PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Metabolome and transcriptome analyses identify the characteristics and expression of related saponins of the three genealogical plants of bead ginseng
items: Over 20% of marine fishes shifting in the North and Barents Seas, but not in the Norwegian Sea
items: Urine based near-infrared spectroscopy analysis reveals a noninvasive and convenient diagnosis method for cancers: a pilot study
items: A decade of study on the condition of western Cuban coral reefs, with low human impact
items: Effectiveness of virtual reality on activities of daily living in children with cerebral palsy: a systematic review and meta-analysis
items: Accumulation and transfer of polystyrene microplastics in Solanum nigrum seedlings
items: Evaluation of the correlation of dorsal root ganglia and spinal nerves with clinical symptoms in patients with postherpetic neuralgia using magnetic resonance neurography
items: A multi-sensor array for detecting and analyzing nocturnal avian migration
items: Adrenal SGLT1 or SGLT2 as predictors of atherosclerosis under chronic stress based on a computer algorithm
items: RNA N6-methyladenosine reader IGF2BP3 promotes acute myeloid leukemia progression by controlling stabilization of EPOR mRNA

Metabolome and transcriptome analyses identify the characteristics and expression of related saponins of the three genealogical plants of bead ginseng
type: item
type: AcademicArticle
description: Objective The classification and clinical usage of the different species of bead ginseng are often confused. Therefore, we conducted an integrated metabolomics and transcriptome analysis of three main species of Panax, including Panax japonicas, Panax pseudoginseng, and Panax pseudo-ginseng var. elegantior. Methods A broad metabolome and transcriptome analysis for three origins of bead ginseng plants was performed using UPLC-ESI-MS/MS, RNA sequencing and annotation, and bioinformatic analysis of transcriptome data. Results The levels of 830 metabolites were determined. A total of 291 differentially accumulated metabolites (DAMs) between Panax pseudo-ginseng var. elegantior and Panax japonicas (Group A), with 73 upregulated and 218 downregulated. A total of 331 DAMs (110 upregulated and 221 downregulated) were found between Panax pseudoginseng and Panax japonicas (group B). There were 160 DAMs (102 up-regulated and 58 down-regulated) between Panax pseudoginseng and Panax pseudo-ginseng var. elegantior (group C). In addition, RNA sequencing was performed in the above three ways. A total of 16,074 differential expression genes (DEGs) were detected between Group A, in which 7,723 genes were upregulated and 8,351 genes were downregulated by RNA sequencing. Similarly, 15,705 genes were differentially expressed between group B, in which 7,436 genes were upregulated and 8,269 genes were downregulated. However, only 1,294 genes were differentially expressed between group C, in which 531 genes were upregulated and 763 genes were downregulated. We performed differential gene analysis on three groups of samples according to the Venn diagram and found that 181 differential genes were present. A total of 3,698 and 2,834 unique genes were in groups A and B, while 130 unique genes were in group C. Conclusions This study provides metabolome and transcriptome information for three bead ginseng plants. The analysis of the metabolite content showed differences in the attributes of the …
format: application/pdf
format: text/html
creator: Yihan Ye
creator: Nan Ma
creator: Yidan Peng
creator: Ying Chen
creator: Yuqu Zhang
creator: Shuyan Zhao
creator: Wei Ren
creator: Yonggang Yan
creator: Gang Zhang
creator: Xinjie Yang
creator: Xiujuan Peng
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.16034
publisher: PeerJ Inc.
rights: © 2023 Ye et al.
abstract: Objective The classification and clinical usage of the different species of bead ginseng are often confused. Therefore, we conducted an integrated metabolomics and transcriptome analysis of three main species of Panax, including Panax japonicas, Panax pseudoginseng, and Panax pseudo-ginseng var. elegantior. Methods A broad metabolome and transcriptome analysis for three origins of bead ginseng plants was performed using UPLC-ESI-MS/MS, RNA sequencing and annotation, and bioinformatic analysis of transcriptome data. Results The levels of 830 metabolites were determined. A total of 291 differentially accumulated metabolites (DAMs) between Panax pseudo-ginseng var. elegantior and Panax japonicas (Group A), with 73 upregulated and 218 downregulated. A total of 331 DAMs (110 upregulated and 221 downregulated) were found between Panax pseudoginseng and Panax japonicas (group B). There were 160 DAMs (102 up-regulated and 58 down-regulated) between Panax pseudoginseng and Panax pseudo-ginseng var. elegantior (group C). In addition, RNA sequencing was performed in the above three ways. A total of 16,074 differential expression genes (DEGs) were detected between Group A, in which 7,723 genes were upregulated and 8,351 genes were downregulated by RNA sequencing. Similarly, 15,705 genes were differentially expressed between group B, in which 7,436 genes were upregulated and 8,269 genes were downregulated. However, only 1,294 genes were differentially expressed between group C, in which 531 genes were upregulated and 763 genes were downregulated. We performed differential gene analysis on three groups of samples according to the Venn diagram and found that 181 differential genes were present. A total of 3,698 and 2,834 unique genes were in groups A and B, while 130 unique genes were in group C. Conclusions This study provides metabolome and transcriptome information for three bead ginseng plants. The analysis of the metabolite content showed differences in the attributes of the …
bibliographic citation: Ye et al. (2023) Metabolome and transcriptome analyses identify the characteristics and expression of related saponins of the three genealogical plants of bead ginseng. PeerJ 11:e16034 https://doi.org/10.7717/peerj.16034
date submitted: 2023-04-06
date accepted: 2023-08-14
issued: 2023-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Yihan
author list: Agent
  family name: Ma
  given name: Nan
author list: Agent
  family name: Peng
  given name: Yidan
author list: Agent
  family name: Chen
  given name: Ying
author list: Agent
  family name: Zhang
  given name: Yuqu
author list: Agent
  family name: Zhao
  given name: Shuyan
author list: Agent
  family name: Ren
  given name: Wei
author list: Agent
  family name: Yan
  given name: Yonggang
author list: Agent
  family name: Zhang
  given name: Gang
author list: Agent
  family name: Yang
  given name: Xinjie
author list: Agent
  family name: Peng
  given name: Xiujuan
doi: 10.7717/peerj.16034
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-01
copyright: © 2023 Ye et al.
attribution name: Ye et al.

Over 20% of marine fishes shifting in the North and Barents Seas, but not in the Norwegian Sea
type: item
type: AcademicArticle
description: Climate warming generally induces poleward range expansions and equatorward range contractions of species’ environmental niches on a global scale. Here, we examined the direction and magnitude of species biomass centroid geographic shifts in relation to temperature and depth for 83 fish species in 9,522 standardised research trawls from the North Sea (1998–2020) to the Norwegian (2000–2020) and Barents Sea (2004–2020). We detected an overall significant northward shift of the marine fish community biomass in the North Sea, and individual species northward shifts in the Barents and North Seas, in 20% and 25% of the species’ biomass centroids in each respective region. We did not detect overall community shifts in the Norwegian Sea, where two species (8%) shifted in each direction (northwards and southwards). Among 9 biological traits, species biogeographic assignation, preferred temperature, age at maturity and maximum depth were significant explanatory variables for species latitudinal shifts in some of the study areas, and Arctic species shifted significantly faster than boreal species in the Barents Sea. Overall, our results suggest a strong influence of other factors, such as biological interactions, in determining several species’ recent geographic shifts.
format: application/pdf
format: text/html
creator: Cesc Gordó-Vilaseca
creator: Laurene Pecuchet
creator: Marta Coll
creator: Henning Reiss
creator: Alexander Jüterbock
creator: Mark John Costello
subject: Aquaculture
subject: Fisheries and Fish Science
subject: Biodiversity
subject: Biogeography
subject: Marine Biology
description: doi:10.7717/peerj.15801
publisher: PeerJ Inc.
rights: © 2023 Gordó-Vilaseca et al.
abstract: Climate warming generally induces poleward range expansions and equatorward range contractions of species’ environmental niches on a global scale. Here, we examined the direction and magnitude of species biomass centroid geographic shifts in relation to temperature and depth for 83 fish species in 9,522 standardised research trawls from the North Sea (1998–2020) to the Norwegian (2000–2020) and Barents Sea (2004–2020). We detected an overall significant northward shift of the marine fish community biomass in the North Sea, and individual species northward shifts in the Barents and North Seas, in 20% and 25% of the species’ biomass centroids in each respective region. We did not detect overall community shifts in the Norwegian Sea, where two species (8%) shifted in each direction (northwards and southwards). Among 9 biological traits, species biogeographic assignation, preferred temperature, age at maturity and maximum depth were significant explanatory variables for species latitudinal shifts in some of the study areas, and Arctic species shifted significantly faster than boreal species in the Barents Sea. Overall, our results suggest a strong influence of other factors, such as biological interactions, in determining several species’ recent geographic shifts.
bibliographic citation: Gordó-Vilaseca et al. (2023) Over 20% of marine fishes shifting in the North and Barents Seas, but not in the Norwegian Sea. PeerJ 11:e15801 https://doi.org/10.7717/peerj.15801
date submitted: 2023-01-31
date accepted: 2023-07-06
issued: 2023-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gordó-Vilaseca
  given name: Cesc
author list: Agent
  family name: Pecuchet
  given name: Laurene
author list: Agent
  family name: Coll
  given name: Marta
author list: Agent
  family name: Reiss
  given name: Henning
author list: Agent
  family name: Jüterbock
  given name: Alexander
author list: Agent
  family name: Costello
  given name: Mark John
doi: 10.7717/peerj.15801
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-31
copyright: © 2023 Gordó-Vilaseca et al.
attribution name: Gordó-Vilaseca et al.

Urine based near-infrared spectroscopy analysis reveals a noninvasive and convenient diagnosis method for cancers: a pilot study
type: item
type: AcademicArticle
description: Background The challenges in cancer diagnosis underline the need for continued research and development of new diagnostic tools and methods. This study aims to explore an effective, noninvasive, and convenient diagnostic tool using urine based near-infrared spectroscopy (NIRS) analysis combined with machine learning algorithm. Methods Urine samples were collected from a total of 327 participants, including 181 cancer cases and 146 healthy controls. These participants were randomly spit into train set (n = 218) and test set (n = 109). NIRS analysis (4,000 ∼10,000 cm−1) was performed for each sample in both train and test sets. Five pretreatment methods, including Savitzky-Golay (SG) smoothing, multiplicative scatter correction (MSC), baseline removal (BSL) with fitting polynomials to be used as baselines, the first derivative (DERIV1), and the second derivative (DERIV2), and combination with “scaling” and “center”, were investigated. Then partial least-squares (PLS) and linear support-vector machine (SVM) classification models were established, and prediction performance was evaluated in test set. Results NIRS had greatly overlapping in peaks, and PCA analysis failed in separation between cancers and healthy controls. In modeling with urine based NIRS data, PLS model showed its highest prediction accuracy of 0.780, with DERIV2, “scaling” and “center” pretreatment, while linear SVM displayed its best prediction accuracy of 0.844, with raw NIRS. With optimization in SVM, the prediction accuracy could improve to 0.862, when the top 262 features were involved as variables. Discussion This pilot study combining urine based NIRS analysis and machine learning is effective and convenient that might facilitate in cancer diagnosis, encouraging further evaluation with a large-size multi-center study.
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creator: Jing Zhu
creator: Siyu Zhang
creator: Ruting Wang
creator: Ruhua Fang
creator: Lan Lei
creator: Ji Zheng
creator: Zhongjian Chen
subject: Epidemiology
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.15895
publisher: PeerJ Inc.
rights: © 2023 Zhu et al.
abstract: Background The challenges in cancer diagnosis underline the need for continued research and development of new diagnostic tools and methods. This study aims to explore an effective, noninvasive, and convenient diagnostic tool using urine based near-infrared spectroscopy (NIRS) analysis combined with machine learning algorithm. Methods Urine samples were collected from a total of 327 participants, including 181 cancer cases and 146 healthy controls. These participants were randomly spit into train set (n = 218) and test set (n = 109). NIRS analysis (4,000 ∼10,000 cm−1) was performed for each sample in both train and test sets. Five pretreatment methods, including Savitzky-Golay (SG) smoothing, multiplicative scatter correction (MSC), baseline removal (BSL) with fitting polynomials to be used as baselines, the first derivative (DERIV1), and the second derivative (DERIV2), and combination with “scaling” and “center”, were investigated. Then partial least-squares (PLS) and linear support-vector machine (SVM) classification models were established, and prediction performance was evaluated in test set. Results NIRS had greatly overlapping in peaks, and PCA analysis failed in separation between cancers and healthy controls. In modeling with urine based NIRS data, PLS model showed its highest prediction accuracy of 0.780, with DERIV2, “scaling” and “center” pretreatment, while linear SVM displayed its best prediction accuracy of 0.844, with raw NIRS. With optimization in SVM, the prediction accuracy could improve to 0.862, when the top 262 features were involved as variables. Discussion This pilot study combining urine based NIRS analysis and machine learning is effective and convenient that might facilitate in cancer diagnosis, encouraging further evaluation with a large-size multi-center study.
bibliographic citation: Zhu et al. (2023) Urine based near-infrared spectroscopy analysis reveals a noninvasive and convenient diagnosis method for cancers: a pilot study. PeerJ 11:e15895 https://doi.org/10.7717/peerj.15895
date submitted: 2023-05-26
date accepted: 2023-07-24
issued: 2023-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Jing
author list: Agent
  family name: Zhang
  given name: Siyu
author list: Agent
  family name: Wang
  given name: Ruting
author list: Agent
  family name: Fang
  given name: Ruhua
author list: Agent
  family name: Lei
  given name: Lan
author list: Agent
  family name: Zheng
  given name: Ji
author list: Agent
  family name: Chen
  given name: Zhongjian
doi: 10.7717/peerj.15895
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-31
copyright: ©2023 Zhu et al.
attribution name: Zhu et al.

A decade of study on the condition of western Cuban coral reefs, with low human impact
type: item
type: AcademicArticle
description: Background The long-time study of coral reefs with low human impacts can provide information on the effects of regional pressures like climate change, and is an opportunity to document how these pressures are reflected in coral communities. An example of minimal local anthropogenic impacts are the Guanahacabibes coral reefs, located in the westernmost region of Cuba. The objectives of this study were: to evaluate the temporal variability of six benthic biological indicators of coral reefs, and to explore the possible relationship between predictive abiotic variables and biological response variables. Methods Four coral reef sites were sampled between 2008 and 2017, to analyze biological indicators (living coral cover, fleshy algae index, coral species richness, coral species abundance, coral trait groups species abundance, Functional Reef Index). Seven abiotic variables (wave exposure, sea surface temperature, degree heating week, chlorophyll-a concentration, particulate organic carbon, photosynthetically available radiation, and the diffuse attenuation coefficient) were compiled between 2007 and 2016, from remote sensing datasets, to analyze their relationship with the biological indicators. Permanova statistical analysis was used to evaluate trends in biological variables between sites and years, and Routine Analysis Based on Linear Distances (DISTLM) was used to explore some dependencies between biotic and abiotic variables. Results We found significant variability in the temporal analysis, with a decrease in living coral cover, a decline in the predominance of the branching and massive framework reef-building species, a decline in Orbicella species abundance, and an increase in the fleshy algae index. Some abiotic variables (average of degree heating weeks, standard deviation of the diffuse attenuation coefficient, average of the sea surface temperature, among others) significantly explained the variability of biological indicators; however, determination coeffi…
format: application/pdf
format: text/html
creator: Hansel Caballero-Aragón
creator: Susana Perera-Valderrama
creator: Dorka Cobián-Rojas
creator: Zaimiuri Hernández Gonzalez
creator: Juliett González Méndez
creator: Elena De la Guardia
subject: Biodiversity
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.15953
publisher: PeerJ Inc.
rights: © 2023 Caballero-Aragón et al.
abstract: Background The long-time study of coral reefs with low human impacts can provide information on the effects of regional pressures like climate change, and is an opportunity to document how these pressures are reflected in coral communities. An example of minimal local anthropogenic impacts are the Guanahacabibes coral reefs, located in the westernmost region of Cuba. The objectives of this study were: to evaluate the temporal variability of six benthic biological indicators of coral reefs, and to explore the possible relationship between predictive abiotic variables and biological response variables. Methods Four coral reef sites were sampled between 2008 and 2017, to analyze biological indicators (living coral cover, fleshy algae index, coral species richness, coral species abundance, coral trait groups species abundance, Functional Reef Index). Seven abiotic variables (wave exposure, sea surface temperature, degree heating week, chlorophyll-a concentration, particulate organic carbon, photosynthetically available radiation, and the diffuse attenuation coefficient) were compiled between 2007 and 2016, from remote sensing datasets, to analyze their relationship with the biological indicators. Permanova statistical analysis was used to evaluate trends in biological variables between sites and years, and Routine Analysis Based on Linear Distances (DISTLM) was used to explore some dependencies between biotic and abiotic variables. Results We found significant variability in the temporal analysis, with a decrease in living coral cover, a decline in the predominance of the branching and massive framework reef-building species, a decline in Orbicella species abundance, and an increase in the fleshy algae index. Some abiotic variables (average of degree heating weeks, standard deviation of the diffuse attenuation coefficient, average of the sea surface temperature, among others) significantly explained the variability of biological indicators; however, determination coeffi…
bibliographic citation: Caballero-Aragón et al. (2023) A decade of study on the condition of western Cuban coral reefs, with low human impact. PeerJ 11:e15953 https://doi.org/10.7717/peerj.15953
date submitted: 2023-01-03
date accepted: 2023-08-01
issued: 2023-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Caballero-Aragón
  given name: Hansel
author list: Agent
  family name: Perera-Valderrama
  given name: Susana
author list: Agent
  family name: Cobián-Rojas
  given name: Dorka
author list: Agent
  family name: Hernández Gonzalez
  given name: Zaimiuri
author list: Agent
  family name: González Méndez
  given name: Juliett
author list: Agent
  family name: De la Guardia
  given name: Elena
doi: 10.7717/peerj.15953
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-31
copyright: ©2023 Caballero-Aragón et al.
attribution name: Caballero-Aragón et al.

Effectiveness of virtual reality on activities of daily living in children with cerebral palsy: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background No meta-analysis has been conducted on the effect of specific virtual reality (VR) treatment modes on activities of daily living (ADL) in children with cerebral palsy (CP). Therefore, this study aimed to confirm whether VR therapy is effective in improving ADL in children with CP according to subgroups. Methodology Literature published in the Cumulated Index to Nursing and Allied Health Literature (CINAHL), Embase, the Physiotherapy Evidence Database (PEDro), and PubMed was reviewed, and Risk of Bias 2.0 (RoB 2) was used to evaluate the quality of the literature. A funnel plot was visually observed to confirm publication bias, supplemented with Egger’s regression test. Data analysis was performed using R version 4.2.1. Subgroup analysis was performed according to the Gross Motor Function Classification System (GMFCS), the Manual Ability Classification System (MACS), treatment minutes per week, treatment period, age, and RoB. Results Eleven of 2,978 studies were included, and the overall effect size was 0.37 (95% confidence interval = 0.17–0.57). Regarding GMFCS, effect sizes of 0.41 and 0.33 was observed for the low- and high-function groups, respectively. For MACS, 0.27 and 0.43 were observed for the low and high-function groups. Regarding treatment minutes per week, the values were 0.22, 0.44, and 0.27 in the 1–100, 101–200, and 201–300 min groups, respectively. In the classification according to age, 0.29 was observed for school-age children and 0.98 for preschool children. Lastly, in the classification according to the RoB, 0.52, −0.01, and 0.23 indicated studies with low risk, some concern, and high risk, respectively. Conclusions The highest effect was observed when VR was applied within 6 weeks of 101-200 per week. Therefore, it is suggested that if the results of this review are applied to children with cerebral palsy in the community, it will be an effective intervention method. Systematic review registration PROPEROS (registration number CRD4202…
format: application/pdf
format: text/html
creator: YongGu Han
creator: SunWook Park
subject: Drugs and Devices
subject: Neurology
subject: Pediatrics
subject: Rehabilitation
description: doi:10.7717/peerj.15964
publisher: PeerJ Inc.
rights: © 2023 Han and Park
abstract: Background No meta-analysis has been conducted on the effect of specific virtual reality (VR) treatment modes on activities of daily living (ADL) in children with cerebral palsy (CP). Therefore, this study aimed to confirm whether VR therapy is effective in improving ADL in children with CP according to subgroups. Methodology Literature published in the Cumulated Index to Nursing and Allied Health Literature (CINAHL), Embase, the Physiotherapy Evidence Database (PEDro), and PubMed was reviewed, and Risk of Bias 2.0 (RoB 2) was used to evaluate the quality of the literature. A funnel plot was visually observed to confirm publication bias, supplemented with Egger’s regression test. Data analysis was performed using R version 4.2.1. Subgroup analysis was performed according to the Gross Motor Function Classification System (GMFCS), the Manual Ability Classification System (MACS), treatment minutes per week, treatment period, age, and RoB. Results Eleven of 2,978 studies were included, and the overall effect size was 0.37 (95% confidence interval = 0.17–0.57). Regarding GMFCS, effect sizes of 0.41 and 0.33 was observed for the low- and high-function groups, respectively. For MACS, 0.27 and 0.43 were observed for the low and high-function groups. Regarding treatment minutes per week, the values were 0.22, 0.44, and 0.27 in the 1–100, 101–200, and 201–300 min groups, respectively. In the classification according to age, 0.29 was observed for school-age children and 0.98 for preschool children. Lastly, in the classification according to the RoB, 0.52, −0.01, and 0.23 indicated studies with low risk, some concern, and high risk, respectively. Conclusions The highest effect was observed when VR was applied within 6 weeks of 101-200 per week. Therefore, it is suggested that if the results of this review are applied to children with cerebral palsy in the community, it will be an effective intervention method. Systematic review registration PROPEROS (registration number CRD4202…
bibliographic citation: Han et al. (2023) Effectiveness of virtual reality on activities of daily living in children with cerebral palsy: a systematic review and meta-analysis. PeerJ 11:e15964 https://doi.org/10.7717/peerj.15964
date submitted: 2023-04-20
date accepted: 2023-08-04
issued: 2023-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: YongGu
author list: Agent
  family name: Park
  given name: SunWook
doi: 10.7717/peerj.15964
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-31
copyright: ©2023 Han and Park
attribution name: Han and Park

Accumulation and transfer of polystyrene microplastics in Solanum nigrum seedlings
type: item
type: AcademicArticle
description: Microplastic (MP) pollution is lately receiving increasing attention owing to its harmful impact on terrestrial ecosystems. In this microcosm study, we assessed the uptake and transfer of MPs in Solanum nigrum seedlings exposed to 50 mg L–1 of 0.2-µm polystyrene (PS) beads for 30 d. Confocal laser scanning micrographs helped detect highly intense red fluorescence signals from PS-MP beads in S. nigrum root compared with the controls. Confocal images revealed that the PS beads were primarily distributed in the epidermis and xylem of roots and vascular systems of stems and leaves. Scanning electron microscopy showed that PS beads were scattered on the cell walls of the root xylem and leaf vascular system. Few PS beads were transferred from roots to stems and leaves via the vascular system following the transpiration stream. In conclusion, our findings showed that PS beads accumulated in S. nigrum roots and were transferred from the roots to the aerial parts.
format: application/pdf
format: text/html
creator: JuKui Zhang
creator: Lian Cao
creator: Xiaoyan Zhu
creator: Hanbo Li
creator: Gang Duan
creator: Ying Wang
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Toxicology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.15967
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Microplastic (MP) pollution is lately receiving increasing attention owing to its harmful impact on terrestrial ecosystems. In this microcosm study, we assessed the uptake and transfer of MPs in Solanum nigrum seedlings exposed to 50 mg L–1 of 0.2-µm polystyrene (PS) beads for 30 d. Confocal laser scanning micrographs helped detect highly intense red fluorescence signals from PS-MP beads in S. nigrum root compared with the controls. Confocal images revealed that the PS beads were primarily distributed in the epidermis and xylem of roots and vascular systems of stems and leaves. Scanning electron microscopy showed that PS beads were scattered on the cell walls of the root xylem and leaf vascular system. Few PS beads were transferred from roots to stems and leaves via the vascular system following the transpiration stream. In conclusion, our findings showed that PS beads accumulated in S. nigrum roots and were transferred from the roots to the aerial parts.
bibliographic citation: Zhang et al. (2023) Accumulation and transfer of polystyrene microplastics in Solanum nigrum seedlings. PeerJ 11:e15967 https://doi.org/10.7717/peerj.15967
date submitted: 2023-03-07
date accepted: 2023-08-04
issued: 2023-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: JuKui
author list: Agent
  family name: Cao
  given name: Lian
author list: Agent
  family name: Zhu
  given name: Xiaoyan
author list: Agent
  family name: Li
  given name: Hanbo
author list: Agent
  family name: Duan
  given name: Gang
author list: Agent
  family name: Wang
  given name: Ying
doi: 10.7717/peerj.15967
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-31
copyright: ©2023 Zhang et al.
attribution name: Zhang et al.

Evaluation of the correlation of dorsal root ganglia and spinal nerves with clinical symptoms in patients with postherpetic neuralgia using magnetic resonance neurography
type: item
type: AcademicArticle
description: Purpose To assess changes of dorsal root ganglia (DRG) and spinal nerves in patients with postherpetic neuralgia (PHN), and investigate the correlation between DRG morphology and clinical symptoms in PHN patients using magnetic resonance neurography (MRN). Methods In this case-control study, forty-nine lesioned DRG in 30 patients and 49 normal DRG in 30 well-matched (age, sex, height, weight) healthy controls were assessed. Clinical symptoms of patients (pain, allodynia, itching, and numbness) were assessed. MRN features (DRG volume (VDRG), the largest diameter (Dmax) of spinal nerves, signal intensity of DRG and spinal nerves (M-value)) were measured in all participants. Multilinear regression analysis was used to evaluate the relationship between the DRG morphology and clinical symptoms in patients. Results The volume and relative M-value of lesioned DRG in patients were significantly higher than those on the same side of healthy controls (p = 0.013, p < 0.001, respectively). The mean Dmax and relative M-value of spinal nerves on the lesioned side were significantly higher than those on the contralateral and same side of healthy controls (p < 0.0001, p = 0.0001, p = 0.0011, p = 0.0053, respectively). No difference was found between the mean VDRG of the lesioned and contralateral sides. Multiple linear regression analysis revealed that disease duration was independent risk factor for the maximum rate of VDRG differences (p = 0.013). Conclusions DRG and spinal nerves on the lesioned side are swollen during PHN. Disease duration is an independent risk factor for morphological differences in the lesioned DRG of PHN patients. This study provides important guidance for individualized treatments of PHN.
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creator: Xueqin Cao
creator: Bo Jiao
creator: Donglin Wen
creator: Guangyou Duan
creator: Mi Zhang
creator: Caixia Zhang
creator: Gang Wu
creator: Xianwei Zhang
subject: Anesthesiology and Pain Management
subject: Anatomy and Physiology
subject: Dermatology
subject: Nephrology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.15998
publisher: PeerJ Inc.
rights: © 2023 Cao et al.
abstract: Purpose To assess changes of dorsal root ganglia (DRG) and spinal nerves in patients with postherpetic neuralgia (PHN), and investigate the correlation between DRG morphology and clinical symptoms in PHN patients using magnetic resonance neurography (MRN). Methods In this case-control study, forty-nine lesioned DRG in 30 patients and 49 normal DRG in 30 well-matched (age, sex, height, weight) healthy controls were assessed. Clinical symptoms of patients (pain, allodynia, itching, and numbness) were assessed. MRN features (DRG volume (VDRG), the largest diameter (Dmax) of spinal nerves, signal intensity of DRG and spinal nerves (M-value)) were measured in all participants. Multilinear regression analysis was used to evaluate the relationship between the DRG morphology and clinical symptoms in patients. Results The volume and relative M-value of lesioned DRG in patients were significantly higher than those on the same side of healthy controls (p = 0.013, p < 0.001, respectively). The mean Dmax and relative M-value of spinal nerves on the lesioned side were significantly higher than those on the contralateral and same side of healthy controls (p < 0.0001, p = 0.0001, p = 0.0011, p = 0.0053, respectively). No difference was found between the mean VDRG of the lesioned and contralateral sides. Multiple linear regression analysis revealed that disease duration was independent risk factor for the maximum rate of VDRG differences (p = 0.013). Conclusions DRG and spinal nerves on the lesioned side are swollen during PHN. Disease duration is an independent risk factor for morphological differences in the lesioned DRG of PHN patients. This study provides important guidance for individualized treatments of PHN.
bibliographic citation: Cao et al. (2023) Evaluation of the correlation of dorsal root ganglia and spinal nerves with clinical symptoms in patients with postherpetic neuralgia using magnetic resonance neurography. PeerJ 11:e15998 https://doi.org/10.7717/peerj.15998
date submitted: 2023-04-28
date accepted: 2023-08-08
issued: 2023-08-31
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Xueqin
author list: Agent
  family name: Jiao
  given name: Bo
author list: Agent
  family name: Wen
  given name: Donglin
author list: Agent
  family name: Duan
  given name: Guangyou
author list: Agent
  family name: Zhang
  given name: Mi
author list: Agent
  family name: Zhang
  given name: Caixia
author list: Agent
  family name: Wu
  given name: Gang
author list: Agent
  family name: Zhang
  given name: Xianwei
doi: 10.7717/peerj.15998
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-31
copyright: © 2023 Cao et al.
attribution name: Cao et al.

A multi-sensor array for detecting and analyzing nocturnal avian migration
type: item
type: AcademicArticle
description: Avian migration has fascinated humans for centuries. Insights into the lives of migrant birds are often elusive; however, recent, standalone technological innovations have revolutionized our understanding of this complex biological phenomenon. A future challenge for following these highly mobile animals is the necessity of bringing multiple technologies together to capture a more complete understanding of their movements. Here, we designed a proof-of-concept multi-sensor array consisting of two weather surveillance radars (WSRs), one local and one regional, an autonomous moon-watching sensor capable of detecting birds flying in front of the moon, and an autonomous recording unit (ARU) capable of recording avian nocturnal flight calls. We deployed this array at a field site in central Oklahoma on select nights in March, April, and May of 2021 and integrated data from this array with wind data corresponding to this site to examine the influence of wind on the movements of spring migrants aloft across these spring nights. We found that regional avian migration intensity is statistically significantly negatively correlated with wind velocity, in line with previous research. Furthermore, we found evidence suggesting that when faced with strong, southerly winds, migrants take advantage of these conditions by adjusting their flight direction by drifting. Importantly, we found that most of the migration intensities detected by the sensors were intercorrelated, except when this correlation could not be ascertained because we lacked the sample size to do so. This study demonstrates the potential for multi-sensor arrays to reveal the detailed ways in which avian migrants move in response to changing atmospheric conditions while in flight.
format: application/pdf
format: text/html
creator: Alva I. Strand
creator: Eli S. Bridge
creator: Jeffrey F. Kelly
creator: Phillip M. Stepanian
creator: David J. Bodine
creator: James R. Soto
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Data Science
subject: Biosphere Interactions
description: doi:10.7717/peerj.15622
publisher: PeerJ Inc.
rights: © 2023 Strand et al.
abstract: Avian migration has fascinated humans for centuries. Insights into the lives of migrant birds are often elusive; however, recent, standalone technological innovations have revolutionized our understanding of this complex biological phenomenon. A future challenge for following these highly mobile animals is the necessity of bringing multiple technologies together to capture a more complete understanding of their movements. Here, we designed a proof-of-concept multi-sensor array consisting of two weather surveillance radars (WSRs), one local and one regional, an autonomous moon-watching sensor capable of detecting birds flying in front of the moon, and an autonomous recording unit (ARU) capable of recording avian nocturnal flight calls. We deployed this array at a field site in central Oklahoma on select nights in March, April, and May of 2021 and integrated data from this array with wind data corresponding to this site to examine the influence of wind on the movements of spring migrants aloft across these spring nights. We found that regional avian migration intensity is statistically significantly negatively correlated with wind velocity, in line with previous research. Furthermore, we found evidence suggesting that when faced with strong, southerly winds, migrants take advantage of these conditions by adjusting their flight direction by drifting. Importantly, we found that most of the migration intensities detected by the sensors were intercorrelated, except when this correlation could not be ascertained because we lacked the sample size to do so. This study demonstrates the potential for multi-sensor arrays to reveal the detailed ways in which avian migrants move in response to changing atmospheric conditions while in flight.
bibliographic citation: Strand et al. (2023) A multi-sensor array for detecting and analyzing nocturnal avian migration. PeerJ 11:e15622 https://doi.org/10.7717/peerj.15622
date submitted: 2022-08-15
date accepted: 2023-06-01
issued: 2023-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Strand
  given name: Alva I.
author list: Agent
  family name: Bridge
  given name: Eli S.
author list: Agent
  family name: Kelly
  given name: Jeffrey F.
author list: Agent
  family name: Stepanian
  given name: Phillip M.
author list: Agent
  family name: Bodine
  given name: David J.
author list: Agent
  family name: Soto
  given name: James R.
doi: 10.7717/peerj.15622
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-30
copyright: © 2023 Strand et al.
attribution name: Strand et al.

Adrenal SGLT1 or SGLT2 as predictors of atherosclerosis under chronic stress based on a computer algorithm
type: item
type: AcademicArticle
description: Background Chronic stress promotes the development of atherosclerosis, causing disruptions in the body’s hormone levels and changes in the structural function of organs. Objective The purpose of this study was to investigate the pathological changes in the adrenal gland in a model of atherosclerosis under chronic stress and to verify the expression levels of Sodium-glucose cotransporter (SGLT) 1 and SGLT2 in the adrenal gland and their significance in the changes of adrenal gland. Methods The model mice were constructed by chronic unpredictable stress, high-fat diet, and Apoe-/- knockout, and they were tested behaviorally at 0, 4, 8 and 12 weeks. The state of the abdominal artery was examined by ultrasound, and the pathological changes of the aorta and adrenal glands were observed by histological methods, and the expression levels and distribution of SGLT1 and SGLT2 in the adrenal gland were observed and analyzed by immunofluorescence and immunohistochemistry. The predictive value of SGLT1 and SGLT2 expression levels on intima-media thickness, internal diameter and adrenal abnormalities were verified by receiver operating characteristic (ROC) curves, support vector machine (SVM) and back-propagation (BP) neural network. Results The results showed that chronic stress mice had elevated expression levels of SGLT1 and SGLT2. The model mice developed thickening intima-media and smaller internal diameter in the aorta, and edema, reticular fiber rupture, increased adrenal glycogen content in the adrenal glands. More importantly, analysis of ROC, SVM and BP showed that SGLT1 and SGLT2 expression levels in the adrenal glands could predict the above changes in the aorta and were also sensitive and specific predictors of adrenal abnormalities. Conclusion SGLT1 and SGLT2 could be potential biomarkers of adrenal injury in atherosclerosis under chronic stress.
format: application/pdf
format: text/html
creator: Jianyi Li
creator: Lingbing Meng
creator: Dishan Wu
creator: Hongxuan Xu
creator: Xing Hu
creator: Gaifeng Hu
creator: Yuhui Chen
creator: Jiapei Xu
creator: Tao Gong
creator: Deping Liu
subject: Biochemistry
subject: Computational Biology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.15647
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background Chronic stress promotes the development of atherosclerosis, causing disruptions in the body’s hormone levels and changes in the structural function of organs. Objective The purpose of this study was to investigate the pathological changes in the adrenal gland in a model of atherosclerosis under chronic stress and to verify the expression levels of Sodium-glucose cotransporter (SGLT) 1 and SGLT2 in the adrenal gland and their significance in the changes of adrenal gland. Methods The model mice were constructed by chronic unpredictable stress, high-fat diet, and Apoe-/- knockout, and they were tested behaviorally at 0, 4, 8 and 12 weeks. The state of the abdominal artery was examined by ultrasound, and the pathological changes of the aorta and adrenal glands were observed by histological methods, and the expression levels and distribution of SGLT1 and SGLT2 in the adrenal gland were observed and analyzed by immunofluorescence and immunohistochemistry. The predictive value of SGLT1 and SGLT2 expression levels on intima-media thickness, internal diameter and adrenal abnormalities were verified by receiver operating characteristic (ROC) curves, support vector machine (SVM) and back-propagation (BP) neural network. Results The results showed that chronic stress mice had elevated expression levels of SGLT1 and SGLT2. The model mice developed thickening intima-media and smaller internal diameter in the aorta, and edema, reticular fiber rupture, increased adrenal glycogen content in the adrenal glands. More importantly, analysis of ROC, SVM and BP showed that SGLT1 and SGLT2 expression levels in the adrenal glands could predict the above changes in the aorta and were also sensitive and specific predictors of adrenal abnormalities. Conclusion SGLT1 and SGLT2 could be potential biomarkers of adrenal injury in atherosclerosis under chronic stress.
bibliographic citation: Li et al. (2023) Adrenal SGLT1 or SGLT2 as predictors of atherosclerosis under chronic stress based on a computer algorithm. PeerJ 11:e15647 https://doi.org/10.7717/peerj.15647
date submitted: 2023-03-23
date accepted: 2023-06-06
issued: 2023-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jianyi
author list: Agent
  family name: Meng
  given name: Lingbing
author list: Agent
  family name: Wu
  given name: Dishan
author list: Agent
  family name: Xu
  given name: Hongxuan
author list: Agent
  family name: Hu
  given name: Xing
author list: Agent
  family name: Hu
  given name: Gaifeng
author list: Agent
  family name: Chen
  given name: Yuhui
author list: Agent
  family name: Xu
  given name: Jiapei
author list: Agent
  family name: Gong
  given name: Tao
author list: Agent
  family name: Liu
  given name: Deping
doi: 10.7717/peerj.15647
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-30
copyright: ©2023 Li et al.
attribution name: Li et al.

RNA N6-methyladenosine reader IGF2BP3 promotes acute myeloid leukemia progression by controlling stabilization of EPOR mRNA
type: item
type: AcademicArticle
description: Background N6-methyladenosine (m6A) methylation epigenetically regulates normal hematopoiesis and plays a role in the pathogenesis of acute myeloid leukemia (AML). However, its potential value for prognosis remains elusive. Methods Analysis of the datasets downloaded from The Cancer Genome Atlas and Genotype Tissue Expression databases revealed that the expression level of 20 regulators related to m6A RNA methylation differ between patients with AML and normal individuals. A prognostic risk model with three genes (YTHDF3, IGF2BP3, and HNRNPA2B1) was developed using univariate Cox regression and the least absolute shrinkage and selection operator Cox regression methods. Results This established signature demonstrated good predictive efficacy with an area under the curve of 0.892 and 0.731 in the training cohort and the validation cohort, respectively. Patients with AML and an increased level of Insulin growth factor 2 mRNA binding protein 3 (IGF2BP3) expression exhibited a poor prognosis. IGF2BP3 knockdown significantly induced G0/G1 phase arrest and inhibited cell proliferation, apoptosis, and/or differentiation. Further, the JAK/STAT pathway may be involved in the regulation of EPOR expression by IGF2BP3-mediated m6A RNA methylation. Conclusion These findings indicate that IGF2BP3 plays a carcinogenic role in AML, implying that it can predict patient survival and could be an effective strategy for AML therapy.
format: application/pdf
format: text/html
creator: Jin Fan
creator: Mengqi Zhuang
creator: Wei Fan
creator: Ming Hou
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Hematology
subject: Oncology
description: doi:10.7717/peerj.15706
publisher: PeerJ Inc.
rights: © 2023 Fan et al.
abstract: Background N6-methyladenosine (m6A) methylation epigenetically regulates normal hematopoiesis and plays a role in the pathogenesis of acute myeloid leukemia (AML). However, its potential value for prognosis remains elusive. Methods Analysis of the datasets downloaded from The Cancer Genome Atlas and Genotype Tissue Expression databases revealed that the expression level of 20 regulators related to m6A RNA methylation differ between patients with AML and normal individuals. A prognostic risk model with three genes (YTHDF3, IGF2BP3, and HNRNPA2B1) was developed using univariate Cox regression and the least absolute shrinkage and selection operator Cox regression methods. Results This established signature demonstrated good predictive efficacy with an area under the curve of 0.892 and 0.731 in the training cohort and the validation cohort, respectively. Patients with AML and an increased level of Insulin growth factor 2 mRNA binding protein 3 (IGF2BP3) expression exhibited a poor prognosis. IGF2BP3 knockdown significantly induced G0/G1 phase arrest and inhibited cell proliferation, apoptosis, and/or differentiation. Further, the JAK/STAT pathway may be involved in the regulation of EPOR expression by IGF2BP3-mediated m6A RNA methylation. Conclusion These findings indicate that IGF2BP3 plays a carcinogenic role in AML, implying that it can predict patient survival and could be an effective strategy for AML therapy.
bibliographic citation: Fan et al. (2023) RNA N6-methyladenosine reader IGF2BP3 promotes acute myeloid leukemia progression by controlling stabilization of EPOR mRNA. PeerJ 11:e15706 https://doi.org/10.7717/peerj.15706
date submitted: 2023-03-03
date accepted: 2023-06-15
issued: 2023-08-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Jin
author list: Agent
  family name: Zhuang
  given name: Mengqi
author list: Agent
  family name: Fan
  given name: Wei
author list: Agent
  family name: Hou
  given name: Ming
doi: 10.7717/peerj.15706
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-30
copyright: © 2023 Fan et al.
attribution name: Fan et al.

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