol et al.
attribution name: Grativol et al.

Diverse and variable virus communities in wild plant populations revealed by metagenomic tools
type: item
type: AcademicArticle
description: Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus c…
format: application/pdf
format: text/html
creator: Hanna Susi
creator: Denis Filloux
creator: Mikko J. Frilander
creator: Philippe Roumagnac
creator: Anna-Liisa Laine
subject: Bioinformatics
subject: Ecology
subject: Plant Science
subject: Virology
subject: Population Biology
description: doi:10.7717/peerj.6140
publisher: PeerJ Inc.
rights: © 2019 Susi et al.
abstract: Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Åland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus c…
bibliographic citation: Susi et al. (2019) Diverse and variable virus communities in wild plant populations revealed by metagenomic tools. PeerJ 7:e6140 https://doi.org/10.7717/peerj.6140
date submitted: 2018-07-12
date accepted: 2018-11-20
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Susi
  given name: Hanna
author list: Agent
  family name: Filloux
  given name: Denis
author list: Agent
  family name: Frilander
  given name: Mikko J.
author list: Agent
  family name: Roumagnac
  given name: Philippe
author list: Agent
  family name: Laine
  given name: Anna-Liisa
doi: 10.7717/peerj.6140
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Susi et al.
attribution name: Susi et al.

Life history responses of two ephemeral plant species to increased precipitation and nitrogen in the Gurbantunggut Desert
type: item
type: AcademicArticle
description: Precipitation change and nitrogen deposition are not only hot topics of current global change but also the main environmental factors affecting plant growth in desert ecosystems. Thus, we performed an experiment of increased precipitation, nitrogen, and precipitation plus nitrogen on the ephemeral annual species Nepeta micrantha and Eremopyrum distans in the Gurbantunggut Desert. We aimed to determine the life history responses of N. micrantha and E. distans to environment changes, and the germination percentage of the offspring (seeds) was also tested in the laboratory. The results showed that increased nitrogen and precipitation plus nitrogen increased the growth of both plant species, whereas increased precipitation inhibited the growth of N. micrantha but increased the growth of E. distans. This differential response of these two species to precipitation and nitrogen also affected the germination of their offspring. In response to increased nitrogen and precipitation plus nitrogen, the germination percentage of the offspring produced by two species decreased in conjunction with the plants exhibiting high reproduction, which may prevent overcrowding during the following year; however, the N. micrantha plants produced more nondormant offspring in conjunction with low reproduction under relatively greater amounts of precipitation, and N. micrantha offspring could occupy their habitat via rapid germination in suitable environments. Therefore, with increased precipitation and nitrogen deposition, these differences in offspring dormancy may affect their ecological niche in the community.
format: application/pdf
format: text/html
creator: Yanfeng Chen
creator: Lingwei Zhang
creator: Xiang Shi
creator: Huiliang Liu
creator: Daoyuan Zhang
subject: Ecology
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.6158
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Precipitation change and nitrogen deposition are not only hot topics of current global change but also the main environmental factors affecting plant growth in desert ecosystems. Thus, we performed an experiment of increased precipitation, nitrogen, and precipitation plus nitrogen on the ephemeral annual species Nepeta micrantha and Eremopyrum distans in the Gurbantunggut Desert. We aimed to determine the life history responses of N. micrantha and E. distans to environment changes, and the germination percentage of the offspring (seeds) was also tested in the laboratory. The results showed that increased nitrogen and precipitation plus nitrogen increased the growth of both plant species, whereas increased precipitation inhibited the growth of N. micrantha but increased the growth of E. distans. This differential response of these two species to precipitation and nitrogen also affected the germination of their offspring. In response to increased nitrogen and precipitation plus nitrogen, the germination percentage of the offspring produced by two species decreased in conjunction with the plants exhibiting high reproduction, which may prevent overcrowding during the following year; however, the N. micrantha plants produced more nondormant offspring in conjunction with low reproduction under relatively greater amounts of precipitation, and N. micrantha offspring could occupy their habitat via rapid germination in suitable environments. Therefore, with increased precipitation and nitrogen deposition, these differences in offspring dormancy may affect their ecological niche in the community.
bibliographic citation: Chen et al. (2019) Life history responses of two ephemeral plant species to increased precipitation and nitrogen in the Gurbantunggut Desert. PeerJ 7:e6158 https://doi.org/10.7717/peerj.6158
date submitted: 2018-08-28
date accepted: 2018-11-26
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yanfeng
author list: Agent
  family name: Zhang
  given name: Lingwei
author list: Agent
  family name: Shi
  given name: Xiang
author list: Agent
  family name: Liu
  given name: Huiliang
author list: Agent
  family name: Zhang
  given name: Daoyuan
doi: 10.7717/peerj.6158
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Chen et al.
attribution name: Chen et al.

Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles
type: item
type: AcademicArticle
description: Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, participants are usually given guidelines on sample packaging and storage, and asked to deliver their stools to a centralised facility. Here, we tested a number of delivery conditions (temperature, duration and addition of preservative medium) and assessed their effects on stool microbial community composition using 16S rRNA gene amplicon sequencing. The largest source of variability in stool community composition was attributable to inter-individual differences regardless of delivery condition. Although the relative effect of delivery condition on community composition was small compared to inter-individual variability (1.6% vs. 60.5%, permutational multivariate analysis of variance [PERMANOVA]) and temporal variation within subjects over 10 weeks (5.2%), shifts in microbial taxa associated with delivery conditions were non-systematic and subject-specific. These findings indicated that it is not possible to model or accurately predict shifts in stool community composition associated with sampling logistics. Based on our findings, we recommend delivery of fresh, preservative-free stool samples to laboratories within 2 hr either at ambient or chilled temperatures to minimise perturbations to microbial community composition. In addition, subsamples from different fractions of the same stool displayed a small (3.3% vs. 72.6% inter-individual variation, PERMANOVA) but significant effect on community composition. Collection of larger sample volumes for homogenisation is recommended.
format: application/pdf
format: text/html
creator: Yun Kit Yeoh
creator: Zigui Chen
creator: Mamie Hui
creator: Martin C.S. Wong
creator: Wendy C.S. Ho
creator: Miu Ling Chin
creator: Siew C. Ng
creator: Francis K.L. Chan
creator: Paul K.S. Chan
subject: Microbiology
subject: Gastroenterology and Hepatology
subject: Public Health
description: doi:10.7717/peerj.6172
publisher: PeerJ Inc.
rights: © 2019 Yeoh et al.
abstract: Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, participants are usually given guidelines on sample packaging and storage, and asked to deliver their stools to a centralised facility. Here, we tested a number of delivery conditions (temperature, duration and addition of preservative medium) and assessed their effects on stool microbial community composition using 16S rRNA gene amplicon sequencing. The largest source of variability in stool community composition was attributable to inter-individual differences regardless of delivery condition. Although the relative effect of delivery condition on community composition was small compared to inter-individual variability (1.6% vs. 60.5%, permutational multivariate analysis of variance [PERMANOVA]) and temporal variation within subjects over 10 weeks (5.2%), shifts in microbial taxa associated with delivery conditions were non-systematic and subject-specific. These findings indicated that it is not possible to model or accurately predict shifts in stool community composition associated with sampling logistics. Based on our findings, we recommend delivery of fresh, preservative-free stool samples to laboratories within 2 hr either at ambient or chilled temperatures to minimise perturbations to microbial community composition. In addition, subsamples from different fractions of the same stool displayed a small (3.3% vs. 72.6% inter-individual variation, PERMANOVA) but significant effect on community composition. Collection of larger sample volumes for homogenisation is recommended.
bibliographic citation: Yeoh et al. (2019) Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles. PeerJ 7:e6172 https://doi.org/10.7717/peerj.6172
date submitted: 2018-08-28
date accepted: 2018-11-28
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yeoh
  given name: Yun Kit
author list: Agent
  family name: Chen
  given name: Zigui
author list: Agent
  family name: Hui
  given name: Mamie
author list: Agent
  family name: Wong
  given name: Martin C.S.
author list: Agent
  family name: Ho
  given name: Wendy C.S.
author list: Agent
  family name: Chin
  given name: Miu Ling
author list: Agent
  family name: Ng
  given name: Siew C.
author list: Agent
  family name: Chan
  given name: Francis K.L.
author list: Agent
  family name: Chan
  given name: Paul K.S.
doi: 10.7717/peerj.6172
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Yeoh et al.
attribution name: Yeoh et al.

Artificial liver research output and citations from 2004 to 2017: a bibliometric analysis
type: item
type: AcademicArticle
description: Background Researches on artificial livers greatly contribute to the clinical treatments for liver failure. This study aimed to evaluate the research output of artificial livers and citations from 2004 to 2017 through a bibliometric analysis. Methods A list of included articles on artificial livers were generated after a comprehensive search of the Web of Science Core Collection (from 2004 to 2017) with the following basic information: number of publications, citations, publication year, country of origin, authors and authorship, funding source, journals, institutions, keywords, and research area. Results A total of 968 included articles ranged from 47 citations to 394 citations with a fluctuation. The publications were distributed in 12 countries, led by China (n = 212) and the US (n = 207). There were strong correlations of the number of citations with authors (r2 = 0.133, p < 0.001), and countries (r2 = 0.275, p < 0.001), while no correlations of the number of citations with the years since publication (r2 = 0.016, p = 0.216), and funding (r2 < 0.001, p = 0.770) were identified. Keyword analysis demonstrated that with the specific change of “acute liver failure,” decrease in “bioartificial livers” and “hepatocyte,” and increase in “tissue engineering” were identified. The top 53 cited keyword and keyword plus (including some duplicates counts) were identified, led by bioartificial liver (405 citations) and hepatocyte (248 citations). The top 50 cited keywords bursts were mainly “Blood” (2004–2008), “hepatocyte like cell” (2008–2015), and “tissue engineering” (2014–2017). All keywords could be classified into four categories: bioartificial livers (57.40%), blood purification (25.00%), clinical (14.81%), and other artificial organs (2.78%). Discussion This study shows the process and tendency of artificial liver research with a comprehensive analysis on artificial livers. However, although it seems that the future of artificial livers seems brighter for hepatocyte …
format: application/pdf
format: text/html
creator: Yan Li
creator: Meizhi He
creator: Ziyuan Zou
creator: Xiaohui Bian
creator: Xiaowen Huang
creator: Chen Yang
creator: Shuyi Wei
creator: Shixue Dai
subject: Gastroenterology and Hepatology
subject: Statistics
subject: Data Science
description: doi:10.7717/peerj.6178
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background Researches on artificial livers greatly contribute to the clinical treatments for liver failure. This study aimed to evaluate the research output of artificial livers and citations from 2004 to 2017 through a bibliometric analysis. Methods A list of included articles on artificial livers were generated after a comprehensive search of the Web of Science Core Collection (from 2004 to 2017) with the following basic information: number of publications, citations, publication year, country of origin, authors and authorship, funding source, journals, institutions, keywords, and research area. Results A total of 968 included articles ranged from 47 citations to 394 citations with a fluctuation. The publications were distributed in 12 countries, led by China (n = 212) and the US (n = 207). There were strong correlations of the number of citations with authors (r2 = 0.133, p < 0.001), and countries (r2 = 0.275, p < 0.001), while no correlations of the number of citations with the years since publication (r2 = 0.016, p = 0.216), and funding (r2 < 0.001, p = 0.770) were identified. Keyword analysis demonstrated that with the specific change of “acute liver failure,” decrease in “bioartificial livers” and “hepatocyte,” and increase in “tissue engineering” were identified. The top 53 cited keyword and keyword plus (including some duplicates counts) were identified, led by bioartificial liver (405 citations) and hepatocyte (248 citations). The top 50 cited keywords bursts were mainly “Blood” (2004–2008), “hepatocyte like cell” (2008–2015), and “tissue engineering” (2014–2017). All keywords could be classified into four categories: bioartificial livers (57.40%), blood purification (25.00%), clinical (14.81%), and other artificial organs (2.78%). Discussion This study shows the process and tendency of artificial liver research with a comprehensive analysis on artificial livers. However, although it seems that the future of artificial livers seems brighter for hepatocyte …
bibliographic citation: Li et al. (2019) Artificial liver research output and citations from 2004 to 2017: a bibliometric analysis. PeerJ 6:e6178 https://doi.org/10.7717/peerj.6178
date submitted: 2018-09-24
date accepted: 2018-11-28
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: He
  given name: Meizhi
author list: Agent
  family name: Zou
  given name: Ziyuan
author list: Agent
  family name: Bian
  given name: Xiaohui
author list: Agent
  family name: Huang
  given name: Xiaowen
author list: Agent
  family name: Yang
  given name: Chen
author list: Agent
  family name: Wei
  given name: Shuyi
author list: Agent
  family name: Dai
  given name: Shixue
doi: 10.7717/peerj.6178
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Li et al.
attribution name: Li et al.

Non-H3 CDR template selection in antibody modeling through machine learning
type: item
type: AcademicArticle
description: Antibodies are proteins generated by the adaptive immune system to recognize and counteract a plethora of pathogens through specific binding. This adaptive binding is mediated by structural diversity in the six complementary determining region (CDR) loops (H1, H2, H3, L1, L2 and L3), which also makes accurate structural modeling of CDRs challenging. Both homology and de novo modeling approaches have been used; to date, the former has achieved greater accuracy for the non-H3 loops. The homology modeling of non-H3 CDRs is more accurate because non-H3 CDR loops of the same length and type can be grouped into a few structural clusters. Most antibody-modeling suites utilize homology modeling for the non-H3 CDRs, differing only in the alignment algorithm and how/if they utilize structural clusters. While RosettaAntibody and SAbPred do not explicitly assign query CDR sequences to clusters, two other approaches, PIGS and Kotai Antibody Builder, utilize sequence-based rules to assign CDR sequences to clusters. While the manually curated sequence rules can identify better structural templates, because their curation requires extensive literature search and human effort, they lag behind the deposition of new antibody structures and are infrequently updated. In this study, we propose a machine learning approach (Gradient Boosting Machine [GBM]) to learn the structural clusters of non-H3 CDRs from sequence alone. The GBM method simplifies feature selection and can easily integrate new data, compared to manual sequence rule curation. We compare the classification results using the GBM method to that of RosettaAntibody in a 3-repeat 10-fold cross-validation (CV) scheme on the cluster-annotated antibody database PyIgClassify and we observe an improvement in the classification accuracy of the concerned loops from 84.5% ± 0.24% to 88.16% ± 0.056%. The GBM models reduce the errors in specific cluster membership misclassifications when the involved clusters have relatively abundant dat…
format: application/pdf
format: text/html
creator: Xiyao Long
creator: Jeliazko R. Jeliazkov
creator: Jeffrey J. Gray
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.6179
publisher: PeerJ Inc.
rights: © 2019 Long et al.
abstract: Antibodies are proteins generated by the adaptive immune system to recognize and counteract a plethora of pathogens through specific binding. This adaptive binding is mediated by structural diversity in the six complementary determining region (CDR) loops (H1, H2, H3, L1, L2 and L3), which also makes accurate structural modeling of CDRs challenging. Both homology and de novo modeling approaches have been used; to date, the former has achieved greater accuracy for the non-H3 loops. The homology modeling of non-H3 CDRs is more accurate because non-H3 CDR loops of the same length and type can be grouped into a few structural clusters. Most antibody-modeling suites utilize homology modeling for the non-H3 CDRs, differing only in the alignment algorithm and how/if they utilize structural clusters. While RosettaAntibody and SAbPred do not explicitly assign query CDR sequences to clusters, two other approaches, PIGS and Kotai Antibody Builder, utilize sequence-based rules to assign CDR sequences to clusters. While the manually curated sequence rules can identify better structural templates, because their curation requires extensive literature search and human effort, they lag behind the deposition of new antibody structures and are infrequently updated. In this study, we propose a machine learning approach (Gradient Boosting Machine [GBM]) to learn the structural clusters of non-H3 CDRs from sequence alone. The GBM method simplifies feature selection and can easily integrate new data, compared to manual sequence rule curation. We compare the classification results using the GBM method to that of RosettaAntibody in a 3-repeat 10-fold cross-validation (CV) scheme on the cluster-annotated antibody database PyIgClassify and we observe an improvement in the classification accuracy of the concerned loops from 84.5% ± 0.24% to 88.16% ± 0.056%. The GBM models reduce the errors in specific cluster membership misclassifications when the involved clusters have relatively abundant dat…
bibliographic citation: Long et al. (2019) Non-H3 CDR template selection in antibody modeling through machine learning. PeerJ 7:e6179 https://doi.org/10.7717/peerj.6179
date submitted: 2018-06-19
date accepted: 2018-11-28
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Long
  given name: Xiyao
author list: Agent
  family name: Jeliazkov
  given name: Jeliazko R.
author list: Agent
  family name: Gray
  given name: Jeffrey J.
doi: 10.7717/peerj.6179
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Long et al.
attribution name: Long et al.

Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia
type: item
type: AcademicArticle
description: Vitex rotundifolia is an important coastal and medicinal plant, and is recorded in the List of the Important Wild Plants for Conservation in China and Japan. However, an effective conservation strategy is lacking. In the present study, the genetic diversity and population structure were analyzed using phylogeographical methods based on the trnH-psbA and trnG-trnS intergenic spacers of the chloroplast DNA (cpDNA) sequences from 157 individuals from 25 sampling sites for V. rotundifolia and V. trifolia plus the internal transcribed spacer (ITS) of the nuclear ribosomal DNA (nrDNA) sequences of 177 individuals from 27 sampling sites. The results showed that V. rotundifolia and V. trifolia had eight cpDNA and two nrDNA haplotypes, respectively, and the V. rotundifolia has a low level of genetic diversity (haplotype diversity hd,cp = 0.360, hd,nr = 0.440), a more pronounced genetic differentiation among populations (population differentiation at the species level (GST) = 0.201, population differentiation at the allele level (NST) = 0.462), and an insignificantly different phylogeographical structure (NST > GST, P > 0.05). In addition, haplotype network analyses indicated that V. rotundifolia and V. trifolia have distinct haplotypes. Divergence dating based on BEAST software analyses showed that most cpDNA clades diverged in the late Pleistocene era. Demographic analysis indicated that V. rotundifolia underwent a rapid demographic expansion. Some scientific strategies are suggested for resource conservation of V. rotundifolia based on its genetic diversity and population structure.
format: application/pdf
format: text/html
creator: Yiqi Sun
creator: Hong Yang
creator: Qiaoyan Zhang
creator: Luping Qin
creator: Pan Li
creator: Joongku Lee
creator: Shichao Chen
creator: Khalid Rahman
creator: Tingguo Kang
creator: Min Jia
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.6194
publisher: PeerJ Inc.
rights: © 2019 Sun et al.
abstract: Vitex rotundifolia is an important coastal and medicinal plant, and is recorded in the List of the Important Wild Plants for Conservation in China and Japan. However, an effective conservation strategy is lacking. In the present study, the genetic diversity and population structure were analyzed using phylogeographical methods based on the trnH-psbA and trnG-trnS intergenic spacers of the chloroplast DNA (cpDNA) sequences from 157 individuals from 25 sampling sites for V. rotundifolia and V. trifolia plus the internal transcribed spacer (ITS) of the nuclear ribosomal DNA (nrDNA) sequences of 177 individuals from 27 sampling sites. The results showed that V. rotundifolia and V. trifolia had eight cpDNA and two nrDNA haplotypes, respectively, and the V. rotundifolia has a low level of genetic diversity (haplotype diversity hd,cp = 0.360, hd,nr = 0.440), a more pronounced genetic differentiation among populations (population differentiation at the species level (GST) = 0.201, population differentiation at the allele level (NST) = 0.462), and an insignificantly different phylogeographical structure (NST > GST, P > 0.05). In addition, haplotype network analyses indicated that V. rotundifolia and V. trifolia have distinct haplotypes. Divergence dating based on BEAST software analyses showed that most cpDNA clades diverged in the late Pleistocene era. Demographic analysis indicated that V. rotundifolia underwent a rapid demographic expansion. Some scientific strategies are suggested for resource conservation of V. rotundifolia based on its genetic diversity and population structure.
bibliographic citation: Sun et al. (2019) Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia. PeerJ 7:e6194 https://doi.org/10.7717/peerj.6194
date submitted: 2018-08-07
date accepted: 2018-12-01
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Yiqi
author list: Agent
  family name: Yang
  given name: Hong
author list: Agent
  family name: Zhang
  given name: Qiaoyan
author list: Agent
  family name: Qin
  given name: Luping
author list: Agent
  family name: Li
  given name: Pan
author list: Agent
  family name: Lee
  given name: Joongku
author list: Agent
  family name: Chen
  given name: Shichao
author list: Agent
  family name: Rahman
  given name: Khalid
author list: Agent
  family name: Kang
  given name: Tingguo
author list: Agent
  family name: Jia
  given name: Min
doi: 10.7717/peerj.6194
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: ©2019 Sun et al.
attribution name: Sun et al.

Local fishermen’s perceptions of the usefulness of artificial reef ecosystem services in Portugal
type: item
type: AcademicArticle
description: Proponents of artificial reef (AR) deployment are often motivated by the usefulness of such structures. The usefulness of ARs is related to their capability of providing ecosystem services/additional functions. We present two distinct Portuguese AR case studies: (1) The Nazaré reef off the central coast of Portugal and (2) the Oura reef off the Algarve coast. Semi-structured interviews were conducted with local fishermen in the fishing towns of Nazaré and Quarteira pre-and post-AR deployment. The main focus of the interviews was to understand fishermen’s perception of AR usefulness (or lack thereof) in terms of nine ecosystem services/additional functions potentially provided by the ARs. We tested the null hypothesis that ARs do not provide additional ecosystem services/additional functions. When queried pre-AR deployment, fishermen indicated that ARs are most likely to provide three ecosystem services: “habitat and refuge,” “biodiversity preservation” and “food production.” Fishermen had similar perceptions post-deployment. For the Nazaré reef, fishermen tended to have a positive or neutral perception of ecosystem services/additional functions being provided by ARs. For the Oura reef, fishermen tended to have a mostly neutral perception of AR ecosystem services; however, there were also some positive and other negative perceptions. It was difficult for stakeholders to conceptualize some of the ecosystem services/additional functions provided by ARs prior to actively using them. As a result, some stakeholders changed their perception of the ecosystem services/additional functions after using the structures. These results indicate that stakeholders likely need to perceive ARs as useful in order for them to provide their support for AR installation. Likewise, their support is often needed to justify the use of public funds to install ARs, therefore making it imperative for resource managers to undertake similar interviews with fishermen when considering the use of ARs…
format: application/pdf
format: text/html
creator: Jorge Ramos
creator: Pedro G. Lino
creator: Amber Himes-Cornell
creator: Miguel N. Santos
subject: Aquaculture, Fisheries and Fish Science
subject: Ecosystem Science
description: doi:10.7717/peerj.6206
publisher: PeerJ Inc.
rights: © 2019 Ramos et al.
abstract: Proponents of artificial reef (AR) deployment are often motivated by the usefulness of such structures. The usefulness of ARs is related to their capability of providing ecosystem services/additional functions. We present two distinct Portuguese AR case studies: (1) The Nazaré reef off the central coast of Portugal and (2) the Oura reef off the Algarve coast. Semi-structured interviews were conducted with local fishermen in the fishing towns of Nazaré and Quarteira pre-and post-AR deployment. The main focus of the interviews was to understand fishermen’s perception of AR usefulness (or lack thereof) in terms of nine ecosystem services/additional functions potentially provided by the ARs. We tested the null hypothesis that ARs do not provide additional ecosystem services/additional functions. When queried pre-AR deployment, fishermen indicated that ARs are most likely to provide three ecosystem services: “habitat and refuge,” “biodiversity preservation” and “food production.” Fishermen had similar perceptions post-deployment. For the Nazaré reef, fishermen tended to have a positive or neutral perception of ecosystem services/additional functions being provided by ARs. For the Oura reef, fishermen tended to have a mostly neutral perception of AR ecosystem services; however, there were also some positive and other negative perceptions. It was difficult for stakeholders to conceptualize some of the ecosystem services/additional functions provided by ARs prior to actively using them. As a result, some stakeholders changed their perception of the ecosystem services/additional functions after using the structures. These results indicate that stakeholders likely need to perceive ARs as useful in order for them to provide their support for AR installation. Likewise, their support is often needed to justify the use of public funds to install ARs, therefore making it imperative for resource managers to undertake similar interviews with fishermen when considering the use of ARs…
bibliographic citation: Ramos et al. (2019) Local fishermen’s perceptions of the usefulness of artificial reef ecosystem services in Portugal. PeerJ 6:e6206 https://doi.org/10.7717/peerj.6206
date submitted: 2018-04-23
date accepted: 2018-11-22
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ramos
  given name: Jorge
author list: Agent
  family name: Lino
  given name: Pedro G.
author list: Agent
  family name: Himes-Cornell
  given name: Amber
author list: Agent
  family name: Santos
  given name: Miguel N.
doi: 10.7717/peerj.6206
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Ramos et al.
attribution name: Ramos et al.

Anuran diversity indicates that Caatinga relictual Neotropical forests are more related to the Atlantic Forest than to the Amazon
type: item
type: AcademicArticle
description: The relationships among the morphoclimatic domains of South America have been a major biogeographical issue of recent years. Palynological, geological and phytogeographical data suggest that the Amazon Forest and the Atlantic Forest were connected during part of the Tertiary and Quaternary periods. This study uses amphibians as model organisms to investigate whether relict northeastern forests are a transition between the Amazon Forest and the Atlantic Forest. We compiled matrices of species composition for four different phytogeographic formations and “Brejos de Altitude,” and analyzed them using clustering methods and Cladistic Analysis of Distributions and Endemism. Our results indicate that the anurofauna of these northeastern forest relicts is most similar in composition to the areas of the Atlantic Forest included in this study, and most dissimilar to the Amazon Forest, which leads us to affirm that events of biotic exchange were more frequent within the Atlantic Forest areas.
format: application/pdf
format: text/html
creator: Deborah P. Castro
creator: João Fabrício M. Rodrigues
creator: Maria Juliana Borges-Leite
creator: Daniel Cassiano Lima
creator: Diva Maria Borges-Nojosa
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.6208
publisher: PeerJ Inc.
rights: © 2019 Castro et al.
abstract: The relationships among the morphoclimatic domains of South America have been a major biogeographical issue of recent years. Palynological, geological and phytogeographical data suggest that the Amazon Forest and the Atlantic Forest were connected during part of the Tertiary and Quaternary periods. This study uses amphibians as model organisms to investigate whether relict northeastern forests are a transition between the Amazon Forest and the Atlantic Forest. We compiled matrices of species composition for four different phytogeographic formations and “Brejos de Altitude,” and analyzed them using clustering methods and Cladistic Analysis of Distributions and Endemism. Our results indicate that the anurofauna of these northeastern forest relicts is most similar in composition to the areas of the Atlantic Forest included in this study, and most dissimilar to the Amazon Forest, which leads us to affirm that events of biotic exchange were more frequent within the Atlantic Forest areas.
bibliographic citation: Castro et al. (2019) Anuran diversity indicates that Caatinga relictual Neotropical forests are more related to the Atlantic Forest than to the Amazon. PeerJ 6:e6208 https://doi.org/10.7717/peerj.6208
date submitted: 2018-03-19
date accepted: 2018-12-04
issued: 2019-01-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Castro
  given name: Deborah P.
author list: Agent
  family name: Rodrigues
  given name: João Fabrício M.
author list: Agent
  family name: Borges-Leite
  given name: Maria Juliana
author list: Agent
  family name: Lima
  given name: Daniel Cassiano
author list: Agent
  family name: Borges-Nojosa
  given name: Diva Maria
doi: 10.7717/peerj.6208
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-11
copyright: © 2019 Authors.
attribution name: Castro et al.

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