PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Prevalence of near-death experiences in people with and without REM sleep intrusion
items: Insights from the proteome profile of Phytophthora capsici in response to the novel fungicide SYP-14288
items: Filter feeding in Late Jurassic pterosaurs supported by coprolite contents
items: The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations
items: Profiling the lncRNA-miRNA-mRNA ceRNA network to reveal potential crosstalk between inflammatory bowel disease and colorectal cancer
items: Effectiveness of small road tunnels and fences in reducing amphibian roadkill and barrier effects at retrofitted roads in Sweden
items: Detecting the impact of land cover change on observed rainfall
items: https://peerj.com/articles/7541
items: https://peerj.com/articles/7555
items: Association between serum uric acid and nonalcoholic fatty liver disease in community patients with type 2 diabetes mellitus

Prevalence of near-death experiences in people with and without REM sleep intrusion
type: item
type: AcademicArticle
description: Background The origin and prevalence of near-death experiences are unknown. A recent study suggested a link with REM sleep intrusion but was criticized for its selection of control participants. We therefore assessed the association of REM intrusion and near-death experiences with different methods. Methods Using a crowd-sourcing platform, we recruited 1,034 lay people from 35 countries to investigate the prevalence of near-death experiences and self-reported REM sleep intrusion. Reports were validated using the Greyson Near-Death Experiences Scale (GNDES) with ≥7 points as cut-off for near-death experiences. Results Near-death experiences were reported by 106 of 1,034 participants (10%; 95% CI [8.5–12%]). Evidence of REM intrusion was more common in people with near-death experiences (n = 50∕106; 47%) than in people with experiences with 6 points or less on the GNDES (n = 47∕183; 26%) or in those without such experiences (n = 107∕744; 14%; p = < 0.0001). Following multivariate regression analysis to adjust for age, gender, place of residence, employment and perceived danger, this association remained highly significant; people with REM intrusion were more likely to exhibit near-death experiences than those without (OR 2.85; 95% CI [1.68–4.88]; p = 0.0001). Discussion Using a crowd-sourcing approach, we found a prevalence of near-death experiences of 10%. While age, gender, place of residence, employment status and perceived threat do not seem to influence the prevalence of near-death experiences, we confirmed a possible association with REM sleep intrusion.
format: application/pdf
format: text/html
creator: Daniel Kondziella
creator: Jens P. Dreier
creator: Markus Harboe Olsen
subject: Emergency and Critical Care
subject: Neurology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.7585
publisher: PeerJ Inc.
rights: © 2019 Kondziella et al.
abstract: Background The origin and prevalence of near-death experiences are unknown. A recent study suggested a link with REM sleep intrusion but was criticized for its selection of control participants. We therefore assessed the association of REM intrusion and near-death experiences with different methods. Methods Using a crowd-sourcing platform, we recruited 1,034 lay people from 35 countries to investigate the prevalence of near-death experiences and self-reported REM sleep intrusion. Reports were validated using the Greyson Near-Death Experiences Scale (GNDES) with ≥7 points as cut-off for near-death experiences. Results Near-death experiences were reported by 106 of 1,034 participants (10%; 95% CI [8.5–12%]). Evidence of REM intrusion was more common in people with near-death experiences (n = 50∕106; 47%) than in people with experiences with 6 points or less on the GNDES (n = 47∕183; 26%) or in those without such experiences (n = 107∕744; 14%; p = < 0.0001). Following multivariate regression analysis to adjust for age, gender, place of residence, employment and perceived danger, this association remained highly significant; people with REM intrusion were more likely to exhibit near-death experiences than those without (OR 2.85; 95% CI [1.68–4.88]; p = 0.0001). Discussion Using a crowd-sourcing approach, we found a prevalence of near-death experiences of 10%. While age, gender, place of residence, employment status and perceived threat do not seem to influence the prevalence of near-death experiences, we confirmed a possible association with REM sleep intrusion.
bibliographic citation: Kondziella et al. (2019) Prevalence of near-death experiences in people with and without REM sleep intrusion. PeerJ 7:e7585 https://doi.org/10.7717/peerj.7585
date submitted: 2019-05-20
date accepted: 2019-07-30
issued: 2019-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kondziella
  given name: Daniel
author list: Agent
  family name: Dreier
  given name: Jens P.
author list: Agent
  family name: Olsen
  given name: Markus Harboe
doi: 10.7717/peerj.7585
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-27
copyright: ©2019 Kondziella et al.
attribution name: Kondziella et al.

Insights from the proteome profile of Phytophthora capsici in response to the novel fungicide SYP-14288
type: item
type: AcademicArticle
description: Phytophthora capsica is a destructive oomycete plant pathogen that causes huge losses to crop production worldwide. However, the novel fungicide SYP-14288 has shown excellent activity against various stages of the oomycete life cycle as well against fungal plant pathogens. The current study utilized isobaric tags for relative and absolute quantitation technology to generate proteome profiles of P. capsici in the presence or absence of SYP-14288 in order to gain a greater understanding of the SYP-14288 mode of action. A total of 1,443 individual proteins were identified during the investigation, of which 599 were considered to have significantly altered expression. Further investigation using Cluster of Orthologous Groups of proteins analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated most of the proteins with altered expression were associated with carbohydrate metabolism, energy metabolism and their downstream biological functions, especially with regard to oxidoreductase activity and subsequent adenosine triphosphate (ATP) production associated pathways. Quantitative expression analysis using qRT-PCR validated the proteomic data. These results seem to indicate that SYP-14288 treatment caused a shift in energy metabolism that resulted in the activation of compensatory mechanisms affecting carbohydrate and lipid metabolism. The study also found evidence that the up-regulation of transmembrane transporters and proteins associated with stress response might also be coopted to compensate for the disrupted proton gradient and other downstream effects. Taken together these results provide strong evidence that SYP-14288 has a similar mode of action to the oxidative phosphorylation uncoupler Fluazinam but further investigation, including molecular studies, is required to completely characterize the SYP-14288 mode of action in P. capsici. However, the proteomic data collected in the current study does provide important insight into the overall ef…
format: application/pdf
format: text/html
creator: Meng Cai
creator: Zhiwen Wang
creator: Xiaoxia Ni
creator: Yanhua Hou
creator: Qin Peng
creator: Xiang Gao
creator: Xili Liu
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.7626
publisher: PeerJ Inc.
rights: © 2019 Cai et al.
abstract: Phytophthora capsica is a destructive oomycete plant pathogen that causes huge losses to crop production worldwide. However, the novel fungicide SYP-14288 has shown excellent activity against various stages of the oomycete life cycle as well against fungal plant pathogens. The current study utilized isobaric tags for relative and absolute quantitation technology to generate proteome profiles of P. capsici in the presence or absence of SYP-14288 in order to gain a greater understanding of the SYP-14288 mode of action. A total of 1,443 individual proteins were identified during the investigation, of which 599 were considered to have significantly altered expression. Further investigation using Cluster of Orthologous Groups of proteins analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated most of the proteins with altered expression were associated with carbohydrate metabolism, energy metabolism and their downstream biological functions, especially with regard to oxidoreductase activity and subsequent adenosine triphosphate (ATP) production associated pathways. Quantitative expression analysis using qRT-PCR validated the proteomic data. These results seem to indicate that SYP-14288 treatment caused a shift in energy metabolism that resulted in the activation of compensatory mechanisms affecting carbohydrate and lipid metabolism. The study also found evidence that the up-regulation of transmembrane transporters and proteins associated with stress response might also be coopted to compensate for the disrupted proton gradient and other downstream effects. Taken together these results provide strong evidence that SYP-14288 has a similar mode of action to the oxidative phosphorylation uncoupler Fluazinam but further investigation, including molecular studies, is required to completely characterize the SYP-14288 mode of action in P. capsici. However, the proteomic data collected in the current study does provide important insight into the overall ef…
bibliographic citation: Cai et al. (2019) Insights from the proteome profile of Phytophthora capsici in response to the novel fungicide SYP-14288. PeerJ 7:e7626 https://doi.org/10.7717/peerj.7626
date submitted: 2019-06-19
date accepted: 2019-08-06
issued: 2019-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cai
  given name: Meng
author list: Agent
  family name: Wang
  given name: Zhiwen
author list: Agent
  family name: Ni
  given name: Xiaoxia
author list: Agent
  family name: Hou
  given name: Yanhua
author list: Agent
  family name: Peng
  given name: Qin
author list: Agent
  family name: Gao
  given name: Xiang
author list: Agent
  family name: Liu
  given name: Xili
doi: 10.7717/peerj.7626
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-27
copyright: © 2019 Cai et al.
attribution name: Cai et al.

Filter feeding in Late Jurassic pterosaurs supported by coprolite contents
type: item
type: AcademicArticle
description: Diets of pterosaurs have mainly been inferred from indirect evidence such as comparative anatomy, associations of co-occurring fossils, and functional morphology. Gut contents are rare, and until now there is only a single coprolite (fossil dropping), with unidentified inclusions, known. Here we describe three coprolites collected from a palaeosurface with numerous pterosaur tracks found in early Kimmeridgian (Hypselocyclum Zone) intertidal deposits of the Wierzbica Quarry, Poland. The specimens’ morphology and association to the tracks suggest a pterosaur producer. Synchrotron scans reveal numerous small inclusions, with foraminifera making up the majority of the identifiable ones. Other small remains include shells/carapaces (of bivalves, ostracods, and other crustaceans/arthropods) and bristles (some possibly of polychaete worms). The high density of the small shelly inclusions suggest that they were not accidently ingested, but constituted an important food source for the pterosaur(s), perhaps together with unpreserved soft-bodied animals. The combined evidence from the tracks and coprolites suggest a filter-feeding ctenochasmatid as the most likely tracemaker. If true, this significantly expands the bromalite record for this pterosaur group, which was previously only known from gastroliths. Moreover, this study also provides the first direct evidence of filter feeding in Jurassic pterosaurs and shows that they had a similar diet to the recent Chilean flamingo (Phoenicopterus chilensis).
format: application/pdf
format: text/html
creator: Martin Qvarnström
creator: Erik Elgh
creator: Krzysztof Owocki
creator: Per E. Ahlberg
creator: Grzegorz Niedźwiedzki
subject: Ecology
subject: Paleontology
description: doi:10.7717/peerj.7375
publisher: PeerJ Inc.
rights: © 2019 Qvarnström et al.
abstract: Diets of pterosaurs have mainly been inferred from indirect evidence such as comparative anatomy, associations of co-occurring fossils, and functional morphology. Gut contents are rare, and until now there is only a single coprolite (fossil dropping), with unidentified inclusions, known. Here we describe three coprolites collected from a palaeosurface with numerous pterosaur tracks found in early Kimmeridgian (Hypselocyclum Zone) intertidal deposits of the Wierzbica Quarry, Poland. The specimens’ morphology and association to the tracks suggest a pterosaur producer. Synchrotron scans reveal numerous small inclusions, with foraminifera making up the majority of the identifiable ones. Other small remains include shells/carapaces (of bivalves, ostracods, and other crustaceans/arthropods) and bristles (some possibly of polychaete worms). The high density of the small shelly inclusions suggest that they were not accidently ingested, but constituted an important food source for the pterosaur(s), perhaps together with unpreserved soft-bodied animals. The combined evidence from the tracks and coprolites suggest a filter-feeding ctenochasmatid as the most likely tracemaker. If true, this significantly expands the bromalite record for this pterosaur group, which was previously only known from gastroliths. Moreover, this study also provides the first direct evidence of filter feeding in Jurassic pterosaurs and shows that they had a similar diet to the recent Chilean flamingo (Phoenicopterus chilensis).
bibliographic citation: Qvarnström et al. (2019) Filter feeding in Late Jurassic pterosaurs supported by coprolite contents. PeerJ 7:e7375 https://doi.org/10.7717/peerj.7375
date submitted: 2019-04-16
date accepted: 2019-06-28
issued: 2019-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qvarnström
  given name: Martin
author list: Agent
  family name: Elgh
  given name: Erik
author list: Agent
  family name: Owocki
  given name: Krzysztof
author list: Agent
  family name: Ahlberg
  given name: Per E.
author list: Agent
  family name: Niedźwiedzki
  given name: Grzegorz
doi: 10.7717/peerj.7375
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-26
copyright: ©2019 Qvarnström et al.
attribution name: Qvarnström et al.

The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations
type: item
type: AcademicArticle
description: Background The RIPper (http://theripper.hawk.rocks) is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in the genome sequences of Ascomycota. The RIP pathway is a fungal genome defense mechanism that is aimed at identifying repeated and duplicated motifs, into which it then introduces cytosine to thymine transition mutations. RIP thus serves to deactivate and counteract the deleterious consequences of selfish or mobile DNA elements in fungal genomes. The occurrence, genetic context and frequency of RIP mutations are widely used to assess the activity of this pathway in genomic regions of interest. Here, we present a bioinformatics tool that is specifically fashioned to automate the investigation of changes in RIP product and substrate nucleotide frequencies in fungal genomes. Results We demonstrated the ability of The RIPper to detect the occurrence and extent of RIP mutations in known RIP affected sequences. Specifically, a sliding window approach was used to perform genome-wide RIP analysis on the genome assembly of Neurospora crassa. Additionally, fine-scale analysis with The RIPper showed that gene regions and transposable element sequences, previously determined to be affected by RIP, were indeed characterized by high frequencies of RIP mutations. Data generated using this software further showed that large proportions of the N. crassa genome constitutes RIP mutations with extensively affected regions displaying reduced GC content. The RIPper was further useful for investigating and visualizing changes in RIP mutations across the length of sequences of interest, allowing for fine-scale analyses. Conclusion This software identified RIP targeted genomic regions and provided RIP statistics for an entire genome assembly, including the genomic proportion affected by RIP. Here, we present The RIPper as an efficient tool for genome-wide RIP analyses.
format: application/pdf
format: text/html
creator: Stephanie van Wyk
creator: Christopher H. Harrison
creator: Brenda D. Wingfield
creator: Lieschen De Vos
creator: Nicolaas A. van der Merwe
creator: Emma T. Steenkamp
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Mycology
description: doi:10.7717/peerj.7447
publisher: PeerJ Inc.
rights: © 2019 van Wyk et al.
abstract: Background The RIPper (http://theripper.hawk.rocks) is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in the genome sequences of Ascomycota. The RIP pathway is a fungal genome defense mechanism that is aimed at identifying repeated and duplicated motifs, into which it then introduces cytosine to thymine transition mutations. RIP thus serves to deactivate and counteract the deleterious consequences of selfish or mobile DNA elements in fungal genomes. The occurrence, genetic context and frequency of RIP mutations are widely used to assess the activity of this pathway in genomic regions of interest. Here, we present a bioinformatics tool that is specifically fashioned to automate the investigation of changes in RIP product and substrate nucleotide frequencies in fungal genomes. Results We demonstrated the ability of The RIPper to detect the occurrence and extent of RIP mutations in known RIP affected sequences. Specifically, a sliding window approach was used to perform genome-wide RIP analysis on the genome assembly of Neurospora crassa. Additionally, fine-scale analysis with The RIPper showed that gene regions and transposable element sequences, previously determined to be affected by RIP, were indeed characterized by high frequencies of RIP mutations. Data generated using this software further showed that large proportions of the N. crassa genome constitutes RIP mutations with extensively affected regions displaying reduced GC content. The RIPper was further useful for investigating and visualizing changes in RIP mutations across the length of sequences of interest, allowing for fine-scale analyses. Conclusion This software identified RIP targeted genomic regions and provided RIP statistics for an entire genome assembly, including the genomic proportion affected by RIP. Here, we present The RIPper as an efficient tool for genome-wide RIP analyses.
bibliographic citation: van Wyk et al. (2019) The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations. PeerJ 7:e7447 https://doi.org/10.7717/peerj.7447
date submitted: 2019-02-22
date accepted: 2019-07-09
issued: 2019-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: van Wyk
  given name: Stephanie
author list: Agent
  family name: Harrison
  given name: Christopher H.
author list: Agent
  family name: Wingfield
  given name: Brenda D.
author list: Agent
  family name: De Vos
  given name: Lieschen
author list: Agent
  family name: van der Merwe
  given name: Nicolaas A.
author list: Agent
  family name: Steenkamp
  given name: Emma T.
doi: 10.7717/peerj.7447
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-26
copyright: ©2019 van Wyk et al.
attribution name: van Wyk et al.

Profiling the lncRNA-miRNA-mRNA ceRNA network to reveal potential crosstalk between inflammatory bowel disease and colorectal cancer
type: item
type: AcademicArticle
description: Background Because of the increasing dysplasia rate in the lifelong course of inflammatory bowel disease (IBD) patients, it is imperative to characterize the crosstalk between IBD and colorectal cancer (CRC). However, there have been no reports revealing the occurrence of the ceRNA network in IBD-related CRC. Methods In this study, we conducted gene expression profile studies of databases and performed an integrated analysis to detect the potential of lncRNA-miRNA-mRNA ceRNA in regulating disease transformation. R packages were used to screen differentially expressed mRNA, lncRNA and miRNA among CRC, IBD and normal tissue. The lncRNA-miRNA-mRNA network was constructed based on predicted miRNA-targeted lncRNAs and miRNA-targeted mRNAs. Functional analyses were then conducted to identify genes involved in the ceRNA network, and key lncRNAs were evaluated based on several clinical outcomes. Results A total of three lncRNAs, 15 miRNAs, and 138 mRNAs were identified as potential mediators in the pathophysiological processes of IBD-related CRC. Gene Ontology annotation enrichment analysis confirmed that the dysplasia process was strongly associated with immune response, response to lipopolysaccharide, and inflammatory response. Survival analysis showed that LINC01106 (HR = 1.7; p < 0.05) were strongly associated with overall survival of colorectal cancer patients. The current study identified a series of IBD-related mRNAs, miRNA, and lncRNAs, and highlighted the important role of ceRNAs in the pathogenesis of IBD-related CRC. Among them, the LINC01106-miRNA-mRNA axis was identified as vital targets for further research.
format: application/pdf
format: text/html
creator: Fangfang Sun
creator: Weiwei Liang
creator: Kejun Tang
creator: Mengying Hong
creator: Jing Qian
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Statistics
subject: Data Science
description: doi:10.7717/peerj.7451
publisher: PeerJ Inc.
rights: © 2019 Sun et al.
abstract: Background Because of the increasing dysplasia rate in the lifelong course of inflammatory bowel disease (IBD) patients, it is imperative to characterize the crosstalk between IBD and colorectal cancer (CRC). However, there have been no reports revealing the occurrence of the ceRNA network in IBD-related CRC. Methods In this study, we conducted gene expression profile studies of databases and performed an integrated analysis to detect the potential of lncRNA-miRNA-mRNA ceRNA in regulating disease transformation. R packages were used to screen differentially expressed mRNA, lncRNA and miRNA among CRC, IBD and normal tissue. The lncRNA-miRNA-mRNA network was constructed based on predicted miRNA-targeted lncRNAs and miRNA-targeted mRNAs. Functional analyses were then conducted to identify genes involved in the ceRNA network, and key lncRNAs were evaluated based on several clinical outcomes. Results A total of three lncRNAs, 15 miRNAs, and 138 mRNAs were identified as potential mediators in the pathophysiological processes of IBD-related CRC. Gene Ontology annotation enrichment analysis confirmed that the dysplasia process was strongly associated with immune response, response to lipopolysaccharide, and inflammatory response. Survival analysis showed that LINC01106 (HR = 1.7; p < 0.05) were strongly associated with overall survival of colorectal cancer patients. The current study identified a series of IBD-related mRNAs, miRNA, and lncRNAs, and highlighted the important role of ceRNAs in the pathogenesis of IBD-related CRC. Among them, the LINC01106-miRNA-mRNA axis was identified as vital targets for further research.
bibliographic citation: Sun et al. (2019) Profiling the lncRNA-miRNA-mRNA ceRNA network to reveal potential crosstalk between inflammatory bowel disease and colorectal cancer. PeerJ 7:e7451 https://doi.org/10.7717/peerj.7451
date submitted: 2019-02-16
date accepted: 2019-07-10
issued: 2019-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Fangfang
author list: Agent
  family name: Liang
  given name: Weiwei
author list: Agent
  family name: Tang
  given name: Kejun
author list: Agent
  family name: Hong
  given name: Mengying
author list: Agent
  family name: Qian
  given name: Jing
doi: 10.7717/peerj.7451
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-26
copyright: ©2019 Sun et al.
attribution name: Sun et al.

Effectiveness of small road tunnels and fences in reducing amphibian roadkill and barrier effects at retrofitted roads in Sweden
type: item
type: AcademicArticle
description: Schemes to reduce road impacts on amphibians have been implemented for decades in Europe, yet, several aspects on the effectiveness of such schemes remain poorly understood. Particularly in northern Europe, including Sweden, there is a lack of available information on road mitigation for amphibians, which is hampering implementation progress and cost-effectiveness analyses of mitigation options. Here, we present data derived from systematic counts of amphibians during spring migration at three previous hot-spots for amphibian roadkill in Sweden, where amphibian tunnels with guiding fences have been installed. We used the data in combination with a risk model to estimate the number of roadkills and successful crossings before vs. after mitigation and mitigated vs. adjacent non-mitigated road sections. In mitigated road sections, the estimated number of amphibians killed or at risk of being killed by car traffic decreased by 85–100% and the estimated number successfully crossing the road increased by 25–340%. Data, however, suggested fence-end effects that may moderate the reduction in roadkill. We discuss possible explanations for the observed differences between sites and construction types, and implications for amphibian conservation. We show how effectiveness estimates can be used for prioritizing amphibian passages along the existing road network. Finally, we emphasize the importance of careful monitoring of amphibian roadkill and successful crossings before and after amphibian passages are constructed.
format: application/pdf
format: text/html
creator: Jan Olof Helldin
creator: Silviu O. Petrovan
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Environmental Impacts
subject: Population Biology
description: doi:10.7717/peerj.7518
publisher: PeerJ Inc.
rights: © 2019 Helldin and Petrovan
abstract: Schemes to reduce road impacts on amphibians have been implemented for decades in Europe, yet, several aspects on the effectiveness of such schemes remain poorly understood. Particularly in northern Europe, including Sweden, there is a lack of available information on road mitigation for amphibians, which is hampering implementation progress and cost-effectiveness analyses of mitigation options. Here, we present data derived from systematic counts of amphibians during spring migration at three previous hot-spots for amphibian roadkill in Sweden, where amphibian tunnels with guiding fences have been installed. We used the data in combination with a risk model to estimate the number of roadkills and successful crossings before vs. after mitigation and mitigated vs. adjacent non-mitigated road sections. In mitigated road sections, the estimated number of amphibians killed or at risk of being killed by car traffic decreased by 85–100% and the estimated number successfully crossing the road increased by 25–340%. Data, however, suggested fence-end effects that may moderate the reduction in roadkill. We discuss possible explanations for the observed differences between sites and construction types, and implications for amphibian conservation. We show how effectiveness estimates can be used for prioritizing amphibian passages along the existing road network. Finally, we emphasize the importance of careful monitoring of amphibian roadkill and successful crossings before and after amphibian passages are constructed.
bibliographic citation: Helldin et al. (2019) Effectiveness of small road tunnels and fences in reducing amphibian roadkill and barrier effects at retrofitted roads in Sweden. PeerJ 7:e7518 https://doi.org/10.7717/peerj.7518
date submitted: 2019-04-17
date accepted: 2019-07-19
issued: 2019-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Helldin
  given name: Jan Olof
author list: Agent
  family name: Petrovan
  given name: Silviu O.
doi: 10.7717/peerj.7518
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-26
copyright: © 2019 Helldin and Petrovan
attribution name: Helldin and Petrovan

Detecting the impact of land cover change on observed rainfall
type: item
type: AcademicArticle
description: Analysis of observational data to pinpoint impact of land cover change on local rainfall is difficult due to multiple environmental factors that cannot be strictly controlled. In this study we use a statistical approach to identify the relationship between removal of tree cover and rainfall with data from best available sources for two large areas in Australia. Gridded rainfall data between 1979 and 2015 was used for the areas, while large scale (exogenous) effects were represented by mean rainfall across a much larger area and climatic indicators, such as Southern Oscillation Index and Indian Ocean Dipole. Both generalised additive modelling and step trend tests were used for the analysis. For a region in south central Queensland, the reported change in tree clearing between 2002–2005 did not result in strong statistically significant precipitation changes. On the other hand, results from a bushfire affected region on the border of New South Wales and Victoria suggest significant changes in the rainfall due to changes in tree cover. This indicates the method works better when an abrupt change in the data can be clearly identified. The results from the step trend test also mainly identified a positive relationship between the tree cover and the rainfall at p < 0.1 at the NSW/Victoria region. High rainfall variability and possible regrowth could have impacted the results in the Queensland region.
format: application/pdf
format: text/html
creator: Chun Xia Liang
creator: Floris F. van Ogtrop
creator: R. Willem Vervoort
subject: Statistics
subject: Coupled Natural and Human Systems
subject: Environmental Impacts
description: doi:10.7717/peerj.7523
publisher: PeerJ Inc.
rights: © 2019 Liang et al.
abstract: Analysis of observational data to pinpoint impact of land cover change on local rainfall is difficult due to multiple environmental factors that cannot be strictly controlled. In this study we use a statistical approach to identify the relationship between removal of tree cover and rainfall with data from best available sources for two large areas in Australia. Gridded rainfall data between 1979 and 2015 was used for the areas, while large scale (exogenous) effects were represented by mean rainfall across a much larger area and climatic indicators, such as Southern Oscillation Index and Indian Ocean Dipole. Both generalised additive modelling and step trend tests were used for the analysis. For a region in south central Queensland, the reported change in tree clearing between 2002–2005 did not result in strong statistically significant precipitation changes. On the other hand, results from a bushfire affected region on the border of New South Wales and Victoria suggest significant changes in the rainfall due to changes in tree cover. This indicates the method works better when an abrupt change in the data can be clearly identified. The results from the step trend test also mainly identified a positive relationship between the tree cover and the rainfall at p < 0.1 at the NSW/Victoria region. High rainfall variability and possible regrowth could have impacted the results in the Queensland region.
bibliographic citation: Liang et al. (2019) Detecting the impact of land cover change on observed rainfall. PeerJ 7:e7523 https://doi.org/10.7717/peerj.7523
date submitted: 2019-03-19
date accepted: 2019-07-21
issued: 2019-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Chun Xia
author list: Agent
  family name: van Ogtrop
  given name: Floris F.
author list: Agent
  family name: Vervoort
  given name: R. Willem
doi: 10.7717/peerj.7523
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-26
copyright: ©2019 Liang et al.
attribution name: Liang et al.

https://peerj.com/articles/7541
type: item
type: AcademicArticle
title: Three new species, one new genus and subfamily of Dorylaimida (de Man, 1876) Pearse, 1942, and revisions on the families Tylencholaimellidae Jairajpuri, 1964 and Mydonomidae Thorne, 1964 (Nematoda: Dorylaimida)
description: Three new species of the order Dorylaimida (de Man, 1876) Pearse, 1942 were identified and described. Paratylencholaimus sanshaensis gen. nov. sp. nov. from Hainan is proposed as a new member of the family Tylencholaimellidae Jairajpuri, 1964. Paratylencholaimus gen. nov. is close to Phellonema Thorne, 1964 and Goferus Jairajpuri & Ahmad, 1992 but can be differentiated mainly by having basal part of odontophore rod-like and without knobs, and basal part of pharynx expanded gradually. Tylencholaimus zhongshanensis sp. nov. from Guangdong and Dorylaimoides shapotouensis sp. nov. from the Ningxia Hui Autonomous Region are also described herein. Phylogenetic analyses based on the 18S rDNA and the D2–D3 region of the 28S rDNA support that the three new species are valid. The classifications of the families Tylencholaimellidae and Mydonomidae Thorne, 1964 are revised mainly based on the analysis of the morphology of odontostyle and odontophore. After these revisions, Paratylencholaiminae subfam. nov. including Paratylencholaimus gen. nov. and Goferus is proposed. Athernema and Agmodorus of Tylencholaimellidae are transferred into Mydonomidae, and the subfamily Athernematinae of Tylencholaimellidae is dismissed. The main characteristics of the family Mydonomidae and Tylencholaimellidae are revised. Keys to the genera of Mydomonidae and Tylencholaimellidae are included.
format: application/pdf
format: text/html
creator: Wen-Jia Wu
creator: Chun-Ling Xu
creator: Hui Xie
creator: Dong-Wei Wang
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7541
publisher: PeerJ Inc.
rights: © 2019 Wu et al.
abstract: Three new species of the order Dorylaimida (de Man, 1876) Pearse, 1942 were identified and described. Paratylencholaimus sanshaensis gen. nov. sp. nov. from Hainan is proposed as a new member of the family Tylencholaimellidae Jairajpuri, 1964. Paratylencholaimus gen. nov. is close to Phellonema Thorne, 1964 and Goferus Jairajpuri & Ahmad, 1992 but can be differentiated mainly by having basal part of odontophore rod-like and without knobs, and basal part of pharynx expanded gradually. Tylencholaimus zhongshanensis sp. nov. from Guangdong and Dorylaimoides shapotouensis sp. nov. from the Ningxia Hui Autonomous Region are also described herein. Phylogenetic analyses based on the 18S rDNA and the D2–D3 region of the 28S rDNA support that the three new species are valid. The classifications of the families Tylencholaimellidae and Mydonomidae Thorne, 1964 are revised mainly based on the analysis of the morphology of odontostyle and odontophore. After these revisions, Paratylencholaiminae subfam. nov. including Paratylencholaimus gen. nov. and Goferus is proposed. Athernema and Agmodorus of Tylencholaimellidae are transferred into Mydonomidae, and the subfamily Athernematinae of Tylencholaimellidae is dismissed. The main characteristics of the family Mydonomidae and Tylencholaimellidae are revised. Keys to the genera of Mydomonidae and Tylencholaimellidae are included.
bibliographic citation: Wu et al. (2019) Three new species, one new genus and subfamily of Dorylaimida (de Man, 1876) Pearse, 1942, and revisions on the families Tylencholaimellidae Jairajpuri, 1964 and Mydonomidae Thorne, 1964 (Nematoda: Dorylaimida). PeerJ 7:e7541 https://doi.org/10.7717/peerj.7541
date submitted: 2019-04-12
date accepted: 2019-07-24
issued: 2019-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Wen-Jia
author list: Agent
  family name: Xu
  given name: Chun-Ling
author list: Agent
  family name: Xie
  given name: Hui
author list: Agent
  family name: Wang
  given name: Dong-Wei
doi: 10.7717/peerj.7541
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-26
copyright: ©2019 Wu et al.
attribution name: Wu et al.

https://peerj.com/articles/7555
type: item
type: AcademicArticle
title: Cell-free supernatants from cultures of lactic acid bacteria isolated from fermented grape as biocontrol against Salmonella Typhi and Salmonella Typhimurium virulence via autoinducer-2 and biofilm interference
description: Background Salmonella Typhi and Salmonella Typhimurium are the causative pathogens of salmonellosis, and they are mostly found in animal source foods (ASF). The inappropriate use of antibiotics enhances the possibility for the emergence of antibiotic resistance in pathogens and antibiotic residue in ASF. One promising alternative to antibiotics in animal farming is the use of lactic acid bacteria (LAB). Methods The present study was carried out the cells and/or the cell-free culture supernatants (CFCS) from beneficial LAB against S. Typhi and S. Typhimurium. The antibacterial mechanisms of LAB-CFCS as biocontrol agents against both Salmonella serovars were investigated through the analysis of anti-salmonella growth activity, biofilm inhibition and quorum quenching activity. Results Among 146 LAB strains isolated from 110 fermented food samples, the 2 strong inhibitory effect strains (WM33 and WM36) from fermented grapes against both Salmonella serovars were selected. Out of the selected strains, WM36 was the most effective inhibitor, which indicated S. Typhi by showing 95.68% biofilm inhibition at 20% biofilm inhibition concentration (BIC) and reduced 99.84% of AI-2 signaling interference. The WM33 was the best to control S. Typhimurium by producing 66.46% biofilm inhibition at only 15% BIC and 99.99% AI-2 signaling a reduction. The 16S rDNA was amplified by a polymerase chain reaction (PCR). The selected isolates were identified as Weissella viridescens WM33 and Weissella confusa WM36 based on nucleotide homology and phylogenetic analysis. Conclusion The metabolic extracts from Weissella spp. inhibit Salmonella serovars with the potential to be used as biocontrol agents to improve microbiological safety in the production of ASF.
format: application/pdf
format: text/html
creator: Wattana Pelyuntha
creator: Chaiyavat Chaiyasut
creator: Duangporn Kantachote
creator: Sasithorn Sirilun
subject: Biotechnology
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.7555
publisher: PeerJ Inc.
rights: © 2019 Pelyuntha et al.
abstract: Background Salmonella Typhi and Salmonella Typhimurium are the causative pathogens of salmonellosis, and they are mostly found in animal source foods (ASF). The inappropriate use of antibiotics enhances the possibility for the emergence of antibiotic resistance in pathogens and antibiotic residue in ASF. One promising alternative to antibiotics in animal farming is the use of lactic acid bacteria (LAB). Methods The present study was carried out the cells and/or the cell-free culture supernatants (CFCS) from beneficial LAB against S. Typhi and S. Typhimurium. The antibacterial mechanisms of LAB-CFCS as biocontrol agents against both Salmonella serovars were investigated through the analysis of anti-salmonella growth activity, biofilm inhibition and quorum quenching activity. Results Among 146 LAB strains isolated from 110 fermented food samples, the 2 strong inhibitory effect strains (WM33 and WM36) from fermented grapes against both Salmonella serovars were selected. Out of the selected strains, WM36 was the most effective inhibitor, which indicated S. Typhi by showing 95.68% biofilm inhibition at 20% biofilm inhibition concentration (BIC) and reduced 99.84% of AI-2 signaling interference. The WM33 was the best to control S. Typhimurium by producing 66.46% biofilm inhibition at only 15% BIC and 99.99% AI-2 signaling a reduction. The 16S rDNA was amplified by a polymerase chain reaction (PCR). The selected isolates were identified as Weissella viridescens WM33 and Weissella confusa WM36 based on nucleotide homology and phylogenetic analysis. Conclusion The metabolic extracts from Weissella spp. inhibit Salmonella serovars with the potential to be used as biocontrol agents to improve microbiological safety in the production of ASF.
bibliographic citation: Pelyuntha et al. (2019) Cell-free supernatants from cultures of lactic acid bacteria isolated from fermented grape as biocontrol against Salmonella Typhi and Salmonella Typhimurium virulence via autoinducer-2 and biofilm interference. PeerJ 7:e7555 https://doi.org/10.7717/peerj.7555
date submitted: 2019-03-29
date accepted: 2019-07-25
issued: 2019-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pelyuntha
  given name: Wattana
author list: Agent
  family name: Chaiyasut
  given name: Chaiyavat
author list: Agent
  family name: Kantachote
  given name: Duangporn
author list: Agent
  family name: Sirilun
  given name: Sasithorn
doi: 10.7717/peerj.7555
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-26
copyright: ©2019 Pelyuntha et al.
attribution name: Pelyuntha et al.

Association between serum uric acid and nonalcoholic fatty liver disease in community patients with type 2 diabetes mellitus
type: item
type: AcademicArticle
description: Background To investigate whether SUA is associated with NAFLD in men and women with T2DM. Methods This cross-sectional study enrolled patients with T2DM at Shanxi High-Tech Development Zone Central Hospital (June 2011 to September 2017). Patients were stratified according to gender and presence/absence of NAFLD. Parameters associated with NAFLD were identified using multivariate stepwise linear regression and univariate/multivariate logistic regression. Results Among 597 patients (325 males) enrolled, 352 had NAFLD. SUA was higher in the NAFLD group than in the non-NAFLD group for both men and women (P < 0.001). Multiple linear regression showed that body mass index (positively), triglycerides (positively) and estimated glomerular filtration rate (negatively) were independently related to SUA (P < 0.001). Univariate logistic regression revealed increased odds of NAFLD for SUA tertiles 2 (P = 0.022) and 3 (P = 0.001) in women and tertile 3 (P = 0.039) in men. After adjustment for multiple clinical parameters, SUA tertiles were significantly associated with NAFLD for tertile 3 in women (P = 0.014), although there were trends toward associations for tertile 2 in women (P = 0.074) and tertiles 2 and 3 in men (P = 0.085 and 0.054, respectively). Conclusion SUA is not independently associated with NAFLD in men or women with T2DM after rigorous adjustment for other metabolic parameters.
format: application/pdf
format: text/html
creator: Linxin Xu
creator: Ting Li
creator: Jianhong Yin
creator: Gang Lin
creator: Yali Xu
creator: Yi Ren
creator: Yan Wang
creator: Jing Yang
creator: Liming Chen
subject: Bioinformatics
subject: Diabetes and Endocrinology
subject: Geriatrics
description: doi:10.7717/peerj.7563
publisher: PeerJ Inc.
rights: © 2019 Xu et al.
abstract: Background To investigate whether SUA is associated with NAFLD in men and women with T2DM. Methods This cross-sectional study enrolled patients with T2DM at Shanxi High-Tech Development Zone Central Hospital (June 2011 to September 2017). Patients were stratified according to gender and presence/absence of NAFLD. Parameters associated with NAFLD were identified using multivariate stepwise linear regression and univariate/multivariate logistic regression. Results Among 597 patients (325 males) enrolled, 352 had NAFLD. SUA was higher in the NAFLD group than in the non-NAFLD group for both men and women (P < 0.001). Multiple linear regression showed that body mass index (positively), triglycerides (positively) and estimated glomerular filtration rate (negatively) were independently related to SUA (P < 0.001). Univariate logistic regression revealed increased odds of NAFLD for SUA tertiles 2 (P = 0.022) and 3 (P = 0.001) in women and tertile 3 (P = 0.039) in men. After adjustment for multiple clinical parameters, SUA tertiles were significantly associated with NAFLD for tertile 3 in women (P = 0.014), although there were trends toward associations for tertile 2 in women (P = 0.074) and tertiles 2 and 3 in men (P = 0.085 and 0.054, respectively). Conclusion SUA is not independently associated with NAFLD in men or women with T2DM after rigorous adjustment for other metabolic parameters.
bibliographic citation: Xu et al. (2019) Association between serum uric acid and nonalcoholic fatty liver disease in community patients with type 2 diabetes mellitus. PeerJ 7:e7563 https://doi.org/10.7717/peerj.7563
date submitted: 2019-04-08
date accepted: 2019-07-29
issued: 2019-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Linxin
author list: Agent
  family name: Li
  given name: Ting
author list: Agent
  family name: Yin
  given name: Jianhong
author list: Agent
  family name: Lin
  given name: Gang
author list: Agent
  family name: Xu
  given name: Yali
author list: Agent
  family name: Ren
  given name: Yi
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Yang
  given name: Jing
author list: Agent
  family name: Chen
  given name: Liming
doi: 10.7717/peerj.7563
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-26
copyright: ©2019 Xu et al.
attribution name: Xu et al.

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