PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Miocene Cupressinoxylon from Gökçeada (Imbros), Turkey with Protophytobia cambium mining and the study of ecological signals of wood anatomy
items: A manikin or human simulator—development of a tool for measuring students’ perception
items: Habitat loss estimation for assessing terrestrial mammalian species extinction risk: an open data framework
items: Wildlife overpass structure size, distribution, effectiveness, and adherence to expert design recommendations
items: Composition of terrestrial mammal assemblages and their habitat use in unflooded and flooded blackwater forests in the Central Amazon
items: Tree variability limits the detection of nutrient treatment effects on sap flux density in a northern hardwood forest
items: Identification of nutritional components in unripe and ripe Docynia delavayi (Franch.) Schneid fruit by widely targeted metabolomics
items: Quantifying the impacts of symbiotic interactions between two invasive species: the tawny crazy ant (Nylanderia fulva) tending the sorghum aphid (Melanaphis sorghi)
items: Widely targeted metabolite profiling of mango stem apex during floral induction by compond of mepiquat chloride, prohexadione-calcium and uniconazole
items: An artificial neural network classification method employing longitudinally monitored immune biomarkers to predict the clinical outcome of critically ill COVID-19 patients

Miocene Cupressinoxylon from Gökçeada (Imbros), Turkey with Protophytobia cambium mining and the study of ecological signals of wood anatomy
type: item
type: AcademicArticle
description: Premise The recognition of the Miocene Climate Optimum (MCO) in terrestrial palaeoenvironments of the Eastern Mediterranean is restricted to Lesbos and Lemnos Islands, Greece. This area is significant for its wood microfossils. A recently-discovered fossil wood assemblage from Gökçeada (Imbros) Island, Turkey, including tree species similar to the Greek findings, is thought to have an early Miocene age. Here, we revise the age of the latter plant fossiliferous locality, re-evaluate the area for the study of MCO for the terrestrial palaeoecosystems of the Eastern Mediterranean and the nomenclature errors referring to the occurrence of fossil wood. We present the plant–insect–environment interactions using detailed anatomical descriptions, of an extinct conifer and its extinct cambium miner feeding traces observed in its secondary xylem. Methods Three thin sections were prepared with standard palaeoxylotomical techniques from a small section of the silicified wood; the sections were observed under a light microscope. The anatomy of the conifer and its damage patterns were compared with those of extant and fossil Cupressaceae and Agromyzidae, respectively. Pivotal results The common anatomical features of the studied wood specimen and Hesperocyparis macrocarpa (Hartw.) Bartel and a shared characteristic (the number of the cross-field pits – a feature we consider of diagnostic value) with Xanthocyparis vietnamensis Farjon & T.H. Nguyên led to its assignment to the Hesperocyparis–Xanthocyparis–Callitropsis clade. The detailed study of the wound scars and anatomical abnormalities, the anatomical–environmental associations, and structural–functional reactions follow the identification of the wood’s anatomy sensu Carlquist providing decisive results. Conclusions Based on the distinctive characteristics presented, we identify our macrofossil as Cupressinoxylon matromnense Grambast, a stem or an extinct lineage of the Hesperocyparis–Xanthocyparis vietnamensis–Callitropsis noo…
format: application/pdf
format: text/html
creator: Dimitra Mantzouka
creator: Ünal Akkemik
creator: Yıldırım Güngör
subject: Ecology
subject: Evolutionary Studies
subject: Paleontology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.14212
publisher: PeerJ Inc.
rights: © 2022 Mantzouka et al.
abstract: Premise The recognition of the Miocene Climate Optimum (MCO) in terrestrial palaeoenvironments of the Eastern Mediterranean is restricted to Lesbos and Lemnos Islands, Greece. This area is significant for its wood microfossils. A recently-discovered fossil wood assemblage from Gökçeada (Imbros) Island, Turkey, including tree species similar to the Greek findings, is thought to have an early Miocene age. Here, we revise the age of the latter plant fossiliferous locality, re-evaluate the area for the study of MCO for the terrestrial palaeoecosystems of the Eastern Mediterranean and the nomenclature errors referring to the occurrence of fossil wood. We present the plant–insect–environment interactions using detailed anatomical descriptions, of an extinct conifer and its extinct cambium miner feeding traces observed in its secondary xylem. Methods Three thin sections were prepared with standard palaeoxylotomical techniques from a small section of the silicified wood; the sections were observed under a light microscope. The anatomy of the conifer and its damage patterns were compared with those of extant and fossil Cupressaceae and Agromyzidae, respectively. Pivotal results The common anatomical features of the studied wood specimen and Hesperocyparis macrocarpa (Hartw.) Bartel and a shared characteristic (the number of the cross-field pits – a feature we consider of diagnostic value) with Xanthocyparis vietnamensis Farjon & T.H. Nguyên led to its assignment to the Hesperocyparis–Xanthocyparis–Callitropsis clade. The detailed study of the wound scars and anatomical abnormalities, the anatomical–environmental associations, and structural–functional reactions follow the identification of the wood’s anatomy sensu Carlquist providing decisive results. Conclusions Based on the distinctive characteristics presented, we identify our macrofossil as Cupressinoxylon matromnense Grambast, a stem or an extinct lineage of the Hesperocyparis–Xanthocyparis vietnamensis–Callitropsis noo…
bibliographic citation: Mantzouka et al. (2022) Miocene Cupressinoxylon from Gökçeada (Imbros), Turkey with Protophytobia cambium mining and the study of ecological signals of wood anatomy. PeerJ 10:e14212 https://doi.org/10.7717/peerj.14212
date submitted: 2021-08-26
date accepted: 2022-09-19
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mantzouka
  given name: Dimitra
author list: Agent
  family name: Akkemik
  given name: Ünal
author list: Agent
  family name: Güngör
  given name: Yıldırım
doi: 10.7717/peerj.14212
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: © 2022 Mantzouka et al.
attribution name: Mantzouka et al.

A manikin or human simulator—development of a tool for measuring students’ perception
type: item
type: AcademicArticle
description: Background Education with the use of medical simulation may involve the use of two modalities: manikins or standardized patients (SPs) to meet specific learning objectives. We have collected students’ opinions about the two modalities which can be helpful in planning and evaluating the curriculum process. Although reviews or comparisons of student opinions appear in the literature, it is difficult to find a scale that would be based on a comparison of specific effects that can be obtained in the educational process. In order to fill this gap, an attempt was made to construct a questionnaire. Methods An experimental version of a questionnaire measuring the final-year students’ (273) opinions about the effectiveness of both simulation techniques has been designed on the basis of semi-structured interviews. They were conducted with 14 final-year students excluded from the subsequently analyzed cohort. The scale has been completed, tested and validated. Results The authors developed a 33-statement questionnaire which contain two scales: teaching medicine with the manikins and with the SPs. Two factors were identified for each scale: Doctor-patient relationship and practical aspects. The scales can be used complementary or separately, as the article reports independent statistics for each scale. The Cronbach’s alpha coefficient for the manikin scale is 0.721 and for the SP scale is 0.758. Conclusions The questionnaire may be applied to medical students to identify their opinions about using manikins and SPs in teaching. It may have an important impact for planning curriculum and implementing particular modalities in accordance with the intended learning objectives.
format: application/pdf
format: text/html
creator: Kamil Torres
creator: Phillip Evans
creator: Izabela Mamcarz
creator: Natalia Radczuk
creator: Anna Torres
subject: Science and Medical Education
subject: Human-Computer Interaction
description: doi:10.7717/peerj.14214
publisher: PeerJ Inc.
rights: © 2022 Torres et al.
abstract: Background Education with the use of medical simulation may involve the use of two modalities: manikins or standardized patients (SPs) to meet specific learning objectives. We have collected students’ opinions about the two modalities which can be helpful in planning and evaluating the curriculum process. Although reviews or comparisons of student opinions appear in the literature, it is difficult to find a scale that would be based on a comparison of specific effects that can be obtained in the educational process. In order to fill this gap, an attempt was made to construct a questionnaire. Methods An experimental version of a questionnaire measuring the final-year students’ (273) opinions about the effectiveness of both simulation techniques has been designed on the basis of semi-structured interviews. They were conducted with 14 final-year students excluded from the subsequently analyzed cohort. The scale has been completed, tested and validated. Results The authors developed a 33-statement questionnaire which contain two scales: teaching medicine with the manikins and with the SPs. Two factors were identified for each scale: Doctor-patient relationship and practical aspects. The scales can be used complementary or separately, as the article reports independent statistics for each scale. The Cronbach’s alpha coefficient for the manikin scale is 0.721 and for the SP scale is 0.758. Conclusions The questionnaire may be applied to medical students to identify their opinions about using manikins and SPs in teaching. It may have an important impact for planning curriculum and implementing particular modalities in accordance with the intended learning objectives.
bibliographic citation: Torres et al. (2022) A manikin or human simulator—development of a tool for measuring students’ perception. PeerJ 10:e14214 https://doi.org/10.7717/peerj.14214
date submitted: 2020-12-28
date accepted: 2022-09-19
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Torres
  given name: Kamil
author list: Agent
  family name: Evans
  given name: Phillip
author list: Agent
  family name: Mamcarz
  given name: Izabela
author list: Agent
  family name: Radczuk
  given name: Natalia
author list: Agent
  family name: Torres
  given name: Anna
doi: 10.7717/peerj.14214
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: ©2022 Torres et al.
attribution name: Torres et al.

Habitat loss estimation for assessing terrestrial mammalian species extinction risk: an open data framework
type: item
type: AcademicArticle
description: Terrestrial mammals face a severe crisis of habitat loss worldwide. Therefore, assessing information on habitat loss throughout different time periods is crucial for assessing species’ conservation statuses based on the IUCN Red List system. To support the national extinction risk assessment in Brazil (2016–2022), we developed a script that uses the MapBiomas Project 6.0 data source of land cover and land use (annual maps at 30 m scale) within the Google Earth Engine (GEE) platform to calculate habitat loss. We defined suitable habitats from the MapBiomas Project land cover classification for 190 mammalian taxa, according to each species range map and ecological characteristics. We considered a period of three generation lengths to assess habitat loss in accordance with the Red List assessment criteria. We used the script to estimate changes in available habitat throughout the analyzed period within the species’ known ranges. The results indicated that habitat loss occurred within 94.3% of the analyzed taxa range, with the Carnivora order suffering the greatest habitat loss, followed by the Cingulata order. These analyses may be decisive for applying criteria, defining categories during the assessment of at least 17 species (9%), enriching discussions, and raising new questions for several other species. We considered the outcome of estimating habitat loss for various taxa when applying criterion A, which refers to population reduction, thus supporting more accurate inferences about past population declines.
format: application/pdf
format: text/html
creator: Mariella Butti
creator: Luciana Pacca
creator: Paloma Santos
creator: André C. Alonso
creator: Gerson Buss
creator: Gabriela Ludwig
creator: Leandro Jerusalinsky
creator: Amely B. Martins
subject: Biodiversity
subject: Conservation Biology
subject: Computational Science
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.14289
publisher: PeerJ Inc.
rights: © 2022 Butti et al.
abstract: Terrestrial mammals face a severe crisis of habitat loss worldwide. Therefore, assessing information on habitat loss throughout different time periods is crucial for assessing species’ conservation statuses based on the IUCN Red List system. To support the national extinction risk assessment in Brazil (2016–2022), we developed a script that uses the MapBiomas Project 6.0 data source of land cover and land use (annual maps at 30 m scale) within the Google Earth Engine (GEE) platform to calculate habitat loss. We defined suitable habitats from the MapBiomas Project land cover classification for 190 mammalian taxa, according to each species range map and ecological characteristics. We considered a period of three generation lengths to assess habitat loss in accordance with the Red List assessment criteria. We used the script to estimate changes in available habitat throughout the analyzed period within the species’ known ranges. The results indicated that habitat loss occurred within 94.3% of the analyzed taxa range, with the Carnivora order suffering the greatest habitat loss, followed by the Cingulata order. These analyses may be decisive for applying criteria, defining categories during the assessment of at least 17 species (9%), enriching discussions, and raising new questions for several other species. We considered the outcome of estimating habitat loss for various taxa when applying criterion A, which refers to population reduction, thus supporting more accurate inferences about past population declines.
bibliographic citation: Butti et al. (2022) Habitat loss estimation for assessing terrestrial mammalian species extinction risk: an open data framework. PeerJ 10:e14289 https://doi.org/10.7717/peerj.14289
date submitted: 2022-07-14
date accepted: 2022-10-02
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Butti
  given name: Mariella
author list: Agent
  family name: Pacca
  given name: Luciana
author list: Agent
  family name: Santos
  given name: Paloma
author list: Agent
  family name: Alonso
  given name: André C.
author list: Agent
  family name: Buss
  given name: Gerson
author list: Agent
  family name: Ludwig
  given name: Gabriela
author list: Agent
  family name: Jerusalinsky
  given name: Leandro
author list: Agent
  family name: Martins
  given name: Amely B.
doi: 10.7717/peerj.14289
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: © 2022 Butti et al.
attribution name: Butti et al.

Wildlife overpass structure size, distribution, effectiveness, and adherence to expert design recommendations
type: item
type: AcademicArticle
description: It is now well evidenced that wildlife crossing structures paired with exclusion fencing reduce wildlife vehicles collisions while facilitating wildlife connectivity across roadways. Managing animal mortality and subpopulation connectivity is crucial to successful species and landscape stewardship. Highway mitigation projects are large economic investments that remain on the landscape for many decades. Governments and planning agents thus strive to balance cost and benefit to build cost-effective structures with the greatest positive impact on local wildlife and motorists. Ideal dimensions of overpasses and underpasses vary by species, but scientists generally suggest that overpasses for large mammals should be approximately 50 m wide. Optimal width also depends on structure length, with longer structures requiring additional width. Accordingly, experts have suggested a width to length ratio of 0.8. We sought to assess how these recommendations manifested in practice—where agencies use this information to design and build structures while also balancing cost and logistical challenges—and the degree to which built structures conform to current recommendations. We identified 120 wildlife overpasses across the world that were constructed to reduce the negative impacts of roads. Using a novel measurement technique, we analyzed the dimensions of these 120 overpasses located in North America, Europe, Asia, and Oceania. The average width of the wildlife overpasses was 34 m. Most wildlife overpasses located in North America and Europe did not meet their respective dimensional expert guidelines. We investigate reasons explaining the non-compliance and provide recommendations for future overpass designs. Building on previous evidence showing that wider overpasses have increased crossing rates, we examined crossing rates for multiple large mammal species across 12 overpasses located in western North America. We qualitatively observed that wider North American overpasses (40–60…
format: application/pdf
format: text/html
creator: Liam Brennan
creator: Emily Chow
creator: Clayton Lamb
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Biosphere Interactions
subject: Natural Resource Management
description: doi:10.7717/peerj.14371
publisher: PeerJ Inc.
rights: © 2022 Brennan et al.
abstract: It is now well evidenced that wildlife crossing structures paired with exclusion fencing reduce wildlife vehicles collisions while facilitating wildlife connectivity across roadways. Managing animal mortality and subpopulation connectivity is crucial to successful species and landscape stewardship. Highway mitigation projects are large economic investments that remain on the landscape for many decades. Governments and planning agents thus strive to balance cost and benefit to build cost-effective structures with the greatest positive impact on local wildlife and motorists. Ideal dimensions of overpasses and underpasses vary by species, but scientists generally suggest that overpasses for large mammals should be approximately 50 m wide. Optimal width also depends on structure length, with longer structures requiring additional width. Accordingly, experts have suggested a width to length ratio of 0.8. We sought to assess how these recommendations manifested in practice—where agencies use this information to design and build structures while also balancing cost and logistical challenges—and the degree to which built structures conform to current recommendations. We identified 120 wildlife overpasses across the world that were constructed to reduce the negative impacts of roads. Using a novel measurement technique, we analyzed the dimensions of these 120 overpasses located in North America, Europe, Asia, and Oceania. The average width of the wildlife overpasses was 34 m. Most wildlife overpasses located in North America and Europe did not meet their respective dimensional expert guidelines. We investigate reasons explaining the non-compliance and provide recommendations for future overpass designs. Building on previous evidence showing that wider overpasses have increased crossing rates, we examined crossing rates for multiple large mammal species across 12 overpasses located in western North America. We qualitatively observed that wider North American overpasses (40–60…
bibliographic citation: Brennan et al. (2022) Wildlife overpass structure size, distribution, effectiveness, and adherence to expert design recommendations. PeerJ 10:e14371 https://doi.org/10.7717/peerj.14371
date submitted: 2022-07-13
date accepted: 2022-10-19
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brennan
  given name: Liam
author list: Agent
  family name: Chow
  given name: Emily
author list: Agent
  family name: Lamb
  given name: Clayton
doi: 10.7717/peerj.14371
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: © 2022 Brennan et al.
attribution name: Brennan et al.

Composition of terrestrial mammal assemblages and their habitat use in unflooded and flooded blackwater forests in the Central Amazon
type: item
type: AcademicArticle
description: Several forest types compose the apparently homogenous forest landscape of the lowland Amazon. The seasonally flooded forests (igapós) of the narrow floodplains of the blackwater rivers of the Amazon basin support their community of animals; however, these animals are required to adapt to survive in this environment. Furthermore, several taxa are an important source of seasonal resources for the animals in the adjacent unflooded forest (terra firme). During the low-water phase, the igapó becomes available to terrestrial species that make use of terra firme and igapó forests. Nonetheless, these lateral movements of terrestrial mammals between hydrologically distinct forest types remain poorly understood. This study tested the hypothesis that the attributes of the assemblages (abundance, richness, evenness, and functional groups) of the terrestrial mammals in both these forest types of the Cuieiras River basin, which is located in the Central Amazon, are distinct and arise from the ecological heterogeneity induced by seasonal floods. After a sampling effort of 10,743 camera trap days over four campaigns, two for the terra firme (6,013 trap days) and two for the igapó forests (4,730 trap days), a total of 31 mammal species (five were considered eventual) were recorded in both forest types. The species richness was similar in the igapó and terra firme forests, and the species abundance and biomass were greater in the terra firme forest, which were probably due to its higher primary productivity; whereas the evenness was increased in the igapós when compared to the terra firme forest. Although both forest types shared 84% of the species, generally a marked difference was observed in the composition of the terrestrial mammal species. These differences were associated with abundances of some specific functional groups, i.e., frugivores/granivores. Within-group variation was explained by balanced variation in abundance and turnover, which the individuals of a given species …
format: application/pdf
format: text/html
creator: André L. S. Gonçalves
creator: Tadeu G. de Oliveira
creator: Alexander R. Arévalo-Sandi
creator: Lucian V. Canto
creator: Tsuneaki Yabe
creator: Wilson R. Spironello
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.14374
publisher: PeerJ Inc.
rights: © 2022 Gonçalves et al.
abstract: Several forest types compose the apparently homogenous forest landscape of the lowland Amazon. The seasonally flooded forests (igapós) of the narrow floodplains of the blackwater rivers of the Amazon basin support their community of animals; however, these animals are required to adapt to survive in this environment. Furthermore, several taxa are an important source of seasonal resources for the animals in the adjacent unflooded forest (terra firme). During the low-water phase, the igapó becomes available to terrestrial species that make use of terra firme and igapó forests. Nonetheless, these lateral movements of terrestrial mammals between hydrologically distinct forest types remain poorly understood. This study tested the hypothesis that the attributes of the assemblages (abundance, richness, evenness, and functional groups) of the terrestrial mammals in both these forest types of the Cuieiras River basin, which is located in the Central Amazon, are distinct and arise from the ecological heterogeneity induced by seasonal floods. After a sampling effort of 10,743 camera trap days over four campaigns, two for the terra firme (6,013 trap days) and two for the igapó forests (4,730 trap days), a total of 31 mammal species (five were considered eventual) were recorded in both forest types. The species richness was similar in the igapó and terra firme forests, and the species abundance and biomass were greater in the terra firme forest, which were probably due to its higher primary productivity; whereas the evenness was increased in the igapós when compared to the terra firme forest. Although both forest types shared 84% of the species, generally a marked difference was observed in the composition of the terrestrial mammal species. These differences were associated with abundances of some specific functional groups, i.e., frugivores/granivores. Within-group variation was explained by balanced variation in abundance and turnover, which the individuals of a given species …
bibliographic citation: Gonçalves et al. (2022) Composition of terrestrial mammal assemblages and their habitat use in unflooded and flooded blackwater forests in the Central Amazon. PeerJ 10:e14374 https://doi.org/10.7717/peerj.14374
date submitted: 2022-07-14
date accepted: 2022-10-19
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gonçalves
  given name: André L. S.
author list: Agent
  family name: de Oliveira
  given name: Tadeu G.
author list: Agent
  family name: Arévalo-Sandi
  given name: Alexander R.
author list: Agent
  family name: Canto
  given name: Lucian V.
author list: Agent
  family name: Yabe
  given name: Tsuneaki
author list: Agent
  family name: Spironello
  given name: Wilson R.
doi: 10.7717/peerj.14374
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: © 2022 Gonçalves et al.
attribution name: Gonçalves et al.

Tree variability limits the detection of nutrient treatment effects on sap flux density in a northern hardwood forest
type: item
type: AcademicArticle
description: The influence of nutrient availability on transpiration is not well understood, in spite of the importance of transpiration to forest water budgets. Soil nutrients have the potential to affect tree water use through indirect effects on leaf area or stomatal conductance. For example, following addition of calcium silicate to a watershed at Hubbard Brook, in New Hampshire, streamflow was reduced for 3 years, which was attributed to a 25% increase in evapotranspiration associated with increased foliar production. The first objective of this study was to quantify the effect of nutrient availability on sap flux density in a nitrogen, phosphorus, and calcium addition experiment in New Hampshire in which tree diameter growth, foliar chemistry, and soil nutrient availability had responded to treatments. We measured sap flux density in American beech (Fagus grandifolia, Ehr.), red maple (Acer rubrum L.), sugar maple (Acer saccharum Marsh.), white birch (Betula papyrifera Marsh.), or yellow birch (Betula alleghaniensis Britton.) trees, over five years of experiments in five stands distributed across three sites. In 2018, 3 years after a calcium silicate addition, sap flux density averaged 36% higher in trees in the treatment than the control plot, but this effect was not very significant (p = 0.07). Our second objective was to determine whether this failure to detect effects with greater statistical confidence was due to small effect sizes or high variability among trees. We found that tree-to-tree variability was high, with coefficients of variation averaging 39% within treatment plots. Depending on the species and year of the study, the minimum difference in sap flux density detectable with our observed variability ranged from 46% to 352%, for a simple ANOVA. We analyzed other studies reported in the literature that compared tree water use among species or treatments and found detectable differences ranging from 16% to 78%. Future sap flux density studies could benefit from…
format: application/pdf
format: text/html
creator: Alexandrea M. Rice
creator: Mariann T. Garrison-Johnston
creator: Arianna J. Libenson
creator: Ruth D. Yanai
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
subject: Forestry
description: doi:10.7717/peerj.14410
publisher: PeerJ Inc.
rights: © 2022 Rice et al.
abstract: The influence of nutrient availability on transpiration is not well understood, in spite of the importance of transpiration to forest water budgets. Soil nutrients have the potential to affect tree water use through indirect effects on leaf area or stomatal conductance. For example, following addition of calcium silicate to a watershed at Hubbard Brook, in New Hampshire, streamflow was reduced for 3 years, which was attributed to a 25% increase in evapotranspiration associated with increased foliar production. The first objective of this study was to quantify the effect of nutrient availability on sap flux density in a nitrogen, phosphorus, and calcium addition experiment in New Hampshire in which tree diameter growth, foliar chemistry, and soil nutrient availability had responded to treatments. We measured sap flux density in American beech (Fagus grandifolia, Ehr.), red maple (Acer rubrum L.), sugar maple (Acer saccharum Marsh.), white birch (Betula papyrifera Marsh.), or yellow birch (Betula alleghaniensis Britton.) trees, over five years of experiments in five stands distributed across three sites. In 2018, 3 years after a calcium silicate addition, sap flux density averaged 36% higher in trees in the treatment than the control plot, but this effect was not very significant (p = 0.07). Our second objective was to determine whether this failure to detect effects with greater statistical confidence was due to small effect sizes or high variability among trees. We found that tree-to-tree variability was high, with coefficients of variation averaging 39% within treatment plots. Depending on the species and year of the study, the minimum difference in sap flux density detectable with our observed variability ranged from 46% to 352%, for a simple ANOVA. We analyzed other studies reported in the literature that compared tree water use among species or treatments and found detectable differences ranging from 16% to 78%. Future sap flux density studies could benefit from…
bibliographic citation: Rice et al. (2022) Tree variability limits the detection of nutrient treatment effects on sap flux density in a northern hardwood forest. PeerJ 10:e14410 https://doi.org/10.7717/peerj.14410
date submitted: 2021-03-24
date accepted: 2022-10-27
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rice
  given name: Alexandrea M.
author list: Agent
  family name: Garrison-Johnston
  given name: Mariann T.
author list: Agent
  family name: Libenson
  given name: Arianna J.
author list: Agent
  family name: Yanai
  given name: Ruth D.
doi: 10.7717/peerj.14410
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: ©2022 Rice et al.
attribution name: Rice et al.

Identification of nutritional components in unripe and ripe Docynia delavayi (Franch.) Schneid fruit by widely targeted metabolomics
type: item
type: AcademicArticle
description: Docynia delavayi (Franch.) Schneid is an evergreen tree with multiple benefits and high development and utilization value. The fruit is consumed as fresh and dry fruit, juices, and other products. However, it is unknown the chemical changes that occur upon fruit maturation. The metabolite content of unripe and ripe fruit was examined using UPLC-MS/MS technology based on a broadly targeted metabolome. We identified 477 metabolites, of which 130 differed between ripe and unripe fruit. These compounds are primarily involved in the biosynthesis of secondary metabolites, such as pantothenic acid, flavonoids, and amino acids. Moreover, in ripe fruit, there are 94 metabolites that are upregulated, particularly flavonoids and terpenoids. In comparison, compounds associated with sour flavors (amino acids, phenolic acids, organic acids) are down-regulated. Remarkably, these metabolites have a strong relationship with the medicinal properties of D. delavayi. This study provides a global perspective of the D. delavayi fruit metabolome and a comprehensive analysis of metabolomic variations during fruit development, thereby increasing the knowledge of the metabolic basis of important fruit quality traits in D. delavayi fruit.
format: application/pdf
format: text/html
creator: Can Chen
creator: Xi Xia
creator: Dawei Wang
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.14441
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: Docynia delavayi (Franch.) Schneid is an evergreen tree with multiple benefits and high development and utilization value. The fruit is consumed as fresh and dry fruit, juices, and other products. However, it is unknown the chemical changes that occur upon fruit maturation. The metabolite content of unripe and ripe fruit was examined using UPLC-MS/MS technology based on a broadly targeted metabolome. We identified 477 metabolites, of which 130 differed between ripe and unripe fruit. These compounds are primarily involved in the biosynthesis of secondary metabolites, such as pantothenic acid, flavonoids, and amino acids. Moreover, in ripe fruit, there are 94 metabolites that are upregulated, particularly flavonoids and terpenoids. In comparison, compounds associated with sour flavors (amino acids, phenolic acids, organic acids) are down-regulated. Remarkably, these metabolites have a strong relationship with the medicinal properties of D. delavayi. This study provides a global perspective of the D. delavayi fruit metabolome and a comprehensive analysis of metabolomic variations during fruit development, thereby increasing the knowledge of the metabolic basis of important fruit quality traits in D. delavayi fruit.
bibliographic citation: Chen et al. (2022) Identification of nutritional components in unripe and ripe Docynia delavayi (Franch.) Schneid fruit by widely targeted metabolomics. PeerJ 10:e14441 https://doi.org/10.7717/peerj.14441
date submitted: 2022-02-21
date accepted: 2022-11-01
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Can
author list: Agent
  family name: Xia
  given name: Xi
author list: Agent
  family name: Wang
  given name: Dawei
doi: 10.7717/peerj.14441
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: ©2022 Chen et al.
attribution name: Chen et al.

Quantifying the impacts of symbiotic interactions between two invasive species: the tawny crazy ant (Nylanderia fulva) tending the sorghum aphid (Melanaphis sorghi)
type: item
type: AcademicArticle
description: The establishment of new symbiotic interactions between introduced species may facilitate invasion success. For instance, tawny crazy ant (Nylanderia fulva Mayr) is known to be an opportunistic tender of honeydew producing insects and this ants’ symbiotic interactions have exacerbated agricultural damage in some invaded regions of the world. The invasive sorghum aphid (Melanaphis sorghi Theobald) was first reported as a pest in the continental United States–in Texas and Louisiana–as recent as 2013, and tawny crazy ant (TCA) was reported in Texas in the early 2000s. Although these introductions are relatively recent, TCA workers tend sorghum aphids in field and greenhouse settings. This study quantified the tending duration of TCA workers to sorghum aphids and the impact of TCA tending on aphid biomass. For this study aphids were collected from three different host plant species (i.e., sugarcane, Johnson grass, and sorghum) and clone colonies were established. Sorghum is the main economic crop in which these aphids occur, hence we focused our study on the potential impacts of interactions on sorghum. Quantification of invasive ant-aphid interactions, on either stems or leaves of sorghum plants, were conducted in greenhouse conditions. Our results show that although these two invasive insect species do not have a long coevolutionary history, TCA developed a tending interaction with sorghum aphid, and aphids were observed excreting honeydew after being antennated by TCA workers. Interestingly, this relatively recent symbiotic interaction significantly increased overall aphid biomass for aphids that were positioned on stems and collected from Johnson grass. It is recommended to continue monitoring the interaction between TCA and sorghum aphid in field conditions due to its potential to increase aphid populations and sorghum plant damage.
format: application/pdf
format: text/html
creator: Jocelyn R. Holt
creator: Antonino Malacrinò
creator: Raul F. Medina
subject: Agricultural Science
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.14448
publisher: PeerJ Inc.
rights: © 2022 Holt et al.
abstract: The establishment of new symbiotic interactions between introduced species may facilitate invasion success. For instance, tawny crazy ant (Nylanderia fulva Mayr) is known to be an opportunistic tender of honeydew producing insects and this ants’ symbiotic interactions have exacerbated agricultural damage in some invaded regions of the world. The invasive sorghum aphid (Melanaphis sorghi Theobald) was first reported as a pest in the continental United States–in Texas and Louisiana–as recent as 2013, and tawny crazy ant (TCA) was reported in Texas in the early 2000s. Although these introductions are relatively recent, TCA workers tend sorghum aphids in field and greenhouse settings. This study quantified the tending duration of TCA workers to sorghum aphids and the impact of TCA tending on aphid biomass. For this study aphids were collected from three different host plant species (i.e., sugarcane, Johnson grass, and sorghum) and clone colonies were established. Sorghum is the main economic crop in which these aphids occur, hence we focused our study on the potential impacts of interactions on sorghum. Quantification of invasive ant-aphid interactions, on either stems or leaves of sorghum plants, were conducted in greenhouse conditions. Our results show that although these two invasive insect species do not have a long coevolutionary history, TCA developed a tending interaction with sorghum aphid, and aphids were observed excreting honeydew after being antennated by TCA workers. Interestingly, this relatively recent symbiotic interaction significantly increased overall aphid biomass for aphids that were positioned on stems and collected from Johnson grass. It is recommended to continue monitoring the interaction between TCA and sorghum aphid in field conditions due to its potential to increase aphid populations and sorghum plant damage.
bibliographic citation: Holt et al. (2022) Quantifying the impacts of symbiotic interactions between two invasive species: the tawny crazy ant (Nylanderia fulva) tending the sorghum aphid (Melanaphis sorghi). PeerJ 10:e14448 https://doi.org/10.7717/peerj.14448
date submitted: 2022-05-16
date accepted: 2022-11-01
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Holt
  given name: Jocelyn R.
author list: Agent
  family name: Malacrinò
  given name: Antonino
author list: Agent
  family name: Medina
  given name: Raul F.
doi: 10.7717/peerj.14448
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: ©2022 Holt et al.
attribution name: Holt et al.

Widely targeted metabolite profiling of mango stem apex during floral induction by compond of mepiquat chloride, prohexadione-calcium and uniconazole
type: item
type: AcademicArticle
description: Background Insufficient low temperatures in winter and soil residues caused by paclobutrazol (PBZ) application pose a considerable challenge for mango floral induction (FI). Gibberellin inhibitors SPD (compound of mepiquat chloride, prohexadione-calcium and uniconazole) had a significant influence on enhancing the flowering rate and yield of mango for two consecutive years (2020–2021). Researchers have indicated that FI is regulated at the metabolic level; however, little is known about the metabolic changes during FI in response to SPD treatment. Methods Here, ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS)-based widely targeted metabolomic analysis was carried out to assess the metabolic differences in the mango stem apex during different stage of mango FI (30, 80, 100 days after SPD/water treatment). Results A total of 582 compounds were annotated and 372 metabolites showed two-fold differences in abundance (variable importance in projection, VIP ≥ 1 and fold change, FC≥ 2 or≤ 0.5) between buds at 30, 80, 100 days after SPD/water treatment or between buds under different treatment. Lipids, phenolic acids, amino acids, carbohydrates, and vitamins were among metabolites showing significant differences over time after SPD treatment. Here, 18 out of 20 lipids, including the lysophosphatidylethanolamine (12, LPE), lysophosphatidylcholine (7, LPC), and free fatty acids (1, FA), were significantly upregulated from 80 to 100 days after SPD treatment comared to water treatment. Meanwhile, the dormancy release of mango buds from 80 to 100 days after SPD treatment was accompanied by the accumulation of proline, ascorbic acid, carbohydrates, and tannins. In addition, metabolites, such as L-homocysteine, L-histidine, and L-homomethionine, showed more than a ten-fold difference in relative abundance from 30 to 100 days after SPD treatment, however, there were no significant changes after water treatment. The present stu…
format: application/pdf
format: text/html
creator: Fei Liang
creator: Wentian Xu
creator: Hongxia Wu
creator: Bin Zheng
creator: Qingzhi Liang
creator: Yingzhi Li
creator: Songbiao Wang
subject: Agricultural Science
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.14458
publisher: PeerJ Inc.
rights: © 2022 Liang et al.
abstract: Background Insufficient low temperatures in winter and soil residues caused by paclobutrazol (PBZ) application pose a considerable challenge for mango floral induction (FI). Gibberellin inhibitors SPD (compound of mepiquat chloride, prohexadione-calcium and uniconazole) had a significant influence on enhancing the flowering rate and yield of mango for two consecutive years (2020–2021). Researchers have indicated that FI is regulated at the metabolic level; however, little is known about the metabolic changes during FI in response to SPD treatment. Methods Here, ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS)-based widely targeted metabolomic analysis was carried out to assess the metabolic differences in the mango stem apex during different stage of mango FI (30, 80, 100 days after SPD/water treatment). Results A total of 582 compounds were annotated and 372 metabolites showed two-fold differences in abundance (variable importance in projection, VIP ≥ 1 and fold change, FC≥ 2 or≤ 0.5) between buds at 30, 80, 100 days after SPD/water treatment or between buds under different treatment. Lipids, phenolic acids, amino acids, carbohydrates, and vitamins were among metabolites showing significant differences over time after SPD treatment. Here, 18 out of 20 lipids, including the lysophosphatidylethanolamine (12, LPE), lysophosphatidylcholine (7, LPC), and free fatty acids (1, FA), were significantly upregulated from 80 to 100 days after SPD treatment comared to water treatment. Meanwhile, the dormancy release of mango buds from 80 to 100 days after SPD treatment was accompanied by the accumulation of proline, ascorbic acid, carbohydrates, and tannins. In addition, metabolites, such as L-homocysteine, L-histidine, and L-homomethionine, showed more than a ten-fold difference in relative abundance from 30 to 100 days after SPD treatment, however, there were no significant changes after water treatment. The present stu…
bibliographic citation: Liang et al. (2022) Widely targeted metabolite profiling of mango stem apex during floral induction by compond of mepiquat chloride, prohexadione-calcium and uniconazole. PeerJ 10:e14458 https://doi.org/10.7717/peerj.14458
date submitted: 2022-05-04
date accepted: 2022-11-02
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Fei
author list: Agent
  family name: Xu
  given name: Wentian
author list: Agent
  family name: Wu
  given name: Hongxia
author list: Agent
  family name: Zheng
  given name: Bin
author list: Agent
  family name: Liang
  given name: Qingzhi
author list: Agent
  family name: Li
  given name: Yingzhi
author list: Agent
  family name: Wang
  given name: Songbiao
doi: 10.7717/peerj.14458
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: ©2022 Liang et al.
attribution name: Liang et al.

An artificial neural network classification method employing longitudinally monitored immune biomarkers to predict the clinical outcome of critically ill COVID-19 patients
type: item
type: AcademicArticle
description: Background The severe form of COVID-19 can cause a dysregulated host immune syndrome that might lead patients to death. To understand the underlying immune mechanisms that contribute to COVID-19 disease we have examined 28 different biomarkers in two cohorts of COVID-19 patients, aiming to systematically capture, quantify, and algorithmize how immune signals might be associated to the clinical outcome of COVID-19 patients. Methods The longitudinal concentration of 28 biomarkers of 95 COVID-19 patients was measured. We performed a dimensionality reduction analysis to determine meaningful biomarkers for explaining the data variability. The biomarkers were used as input of artificial neural network, random forest, classification and regression trees, k-nearest neighbors and support vector machines. Two different clinical cohorts were used to grant validity to the findings. Results We benchmarked the classification capacity of two COVID-19 clinicals studies with different models and found that artificial neural networks was the best classifier. From it, we could employ different sets of biomarkers to predict the clinical outcome of COVID-19 patients. First, all the biomarkers available yielded a satisfactory classification. Next, we assessed the prediction capacity of each protein separated. With a reduced set of biomarkers, our model presented 94% accuracy, 96.6% precision, 91.6% recall, and 95% of specificity upon the testing data. We used the same model to predict 83% and 87% (recovered and deceased) of unseen data, granting validity to the results obtained. Conclusions In this work, using state-of-the-art computational techniques, we systematically identified an optimal set of biomarkers that are related to a prediction capacity of COVID-19 patients. The screening of such biomarkers might assist in understanding the underlying immune response towards inflammatory diseases.
format: application/pdf
format: text/html
creator: Gustavo Martinez
creator: Alexis Garduno
creator: Abdullah Mahmud-Al-Rafat
creator: Ali Toloue Ostadgavahi
creator: Ann Avery
creator: Scheila de Avila e Silva
creator: Rachael Cusack
creator: Cheryl Cameron
creator: Mark Cameron
creator: Ignacio Martin-Loeches
creator: David Kelvin
subject: Bioinformatics
subject: Immunology
subject: Data Mining and Machine Learning
subject: COVID-19
description: doi:10.7717/peerj.14487
publisher: PeerJ Inc.
rights: © 2022 Martinez et al.
abstract: Background The severe form of COVID-19 can cause a dysregulated host immune syndrome that might lead patients to death. To understand the underlying immune mechanisms that contribute to COVID-19 disease we have examined 28 different biomarkers in two cohorts of COVID-19 patients, aiming to systematically capture, quantify, and algorithmize how immune signals might be associated to the clinical outcome of COVID-19 patients. Methods The longitudinal concentration of 28 biomarkers of 95 COVID-19 patients was measured. We performed a dimensionality reduction analysis to determine meaningful biomarkers for explaining the data variability. The biomarkers were used as input of artificial neural network, random forest, classification and regression trees, k-nearest neighbors and support vector machines. Two different clinical cohorts were used to grant validity to the findings. Results We benchmarked the classification capacity of two COVID-19 clinicals studies with different models and found that artificial neural networks was the best classifier. From it, we could employ different sets of biomarkers to predict the clinical outcome of COVID-19 patients. First, all the biomarkers available yielded a satisfactory classification. Next, we assessed the prediction capacity of each protein separated. With a reduced set of biomarkers, our model presented 94% accuracy, 96.6% precision, 91.6% recall, and 95% of specificity upon the testing data. We used the same model to predict 83% and 87% (recovered and deceased) of unseen data, granting validity to the results obtained. Conclusions In this work, using state-of-the-art computational techniques, we systematically identified an optimal set of biomarkers that are related to a prediction capacity of COVID-19 patients. The screening of such biomarkers might assist in understanding the underlying immune response towards inflammatory diseases.
bibliographic citation: Martinez et al. (2022) An artificial neural network classification method employing longitudinally monitored immune biomarkers to predict the clinical outcome of critically ill COVID-19 patients. PeerJ 10:e14487 https://doi.org/10.7717/peerj.14487
date submitted: 2022-07-25
date accepted: 2022-11-08
issued: 2022-12-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martinez
  given name: Gustavo
author list: Agent
  family name: Garduno
  given name: Alexis
author list: Agent
  family name: Mahmud-Al-Rafat
  given name: Abdullah
author list: Agent
  family name: Ostadgavahi
  given name: Ali Toloue
author list: Agent
  family name: Avery
  given name: Ann
author list: Agent
  family name: de Avila e Silva
  given name: Scheila
author list: Agent
  family name: Cusack
  given name: Rachael
author list: Agent
  family name: Cameron
  given name: Cheryl
author list: Agent
  family name: Cameron
  given name: Mark
author list: Agent
  family name: Martin-Loeches
  given name: Ignacio
author list: Agent
  family name: Kelvin
  given name: David
doi: 10.7717/peerj.14487
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-12-12
copyright: ©2022 Martinez et al.
attribution name: Martinez et al.

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