PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A new species of Pristimantis (Anura: Strabomantidae) from white-sand forests of central Amazonia, Brazil
items: Reliability of sonographic measurements of the ulnar collateral ligament: a multi-rater prospective study
items: Assessment of aquatic food web and trophic niche as a measurement of recovery function in restored mangroves in the Southern Gulf of Mexico
items: Isoscapes of remnant and restored Hawaiian montane forests reveal differences in biological nitrogen fixation and carbon inputs
items: Pollution and health risk assessment of rare earth elements in Citrus sinensis growing soil in mining area of southern China
items: Neutrophil extracellular trap burden correlates with the stenosis of coronary atherosclerosis
items: Ecodatacube.eu: analysis-ready open environmental data cube for Europe
items: Influence of geographic origin and tissue type on the medicinal chemical compounds of Semiliquidambar cathayensis
items: Fasudil may alleviate alcohol-induced astrocyte damage by modifying lipid metabolism, as determined by metabonomics analysis
items: Temporal and inter-individual changes in the integrated biochemical condition of the gonads of female swordfish (Xiphias gladius) from the Southeastern Pacific Ocean

A new species of Pristimantis (Anura: Strabomantidae) from white-sand forests of central Amazonia, Brazil
type: item
type: AcademicArticle
description: The white-sand ecosystems in the Solimões-Negro Interfluve are among the less studied in Amazonia. Recent herpetological surveys conducted west of Manaus, Brazil (central Amazonia) indicate that white-sand forests host a unique anuran fauna comprising habitat specialized and endemic species. In the present study we describe a new species of rain frog belonging to the Pristimantis unistrigatus species group from the white-sand forest locally called “campinarana” (thin-trunked forests with canopy height below 20 m). The new species is phylogenetically close to rain frogs from western Amazonian lowlands (P. delius, P. librarius, P. matidiktyo and P. ockendeni). It differs from its closest relatives mainly by its size (male SVL of 17.3–20.1 mm, n = 16; female SVL of 23.2–26.5 mm, n = 6), presence of tympanum, tarsal tubercles and dentigerous processes of vomers, its translucent groin without bright colored blotches or marks, and by its advertisement call (composed of 5–10 notes, call duration of 550–1,061 ms, dominant frequency of 3,295–3,919 Hz). Like other anuran species recently discovered in the white-sand forests west of Manaus, the new species seems to be restricted to this peculiar ecosystem.
format: application/pdf
format: text/html
creator: Alexander Tamanini Mônico
creator: Miquéias Ferrão
creator: Jiří Moravec
creator: Antoine Fouquet
creator: Albertina P. Lima
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15399
publisher: PeerJ Inc.
rights: © 2023 Mônico et al.
abstract: The white-sand ecosystems in the Solimões-Negro Interfluve are among the less studied in Amazonia. Recent herpetological surveys conducted west of Manaus, Brazil (central Amazonia) indicate that white-sand forests host a unique anuran fauna comprising habitat specialized and endemic species. In the present study we describe a new species of rain frog belonging to the Pristimantis unistrigatus species group from the white-sand forest locally called “campinarana” (thin-trunked forests with canopy height below 20 m). The new species is phylogenetically close to rain frogs from western Amazonian lowlands (P. delius, P. librarius, P. matidiktyo and P. ockendeni). It differs from its closest relatives mainly by its size (male SVL of 17.3–20.1 mm, n = 16; female SVL of 23.2–26.5 mm, n = 6), presence of tympanum, tarsal tubercles and dentigerous processes of vomers, its translucent groin without bright colored blotches or marks, and by its advertisement call (composed of 5–10 notes, call duration of 550–1,061 ms, dominant frequency of 3,295–3,919 Hz). Like other anuran species recently discovered in the white-sand forests west of Manaus, the new species seems to be restricted to this peculiar ecosystem.
bibliographic citation: Mônico et al. (2023) A new species of Pristimantis (Anura: Strabomantidae) from white-sand forests of central Amazonia, Brazil. PeerJ 11:e15399 https://doi.org/10.7717/peerj.15399
date submitted: 2022-12-20
date accepted: 2023-04-20
issued: 2023-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mônico
  given name: Alexander Tamanini
author list: Agent
  family name: Ferrão
  given name: Miquéias
author list: Agent
  family name: Moravec
  given name: Jiří
author list: Agent
  family name: Fouquet
  given name: Antoine
author list: Agent
  family name: Lima
  given name: Albertina P.
doi: 10.7717/peerj.15399
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-06
copyright: ©2023 Mônico et al.
attribution name: Mônico et al.

Reliability of sonographic measurements of the ulnar collateral ligament: a multi-rater prospective study
type: item
type: AcademicArticle
description: Background The use of sonography is a cost-effective and reliable method to evaluate upper extremity superficial tissue structural integrity and pathology. Establishing the measurement reliability of widely used diagnostic ultrasound evaluation for musculoskeletal assessment is paramount enhance accurate clinical evaluations. The objective of this study was to establish the inter-rater and intra-rater reliability of select ulnar collateral ligament (UCL) thickness measures at two distinct anatomical locations in intercollegiate baseball athletes using ultrasound imaging (USI). Methods This was a prospective cohort study conducted in a university research laboratory and included a total of 17 NCAA Division I baseball athletes (age 20.4 ± 1.43, height = 183.63 cm ± 6.27 cm, mass = 89.28 kg ± 8.24 kg). Two trained clinicians measured UCL mid-substance and apex thickness in the throwing extremity, prospectively, on 5 occasions at 1-month intervals during rest. Intraclass correlation coefficients (ICCs) (model 3,3), associated standard error of measurement, and 95% minimal detectable change in thickness were derived. Results Intrarater reliability estimates for operator 1 were 0.90–0.98 (mid-substance) and 0.91–0.99 (apex). Operator 2’s values were 0.92–0.97 and 0.93–0.99, respectively. The standard error of measurement (SEM) ranged from 0.045–0.071 cm (mid-substance) and 0.023–0.067 cm (apex). The minimal detectable difference (MDD95) was 0.12–0.20 cm (mid-substance) and 0.07–0.19 cm (apex). Interrater reliability was 0.86–0.96 (mid-substance) and 0.79–0.98 (apex); most ICCs were >0.90. Measurement of UCL thickness at two locations demonstrated very good to excellent reliability with high precision. Using this protocol, two evaluators can obtain consistent UCL measurement at two positions. This finding has significant implications for the clinical evaluation of superficial tissue pathology of the same individual by two experienced practitioners.
format: application/pdf
format: text/html
creator: Shawn D. Felton
creator: Arie J. Van Duijn
creator: Mitchell L. Cordova
subject: Anatomy and Physiology
subject: Kinesiology
subject: Orthopedics
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.15418
publisher: PeerJ Inc.
rights: © 2023 Felton et al.
abstract: Background The use of sonography is a cost-effective and reliable method to evaluate upper extremity superficial tissue structural integrity and pathology. Establishing the measurement reliability of widely used diagnostic ultrasound evaluation for musculoskeletal assessment is paramount enhance accurate clinical evaluations. The objective of this study was to establish the inter-rater and intra-rater reliability of select ulnar collateral ligament (UCL) thickness measures at two distinct anatomical locations in intercollegiate baseball athletes using ultrasound imaging (USI). Methods This was a prospective cohort study conducted in a university research laboratory and included a total of 17 NCAA Division I baseball athletes (age 20.4 ± 1.43, height = 183.63 cm ± 6.27 cm, mass = 89.28 kg ± 8.24 kg). Two trained clinicians measured UCL mid-substance and apex thickness in the throwing extremity, prospectively, on 5 occasions at 1-month intervals during rest. Intraclass correlation coefficients (ICCs) (model 3,3), associated standard error of measurement, and 95% minimal detectable change in thickness were derived. Results Intrarater reliability estimates for operator 1 were 0.90–0.98 (mid-substance) and 0.91–0.99 (apex). Operator 2’s values were 0.92–0.97 and 0.93–0.99, respectively. The standard error of measurement (SEM) ranged from 0.045–0.071 cm (mid-substance) and 0.023–0.067 cm (apex). The minimal detectable difference (MDD95) was 0.12–0.20 cm (mid-substance) and 0.07–0.19 cm (apex). Interrater reliability was 0.86–0.96 (mid-substance) and 0.79–0.98 (apex); most ICCs were >0.90. Measurement of UCL thickness at two locations demonstrated very good to excellent reliability with high precision. Using this protocol, two evaluators can obtain consistent UCL measurement at two positions. This finding has significant implications for the clinical evaluation of superficial tissue pathology of the same individual by two experienced practitioners.
bibliographic citation: Felton et al. (2023) Reliability of sonographic measurements of the ulnar collateral ligament: a multi-rater prospective study. PeerJ 11:e15418 https://doi.org/10.7717/peerj.15418
date submitted: 2022-11-09
date accepted: 2023-04-25
issued: 2023-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Felton
  given name: Shawn D.
author list: Agent
  family name: Van Duijn
  given name: Arie J.
author list: Agent
  family name: Cordova
  given name: Mitchell L.
doi: 10.7717/peerj.15418
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-06
copyright: ©2023 Felton et al.
attribution name: Felton et al.

Assessment of aquatic food web and trophic niche as a measurement of recovery function in restored mangroves in the Southern Gulf of Mexico
type: item
type: AcademicArticle
description: Mangroves are coastal wetlands with high biodiversity and productivity, with great interaction with coastal environments. In the face of worldwide mangrove loss, restoration projects attempt to recover ecosystem composition and functioning over time. Our objective was to examine and compare the food webs in mangrove areas with different restoration times and in a reference mangrove in Términos Lagoon, Mexico. We estimated the trophic structure, identified the carbon resources that maintain aquatic consumers through the analysis of stable isotopes, and compared the trophic niche of the restored mangroves with the reference mangrove. We analyzed environmental variables, trophic structure, and contributions of resources during three seasons: rainy, dry, and “nortes”. Environmental changes and food structure changed in response to regional seasons. Bayesian mixing models indicated that food webs varied seasonally as a response to the primary productivity developed at Términos Lagoon. As expected, the assimilation of C3 plants in the reference mangrove was highest, as a primary (“nortes” season) and secondary resource (dry and rainy seasons). The restored mangroves depended mainly on allochthonous resources (seagrass, epiphytes, and phytoplankton). The assimilation of these resources highlighted the importance of connectivity and the input of sources of carbon from nearby coastal environments. Trophic niche analysis showed that the area with longer restoration time was more similar to the reference mangrove, which is evidence of the importance and efficacy of the restoration process, as well as the restoration of the ecosystem function over time.
format: application/pdf
format: text/html
creator: Miriam Soria-Barreto
creator: Rosela Pérez-Ceballos
creator: Arturo Zaldívar-Jiménez
creator: Rolando Gelabert Fernández
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.15422
publisher: PeerJ Inc.
rights: © 2023 Soria-Barreto et al.
abstract: Mangroves are coastal wetlands with high biodiversity and productivity, with great interaction with coastal environments. In the face of worldwide mangrove loss, restoration projects attempt to recover ecosystem composition and functioning over time. Our objective was to examine and compare the food webs in mangrove areas with different restoration times and in a reference mangrove in Términos Lagoon, Mexico. We estimated the trophic structure, identified the carbon resources that maintain aquatic consumers through the analysis of stable isotopes, and compared the trophic niche of the restored mangroves with the reference mangrove. We analyzed environmental variables, trophic structure, and contributions of resources during three seasons: rainy, dry, and “nortes”. Environmental changes and food structure changed in response to regional seasons. Bayesian mixing models indicated that food webs varied seasonally as a response to the primary productivity developed at Términos Lagoon. As expected, the assimilation of C3 plants in the reference mangrove was highest, as a primary (“nortes” season) and secondary resource (dry and rainy seasons). The restored mangroves depended mainly on allochthonous resources (seagrass, epiphytes, and phytoplankton). The assimilation of these resources highlighted the importance of connectivity and the input of sources of carbon from nearby coastal environments. Trophic niche analysis showed that the area with longer restoration time was more similar to the reference mangrove, which is evidence of the importance and efficacy of the restoration process, as well as the restoration of the ecosystem function over time.
bibliographic citation: Soria-Barreto et al. (2023) Assessment of aquatic food web and trophic niche as a measurement of recovery function in restored mangroves in the Southern Gulf of Mexico. PeerJ 11:e15422 https://doi.org/10.7717/peerj.15422
date submitted: 2022-01-31
date accepted: 2023-04-25
issued: 2023-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soria-Barreto
  given name: Miriam
author list: Agent
  family name: Pérez-Ceballos
  given name: Rosela
author list: Agent
  family name: Zaldívar-Jiménez
  given name: Arturo
author list: Agent
  family name: Gelabert Fernández
  given name: Rolando
doi: 10.7717/peerj.15422
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-06
copyright: ©2023 Soria-Barreto et al.
attribution name: Soria-Barreto et al.

Isoscapes of remnant and restored Hawaiian montane forests reveal differences in biological nitrogen fixation and carbon inputs
type: item
type: AcademicArticle
description: Deforestation and subsequent land-use conversion has altered ecosystems and led to negative effects on biodiversity. To ameliorate these effects, nitrogen-fixing (N2-fixing) trees are frequently used in the reforestation of degraded landscapes, especially in the tropics; however, their influence on ecosystem properties such as nitrogen (N) availability and carbon (C) stocks are understudied. Here, we use a 30-y old reforestation site of outplanted native N2-fixing trees (Acacia koa) dominated by exotic grass understory, and a neighboring remnant forest dominated by A. koa canopy trees and native understory, to assess whether restoration is leading to similar N and C biogeochemical landscapes and soil and plant properties as a target remnant forest ecosystem. We measured nutrient contents and isotope values (δ15N, δ13C) in soils, A. koa, and non-N2-fixing understory plants (Rubus spp.) and generated δ15N and δ13C isoscapes of the two forests to test for (1) different levels of biological nitrogen fixation (BNF) and its contribution to non-N2-fixing understory plants, and (2) the influence of historic land conversion and more recent afforestation on plant and soil δ13C. In the plantation, A. koa densities were higher and foliar δ15N values for A. koa and Rubus spp. were lower than in the remnant forest. Foliar and soil isoscapes also showed a more homogeneous distribution of low δ15N values in the plantation and greater influence of A. koa on neighboring plants and soil, suggesting greater BNF. Foliar δ13C also indicated higher water use efficiency (WUEi) in the plantation, indicative of differences in plant-water relations or soil water status between the two forest types. Plantation soil δ13C was higher than the remnant forest, consistent with greater contributions of exotic C4-pasture grasses to soil C pools, possibly due to facilitation of non-native grasses by the dense A. koa canopy. These findings are consequential for forest restoration, as they contribute to …
format: application/pdf
format: text/html
creator: Christopher B. Wall
creator: Sean O. I. Swift
creator: Carla M. D’Antonio
creator: Gerhard Gebauer
creator: Nicole A. Hynson
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Natural Resource Management
subject: Forestry
description: doi:10.7717/peerj.15468
publisher: PeerJ Inc.
rights: © 2023 Wall et al.
abstract: Deforestation and subsequent land-use conversion has altered ecosystems and led to negative effects on biodiversity. To ameliorate these effects, nitrogen-fixing (N2-fixing) trees are frequently used in the reforestation of degraded landscapes, especially in the tropics; however, their influence on ecosystem properties such as nitrogen (N) availability and carbon (C) stocks are understudied. Here, we use a 30-y old reforestation site of outplanted native N2-fixing trees (Acacia koa) dominated by exotic grass understory, and a neighboring remnant forest dominated by A. koa canopy trees and native understory, to assess whether restoration is leading to similar N and C biogeochemical landscapes and soil and plant properties as a target remnant forest ecosystem. We measured nutrient contents and isotope values (δ15N, δ13C) in soils, A. koa, and non-N2-fixing understory plants (Rubus spp.) and generated δ15N and δ13C isoscapes of the two forests to test for (1) different levels of biological nitrogen fixation (BNF) and its contribution to non-N2-fixing understory plants, and (2) the influence of historic land conversion and more recent afforestation on plant and soil δ13C. In the plantation, A. koa densities were higher and foliar δ15N values for A. koa and Rubus spp. were lower than in the remnant forest. Foliar and soil isoscapes also showed a more homogeneous distribution of low δ15N values in the plantation and greater influence of A. koa on neighboring plants and soil, suggesting greater BNF. Foliar δ13C also indicated higher water use efficiency (WUEi) in the plantation, indicative of differences in plant-water relations or soil water status between the two forest types. Plantation soil δ13C was higher than the remnant forest, consistent with greater contributions of exotic C4-pasture grasses to soil C pools, possibly due to facilitation of non-native grasses by the dense A. koa canopy. These findings are consequential for forest restoration, as they contribute to …
bibliographic citation: Wall et al. (2023) Isoscapes of remnant and restored Hawaiian montane forests reveal differences in biological nitrogen fixation and carbon inputs. PeerJ 11:e15468 https://doi.org/10.7717/peerj.15468
date submitted: 2023-02-16
date accepted: 2023-05-05
issued: 2023-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wall
  given name: Christopher B.
author list: Agent
  family name: Swift
  given name: Sean O. I.
author list: Agent
  family name: D’Antonio
  given name: Carla M.
author list: Agent
  family name: Gebauer
  given name: Gerhard
author list: Agent
  family name: Hynson
  given name: Nicole A.
doi: 10.7717/peerj.15468
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-06
copyright: © 2023 Wall et al.
attribution name: Wall et al.

Pollution and health risk assessment of rare earth elements in Citrus sinensis growing soil in mining area of southern China
type: item
type: AcademicArticle
description: Background Analyzing the pollution and health risk of rare earth elements (REEs) in crop-growing soils around rare earth deposits can facilitate the improvement of REE mining-influenced area. In this study, pollution status, fraction and anomaly, plant accumulation characteristics, and potential risks of REEs (including heavy and light rare earth elements, HREEs and LREEs) in C. sinensis planting soil near ion-adsorption deposits in southern Ganzhou were analyzed. The influence of the soil environment on REEs in soil and fruit of C. sinensis was also explored. Methods The geo-accumulation index (Igeo) and ecological risk index(RI) were used to analyze the pollution potential and ecological risks of REEs in soils, respectively. Health risk index and translocation factor (TF) were applied to analyze the accumulation and health risks of REEs in fruit of C. sinensis. The influence of soil factors on REEs in soil and fruit of C. sinensis were determined via correlation and redundancy analysis. Results Comparison with background values and assessment of Igeo and RI indicated that the soil was polluted by REEs, albeit at varying degrees. Fractionation between LREEs and HREEs occurred, along with significant positive Ce anomaly and negative Eu anomaly. With TF values < 1, our results suggest that C. sinensis has a weak ability to accumulate REEs in its fruit. The concentrations of REEs in fruit differed between LREEs and HREEs, with content of HREE in fruit ordered as Jiading > Anxi > Wuyang and of LREE in fruit higher in Wuyang. Correlation and redundancy analysis indicated that K2O, Fe2O3 and TOC are important soil factors influencing REE accumulation by C. sinensis, with K2O positively related and Fe2O3 and TOC negatively related to the accumulation process.
format: application/pdf
format: text/html
creator: Jinhu Lai
creator: Jinfu Liu
creator: Daishe Wu
creator: Jinying Xu
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.15470
publisher: PeerJ Inc.
rights: © 2023 Lai et al.
abstract: Background Analyzing the pollution and health risk of rare earth elements (REEs) in crop-growing soils around rare earth deposits can facilitate the improvement of REE mining-influenced area. In this study, pollution status, fraction and anomaly, plant accumulation characteristics, and potential risks of REEs (including heavy and light rare earth elements, HREEs and LREEs) in C. sinensis planting soil near ion-adsorption deposits in southern Ganzhou were analyzed. The influence of the soil environment on REEs in soil and fruit of C. sinensis was also explored. Methods The geo-accumulation index (Igeo) and ecological risk index(RI) were used to analyze the pollution potential and ecological risks of REEs in soils, respectively. Health risk index and translocation factor (TF) were applied to analyze the accumulation and health risks of REEs in fruit of C. sinensis. The influence of soil factors on REEs in soil and fruit of C. sinensis were determined via correlation and redundancy analysis. Results Comparison with background values and assessment of Igeo and RI indicated that the soil was polluted by REEs, albeit at varying degrees. Fractionation between LREEs and HREEs occurred, along with significant positive Ce anomaly and negative Eu anomaly. With TF values < 1, our results suggest that C. sinensis has a weak ability to accumulate REEs in its fruit. The concentrations of REEs in fruit differed between LREEs and HREEs, with content of HREE in fruit ordered as Jiading > Anxi > Wuyang and of LREE in fruit higher in Wuyang. Correlation and redundancy analysis indicated that K2O, Fe2O3 and TOC are important soil factors influencing REE accumulation by C. sinensis, with K2O positively related and Fe2O3 and TOC negatively related to the accumulation process.
bibliographic citation: Lai et al. (2023) Pollution and health risk assessment of rare earth elements in Citrus sinensis growing soil in mining area of southern China. PeerJ 11:e15470 https://doi.org/10.7717/peerj.15470
date submitted: 2022-11-25
date accepted: 2023-05-07
issued: 2023-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lai
  given name: Jinhu
author list: Agent
  family name: Liu
  given name: Jinfu
author list: Agent
  family name: Wu
  given name: Daishe
author list: Agent
  family name: Xu
  given name: Jinying
doi: 10.7717/peerj.15470
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-06
copyright: ©2023 Lai et al.
attribution name: Lai et al.

Neutrophil extracellular trap burden correlates with the stenosis of coronary atherosclerosis
type: item
type: AcademicArticle
description: Background Coronary atherosclerosis diseases (CADs) are associated with chronic inflammation. Neutrophil extracellular traps (NETs) are a type of novel proinflammatory cytokines whose levels are dramatically elevated in acute coronary syndrome. We conducted this study to further evaluate the association between circulating NET-associated markers and CAD in Chinese adults. Methods A total of 174 patients with CAD and 55 healthy controls were screened using percutaneous coronary intervention or coronary computed tomography angiography. Blood lipid levels, blood glucose levels, and blood cell counts were determined using commercial kits. Serum levels of myeloperoxidase (MPO) and neutrophil elastase (NE) were measured using ELISA. Double-stranded DNA (dsDNA) in serum was quantified using the Quant-iT PicoGreen assay. We also compared the circulating NET levels with various parameters in the study subjects. Results The levels of serum NET markers, dsDNA, MPO, and NE, were significantly elevated in patients with CAD, particularly in the severe group, consistent with the increase in neutrophil counts. The levels of NET markers correlated with the risk factors of AS, increasing with the number of risk factors. NET markers were identified as independent risk factors for severe coronary stenosis and also as predictors of severe CAD. Conclusion NETs may be related to AS and serve as indicators or predictors of stenosis in patients with severe CAD.
format: application/pdf
format: text/html
creator: Yan Wang
creator: Mao Yang
creator: Yuanyuan Xu
creator: Shujun Yan
creator: Enze Jin
creator: Xueqi Li
subject: Cardiology
subject: Hematology
subject: Immunology
subject: Pathology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.15471
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Background Coronary atherosclerosis diseases (CADs) are associated with chronic inflammation. Neutrophil extracellular traps (NETs) are a type of novel proinflammatory cytokines whose levels are dramatically elevated in acute coronary syndrome. We conducted this study to further evaluate the association between circulating NET-associated markers and CAD in Chinese adults. Methods A total of 174 patients with CAD and 55 healthy controls were screened using percutaneous coronary intervention or coronary computed tomography angiography. Blood lipid levels, blood glucose levels, and blood cell counts were determined using commercial kits. Serum levels of myeloperoxidase (MPO) and neutrophil elastase (NE) were measured using ELISA. Double-stranded DNA (dsDNA) in serum was quantified using the Quant-iT PicoGreen assay. We also compared the circulating NET levels with various parameters in the study subjects. Results The levels of serum NET markers, dsDNA, MPO, and NE, were significantly elevated in patients with CAD, particularly in the severe group, consistent with the increase in neutrophil counts. The levels of NET markers correlated with the risk factors of AS, increasing with the number of risk factors. NET markers were identified as independent risk factors for severe coronary stenosis and also as predictors of severe CAD. Conclusion NETs may be related to AS and serve as indicators or predictors of stenosis in patients with severe CAD.
bibliographic citation: Wang et al. (2023) Neutrophil extracellular trap burden correlates with the stenosis of coronary atherosclerosis. PeerJ 11:e15471 https://doi.org/10.7717/peerj.15471
date submitted: 2023-02-17
date accepted: 2023-05-07
issued: 2023-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Yang
  given name: Mao
author list: Agent
  family name: Xu
  given name: Yuanyuan
author list: Agent
  family name: Yan
  given name: Shujun
author list: Agent
  family name: Jin
  given name: Enze
author list: Agent
  family name: Li
  given name: Xueqi
doi: 10.7717/peerj.15471
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-06
copyright: ©2023 Wang et al.
attribution name: Wang et al.

Ecodatacube.eu: analysis-ready open environmental data cube for Europe
type: item
type: AcademicArticle
description: The article describes the production steps and accuracy assessment of an analysis-ready, open-access European data cube consisting of 2000–2020+ Landsat data, 2017–2021+ Sentinel-2 data and a 30 m resolution digital terrain model (DTM). The main purpose of the data cube is to make annual continental-scale spatiotemporal machine learning tasks accessible to a wider user base by providing a spatially and temporally consistent multidimensional feature space. This has required systematic spatiotemporal harmonization, efficient compression, and imputation of missing values. Sentinel-2 and Landsat reflectance values were aggregated into four quarterly averages approximating the four seasons common in Europe (winter, spring, summer and autumn), as well as the 25th and 75th percentile, in order to retain intra-seasonal variance. Remaining missing data in the Landsat time-series was imputed with a temporal moving window median (TMWM) approach. An accuracy assessment shows TMWM performs relatively better in Southern Europe and lower in mountainous regions such as the Scandinavian Mountains, the Alps, and the Pyrenees. We quantify the usability of the different component data sets for spatiotemporal machine learning tasks with a series of land cover classification experiments, which show that models utilizing the full feature space (30 m DTM, 30 m Landsat, 30 m and 10 m Sentinel-2) yield the highest land cover classification accuracy, with different data sets improving the results for different land cover classes. The data sets presented in the article are part of the EcoDataCube platform, which also hosts open vegetation, soil, and land use/land cover (LULC) maps created. All data sets are available under CC-BY license as Cloud-Optimized GeoTIFFs (ca. 12 TB in size) through SpatioTemporal Asset Catalog (STAC) and the EcoDataCube data portal.
format: application/pdf
format: text/html
creator: Martijn Witjes
creator: Leandro Parente
creator: Josip Križan
creator: Tomislav Hengl
creator: Luka Antonić
subject: Ecosystem Science
subject: Computational Science
subject: Data Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.15478
publisher: PeerJ Inc.
rights: © 2023 Witjes et al.
abstract: The article describes the production steps and accuracy assessment of an analysis-ready, open-access European data cube consisting of 2000–2020+ Landsat data, 2017–2021+ Sentinel-2 data and a 30 m resolution digital terrain model (DTM). The main purpose of the data cube is to make annual continental-scale spatiotemporal machine learning tasks accessible to a wider user base by providing a spatially and temporally consistent multidimensional feature space. This has required systematic spatiotemporal harmonization, efficient compression, and imputation of missing values. Sentinel-2 and Landsat reflectance values were aggregated into four quarterly averages approximating the four seasons common in Europe (winter, spring, summer and autumn), as well as the 25th and 75th percentile, in order to retain intra-seasonal variance. Remaining missing data in the Landsat time-series was imputed with a temporal moving window median (TMWM) approach. An accuracy assessment shows TMWM performs relatively better in Southern Europe and lower in mountainous regions such as the Scandinavian Mountains, the Alps, and the Pyrenees. We quantify the usability of the different component data sets for spatiotemporal machine learning tasks with a series of land cover classification experiments, which show that models utilizing the full feature space (30 m DTM, 30 m Landsat, 30 m and 10 m Sentinel-2) yield the highest land cover classification accuracy, with different data sets improving the results for different land cover classes. The data sets presented in the article are part of the EcoDataCube platform, which also hosts open vegetation, soil, and land use/land cover (LULC) maps created. All data sets are available under CC-BY license as Cloud-Optimized GeoTIFFs (ca. 12 TB in size) through SpatioTemporal Asset Catalog (STAC) and the EcoDataCube data portal.
bibliographic citation: Witjes et al. (2023) Ecodatacube.eu: analysis-ready open environmental data cube for Europe. PeerJ 11:e15478 https://doi.org/10.7717/peerj.15478
date submitted: 2022-11-22
date accepted: 2023-05-08
issued: 2023-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Witjes
  given name: Martijn
author list: Agent
  family name: Parente
  given name: Leandro
author list: Agent
  family name: Križan
  given name: Josip
author list: Agent
  family name: Hengl
  given name: Tomislav
author list: Agent
  family name: Antonić
  given name: Luka
doi: 10.7717/peerj.15478
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-06
copyright: © 2023 Witjes et al.
attribution name: Witjes et al.

Influence of geographic origin and tissue type on the medicinal chemical compounds of Semiliquidambar cathayensis
type: item
type: AcademicArticle
description: Semiliquidambar cathayensis is widely used in traditional Chinese medicine owing its high concentrations of polyphenol, triterpenoidic acid, and flavonoids. This study aimed to explore the impact of geographical origin and tissue type on the contents of chemical compounds of S. cathayensis, as determined by colorimetric and chromatographic methods. Therefore, we quantitively evaluated chemical compounds found in the tissues of various organs of plants collected in six different regions. Overall, we found that geographical origin affected the content of medicinal compounds in S. cathayensis leaves, with plants from Jingzhou county showing the best therapeutic potential. However, no specific correlation was observed with latitude. It is noteworthy that the amount of paeoniflorin and other compounds can be used as biomarkers of geographical origin and tissue type. Most medicinal compounds accumulated mainly in the leaves, whereas ursolic and oleanolic acids accumulated in the roots. These results show that the comprehensive medicinal value of the leaves of S. cathayensis in Jingzhou county is the highest, but the root should be selected first to collect oleanolic acid and ursolic acid.
format: application/pdf
format: text/html
creator: Xiaoming Tian
creator: Hao Lv
creator: Guangfeng Xiang
creator: Jing Peng
creator: Gaofei Li
creator: Yan He
creator: Fan Zhang
creator: Cun Mou
subject: Agricultural Science
subject: Translational Medicine
description: doi:10.7717/peerj.15484
publisher: PeerJ Inc.
rights: © 2023 Tian et al.
abstract: Semiliquidambar cathayensis is widely used in traditional Chinese medicine owing its high concentrations of polyphenol, triterpenoidic acid, and flavonoids. This study aimed to explore the impact of geographical origin and tissue type on the contents of chemical compounds of S. cathayensis, as determined by colorimetric and chromatographic methods. Therefore, we quantitively evaluated chemical compounds found in the tissues of various organs of plants collected in six different regions. Overall, we found that geographical origin affected the content of medicinal compounds in S. cathayensis leaves, with plants from Jingzhou county showing the best therapeutic potential. However, no specific correlation was observed with latitude. It is noteworthy that the amount of paeoniflorin and other compounds can be used as biomarkers of geographical origin and tissue type. Most medicinal compounds accumulated mainly in the leaves, whereas ursolic and oleanolic acids accumulated in the roots. These results show that the comprehensive medicinal value of the leaves of S. cathayensis in Jingzhou county is the highest, but the root should be selected first to collect oleanolic acid and ursolic acid.
bibliographic citation: Tian et al. (2023) Influence of geographic origin and tissue type on the medicinal chemical compounds of Semiliquidambar cathayensis. PeerJ 11:e15484 https://doi.org/10.7717/peerj.15484
date submitted: 2022-11-10
date accepted: 2023-05-10
issued: 2023-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tian
  given name: Xiaoming
author list: Agent
  family name: Lv
  given name: Hao
author list: Agent
  family name: Xiang
  given name: Guangfeng
author list: Agent
  family name: Peng
  given name: Jing
author list: Agent
  family name: Li
  given name: Gaofei
author list: Agent
  family name: He
  given name: Yan
author list: Agent
  family name: Zhang
  given name: Fan
author list: Agent
  family name: Mou
  given name: Cun
doi: 10.7717/peerj.15484
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-06
copyright: ©2023 Tian et al.
attribution name: Tian et al.

Fasudil may alleviate alcohol-induced astrocyte damage by modifying lipid metabolism, as determined by metabonomics analysis
type: item
type: AcademicArticle
description: Alcohol dependence is a chronic, relapsing encephalopathy characterized by compulsive craving for alcohol, loss of control over alcohol use, and the presence of negative emotions and physical discomfort when alcohol is unavailable. Harmful use of alcohol is one of the greatest risk factors for death, illness, and disability. Rho kinase inhibitors have neuroprotective effects. This study used metabonomics analysis to assess untreated astrocytes, astrocytes exposed to 75 mmol/L of alcohol, and astrocytes exposed to 75 mmol/L of alcohol and treated with 15 µg/mL fasudil for 24 h. One of the clearest differences between the alcohol-exposed and fasudil-treated alcohol-exposed groups was the abundance of lipids and lipid-like molecules, although glycerophospholipid metabolism was comparable in both groups. Our findings show that fasudil may alleviate alcohol-induced astrocyte damage by modifying lipid metabolism, providing a new approach for preventing and treating alcohol dependence.
format: application/pdf
format: text/html
creator: Huiying Zhao
creator: Xintong Li
creator: Yongqi Zheng
creator: Xiaofeng Zhu
creator: Xunzhong Qi
creator: Xinyan Huang
creator: Shunjie Bai
creator: Chengji Wu
creator: Guangtao Sun
subject: Cell Biology
subject: Genomics
subject: Neuroscience
subject: Cognitive Disorders
subject: Neurology
description: doi:10.7717/peerj.15494
publisher: PeerJ Inc.
rights: © 2023 Zhao et al.
abstract: Alcohol dependence is a chronic, relapsing encephalopathy characterized by compulsive craving for alcohol, loss of control over alcohol use, and the presence of negative emotions and physical discomfort when alcohol is unavailable. Harmful use of alcohol is one of the greatest risk factors for death, illness, and disability. Rho kinase inhibitors have neuroprotective effects. This study used metabonomics analysis to assess untreated astrocytes, astrocytes exposed to 75 mmol/L of alcohol, and astrocytes exposed to 75 mmol/L of alcohol and treated with 15 µg/mL fasudil for 24 h. One of the clearest differences between the alcohol-exposed and fasudil-treated alcohol-exposed groups was the abundance of lipids and lipid-like molecules, although glycerophospholipid metabolism was comparable in both groups. Our findings show that fasudil may alleviate alcohol-induced astrocyte damage by modifying lipid metabolism, providing a new approach for preventing and treating alcohol dependence.
bibliographic citation: Zhao et al. (2023) Fasudil may alleviate alcohol-induced astrocyte damage by modifying lipid metabolism, as determined by metabonomics analysis. PeerJ 11:e15494 https://doi.org/10.7717/peerj.15494
date submitted: 2023-01-12
date accepted: 2023-05-11
issued: 2023-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Huiying
author list: Agent
  family name: Li
  given name: Xintong
author list: Agent
  family name: Zheng
  given name: Yongqi
author list: Agent
  family name: Zhu
  given name: Xiaofeng
author list: Agent
  family name: Qi
  given name: Xunzhong
author list: Agent
  family name: Huang
  given name: Xinyan
author list: Agent
  family name: Bai
  given name: Shunjie
author list: Agent
  family name: Wu
  given name: Chengji
author list: Agent
  family name: Sun
  given name: Guangtao
doi: 10.7717/peerj.15494
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-06
copyright: © 2023 Zhao et al.
attribution name: Zhao et al.

Temporal and inter-individual changes in the integrated biochemical condition of the gonads of female swordfish (Xiphias gladius) from the Southeastern Pacific Ocean
type: item
type: AcademicArticle
description: The integrated biochemical condition (IBC) of gonads is closely related to the reproductive success of highly migratory marine species. The IBC of gonads can be influenced not only by size and/or age, but also by environmental conditions. Here, female swordfish, Xiphias gladius, that migrate to temperate regions with a marked seasonality (e.g., the Southeastern Pacific Ocean, SEPO) were compared in relation to the IBCs (lipids, proteins, glucose and, fatty acid profiles) of their gonads; individuals with two body size ranges and distinct degrees of sexual maturity were evaluated, and considered as: small and/or virginal (SV: <170 cm lower jaw fork-length (LJFL), oocyte size (OS) <0.08 mm) vs large and/or maturing females (LM: >190 cm LJFL, OS >0.133 mm). This comparison was conducted in two environmentally contrasting seasons (winter vs spring). Our results showed that the gonadosomatic index (GSI) was significantly higher in LM than SV. Lipid contents varied significantly between seasons and body sizes. The highest lipid concentrations were recorded in the spring in large females. No significant differences were found when comparing the protein and glucose contents of the two evaluated seasons or body size ranges of the studied females. In turn, the fatty acid (FA) profiles of female gonads significantly varied for both seasons and body size ranges. A high content of saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs) and poly-unsaturated fatty acids (PUFAs) were recorded in female gonads in the spring. The SFAs C16:0 and C18:0, the MUFA C18:1n9, and the essential PUFA C22:6n3 were the main contributors to the observed differences between spring and winter. These results could be used as indicators of the nutritional condition and health status of swordfish individuals. Hence, the IBC of female swordfish gonads have great potential to aid in estimating survival rates and stock abundances of this species. The integration of this information constitutes…
format: application/pdf
format: text/html
creator: Fabián Guzmán-Rivas
creator: Juan Ortega
creator: Sergio Mora
creator: Patricio Barría
creator: Rodrigo Riera
creator: Ángel Urzúa
subject: Aquaculture
subject: Fisheries and Fish Science
subject: Biochemistry
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.15524
publisher: PeerJ Inc.
rights: © 2023 Guzmán-Rivas et al.
abstract: The integrated biochemical condition (IBC) of gonads is closely related to the reproductive success of highly migratory marine species. The IBC of gonads can be influenced not only by size and/or age, but also by environmental conditions. Here, female swordfish, Xiphias gladius, that migrate to temperate regions with a marked seasonality (e.g., the Southeastern Pacific Ocean, SEPO) were compared in relation to the IBCs (lipids, proteins, glucose and, fatty acid profiles) of their gonads; individuals with two body size ranges and distinct degrees of sexual maturity were evaluated, and considered as: small and/or virginal (SV: <170 cm lower jaw fork-length (LJFL), oocyte size (OS) <0.08 mm) vs large and/or maturing females (LM: >190 cm LJFL, OS >0.133 mm). This comparison was conducted in two environmentally contrasting seasons (winter vs spring). Our results showed that the gonadosomatic index (GSI) was significantly higher in LM than SV. Lipid contents varied significantly between seasons and body sizes. The highest lipid concentrations were recorded in the spring in large females. No significant differences were found when comparing the protein and glucose contents of the two evaluated seasons or body size ranges of the studied females. In turn, the fatty acid (FA) profiles of female gonads significantly varied for both seasons and body size ranges. A high content of saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs) and poly-unsaturated fatty acids (PUFAs) were recorded in female gonads in the spring. The SFAs C16:0 and C18:0, the MUFA C18:1n9, and the essential PUFA C22:6n3 were the main contributors to the observed differences between spring and winter. These results could be used as indicators of the nutritional condition and health status of swordfish individuals. Hence, the IBC of female swordfish gonads have great potential to aid in estimating survival rates and stock abundances of this species. The integration of this information constitutes…
bibliographic citation: Guzmán-Rivas et al. (2023) Temporal and inter-individual changes in the integrated biochemical condition of the gonads of female swordfish (Xiphias gladius) from the Southeastern Pacific Ocean. PeerJ 11:e15524 https://doi.org/10.7717/peerj.15524
date submitted: 2022-12-19
date accepted: 2023-05-18
issued: 2023-06-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guzmán-Rivas
  given name: Fabián
author list: Agent
  family name: Ortega
  given name: Juan
author list: Agent
  family name: Mora
  given name: Sergio
author list: Agent
  family name: Barría
  given name: Patricio
author list: Agent
  family name: Riera
  given name: Rodrigo
author list: Agent
  family name: Urzúa
  given name: Ángel
doi: 10.7717/peerj.15524
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-06
copyright: © 2023 Guzmán-Rivas et al.
attribution name: Guzmán-Rivas et al.

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