PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Construction and validation of a PANoptosis-related lncRNA signature for predicting prognosis and targeted drug response in thyroid cancer
items: Effects of home-based telerehabilitation on dynamic alterations in regional intrinsic neural activity and degree centrality in stroke patients
items: Wheat gibberellin oxidase genes and their functions in regulating tillering
items: Assessment of selection criteria using multi-year study for effective breeding program of Zingiber officinale L
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

Construction and validation of a PANoptosis-related lncRNA signature for predicting prognosis and targeted drug response in thyroid cancer
type: item
type: AcademicArticle
description: Thyroid cancer (TC) is the most prevalent malignancy of the endocrine system. PANoptosis, a newly discovered cell death pathway, is of interest in tumor research. However, the relationship between PANoptosis-related lncRNAs (PRlncRNAs) and TC remains unclear. The study aimed to develop a prognostic model based on PRlncRNAs in TC. Gene expression data of PANoptosis-associated genes and clinical information on TC from The Cancer Genome Atlas (TCGA) database were analyzed by Pearson correlation analysis, univariate/multivariate Cox analysis, and Lasso Cox regression analysis. A PRlncRNA signature was constructed and used to develop a nomogram to predict overall survival (OS). We further explored the correlation between the risk score and tumor immune microenvironment, immune checkpoints, and drug sensitivity. Moreover, we verified the expression and biological function of lncRNAs in TC cell lines. Finally, seven PRlncRNAs were used to construct a prognostic model for predicting the OS of TC patients. We found that the risk score was associated with the tumor microenvironment (TME) and the expression of critical immune checkpoints. In addition, we screened for drugs that high- or low-risk TC groups might be sensitive to. Quantitative real-time polymerase chain reaction (qRT-PCR) results showed differential expression of four PRlncRNAs (GAPLINC, IDI2-AS1, LINC02154, and RBPMS-AS1) between tumor and normal tissues. Besides, a GEO database (GSE33630) was used to verify the expression differences of PRLncRNAs in THCA tissues and normal tissues. Finally, RBPMS-AS1 was found to inhibit the proliferation and migration of TC cells. In conclusion, we developed a PANoptosis-related lncRNA prognostic risk model that offers a comprehensive understanding of TME status in patients with TC and establishes a foundation for the choice of sensitive medications and immunotherapy.
format: application/pdf
format: text/html
creator: Ruowen Li
creator: Mingjian Zhao
creator: Min Sun
creator: Chengxu Miao
creator: Jinghui Lu
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Oncology
description: doi:10.7717/peerj.15884
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Thyroid cancer (TC) is the most prevalent malignancy of the endocrine system. PANoptosis, a newly discovered cell death pathway, is of interest in tumor research. However, the relationship between PANoptosis-related lncRNAs (PRlncRNAs) and TC remains unclear. The study aimed to develop a prognostic model based on PRlncRNAs in TC. Gene expression data of PANoptosis-associated genes and clinical information on TC from The Cancer Genome Atlas (TCGA) database were analyzed by Pearson correlation analysis, univariate/multivariate Cox analysis, and Lasso Cox regression analysis. A PRlncRNA signature was constructed and used to develop a nomogram to predict overall survival (OS). We further explored the correlation between the risk score and tumor immune microenvironment, immune checkpoints, and drug sensitivity. Moreover, we verified the expression and biological function of lncRNAs in TC cell lines. Finally, seven PRlncRNAs were used to construct a prognostic model for predicting the OS of TC patients. We found that the risk score was associated with the tumor microenvironment (TME) and the expression of critical immune checkpoints. In addition, we screened for drugs that high- or low-risk TC groups might be sensitive to. Quantitative real-time polymerase chain reaction (qRT-PCR) results showed differential expression of four PRlncRNAs (GAPLINC, IDI2-AS1, LINC02154, and RBPMS-AS1) between tumor and normal tissues. Besides, a GEO database (GSE33630) was used to verify the expression differences of PRLncRNAs in THCA tissues and normal tissues. Finally, RBPMS-AS1 was found to inhibit the proliferation and migration of TC cells. In conclusion, we developed a PANoptosis-related lncRNA prognostic risk model that offers a comprehensive understanding of TME status in patients with TC and establishes a foundation for the choice of sensitive medications and immunotherapy.
bibliographic citation: Li et al. (2023) Construction and validation of a PANoptosis-related lncRNA signature for predicting prognosis and targeted drug response in thyroid cancer. PeerJ 11:e15884 https://doi.org/10.7717/peerj.15884
date submitted: 2023-04-12
date accepted: 2023-07-20
issued: 2023-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Ruowen
author list: Agent
  family name: Zhao
  given name: Mingjian
author list: Agent
  family name: Sun
  given name: Min
author list: Agent
  family name: Miao
  given name: Chengxu
author list: Agent
  family name: Lu
  given name: Jinghui
doi: 10.7717/peerj.15884
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-01
copyright: © 2023 Li et al.
attribution name: Li et al.

Effects of home-based telerehabilitation on dynamic alterations in regional intrinsic neural activity and degree centrality in stroke patients
type: item
type: AcademicArticle
description: Objective To explore the effects of home-based telerehabilitation (TR) on dynamic alterations in regional intrinsic neural activity and degree centrality in stroke patients by resting-state functional MRI (fMRI) methods. Methods The neuroimaging data of 52 stroke patients were analyzed. Dynamic regional spontaneous neural activity (dynamic amplitude of low-frequency fluctuations, dALFF; and dynamic regional homogeneity, dReHo) and dynamic degree centrality (dDC) were compared between the TR and conventional rehabilitation (CR) groups. A flexible factorial model was employed to investigate the expected effects. Results The patients in the TR group showed increased dALFF in the right precuneus and bilateral precentral gyrus (PreCG) and reduced dALFF in the right inferior parietal lobule by the analysis of main effects. Significant differences between groups were detected in the right precuneus, right fusiform gyrus and left middle frontal gyrus for dReHo and in the left cingulate gyrus, right middle temporal gyrus and left precuneus for dDC. A significant correlation was found in the TR group between the changed dALFF in the left PreCG and the changed Fugl-Meyer assessment (FMA) scores from baseline to postrehabilitation. Conclusions This study implied that home-based TR training can alter the patterns of dynamic spontaneous brain activity and functional connectivity in certain brain regions. The identification of key brain regions by neuroimaging indicators such as dynamic regional brain activity and degree centrality in the recovery process would provide a theoretical basis for noninvasive brain stimulation technology and strategies for formulating targeted rehabilitation programs for stroke patients with motor dysfunction.
format: application/pdf
format: text/html
creator: Jing Chen
creator: Jing Li
creator: Fenglei Qiao
creator: Zhang Shi
creator: Weiwei Lu
subject: Clinical Trials
subject: Neurology
subject: Radiology and Medical Imaging
subject: Rehabilitation
description: doi:10.7717/peerj.15903
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Objective To explore the effects of home-based telerehabilitation (TR) on dynamic alterations in regional intrinsic neural activity and degree centrality in stroke patients by resting-state functional MRI (fMRI) methods. Methods The neuroimaging data of 52 stroke patients were analyzed. Dynamic regional spontaneous neural activity (dynamic amplitude of low-frequency fluctuations, dALFF; and dynamic regional homogeneity, dReHo) and dynamic degree centrality (dDC) were compared between the TR and conventional rehabilitation (CR) groups. A flexible factorial model was employed to investigate the expected effects. Results The patients in the TR group showed increased dALFF in the right precuneus and bilateral precentral gyrus (PreCG) and reduced dALFF in the right inferior parietal lobule by the analysis of main effects. Significant differences between groups were detected in the right precuneus, right fusiform gyrus and left middle frontal gyrus for dReHo and in the left cingulate gyrus, right middle temporal gyrus and left precuneus for dDC. A significant correlation was found in the TR group between the changed dALFF in the left PreCG and the changed Fugl-Meyer assessment (FMA) scores from baseline to postrehabilitation. Conclusions This study implied that home-based TR training can alter the patterns of dynamic spontaneous brain activity and functional connectivity in certain brain regions. The identification of key brain regions by neuroimaging indicators such as dynamic regional brain activity and degree centrality in the recovery process would provide a theoretical basis for noninvasive brain stimulation technology and strategies for formulating targeted rehabilitation programs for stroke patients with motor dysfunction.
bibliographic citation: Chen et al. (2023) Effects of home-based telerehabilitation on dynamic alterations in regional intrinsic neural activity and degree centrality in stroke patients. PeerJ 11:e15903 https://doi.org/10.7717/peerj.15903
date submitted: 2023-04-09
date accepted: 2023-07-25
issued: 2023-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jing
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Qiao
  given name: Fenglei
author list: Agent
  family name: Shi
  given name: Zhang
author list: Agent
  family name: Lu
  given name: Weiwei
doi: 10.7717/peerj.15903
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-01
copyright: ©2023 Chen et al.
attribution name: Chen et al.

Wheat gibberellin oxidase genes and their functions in regulating tillering
type: item
type: AcademicArticle
description: Multiple genetic factors control tillering, a key agronomy trait for wheat (Triticum aestivum L.) yield. Previously, we reported a dwarf-monoculm mutant (dmc) derived from wheat cultivar Guomai 301, and found that the contents of gibberellic acid 3 (GA3) in the tiller primordia of dmc were significantly higher. Transcriptome analysis indicated that some wheat gibberellin oxidase (TaGAox) genes TaGA20ox-A2, TaGA20ox-B2, TaGA3ox-A2, TaGA20ox-A4, TaGA2ox-A10 and TaGA2ox-B10 were differentially expressed in dmc. Therefore, this study systematically analyzed the roles of gibberellin oxidase genes during wheat tillering. A total of 63 TaGAox genes were identified by whole genome analysis. The TaGAoxs were clustered to four subfamilies, GA20oxs, GA2oxs, GA3oxs and GA7oxs, including seven subgroups based on their protein structures. The promoter regions of TaGAox genes contain a large number of cis-acting elements closely related to hormone, plant growth and development, light, and abiotic stress responses. Segmental duplication events played a major role in TaGAoxs expansion. Compared to Arabidopsis, the gene collinearity degrees of the GAoxs were significantly higher among wheat, rice and maize. TaGAox genes showed tissue-specific expression patterns. The expressions of TaGAox genes (TaGA20ox-B2, TaGA7ox-A1, TaGA2ox10 and TaGA3ox-A2) were significantly affected by exogenous GA3 applications, which also significantly promoted tillering of Guomai 301, but didn’t promote dmc. TaGA7ox-A1 overexpression transgenic wheat lines were obtained by Agrobacterium mediated transformation. Genomic PCR and first-generation sequencing demonstrated that the gene was integrated into the wheat genome. Association analysis of TaGA7ox-A1 expression level and tiller number per plant demonstrated that the tillering capacities of some TaGA7ox-A1 transgenic lines were increased. These data demonstrated that some TaGAoxs as well as GA signaling were involved in regulating wheat tillering, but the …
format: application/pdf
format: text/html
creator: Ting Wang
creator: Junchang Li
creator: Yumei Jiang
creator: Jing Zhang
creator: Yongjing Ni
creator: Peipei Zhang
creator: Ziping Yao
creator: Zhixin Jiao
creator: Huijuan Li
creator: Lei Li
creator: Yufan Niu
creator: Qiaoyun Li
creator: Guihong Yin
creator: Jishan Niu
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15924
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Multiple genetic factors control tillering, a key agronomy trait for wheat (Triticum aestivum L.) yield. Previously, we reported a dwarf-monoculm mutant (dmc) derived from wheat cultivar Guomai 301, and found that the contents of gibberellic acid 3 (GA3) in the tiller primordia of dmc were significantly higher. Transcriptome analysis indicated that some wheat gibberellin oxidase (TaGAox) genes TaGA20ox-A2, TaGA20ox-B2, TaGA3ox-A2, TaGA20ox-A4, TaGA2ox-A10 and TaGA2ox-B10 were differentially expressed in dmc. Therefore, this study systematically analyzed the roles of gibberellin oxidase genes during wheat tillering. A total of 63 TaGAox genes were identified by whole genome analysis. The TaGAoxs were clustered to four subfamilies, GA20oxs, GA2oxs, GA3oxs and GA7oxs, including seven subgroups based on their protein structures. The promoter regions of TaGAox genes contain a large number of cis-acting elements closely related to hormone, plant growth and development, light, and abiotic stress responses. Segmental duplication events played a major role in TaGAoxs expansion. Compared to Arabidopsis, the gene collinearity degrees of the GAoxs were significantly higher among wheat, rice and maize. TaGAox genes showed tissue-specific expression patterns. The expressions of TaGAox genes (TaGA20ox-B2, TaGA7ox-A1, TaGA2ox10 and TaGA3ox-A2) were significantly affected by exogenous GA3 applications, which also significantly promoted tillering of Guomai 301, but didn’t promote dmc. TaGA7ox-A1 overexpression transgenic wheat lines were obtained by Agrobacterium mediated transformation. Genomic PCR and first-generation sequencing demonstrated that the gene was integrated into the wheat genome. Association analysis of TaGA7ox-A1 expression level and tiller number per plant demonstrated that the tillering capacities of some TaGA7ox-A1 transgenic lines were increased. These data demonstrated that some TaGAoxs as well as GA signaling were involved in regulating wheat tillering, but the …
bibliographic citation: Wang et al. (2023) Wheat gibberellin oxidase genes and their functions in regulating tillering. PeerJ 11:e15924 https://doi.org/10.7717/peerj.15924
date submitted: 2022-12-28
date accepted: 2023-07-30
issued: 2023-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Ting
author list: Agent
  family name: Li
  given name: Junchang
author list: Agent
  family name: Jiang
  given name: Yumei
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Ni
  given name: Yongjing
author list: Agent
  family name: Zhang
  given name: Peipei
author list: Agent
  family name: Yao
  given name: Ziping
author list: Agent
  family name: Jiao
  given name: Zhixin
author list: Agent
  family name: Li
  given name: Huijuan
author list: Agent
  family name: Li
  given name: Lei
author list: Agent
  family name: Niu
  given name: Yufan
author list: Agent
  family name: Li
  given name: Qiaoyun
author list: Agent
  family name: Yin
  given name: Guihong
author list: Agent
  family name: Niu
  given name: Jishan
doi: 10.7717/peerj.15924
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-01
copyright: © 2023 Wang et al.
attribution name: Wang et al.

Assessment of selection criteria using multi-year study for effective breeding program of Zingiber officinale L
type: item
type: AcademicArticle
description: Background Ginger has been an important cash crop with numerous applications since ancient times. As the demand for ginger is ever-growing and being a seasonal crop, a high-yielding variety of ginger would be economically profitable. Methods In this study, 150 germplasm were collected from different regions of NE India and evaluated for three years in CRBD design with three replications. The present study thus focused on the variability, association, and diversity studies for the first time on 150 ginger germplasm from across North East India. The genotypic and phenotypic coefficient of variation, heritability, correlation, and path analysis were evaluated for the germplasm. Results Analysis of variance (ANOVA) revealed considerable differences among the studied germplasm for studied characters, revealing sufficient variability in the materials. The Mahalanobis D2 and Tocher methods grouped the 150 ginger germplasm into ten clusters. Based on the results of the path coefficient analysis determined for essential oil yield and rhizome yield per plant, it can be concluded that the characters’ initial rhizome weight, the weight of mother rhizome, and weight of secondary rhizome were the most important and appeared promising in improving the overall yield potential of ginger rhizome and essential oil yield. Thus, selection based on the identified traits would lead to an effective ginger breeding program for higher rhizome and essential oil yield.
format: application/pdf
format: text/html
creator: Twahira Begum
creator: Roktim Gogoi
creator: Ankita Gogoi
creator: Tanmita Gupta
creator: Sanjoy Kumar Chanda
creator: Himangshu Lekhak
creator: Mohan Lal
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.15966
publisher: PeerJ Inc.
rights: © 2023 Begum et al.
abstract: Background Ginger has been an important cash crop with numerous applications since ancient times. As the demand for ginger is ever-growing and being a seasonal crop, a high-yielding variety of ginger would be economically profitable. Methods In this study, 150 germplasm were collected from different regions of NE India and evaluated for three years in CRBD design with three replications. The present study thus focused on the variability, association, and diversity studies for the first time on 150 ginger germplasm from across North East India. The genotypic and phenotypic coefficient of variation, heritability, correlation, and path analysis were evaluated for the germplasm. Results Analysis of variance (ANOVA) revealed considerable differences among the studied germplasm for studied characters, revealing sufficient variability in the materials. The Mahalanobis D2 and Tocher methods grouped the 150 ginger germplasm into ten clusters. Based on the results of the path coefficient analysis determined for essential oil yield and rhizome yield per plant, it can be concluded that the characters’ initial rhizome weight, the weight of mother rhizome, and weight of secondary rhizome were the most important and appeared promising in improving the overall yield potential of ginger rhizome and essential oil yield. Thus, selection based on the identified traits would lead to an effective ginger breeding program for higher rhizome and essential oil yield.
bibliographic citation: Begum et al. (2023) Assessment of selection criteria using multi-year study for effective breeding program of Zingiber officinale L. PeerJ 11:e15966 https://doi.org/10.7717/peerj.15966
date submitted: 2023-02-02
date accepted: 2023-08-04
issued: 2023-09-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Begum
  given name: Twahira
author list: Agent
  family name: Gogoi
  given name: Roktim
author list: Agent
  family name: Gogoi
  given name: Ankita
author list: Agent
  family name: Gupta
  given name: Tanmita
author list: Agent
  family name: Chanda
  given name: Sanjoy Kumar
author list: Agent
  family name: Lekhak
  given name: Himangshu
author list: Agent
  family name: Lal
  given name: Mohan
doi: 10.7717/peerj.15966
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-09-01
copyright: ©2023 Begum et al.
attribution name: Begum et al.

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.
format: application/pdf
format: text/html
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.

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