PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Disturbance has lasting effects on functional traits and diversity of grassland plant communities
items: A longitudinal study of risk factors associated with white spot disease occurrence in marine shrimp farming in Rayong, Thailand
items: Acute kidney injury-attributable mortality in critically ill patients with sepsis
items: Crop damage by vertebrates in Latin America: current knowledge and potential future management directions
items: A worldwide comparison of long-distance running training in 2019 and 2020: associated effects of the COVID-19 pandemic
items: Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study
items: First fossil-leaf floras from Brunei Darussalam show dipterocarp dominance in Borneo by the Pliocene
items: Genome-wide characterization and expression of the TLP gene family associated with Colletotrichum gloeosporioides inoculation in Fragaria × ananassa
items: A prognostic risk model based on DNA methylation levels of genes and lncRNAs in lung squamous cell carcinoma
items: Development of a Japanese version of the Psychological Ownership Scale

Disturbance has lasting effects on functional traits and diversity of grassland plant communities
type: item
type: AcademicArticle
description: Background Localized disturbances within grasslands alter biological properties and may shift species composition. For example, rare species in established communities may become dominant in successional communities if they exhibit traits well-suited to disturbance conditions. Although the idea that plant species exhibit different trait ‘strategies’ is well established, it is unclear how ecological selection for specific traits may change as a function of disturbance. Further, there is little data available testing whether disturbances select for single trait-characters within communities (homogenization), or allow multiple trait-types to persist (diversification). We investigated how (a) traits and (b) functional diversity of post-disturbance gap communities compared to those in adjacent undisturbed grasslands, and (c) if altered functional diversity resulted in the homogenization or diversification of functional traits. Methods Here we emulate the impacts of an extreme disturbance in a native grassland site. We measured plant community composition of twelve paired 50 × 50 cm plots (24 total) in Alberta, Canada. Each pair consisted of one undisturbed plot and one which had all plants terminated 2 years prior. We used species abundances and a local trait database to calculate community weighted means for maximum height, specific leaf area, specific root length, leaf nitrogen percent, and root nitrogen percent. To test the impacts of disturbance on community functional traits, we calculated functional diversity measures and compared them between disturbed and undisturbed communities. Results Within 2 years, species richness and evenness in disturbed communities had recovered and was equivalent to undisturbed communities. However, disturbed and undisturbed communities had distinct community compositions, resulting in lower functional divergence in disturbed plots. Further, disturbance was linked to increases in community-weighted mean trait values for resource-acquisi…
format: application/pdf
format: text/html
creator: Ellen A. Smith
creator: Emily M. Holden
creator: Charlotte Brown
creator: James F. Cahill Jr
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.13179
publisher: PeerJ Inc.
rights: © 2022 Smith et al.
abstract: Background Localized disturbances within grasslands alter biological properties and may shift species composition. For example, rare species in established communities may become dominant in successional communities if they exhibit traits well-suited to disturbance conditions. Although the idea that plant species exhibit different trait ‘strategies’ is well established, it is unclear how ecological selection for specific traits may change as a function of disturbance. Further, there is little data available testing whether disturbances select for single trait-characters within communities (homogenization), or allow multiple trait-types to persist (diversification). We investigated how (a) traits and (b) functional diversity of post-disturbance gap communities compared to those in adjacent undisturbed grasslands, and (c) if altered functional diversity resulted in the homogenization or diversification of functional traits. Methods Here we emulate the impacts of an extreme disturbance in a native grassland site. We measured plant community composition of twelve paired 50 × 50 cm plots (24 total) in Alberta, Canada. Each pair consisted of one undisturbed plot and one which had all plants terminated 2 years prior. We used species abundances and a local trait database to calculate community weighted means for maximum height, specific leaf area, specific root length, leaf nitrogen percent, and root nitrogen percent. To test the impacts of disturbance on community functional traits, we calculated functional diversity measures and compared them between disturbed and undisturbed communities. Results Within 2 years, species richness and evenness in disturbed communities had recovered and was equivalent to undisturbed communities. However, disturbed and undisturbed communities had distinct community compositions, resulting in lower functional divergence in disturbed plots. Further, disturbance was linked to increases in community-weighted mean trait values for resource-acquisi…
bibliographic citation: Smith et al. (2022) Disturbance has lasting effects on functional traits and diversity of grassland plant communities. PeerJ 10:e13179 https://doi.org/10.7717/peerj.13179
date submitted: 2021-10-05
date accepted: 2022-03-07
issued: 2022-03-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smith
  given name: Ellen A.
author list: Agent
  family name: Holden
  given name: Emily M.
author list: Agent
  family name: Brown
  given name: Charlotte
author list: Agent
  family name: Cahill Jr
  given name: James F.
doi: 10.7717/peerj.13179
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-25
copyright: © 2022 Smith et al.
attribution name: Smith et al.

A longitudinal study of risk factors associated with white spot disease occurrence in marine shrimp farming in Rayong, Thailand
type: item
type: AcademicArticle
description: Background A longitudinal study was conducted to analyze farm characteristics, farm practices, and biosecurity measures that influenced the occurrence of white spot disease (WSD) in shrimp farming in Rayong, Thailand. Methods Data were collected using a structured interview schedule administered between October 2017 and September 2019. A generalized estimating equations (GEE) model was used to identify risk factors. From the 270 responses, 86 possible risk factors were analyzed using univariate and multivariate analysis. Results We found that 17 possible risk factors were statistically significant with an alpha level of 1% and associated with WSD status. In the final model, multivariate analysis found that two independent variables were statistically significant. First, the absence of inclement weather during ponding was a statistically significant factor associated with WSD occurrence and it prevented WSD occurrence as the odds ratio (OR) was <1 (OR = 0.196, P = 1.3 × 10−5). Second, the separation of ponds into three specific types (cultured, water treatment, and pond for water reservoir) was significantly associated with WSD occurrence. Likewise, the presence of this ponding system was a protective factor against WSD (OR = 0.0828, P = 0.001). Conclusions The results of this study offer a reference for farmers and relevant authorities when addressing WSD occurrence in shrimp farming. In addition, our results can help relevant authorities in controlling WSD in other endemic areas.
format: application/pdf
format: text/html
creator: Sompit Yaemkasem
creator: Visanu Boonyawiwat
creator: Manakorn Sukmak
creator: Sukanya Thongratsakul
creator: Chaithep Poolkhet
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.13182
publisher: PeerJ Inc.
rights: © 2022 Yaemkasem et al.
abstract: Background A longitudinal study was conducted to analyze farm characteristics, farm practices, and biosecurity measures that influenced the occurrence of white spot disease (WSD) in shrimp farming in Rayong, Thailand. Methods Data were collected using a structured interview schedule administered between October 2017 and September 2019. A generalized estimating equations (GEE) model was used to identify risk factors. From the 270 responses, 86 possible risk factors were analyzed using univariate and multivariate analysis. Results We found that 17 possible risk factors were statistically significant with an alpha level of 1% and associated with WSD status. In the final model, multivariate analysis found that two independent variables were statistically significant. First, the absence of inclement weather during ponding was a statistically significant factor associated with WSD occurrence and it prevented WSD occurrence as the odds ratio (OR) was <1 (OR = 0.196, P = 1.3 × 10−5). Second, the separation of ponds into three specific types (cultured, water treatment, and pond for water reservoir) was significantly associated with WSD occurrence. Likewise, the presence of this ponding system was a protective factor against WSD (OR = 0.0828, P = 0.001). Conclusions The results of this study offer a reference for farmers and relevant authorities when addressing WSD occurrence in shrimp farming. In addition, our results can help relevant authorities in controlling WSD in other endemic areas.
bibliographic citation: Yaemkasem et al. (2022) A longitudinal study of risk factors associated with white spot disease occurrence in marine shrimp farming in Rayong, Thailand. PeerJ 10:e13182 https://doi.org/10.7717/peerj.13182
date submitted: 2021-12-09
date accepted: 2022-03-07
issued: 2022-03-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yaemkasem
  given name: Sompit
author list: Agent
  family name: Boonyawiwat
  given name: Visanu
author list: Agent
  family name: Sukmak
  given name: Manakorn
author list: Agent
  family name: Thongratsakul
  given name: Sukanya
author list: Agent
  family name: Poolkhet
  given name: Chaithep
doi: 10.7717/peerj.13182
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-25
copyright: © 2022 Yaemkasem et al.
attribution name: Yaemkasem et al.

Acute kidney injury-attributable mortality in critically ill patients with sepsis
type: item
type: AcademicArticle
description: Background To assess whether acute kidney injury (AKI) is independently associated with hospital mortality in ICU patients with sepsis, and estimate the excess AKI-related mortality attributable to AKI. Methods We analyzed adult patients from two distinct retrospective critically ill cohorts: (1) Medical Information Mart for Intensive Care IV (MIMIC IV; n = 15,610) cohort and (2) Wenzhou (n = 1,341) cohort. AKI was defined by Kidney Disease: Improving Global Outcomes (KDIGO) criteria. We applied multivariate logistic and linear regression models to assess the hospital and ICU mortality, hospital length-of-stay (LOS), and ICU LOS. The excess attributable mortality for AKI in ICU patients with sepsis was further evaluated. Results AKI occurred in 5,225 subjects in the MIMIC IV cohort (33.5%) and 494 in the Wenzhou cohort (36.8%). Each stage of AKI was an independent risk factor for hospital mortality in multivariate logistic regression after adjusting for baseline illness severity. The excess attributable mortality for AKI was 58.6% (95% CI [46.8%–70.3%]) in MIMIC IV and 44.6% (95% CI [12.7%–76.4%]) in Wenzhou. Additionally, AKI was independently associated with increased ICU mortality, hospital LOS, and ICU LOS. Conclusion Acute kidney injury is an independent risk factor for hospital and ICU mortality, as well as hospital and ICU LOS in critically ill patients with sepsis. Thus, AKI is associated with excess attributable mortality.
format: application/pdf
format: text/html
creator: Zhiyi Wang
creator: Jie Weng
creator: Jinwen Yang
creator: Xiaoming Zhou
creator: Zhe Xu
creator: Ruonan Hou
creator: Zhiliang Zhou
creator: Liang Wang
creator: Chan Chen
creator: Shengwei Jin
subject: Emergency and Critical Care
subject: Infectious Diseases
subject: Nephrology
description: doi:10.7717/peerj.13184
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background To assess whether acute kidney injury (AKI) is independently associated with hospital mortality in ICU patients with sepsis, and estimate the excess AKI-related mortality attributable to AKI. Methods We analyzed adult patients from two distinct retrospective critically ill cohorts: (1) Medical Information Mart for Intensive Care IV (MIMIC IV; n = 15,610) cohort and (2) Wenzhou (n = 1,341) cohort. AKI was defined by Kidney Disease: Improving Global Outcomes (KDIGO) criteria. We applied multivariate logistic and linear regression models to assess the hospital and ICU mortality, hospital length-of-stay (LOS), and ICU LOS. The excess attributable mortality for AKI in ICU patients with sepsis was further evaluated. Results AKI occurred in 5,225 subjects in the MIMIC IV cohort (33.5%) and 494 in the Wenzhou cohort (36.8%). Each stage of AKI was an independent risk factor for hospital mortality in multivariate logistic regression after adjusting for baseline illness severity. The excess attributable mortality for AKI was 58.6% (95% CI [46.8%–70.3%]) in MIMIC IV and 44.6% (95% CI [12.7%–76.4%]) in Wenzhou. Additionally, AKI was independently associated with increased ICU mortality, hospital LOS, and ICU LOS. Conclusion Acute kidney injury is an independent risk factor for hospital and ICU mortality, as well as hospital and ICU LOS in critically ill patients with sepsis. Thus, AKI is associated with excess attributable mortality.
bibliographic citation: Wang et al. (2022) Acute kidney injury-attributable mortality in critically ill patients with sepsis. PeerJ 10:e13184 https://doi.org/10.7717/peerj.13184
date submitted: 2022-01-11
date accepted: 2022-03-07
issued: 2022-03-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhiyi
author list: Agent
  family name: Weng
  given name: Jie
author list: Agent
  family name: Yang
  given name: Jinwen
author list: Agent
  family name: Zhou
  given name: Xiaoming
author list: Agent
  family name: Xu
  given name: Zhe
author list: Agent
  family name: Hou
  given name: Ruonan
author list: Agent
  family name: Zhou
  given name: Zhiliang
author list: Agent
  family name: Wang
  given name: Liang
author list: Agent
  family name: Chen
  given name: Chan
author list: Agent
  family name: Jin
  given name: Shengwei
doi: 10.7717/peerj.13184
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-25
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Crop damage by vertebrates in Latin America: current knowledge and potential future management directions
type: item
type: AcademicArticle
description: Background Crop farming contributes to one of the most extensive land use activities in the world, and cropland areas continue to rise. Many vertebrate species feed on crops, which has caused an increase in human-wildlife conflicts in croplands. Crop-feeding damages the economy of local communities and causes retaliation against the responsible vertebrates in several forms, including lethal practices such as hunting and poisoning. Lethal control may cause the local extirpation of some species, affecting ecological processes and patterns. Therefore, it is necessary to find non-lethal alternatives that can protect both local economies and wildlife. Research has been conducted in Africa and Asia, focusing on elephants and primates, and the effectiveness of some non-lethal alternatives, such as chili-based repellents and beehives, is being investigated. However, there has been very little research on this topic in Central and South America. The goal of this review is to assess the current knowledge on crop damage by vertebrates in Central and South America and indicate future research directions. Survey methodology We reviewed the available scientific literature reporting crop damage by vertebrates in Central and South America, and the Caribbean, published between 1980 and 2020, through systematic searches on Web of Science, Scopus, and Google Scholar. We analyzed the temporal and geographical distributions of the studies, the crops and vertebrate species these studies considered, the crop protection techniques used, and their effectiveness. Results We retrieved only 113 studies on crop damage by vertebrates in Latin America, but there was an increasing trend in the number of studies published over time. Most of the studies were conducted in Brazil, Argentina, Mexico, and Costa Rica. Four orders of mammals (Rodentia, Carnivora, Artiodactyla, and Primates) and four orders of birds (Passeriformes, Columbiformes, Psittaciformes, and Anseriformes) were the most common group…
format: application/pdf
format: text/html
creator: Adrián Alejandro Cuesta Hermira
creator: Fernanda Michalski
subject: Agricultural Science
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Natural Resource Management
description: doi:10.7717/peerj.13185
publisher: PeerJ Inc.
rights: © 2022 Alejandro Cuesta Hermira and Michalski
abstract: Background Crop farming contributes to one of the most extensive land use activities in the world, and cropland areas continue to rise. Many vertebrate species feed on crops, which has caused an increase in human-wildlife conflicts in croplands. Crop-feeding damages the economy of local communities and causes retaliation against the responsible vertebrates in several forms, including lethal practices such as hunting and poisoning. Lethal control may cause the local extirpation of some species, affecting ecological processes and patterns. Therefore, it is necessary to find non-lethal alternatives that can protect both local economies and wildlife. Research has been conducted in Africa and Asia, focusing on elephants and primates, and the effectiveness of some non-lethal alternatives, such as chili-based repellents and beehives, is being investigated. However, there has been very little research on this topic in Central and South America. The goal of this review is to assess the current knowledge on crop damage by vertebrates in Central and South America and indicate future research directions. Survey methodology We reviewed the available scientific literature reporting crop damage by vertebrates in Central and South America, and the Caribbean, published between 1980 and 2020, through systematic searches on Web of Science, Scopus, and Google Scholar. We analyzed the temporal and geographical distributions of the studies, the crops and vertebrate species these studies considered, the crop protection techniques used, and their effectiveness. Results We retrieved only 113 studies on crop damage by vertebrates in Latin America, but there was an increasing trend in the number of studies published over time. Most of the studies were conducted in Brazil, Argentina, Mexico, and Costa Rica. Four orders of mammals (Rodentia, Carnivora, Artiodactyla, and Primates) and four orders of birds (Passeriformes, Columbiformes, Psittaciformes, and Anseriformes) were the most common group…
bibliographic citation: Cuesta Hermira et al. (2022) Crop damage by vertebrates in Latin America: current knowledge and potential future management directions. PeerJ 10:e13185 https://doi.org/10.7717/peerj.13185
date submitted: 2021-10-18
date accepted: 2022-03-08
issued: 2022-03-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cuesta Hermira
  given name: Adrián Alejandro
author list: Agent
  family name: Michalski
  given name: Fernanda
doi: 10.7717/peerj.13185
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-25
copyright: © 2022 Alejandro Cuesta Hermira and Michalski
attribution name: Alejandro Cuesta Hermira and Michalski

A worldwide comparison of long-distance running training in 2019 and 2020: associated effects of the COVID-19 pandemic
type: item
type: AcademicArticle
description: Objective The goal of the present study was to investigate possible effects of the COVID-19 pandemic on long-distance running training. Methods This is a retrospective study with a within-subject design. We analyzed 10,703,690 records of running training during 2019 and 2020, from 36,412 athletes from around the world. The records were obtained through web scraping of a large social network for athletes on the internet. A potential long-distance runner was defined as a user of the social network who had a record of running at least one of the six World Marathon Majors by 2019. Results In 2020, compared with 2019, in total there was a 3.6% decrease in the number of athletes running, a 7.5% decrease in the distance and 6.7% in the duration of running training. There were large variations in these variables throughout 2020, reaching 16% fewer athletes running weekly and 35% lower running distance (Cohen’s d = 0.34, p < 0.001) and 33% lower running duration (Cohen’s d = 0.30, p < 0.001) in September 2020. The beginning of the decrease in running training in the first quarter of 2020 coincides with the beginning of the adoption of measures to restrict the COVID-19 pandemic; but as of the second quarter of 2020, running training appears to have undergone variations unrelated to the preventive measures. Among the ten most represented countries in the dataset, running training in Brazil appears to have been the most affected by the COVID-19 pandemic and restriction measures. Conclusion The wide variations in long-distance running training throughout 2020 are likely related to the COVID-19 pandemic. As for the total volume, the observed decreases of up to 7.5% in the outcome variables related to running training in 2020 could also be attributed to the COVID-19 pandemic, but other factors such as injury, illness or lack of interest, may also have contributed to these decreases.
format: application/pdf
format: text/html
creator: Leonardo A. Afonseca
creator: Renato N. Watanabe
creator: Marcos Duarte
subject: Kinesiology
subject: Public Health
subject: Statistics
subject: Data Science
subject: COVID-19
description: doi:10.7717/peerj.13192
publisher: PeerJ Inc.
rights: © 2022 Afonseca et al.
abstract: Objective The goal of the present study was to investigate possible effects of the COVID-19 pandemic on long-distance running training. Methods This is a retrospective study with a within-subject design. We analyzed 10,703,690 records of running training during 2019 and 2020, from 36,412 athletes from around the world. The records were obtained through web scraping of a large social network for athletes on the internet. A potential long-distance runner was defined as a user of the social network who had a record of running at least one of the six World Marathon Majors by 2019. Results In 2020, compared with 2019, in total there was a 3.6% decrease in the number of athletes running, a 7.5% decrease in the distance and 6.7% in the duration of running training. There were large variations in these variables throughout 2020, reaching 16% fewer athletes running weekly and 35% lower running distance (Cohen’s d = 0.34, p < 0.001) and 33% lower running duration (Cohen’s d = 0.30, p < 0.001) in September 2020. The beginning of the decrease in running training in the first quarter of 2020 coincides with the beginning of the adoption of measures to restrict the COVID-19 pandemic; but as of the second quarter of 2020, running training appears to have undergone variations unrelated to the preventive measures. Among the ten most represented countries in the dataset, running training in Brazil appears to have been the most affected by the COVID-19 pandemic and restriction measures. Conclusion The wide variations in long-distance running training throughout 2020 are likely related to the COVID-19 pandemic. As for the total volume, the observed decreases of up to 7.5% in the outcome variables related to running training in 2020 could also be attributed to the COVID-19 pandemic, but other factors such as injury, illness or lack of interest, may also have contributed to these decreases.
bibliographic citation: Afonseca et al. (2022) A worldwide comparison of long-distance running training in 2019 and 2020: associated effects of the COVID-19 pandemic. PeerJ 10:e13192 https://doi.org/10.7717/peerj.13192
date submitted: 2021-10-14
date accepted: 2022-03-08
issued: 2022-03-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Afonseca
  given name: Leonardo A.
author list: Agent
  family name: Watanabe
  given name: Renato N.
author list: Agent
  family name: Duarte
  given name: Marcos
doi: 10.7717/peerj.13192
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-25
copyright: ©2022 Afonseca et al.
attribution name: Afonseca et al.

Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study
type: item
type: AcademicArticle
description: Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. Across most simulations, more than 228 out of the 233 simulated viruses were recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovered only around one third. Overall, Centrifuge and Kraken2 had the best performance with the highest values of sensitivity and precision. We found that deamination damage had little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) an…
format: application/pdf
format: text/html
creator: Yami Ommar Arizmendi Cárdenas
creator: Samuel Neuenschwander
creator: Anna-Sapfo Malaspinas
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
subject: Genomics
subject: Virology
description: doi:10.7717/peerj.12784
publisher: PeerJ Inc.
rights: © 2022 Arizmendi Cárdenas et al.
abstract: Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. Across most simulations, more than 228 out of the 233 simulated viruses were recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovered only around one third. Overall, Centrifuge and Kraken2 had the best performance with the highest values of sensitivity and precision. We found that deamination damage had little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) an…
bibliographic citation: Arizmendi Cárdenas et al. (2022) Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study. PeerJ 10:e12784 https://doi.org/10.7717/peerj.12784
date submitted: 2021-04-12
date accepted: 2021-12-21
issued: 2022-03-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arizmendi Cárdenas
  given name: Yami Ommar
author list: Agent
  family name: Neuenschwander
  given name: Samuel
author list: Agent
  family name: Malaspinas
  given name: Anna-Sapfo
doi: 10.7717/peerj.12784
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-24
copyright: ©2022 Arizmendi Cárdenas et al.
attribution name: Arizmendi Cárdenas et al.

First fossil-leaf floras from Brunei Darussalam show dipterocarp dominance in Borneo by the Pliocene
type: item
type: AcademicArticle
description: The Malay Archipelago is one of the most biodiverse regions on Earth, but it suffers high extinction risks due to severe anthropogenic pressures. Paleobotanical knowledge provides baselines for the conservation of living analogs and improved understanding of vegetation, biogeography, and paleoenvironments through time. The Malesian bioregion is well studied palynologically, but there have been very few investigations of Cenozoic paleobotany (plant macrofossils) in a century or more. We report the first paleobotanical survey of Brunei Darussalam, a sultanate on the north coast of Borneo that still preserves the majority of its extraordinarily diverse, old-growth tropical rainforests. We discovered abundant compression floras dominated by angiosperm leaves at two sites of probable Pliocene age: Berakas Beach, in the Liang Formation, and Kampong Lugu, in an undescribed stratigraphic unit. Both sites also yielded rich palynofloral assemblages from the macrofossil-bearing beds, indicating lowland fern-dominated swamp (Berakas Beach) and mangrove swamp (Kampong Lugu) depositional environments. Fern spores from at least nine families dominate both palynological assemblages, along with abundant fungal and freshwater algal remains, rare marine microplankton, at least four mangrove genera, and a diverse rainforest tree and liana contribution (at least 19 families) with scarce pollen of Dipterocarpaceae, today’s dominant regional life form. Compressed leaves and rare reproductive material represent influx to the depocenters from the adjacent coastal rainforests. Although only about 40% of specimens preserve informative details, we can distinguish 23 leaf and two reproductive morphotypes among the two sites. Dipterocarps are by far the most abundant group in both compression assemblages, providing rare, localized evidence for dipterocarp-dominated lowland rainforests in the Malay Archipelago before the Pleistocene. The dipterocarp fossils include winged Shorea fruits, at least …
format: application/pdf
format: text/html
creator: Peter Wilf
creator: Xiaoyu Zou
creator: Michael P. Donovan
creator: László Kocsis
creator: Antonino Briguglio
creator: David Shaw
creator: JW Ferry Slik
creator: Joseph J. Lambiase
subject: Biodiversity
subject: Ecosystem Science
subject: Evolutionary Studies
subject: Paleontology
subject: Plant Science
description: doi:10.7717/peerj.12949
publisher: PeerJ Inc.
rights: © 2022 Wilf et al.
abstract: The Malay Archipelago is one of the most biodiverse regions on Earth, but it suffers high extinction risks due to severe anthropogenic pressures. Paleobotanical knowledge provides baselines for the conservation of living analogs and improved understanding of vegetation, biogeography, and paleoenvironments through time. The Malesian bioregion is well studied palynologically, but there have been very few investigations of Cenozoic paleobotany (plant macrofossils) in a century or more. We report the first paleobotanical survey of Brunei Darussalam, a sultanate on the north coast of Borneo that still preserves the majority of its extraordinarily diverse, old-growth tropical rainforests. We discovered abundant compression floras dominated by angiosperm leaves at two sites of probable Pliocene age: Berakas Beach, in the Liang Formation, and Kampong Lugu, in an undescribed stratigraphic unit. Both sites also yielded rich palynofloral assemblages from the macrofossil-bearing beds, indicating lowland fern-dominated swamp (Berakas Beach) and mangrove swamp (Kampong Lugu) depositional environments. Fern spores from at least nine families dominate both palynological assemblages, along with abundant fungal and freshwater algal remains, rare marine microplankton, at least four mangrove genera, and a diverse rainforest tree and liana contribution (at least 19 families) with scarce pollen of Dipterocarpaceae, today’s dominant regional life form. Compressed leaves and rare reproductive material represent influx to the depocenters from the adjacent coastal rainforests. Although only about 40% of specimens preserve informative details, we can distinguish 23 leaf and two reproductive morphotypes among the two sites. Dipterocarps are by far the most abundant group in both compression assemblages, providing rare, localized evidence for dipterocarp-dominated lowland rainforests in the Malay Archipelago before the Pleistocene. The dipterocarp fossils include winged Shorea fruits, at least …
bibliographic citation: Wilf et al. (2022) First fossil-leaf floras from Brunei Darussalam show dipterocarp dominance in Borneo by the Pliocene. PeerJ 10:e12949 https://doi.org/10.7717/peerj.12949
date submitted: 2021-10-17
date accepted: 2022-01-26
issued: 2022-03-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilf
  given name: Peter
author list: Agent
  family name: Zou
  given name: Xiaoyu
author list: Agent
  family name: Donovan
  given name: Michael P.
author list: Agent
  family name: Kocsis
  given name: László
author list: Agent
  family name: Briguglio
  given name: Antonino
author list: Agent
  family name: Shaw
  given name: David
author list: Agent
  family name: Slik
  given name: JW Ferry
author list: Agent
  family name: Lambiase
  given name: Joseph J.
doi: 10.7717/peerj.12949
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-24
copyright: © 2022 Wilf et al.
attribution name: Wilf et al.

Genome-wide characterization and expression of the TLP gene family associated with Colletotrichum gloeosporioides inoculation in Fragaria × ananassa
type: item
type: AcademicArticle
description: Background Colletotrichum gloeosporioides, a soil-borne fungal pathogen, causes significant yield losses in many plants, including cultivated strawberry (Fragaria × ananassa, 2n = 8x = 56). Thaumatin-like proteins (TLPs) are a large and complex family of proteins that play a vital role in plant host defense and other physiological processes. Methods To enhance our understanding of the antifungal activity of F. × ananassa TLPs (FaTLP), we investigated the genome-wide identification of FaTLP gene families and their expression patterns in F. × ananassa plants upon pathogen infection. Moreover, we used RNA sequencing (RNA-seq) to detect the differences in the expression patterns of TLP genes between different resistant strawberry cultivars in response to C. gloeosporioides infection. Results In total, 76 TLP genes were identified from the octoploid cultivated strawberry genome with a mean length of 1,439 bp. They were distributed on 24 F. × ananassa chromosomes. The FaTLP family was then divided into ten groups (Group I–X) according to the comparative phylogenetic results. Group VIII contained the highest number of TLP family genes. qRT-PCR analysis results indicated that FaTLP40, FaTLP41, FaTLP43, FaTLP68, and FaTLP75 were upregulated following C. gloeosporioides infection in the resistant octoploid strawberry. Conclusions The data showed some differences in TLP gene expression patterns across different resistant strawberry cultivars, as well as faster TLP defense responses to pathogenic fungi in resistant cultivars. This study will aid in the characterization of TLP gene family members found in octoploid strawberries and their potential biological functions in plants’ defenses against pathogenic fungi.
format: application/pdf
format: text/html
creator: Yuchao Zhang
creator: Lixiang Miao
creator: Xiaofang Yang
creator: Guihua Jiang
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12979
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Colletotrichum gloeosporioides, a soil-borne fungal pathogen, causes significant yield losses in many plants, including cultivated strawberry (Fragaria × ananassa, 2n = 8x = 56). Thaumatin-like proteins (TLPs) are a large and complex family of proteins that play a vital role in plant host defense and other physiological processes. Methods To enhance our understanding of the antifungal activity of F. × ananassa TLPs (FaTLP), we investigated the genome-wide identification of FaTLP gene families and their expression patterns in F. × ananassa plants upon pathogen infection. Moreover, we used RNA sequencing (RNA-seq) to detect the differences in the expression patterns of TLP genes between different resistant strawberry cultivars in response to C. gloeosporioides infection. Results In total, 76 TLP genes were identified from the octoploid cultivated strawberry genome with a mean length of 1,439 bp. They were distributed on 24 F. × ananassa chromosomes. The FaTLP family was then divided into ten groups (Group I–X) according to the comparative phylogenetic results. Group VIII contained the highest number of TLP family genes. qRT-PCR analysis results indicated that FaTLP40, FaTLP41, FaTLP43, FaTLP68, and FaTLP75 were upregulated following C. gloeosporioides infection in the resistant octoploid strawberry. Conclusions The data showed some differences in TLP gene expression patterns across different resistant strawberry cultivars, as well as faster TLP defense responses to pathogenic fungi in resistant cultivars. This study will aid in the characterization of TLP gene family members found in octoploid strawberries and their potential biological functions in plants’ defenses against pathogenic fungi.
bibliographic citation: Zhang et al. (2022) Genome-wide characterization and expression of the TLP gene family associated with Colletotrichum gloeosporioides inoculation in Fragaria × ananassa. PeerJ 10:e12979 https://doi.org/10.7717/peerj.12979
date submitted: 2021-09-01
date accepted: 2022-01-31
issued: 2022-03-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yuchao
author list: Agent
  family name: Miao
  given name: Lixiang
author list: Agent
  family name: Yang
  given name: Xiaofang
author list: Agent
  family name: Jiang
  given name: Guihua
doi: 10.7717/peerj.12979
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-24
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

A prognostic risk model based on DNA methylation levels of genes and lncRNAs in lung squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Recurrence is a risk factor for the prognosis of lung squamous carcinoma (LUSC). DNA methylation levels of RNAs are also associated with LUSC prognosis. This study aimed to construct a prognostic model with high performance in predicting LUSC prognosis using the methylation levels of lncRNAs and genes. Methods The differentially expressed RNAs (DERs) and differentially methylated RNAs (DMRs) between the recurrent and non-recurrent LUSC tissues in The Cancer Genome Atlas (TCGA; training dataset) were identified. Weighted correlation network analysis was performed to identify co-methylation networks. Differentially methylated genes and lncRNAs with opposite expression-methylation levels were used for the screening of prognosis-associated RNAs. The prognostic model was constructed and its performance was validated in the GSE39279 dataset. Results A total of 664 DERs and 981 DMRs (including 972 genes) in recurrent LUSC tissues were identified. Three co-methylation modules, including 226 differentially methylated genes, were significantly associated with LUSC. Among prognosis-associated RNAs, 18 DERs/DMRs with opposite methylation-expression levels were included in the methylation prognostic risk model. LUSC patients with high risk scores had a poor prognosis compared with patients who had low risk scores (TCGA: HR = 3.856, 95% CI [2.297–6.471]; GSE39279: HR = 3.040, 95% CI [1.435–6.437]). This model had a high accuracy in predicting the prognosis (AUC = 0.903 and 0.800, respectively), equivalent to the nomogram model inclusive of clinical variables. Conclusions Referring to the methylation levels of the 16-RNAs might help to predict the survival outcomes in LUSC.
format: application/pdf
format: text/html
creator: Weiqing Wang
creator: Ming Xiang
creator: Hui Liu
creator: Xiao Chu
creator: Zhaoyun Sun
creator: Liang Feng
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.13057
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Recurrence is a risk factor for the prognosis of lung squamous carcinoma (LUSC). DNA methylation levels of RNAs are also associated with LUSC prognosis. This study aimed to construct a prognostic model with high performance in predicting LUSC prognosis using the methylation levels of lncRNAs and genes. Methods The differentially expressed RNAs (DERs) and differentially methylated RNAs (DMRs) between the recurrent and non-recurrent LUSC tissues in The Cancer Genome Atlas (TCGA; training dataset) were identified. Weighted correlation network analysis was performed to identify co-methylation networks. Differentially methylated genes and lncRNAs with opposite expression-methylation levels were used for the screening of prognosis-associated RNAs. The prognostic model was constructed and its performance was validated in the GSE39279 dataset. Results A total of 664 DERs and 981 DMRs (including 972 genes) in recurrent LUSC tissues were identified. Three co-methylation modules, including 226 differentially methylated genes, were significantly associated with LUSC. Among prognosis-associated RNAs, 18 DERs/DMRs with opposite methylation-expression levels were included in the methylation prognostic risk model. LUSC patients with high risk scores had a poor prognosis compared with patients who had low risk scores (TCGA: HR = 3.856, 95% CI [2.297–6.471]; GSE39279: HR = 3.040, 95% CI [1.435–6.437]). This model had a high accuracy in predicting the prognosis (AUC = 0.903 and 0.800, respectively), equivalent to the nomogram model inclusive of clinical variables. Conclusions Referring to the methylation levels of the 16-RNAs might help to predict the survival outcomes in LUSC.
bibliographic citation: Wang et al. (2022) A prognostic risk model based on DNA methylation levels of genes and lncRNAs in lung squamous cell carcinoma. PeerJ 10:e13057 https://doi.org/10.7717/peerj.13057
date submitted: 2021-03-31
date accepted: 2022-02-13
issued: 2022-03-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Weiqing
author list: Agent
  family name: Xiang
  given name: Ming
author list: Agent
  family name: Liu
  given name: Hui
author list: Agent
  family name: Chu
  given name: Xiao
author list: Agent
  family name: Sun
  given name: Zhaoyun
author list: Agent
  family name: Feng
  given name: Liang
doi: 10.7717/peerj.13057
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-24
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Development of a Japanese version of the Psychological Ownership Scale
type: item
type: AcademicArticle
description: The present study addresses the need for a valid instrument for measuring dimensions of psychological ownership, including that of owned and non-owned objects, for use in the language and culture of Japan. Although the theory of psychological ownership has expanded self-extension theory, the most widely used scale of psychological ownership does not measure the extent to which one feels that it (the owned object) is a part of them. Thus, the present study aimed to develop a Japanese version of the Psychological Ownership Scale (POS-J) and examine its reliability and validity. Study 1 measured the POS-J of an owned object, finding the POS-J to have a two-factor structure (possession-self link and feeling of ownership) and its internal consistency and reliability to be adequate. Moreover, POS-J scores were positively correlated with perceived control and self-extension tendency, but not monetary value, indicating that conceptual validity was generally supported. To confirm whether the POS-J could be used for a non-owned object, Study 2 rephrased the expressions of item descriptions and examined the effect of imagining touching a non-owned object on the POS-J scores, showing that doing so increased the POS-J scores for the object. Our findings suggest that the POS-J is a reliable and valid measure of the psychological ownership of owned and non-owned objects for use in Japan.
format: application/pdf
format: text/html
creator: Sayo Iseki
creator: Kyoshiro Sasaki
creator: Shinji Kitagami
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.13063
publisher: PeerJ Inc.
rights: © 2022 Iseki et al.
abstract: The present study addresses the need for a valid instrument for measuring dimensions of psychological ownership, including that of owned and non-owned objects, for use in the language and culture of Japan. Although the theory of psychological ownership has expanded self-extension theory, the most widely used scale of psychological ownership does not measure the extent to which one feels that it (the owned object) is a part of them. Thus, the present study aimed to develop a Japanese version of the Psychological Ownership Scale (POS-J) and examine its reliability and validity. Study 1 measured the POS-J of an owned object, finding the POS-J to have a two-factor structure (possession-self link and feeling of ownership) and its internal consistency and reliability to be adequate. Moreover, POS-J scores were positively correlated with perceived control and self-extension tendency, but not monetary value, indicating that conceptual validity was generally supported. To confirm whether the POS-J could be used for a non-owned object, Study 2 rephrased the expressions of item descriptions and examined the effect of imagining touching a non-owned object on the POS-J scores, showing that doing so increased the POS-J scores for the object. Our findings suggest that the POS-J is a reliable and valid measure of the psychological ownership of owned and non-owned objects for use in Japan.
bibliographic citation: Iseki et al. (2022) Development of a Japanese version of the Psychological Ownership Scale. PeerJ 10:e13063 https://doi.org/10.7717/peerj.13063
date submitted: 2021-09-21
date accepted: 2022-02-14
issued: 2022-03-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Iseki
  given name: Sayo
author list: Agent
  family name: Sasaki
  given name: Kyoshiro
author list: Agent
  family name: Kitagami
  given name: Shinji
doi: 10.7717/peerj.13063
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-03-24
copyright: © 2022 Iseki et al.
attribution name: Iseki et al.

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