PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Awareness and attitudes towards eye donation among medical and allied health students in Jeddah, Saudi Arabia
items: Estimates on age, growth, and mortality of Leuciscus chuanchicus (Kessler 1876) in the Ningxia section of the upper reaches of the Yellow River, China
items: Measuring multi-year changes in the Symbiodiniaceae algae in Caribbean corals on coral-depleted reefs
items: Pseudotargeted lipidomics analysis of scoparone on glycerophospholipid metabolism in non-alcoholic steatohepatitis mice by LC-MRM-MS
items: Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.)
items: Improving plant miRNA-target prediction with self-supervised k-mer embedding and spectral graph convolutional neural network
items: CircCamsap1 is dispensable for male fertility in mice
items: No benefit of higher protein dosing in critically ill patients: a systematic review and meta-analysis of randomized controlled trials
items: Exploring the influence of self-identification on perceptual judgments of physical and social causality
items: Alteration of RNA m6A methylation mediates aberrant RNA binding protein expression and alternative splicing in condyloma acuminatum

Awareness and attitudes towards eye donation among medical and allied health students in Jeddah, Saudi Arabia
type: item
type: AcademicArticle
description: Background Many national studies in Saudi Arabia have revealed a lack of knowledge about eye donation. The current study assessed awareness and attitudes towards eye donation among health faculty students in Jeddah, Saudi Arabia. It aims to increase their awareness as future healthcare providers are expected to raise general awareness to attain more local corneal donations. Methods A cross-sectional study including 1,060 health faculty students was conducted at King Abdulaziz University. Data were collected through an online questionnaire that covered participants’ demographics, academic year, knowledge, and attitudes regarding eye donation. Results Thirty-five percent of students had heard about eye donation, with the most common sources of information being social media (29%) and health workers (24%). Most respondents, 61% (n = 643), indicated willingness to donate their eyes after death. Of these respondents, 93% (n = 986), 6.8% (n = 72), and 0.2% (n = 2) had poor, fair, and good knowledge levels, respectively. A total of 66% (n = 696) and 34% (n = 364) had negative and positive attitudes, respectively. Conclusion Students in this study showed low levels of knowledge and negative attitudes about eye donation. Students should be adequately educated about the significance of eye donation.
format: application/pdf
format: text/html
creator: Mahmood Showail
creator: Turki A. AlAmoudi
creator: Esraa Basalem
creator: Khalid Alshebl
creator: Nawaf Meshal Almalki
creator: Abdullah Al Matrafi
creator: Mohammed Ashour
subject: Irrelevant Subject
subject: Health Policy
subject: Ophthalmology
subject: Ethical Issues
subject: Science and Medical Education
description: doi:10.7717/peerj.17334
publisher: PeerJ Inc.
rights: © 2024 Showail et al.
abstract: Background Many national studies in Saudi Arabia have revealed a lack of knowledge about eye donation. The current study assessed awareness and attitudes towards eye donation among health faculty students in Jeddah, Saudi Arabia. It aims to increase their awareness as future healthcare providers are expected to raise general awareness to attain more local corneal donations. Methods A cross-sectional study including 1,060 health faculty students was conducted at King Abdulaziz University. Data were collected through an online questionnaire that covered participants’ demographics, academic year, knowledge, and attitudes regarding eye donation. Results Thirty-five percent of students had heard about eye donation, with the most common sources of information being social media (29%) and health workers (24%). Most respondents, 61% (n = 643), indicated willingness to donate their eyes after death. Of these respondents, 93% (n = 986), 6.8% (n = 72), and 0.2% (n = 2) had poor, fair, and good knowledge levels, respectively. A total of 66% (n = 696) and 34% (n = 364) had negative and positive attitudes, respectively. Conclusion Students in this study showed low levels of knowledge and negative attitudes about eye donation. Students should be adequately educated about the significance of eye donation.
bibliographic citation: Showail et al. (2024) Awareness and attitudes towards eye donation among medical and allied health students in Jeddah, Saudi Arabia. PeerJ 12:e17334 https://doi.org/10.7717/peerj.17334
date submitted: 2023-07-20
date accepted: 2024-04-12
issued: 2024-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Showail
  given name: Mahmood
author list: Agent
  family name: AlAmoudi
  given name: Turki A.
author list: Agent
  family name: Basalem
  given name: Esraa
author list: Agent
  family name: Alshebl
  given name: Khalid
author list: Agent
  family name: Almalki
  given name: Nawaf Meshal
author list: Agent
  family name: Al Matrafi
  given name: Abdullah
author list: Agent
  family name: Ashour
  given name: Mohammed
doi: 10.7717/peerj.17334
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-21
copyright: © 2024 Showail et al.
attribution name: Showail et al.

Estimates on age, growth, and mortality of Leuciscus chuanchicus (Kessler 1876) in the Ningxia section of the upper reaches of the Yellow River, China
type: item
type: AcademicArticle
description: To investigate the age structure, growth pattern, mortality and exploitation rates of Leuciscus chuanchicus in the upstream Ningxia section of the Yellow River, four sampling surveys were conducted between 2022 and 2023. A total of 472 individuals were measured for their total length (TL) and body weight (W). Age determination was performed using otoliths. The collected samples had a range of total lengths from 4.52 to 37.45 cm, body weights ranging from 0.68 to 552.43 g, and ages ranging from 1 to 7 years old. The relationship between total length and body weight was expressed as W = 0.0052 L3.19 for all samples, which indicates that the growth of L. chuanchicus adheres to allometry. The Von Bertalanffy growth equation revealed that the fish had an asymptotic total length (L∞) of approximately 37.9 cm with a growth coefficient (K) value of approximately 0.461 yr−1. Using the age-based catch curve method, the calculated total instantaneous mortality rate (Z) for all samples was determined as being equal to approximately 1.1302 yr−1. Additionally, three methods were used to estimate the average instantaneous rate of natural mortality (M), resulting in an approximate value of 0.7167 yr−1 for all samples. Furthermore, the instantaneous rate of fishing mortality (F) for all samples was calculated as 0.4134 yr−1, leading us to determine that the exploitation rate (E) is 0.3658. It was concluded that the growth rate of L. chuanchicus in the upstream of the Yellow River is relatively fast, and L. chuanchicus has not been subjected to excessive exploitation, yet its relatively high natural mortality rate underscores the need for targeted management measures aimed at preserving its habitat.
format: application/pdf
format: text/html
creator: Shuhan Xiong
creator: Jiacheng Liu
creator: Peilun Li
creator: Yanbin Liu
creator: Kai Liu
creator: Yongjie Wang
creator: Jilong Wang
subject: Aquaculture, Fisheries and Fish Science
subject: Freshwater Biology
description: doi:10.7717/peerj.17351
publisher: PeerJ Inc.
rights: © 2024 Xiong et al.
abstract: To investigate the age structure, growth pattern, mortality and exploitation rates of Leuciscus chuanchicus in the upstream Ningxia section of the Yellow River, four sampling surveys were conducted between 2022 and 2023. A total of 472 individuals were measured for their total length (TL) and body weight (W). Age determination was performed using otoliths. The collected samples had a range of total lengths from 4.52 to 37.45 cm, body weights ranging from 0.68 to 552.43 g, and ages ranging from 1 to 7 years old. The relationship between total length and body weight was expressed as W = 0.0052 L3.19 for all samples, which indicates that the growth of L. chuanchicus adheres to allometry. The Von Bertalanffy growth equation revealed that the fish had an asymptotic total length (L∞) of approximately 37.9 cm with a growth coefficient (K) value of approximately 0.461 yr−1. Using the age-based catch curve method, the calculated total instantaneous mortality rate (Z) for all samples was determined as being equal to approximately 1.1302 yr−1. Additionally, three methods were used to estimate the average instantaneous rate of natural mortality (M), resulting in an approximate value of 0.7167 yr−1 for all samples. Furthermore, the instantaneous rate of fishing mortality (F) for all samples was calculated as 0.4134 yr−1, leading us to determine that the exploitation rate (E) is 0.3658. It was concluded that the growth rate of L. chuanchicus in the upstream of the Yellow River is relatively fast, and L. chuanchicus has not been subjected to excessive exploitation, yet its relatively high natural mortality rate underscores the need for targeted management measures aimed at preserving its habitat.
bibliographic citation: Xiong et al. (2024) Estimates on age, growth, and mortality of Leuciscus chuanchicus (Kessler 1876) in the Ningxia section of the upper reaches of the Yellow River, China. PeerJ 12:e17351 https://doi.org/10.7717/peerj.17351
date submitted: 2024-01-29
date accepted: 2024-04-17
issued: 2024-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiong
  given name: Shuhan
author list: Agent
  family name: Liu
  given name: Jiacheng
author list: Agent
  family name: Li
  given name: Peilun
author list: Agent
  family name: Liu
  given name: Yanbin
author list: Agent
  family name: Liu
  given name: Kai
author list: Agent
  family name: Wang
  given name: Yongjie
author list: Agent
  family name: Wang
  given name: Jilong
doi: 10.7717/peerj.17351
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-21
copyright: © 2024 Xiong et al.
attribution name: Xiong et al.

Measuring multi-year changes in the Symbiodiniaceae algae in Caribbean corals on coral-depleted reefs
type: item
type: AcademicArticle
description: Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from nine species were marked and sampled in 2017. Of these colonies, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes (2017) and the regional onset of stony coral tissue loss disease (2019). While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together, these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals.
format: application/pdf
format: text/html
creator: Ross Cunning
creator: Elizabeth A. Lenz
creator: Peter J. Edmunds
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Climate Change Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.17358
publisher: PeerJ Inc.
rights: © 2024 Cunning et al.
abstract: Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from nine species were marked and sampled in 2017. Of these colonies, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes (2017) and the regional onset of stony coral tissue loss disease (2019). While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together, these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals.
bibliographic citation: Cunning et al. (2024) Measuring multi-year changes in the Symbiodiniaceae algae in Caribbean corals on coral-depleted reefs. PeerJ 12:e17358 https://doi.org/10.7717/peerj.17358
date submitted: 2023-12-07
date accepted: 2024-04-18
issued: 2024-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cunning
  given name: Ross
author list: Agent
  family name: Lenz
  given name: Elizabeth A.
author list: Agent
  family name: Edmunds
  given name: Peter J.
doi: 10.7717/peerj.17358
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-21
copyright: © 2024 Cunning et al.
attribution name: Cunning et al.

Pseudotargeted lipidomics analysis of scoparone on glycerophospholipid metabolism in non-alcoholic steatohepatitis mice by LC-MRM-MS
type: item
type: AcademicArticle
description: As the inflammatory subtype of nonalcoholic fatty liver disease (NAFLD), the progression of nonalcoholic steatohepatitis (NASH) is associated with disorders of glycerophospholipid metabolism. Scoparone is the major bioactive component in Artemisia capillaris which has been widely used to treat NASH in traditional Chinese medicine. However, the underlying mechanisms of scoparone against NASH are not yet fully understood, which hinders the development of effective therapeutic agents for NASH. Given the crucial role of glycerophospholipid metabolism in NASH progression, this study aimed to characterize the differential expression of glycerophospholipids that is responsible for scoparone’s pharmacological effects and assess its efficacy against NASH. Liquid chromatography-multiple reaction monitoring-mass spectrometry (LC-MRM-MS) was performed to get the concentrations of glycerophospholipids, clarify mechanisms of disease, and highlight insights into drug discovery. Additionally, pathologic findings also presented consistent changes in high-fat diet-induced NASH model, and after scoparone treatment, both the levels of glycerophospholipids and histopathology were similar to normal levels, indicating a beneficial effect during the observation time. Altogether, these results refined the insights on the mechanisms of scoparone against NASH and suggested a route to relieve NASH with glycerophospholipid metabolism. In addition, the current work demonstrated that a pseudotargeted lipidomic platform provided a novel insight into the potential mechanism of scoparone action.
format: application/pdf
format: text/html
creator: Qi Song
creator: Ziyi Zhao
creator: Hu Liu
creator: Jinling Zhang
creator: Zhiqiang Wang
creator: Yunqi Zhang
creator: Guowei Ma
creator: Shaoqin Ge
subject: Biochemistry
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Metabolic Sciences
description: doi:10.7717/peerj.17380
publisher: PeerJ Inc.
rights: © 2024 Song et al.
abstract: As the inflammatory subtype of nonalcoholic fatty liver disease (NAFLD), the progression of nonalcoholic steatohepatitis (NASH) is associated with disorders of glycerophospholipid metabolism. Scoparone is the major bioactive component in Artemisia capillaris which has been widely used to treat NASH in traditional Chinese medicine. However, the underlying mechanisms of scoparone against NASH are not yet fully understood, which hinders the development of effective therapeutic agents for NASH. Given the crucial role of glycerophospholipid metabolism in NASH progression, this study aimed to characterize the differential expression of glycerophospholipids that is responsible for scoparone’s pharmacological effects and assess its efficacy against NASH. Liquid chromatography-multiple reaction monitoring-mass spectrometry (LC-MRM-MS) was performed to get the concentrations of glycerophospholipids, clarify mechanisms of disease, and highlight insights into drug discovery. Additionally, pathologic findings also presented consistent changes in high-fat diet-induced NASH model, and after scoparone treatment, both the levels of glycerophospholipids and histopathology were similar to normal levels, indicating a beneficial effect during the observation time. Altogether, these results refined the insights on the mechanisms of scoparone against NASH and suggested a route to relieve NASH with glycerophospholipid metabolism. In addition, the current work demonstrated that a pseudotargeted lipidomic platform provided a novel insight into the potential mechanism of scoparone action.
bibliographic citation: Song et al. (2024) Pseudotargeted lipidomics analysis of scoparone on glycerophospholipid metabolism in non-alcoholic steatohepatitis mice by LC-MRM-MS. PeerJ 12:e17380 https://doi.org/10.7717/peerj.17380
date submitted: 2023-11-28
date accepted: 2024-04-21
issued: 2024-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Qi
author list: Agent
  family name: Zhao
  given name: Ziyi
author list: Agent
  family name: Liu
  given name: Hu
author list: Agent
  family name: Zhang
  given name: Jinling
author list: Agent
  family name: Wang
  given name: Zhiqiang
author list: Agent
  family name: Zhang
  given name: Yunqi
author list: Agent
  family name: Ma
  given name: Guowei
author list: Agent
  family name: Ge
  given name: Shaoqin
doi: 10.7717/peerj.17380
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-21
copyright: ©2024 Song et al.
attribution name: Song et al.

Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.)
type: item
type: AcademicArticle
description: The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.
format: application/pdf
format: text/html
creator: Peiqi Ye
creator: Xiaoliang Che
creator: Yang Liu
creator: Ming Zeng
creator: Wenbing Guo
creator: Yongbin Long
creator: Tianyi Liu
creator: Zhe Wang
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.17388
publisher: PeerJ Inc.
rights: © 2024 Ye et al.
abstract: The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.
bibliographic citation: Ye et al. (2024) Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.). PeerJ 12:e17388 https://doi.org/10.7717/peerj.17388
date submitted: 2024-01-25
date accepted: 2024-04-23
issued: 2024-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Peiqi
author list: Agent
  family name: Che
  given name: Xiaoliang
author list: Agent
  family name: Liu
  given name: Yang
author list: Agent
  family name: Zeng
  given name: Ming
author list: Agent
  family name: Guo
  given name: Wenbing
author list: Agent
  family name: Long
  given name: Yongbin
author list: Agent
  family name: Liu
  given name: Tianyi
author list: Agent
  family name: Wang
  given name: Zhe
doi: 10.7717/peerj.17388
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-21
copyright: © 2024 Ye et al.
attribution name: Ye et al.

Improving plant miRNA-target prediction with self-supervised k-mer embedding and spectral graph convolutional neural network
type: item
type: AcademicArticle
description: Deciphering the targets of microRNAs (miRNAs) in plants is crucial for comprehending their function and the variation in phenotype that they cause. As the highly cell-specific nature of miRNA regulation, recent computational approaches usually utilize expression data to identify the most physiologically relevant targets. Although these methods are effective, they typically require a large sample size and high-depth sequencing to detect potential miRNA-target pairs, thereby limiting their applicability in improving plant breeding. In this study, we propose a novel miRNA-target prediction framework named kmerPMTF (k-mer-based prediction framework for plant miRNA-target). Our framework effectively extracts the latent semantic embeddings of sequences by utilizing k-mer splitting and a deep self-supervised neural network. We construct multiple similarity networks based on k-mer embeddings and employ graph convolutional networks to derive deep representations of miRNAs and targets and calculate the probabilities of potential associations. We evaluated the performance of kmerPMTF on four typical plant datasets: Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum, and Prunus persica. The results demonstrate its ability to achieve AUPRC values of 84.9%, 91.0%, 80.1%, and 82.1% in 5-fold cross-validation, respectively. Compared with several state-of-the-art existing methods, our framework achieves better performance on threshold-independent evaluation metrics. Overall, our study provides an efficient and simplified methodology for identifying plant miRNA-target associations, which will contribute to a deeper comprehension of miRNA regulatory mechanisms in plants.
format: application/pdf
format: text/html
creator: Weihan Zhang
creator: Ping Zhang
creator: Weicheng Sun
creator: Jinsheng Xu
creator: Liao Liao
creator: Yunpeng Cao
creator: Yuepeng Han
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.17396
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Deciphering the targets of microRNAs (miRNAs) in plants is crucial for comprehending their function and the variation in phenotype that they cause. As the highly cell-specific nature of miRNA regulation, recent computational approaches usually utilize expression data to identify the most physiologically relevant targets. Although these methods are effective, they typically require a large sample size and high-depth sequencing to detect potential miRNA-target pairs, thereby limiting their applicability in improving plant breeding. In this study, we propose a novel miRNA-target prediction framework named kmerPMTF (k-mer-based prediction framework for plant miRNA-target). Our framework effectively extracts the latent semantic embeddings of sequences by utilizing k-mer splitting and a deep self-supervised neural network. We construct multiple similarity networks based on k-mer embeddings and employ graph convolutional networks to derive deep representations of miRNAs and targets and calculate the probabilities of potential associations. We evaluated the performance of kmerPMTF on four typical plant datasets: Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum, and Prunus persica. The results demonstrate its ability to achieve AUPRC values of 84.9%, 91.0%, 80.1%, and 82.1% in 5-fold cross-validation, respectively. Compared with several state-of-the-art existing methods, our framework achieves better performance on threshold-independent evaluation metrics. Overall, our study provides an efficient and simplified methodology for identifying plant miRNA-target associations, which will contribute to a deeper comprehension of miRNA regulatory mechanisms in plants.
bibliographic citation: Zhang et al. (2024) Improving plant miRNA-target prediction with self-supervised k-mer embedding and spectral graph convolutional neural network. PeerJ 12:e17396 https://doi.org/10.7717/peerj.17396
date submitted: 2024-01-08
date accepted: 2024-04-25
issued: 2024-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Weihan
author list: Agent
  family name: Zhang
  given name: Ping
author list: Agent
  family name: Sun
  given name: Weicheng
author list: Agent
  family name: Xu
  given name: Jinsheng
author list: Agent
  family name: Liao
  given name: Liao
author list: Agent
  family name: Cao
  given name: Yunpeng
author list: Agent
  family name: Han
  given name: Yuepeng
doi: 10.7717/peerj.17396
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-21
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

CircCamsap1 is dispensable for male fertility in mice
type: item
type: AcademicArticle
description: Background Circular RNAs (circRNAs) are a large class of RNAs present in mammals. Among these, circCamsap1 is a well-acknowledged circRNA with significant implications, particularly in the development and progression of diverse tumors. However, the potential consequences of circCamsap1 depletion in vivo on male reproduction are yet to be thoroughly investigated. Methods The presence of circCamsap1 in the mouse testes was confirmed, and gene expression analysis was performed using reverse transcription quantitative polymerase chain reaction. CircCamsap1 knockout mice were generated utilizing the CRISPR/Cas9 system. Phenotypic analysis of both the testes and epididymis was conducted using histological and immunofluorescence staining. Additionally, fertility and sperm motility were assessed. Results Here, we successfully established a circCamsap1 knockout mouse model without affecting the expression of parental gene. Surprisingly, male mice lacking circCamsap1 (circCamsap1−/−) exhibited normal fertility, with no discernible differences in testicular and epididymal histology, spermatogenesis, sperm counts or sperm motility compared to circCamsap1+/+ mice. These findings suggest that circCamsap1 may not play an essential role in physiological spermatogenesis. Nonetheless, this result also underscores the complexity of circRNA function in male reproductive biology. Therefore, further research is necessary to elucidate the precise roles of other circRNAs in regulating male fertility.
format: application/pdf
format: text/html
creator: Shu Zhang
creator: Haojie Li
creator: Wei Jiang
creator: Xia Chen
creator: Han Zhou
creator: Chang Wang
creator: Hao Kong
creator: Yichao Shi
creator: Xiaodan Shi
subject: Biochemistry
subject: Developmental Biology
subject: Molecular Biology
subject: Andrology
subject: Histology
description: doi:10.7717/peerj.17399
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Background Circular RNAs (circRNAs) are a large class of RNAs present in mammals. Among these, circCamsap1 is a well-acknowledged circRNA with significant implications, particularly in the development and progression of diverse tumors. However, the potential consequences of circCamsap1 depletion in vivo on male reproduction are yet to be thoroughly investigated. Methods The presence of circCamsap1 in the mouse testes was confirmed, and gene expression analysis was performed using reverse transcription quantitative polymerase chain reaction. CircCamsap1 knockout mice were generated utilizing the CRISPR/Cas9 system. Phenotypic analysis of both the testes and epididymis was conducted using histological and immunofluorescence staining. Additionally, fertility and sperm motility were assessed. Results Here, we successfully established a circCamsap1 knockout mouse model without affecting the expression of parental gene. Surprisingly, male mice lacking circCamsap1 (circCamsap1−/−) exhibited normal fertility, with no discernible differences in testicular and epididymal histology, spermatogenesis, sperm counts or sperm motility compared to circCamsap1+/+ mice. These findings suggest that circCamsap1 may not play an essential role in physiological spermatogenesis. Nonetheless, this result also underscores the complexity of circRNA function in male reproductive biology. Therefore, further research is necessary to elucidate the precise roles of other circRNAs in regulating male fertility.
bibliographic citation: Zhang et al. (2024) CircCamsap1 is dispensable for male fertility in mice. PeerJ 12:e17399 https://doi.org/10.7717/peerj.17399
date submitted: 2024-01-10
date accepted: 2024-04-25
issued: 2024-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Shu
author list: Agent
  family name: Li
  given name: Haojie
author list: Agent
  family name: Jiang
  given name: Wei
author list: Agent
  family name: Chen
  given name: Xia
author list: Agent
  family name: Zhou
  given name: Han
author list: Agent
  family name: Wang
  given name: Chang
author list: Agent
  family name: Kong
  given name: Hao
author list: Agent
  family name: Shi
  given name: Yichao
author list: Agent
  family name: Shi
  given name: Xiaodan
doi: 10.7717/peerj.17399
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-21
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

No benefit of higher protein dosing in critically ill patients: a systematic review and meta-analysis of randomized controlled trials
type: item
type: AcademicArticle
description: Purpose The optimal range of protein dosage and effect of high-dose protein on critically ill patients remain controversial. We conducted a meta-analysis to compare higher and lower doses of protein supplementation for nutritional support in critically ill patients. Methods We searched the PubMed, Embase, Scopus, and Cochrane Library databases for randomized controlled trials that compared higher (≥1.2 g/kg per day) versus lower (<1.2 g/kg per day) doses of protein supplementation among critically ill adult patients. This search spanned from the inception of relevant databases to November 20, 2023. Our primary endpoint of interest was overall mortality, while secondary endpoints included length of stay in the intensive care unit, length of hospital stay, duration of mechanical ventilation, and incidence of acute kidney injury. Results Seventeen studies including 2,965 critically ill patients were included in our meta-analysis. The pooled analyses showed no significant difference in overall mortality (RR 1.03, 95%CI [0.92–1.15], P = 0.65, I2 = 0%), length of intensive care unit stay (MD 0.19, 95%CI [−0.67 to 1.04], P = 0.66, I2 = 25%), length of hospital stay (MD 0.73, 95%CI [−1.59 to 3.04], P = 0.54, I2 = 27%), duration of mechanical ventilation (MD −0.14, 95%CI [−0.83 to 0.54], P = 0.68, I2 = 8%), and incidence of acute kidney injury (RR 1.11, 95%CI [0.87–1.41], P = 0.38, I2 = 0%) between critically ill patients receiving higher or lower doses of protein supplementation. Conclusions For critically ill patients, the protein supplementation dose had no significant effect on clinical outcomes, including overall mortality, length of intensive care unit and hospital stay, duration of mechanical ventilation, and incidence of acute kidney injury.
format: application/pdf
format: text/html
creator: Yonggen Qin
creator: Jian Huang
creator: Xiaofeng Ping
creator: Hui Zheng
creator: Kai Zhang
creator: Xiaoya Xu
creator: Jiuqing Yu
subject: Emergency and Critical Care
subject: Evidence Based Medicine
subject: Nutrition
description: doi:10.7717/peerj.17433
publisher: PeerJ Inc.
rights: © 2024 Qin et al.
abstract: Purpose The optimal range of protein dosage and effect of high-dose protein on critically ill patients remain controversial. We conducted a meta-analysis to compare higher and lower doses of protein supplementation for nutritional support in critically ill patients. Methods We searched the PubMed, Embase, Scopus, and Cochrane Library databases for randomized controlled trials that compared higher (≥1.2 g/kg per day) versus lower (<1.2 g/kg per day) doses of protein supplementation among critically ill adult patients. This search spanned from the inception of relevant databases to November 20, 2023. Our primary endpoint of interest was overall mortality, while secondary endpoints included length of stay in the intensive care unit, length of hospital stay, duration of mechanical ventilation, and incidence of acute kidney injury. Results Seventeen studies including 2,965 critically ill patients were included in our meta-analysis. The pooled analyses showed no significant difference in overall mortality (RR 1.03, 95%CI [0.92–1.15], P = 0.65, I2 = 0%), length of intensive care unit stay (MD 0.19, 95%CI [−0.67 to 1.04], P = 0.66, I2 = 25%), length of hospital stay (MD 0.73, 95%CI [−1.59 to 3.04], P = 0.54, I2 = 27%), duration of mechanical ventilation (MD −0.14, 95%CI [−0.83 to 0.54], P = 0.68, I2 = 8%), and incidence of acute kidney injury (RR 1.11, 95%CI [0.87–1.41], P = 0.38, I2 = 0%) between critically ill patients receiving higher or lower doses of protein supplementation. Conclusions For critically ill patients, the protein supplementation dose had no significant effect on clinical outcomes, including overall mortality, length of intensive care unit and hospital stay, duration of mechanical ventilation, and incidence of acute kidney injury.
bibliographic citation: Qin et al. (2024) No benefit of higher protein dosing in critically ill patients: a systematic review and meta-analysis of randomized controlled trials. PeerJ 12:e17433 https://doi.org/10.7717/peerj.17433
date submitted: 2024-01-25
date accepted: 2024-04-29
issued: 2024-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qin
  given name: Yonggen
author list: Agent
  family name: Huang
  given name: Jian
author list: Agent
  family name: Ping
  given name: Xiaofeng
author list: Agent
  family name: Zheng
  given name: Hui
author list: Agent
  family name: Zhang
  given name: Kai
author list: Agent
  family name: Xu
  given name: Xiaoya
author list: Agent
  family name: Yu
  given name: Jiuqing
doi: 10.7717/peerj.17433
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-21
copyright: © 2024 Qin et al.
attribution name: Qin et al.

Exploring the influence of self-identification on perceptual judgments of physical and social causality
type: item
type: AcademicArticle
description: People tend to overestimate the causal contribution of the self to the observed outcome in various situations, a cognitive bias known as the ‘illusion of control.’ This study delves into whether this cognitive bias impacts causality judgments in animations depicting physical and social causal interactions. In two experiments, participants were instructed to associate themselves and a hypothetical stranger identity with two geometrical shapes (a circle and a square). Subsequently, they viewed animations portraying these shapes assuming the roles of agent and patient in causal interactions. Within one block, the shape related to the self served as the agent, while the shape associated with the stranger played the role of the patient. Conversely, in the other block, the identity-role association was reversed. We posited that the perception of the self as a causal agent might influence explicit judgments of physical and social causality. Experiment 1 demonstrated that physical causality ratings were solely shaped by kinematic cues. In Experiment 2, emphasising social causality, the dominance of kinematic parameters was confirmed. Therefore, contrary to the hypothesis anticipating diminished causality ratings with specific identity-role associations, results indicated negligible impact of our manipulation. The study contributes to understanding the interplay between kinematic and non-kinematic cues in human causal reasoning. It suggests that explicit judgments of causality in simple animations primarily rely on low-level kinematic cues, with the cognitive bias of overestimating the self’s contribution playing a negligible role.
format: application/pdf
format: text/html
creator: Michele Vicovaro
creator: Francesca Squadrelli Saraceno
creator: Mario Dalmaso
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.17449
publisher: PeerJ Inc.
rights: © 2024 Vicovaro et al.
abstract: People tend to overestimate the causal contribution of the self to the observed outcome in various situations, a cognitive bias known as the ‘illusion of control.’ This study delves into whether this cognitive bias impacts causality judgments in animations depicting physical and social causal interactions. In two experiments, participants were instructed to associate themselves and a hypothetical stranger identity with two geometrical shapes (a circle and a square). Subsequently, they viewed animations portraying these shapes assuming the roles of agent and patient in causal interactions. Within one block, the shape related to the self served as the agent, while the shape associated with the stranger played the role of the patient. Conversely, in the other block, the identity-role association was reversed. We posited that the perception of the self as a causal agent might influence explicit judgments of physical and social causality. Experiment 1 demonstrated that physical causality ratings were solely shaped by kinematic cues. In Experiment 2, emphasising social causality, the dominance of kinematic parameters was confirmed. Therefore, contrary to the hypothesis anticipating diminished causality ratings with specific identity-role associations, results indicated negligible impact of our manipulation. The study contributes to understanding the interplay between kinematic and non-kinematic cues in human causal reasoning. It suggests that explicit judgments of causality in simple animations primarily rely on low-level kinematic cues, with the cognitive bias of overestimating the self’s contribution playing a negligible role.
bibliographic citation: Vicovaro et al. (2024) Exploring the influence of self-identification on perceptual judgments of physical and social causality. PeerJ 12:e17449 https://doi.org/10.7717/peerj.17449
date submitted: 2024-02-14
date accepted: 2024-05-02
issued: 2024-05-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vicovaro
  given name: Michele
author list: Agent
  family name: Squadrelli Saraceno
  given name: Francesca
author list: Agent
  family name: Dalmaso
  given name: Mario
doi: 10.7717/peerj.17449
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-21
copyright: © 2024 Vicovaro et al.
attribution name: Vicovaro et al.

Alteration of RNA m6A methylation mediates aberrant RNA binding protein expression and alternative splicing in condyloma acuminatum
type: item
type: AcademicArticle
description: Background Condyloma acuminatum (CA) is caused by low-risk human papillomavirus, and is characterized by high recurrence after treatment. The RNA modification N6-methyladenosine (m6A) plays an important role during diverse viral infections, including high-risk HPV infection in cervical cancer. However, it is unclear whether low-risk HPV infection changes the RNA m6A methylation in CA. Methods High-throughputm6A-sequencing was performed to profile the transcriptome-wide mRNA modifications of CA tissues infected by LR-HPVs and the paired normal tissues from CA patients. We further investigated the regulation of alternative splicing by RNA binding proteins (RBPs) with altered m6A modification and constructed a regulatory network among these RBPs, regulated alternative splicing events (RASEs) and regulated alternative splicing genes (RASGs) in CA. Results The results show that the m6A level in CA tissues differed from that in the paired controls. Furthermore, cell cycle- and cell adhesion- associated genes with m6A modification were differentially expressed in CA tissues compared to the paired controls. In particular, seven RNA binding protein genes with specific m6A methylated sites, showed a higher or lower expression at the mRNA level in CA tissues than in the paired normal tissues. In addition, these differentially expressed RNA binding protein genes would regulate the alternative splicing pattern of apoptotic process genes in CA tissue. Conclusions Our study reveals a sophisticated m6A modification profile in CA tissue that affects the response of host cells to HPV infection, and provides cues for the further exploration of the roles of m6A and the development of a novel treatment strategy for CA.
format: application/pdf
format: text/html
creator: Xiaoyan Liu
creator: Bo Xie
creator: Su Wang
creator: Yinhua Wu
creator: Yu Zhang
creator: Liming Ruan
subject: Molecular Biology
subject: Dermatology
subject: Infectious Diseases
subject: Women’s Health
description: doi:10.7717/peerj.17376
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Background Condyloma acuminatum (CA) is caused by low-risk human papillomavirus, and is characterized by high recurrence after treatment. The RNA modification N6-methyladenosine (m6A) plays an important role during diverse viral infections, including high-risk HPV infection in cervical cancer. However, it is unclear whether low-risk HPV infection changes the RNA m6A methylation in CA. Methods High-throughputm6A-sequencing was performed to profile the transcriptome-wide mRNA modifications of CA tissues infected by LR-HPVs and the paired normal tissues from CA patients. We further investigated the regulation of alternative splicing by RNA binding proteins (RBPs) with altered m6A modification and constructed a regulatory network among these RBPs, regulated alternative splicing events (RASEs) and regulated alternative splicing genes (RASGs) in CA. Results The results show that the m6A level in CA tissues differed from that in the paired controls. Furthermore, cell cycle- and cell adhesion- associated genes with m6A modification were differentially expressed in CA tissues compared to the paired controls. In particular, seven RNA binding protein genes with specific m6A methylated sites, showed a higher or lower expression at the mRNA level in CA tissues than in the paired normal tissues. In addition, these differentially expressed RNA binding protein genes would regulate the alternative splicing pattern of apoptotic process genes in CA tissue. Conclusions Our study reveals a sophisticated m6A modification profile in CA tissue that affects the response of host cells to HPV infection, and provides cues for the further exploration of the roles of m6A and the development of a novel treatment strategy for CA.
bibliographic citation: Liu et al. (2024) Alteration of RNA m6A methylation mediates aberrant RNA binding protein expression and alternative splicing in condyloma acuminatum. PeerJ 12:e17376 https://doi.org/10.7717/peerj.17376
date submitted: 2023-12-26
date accepted: 2024-04-19
issued: 2024-05-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xiaoyan
author list: Agent
  family name: Xie
  given name: Bo
author list: Agent
  family name: Wang
  given name: Su
author list: Agent
  family name: Wu
  given name: Yinhua
author list: Agent
  family name: Zhang
  given name: Yu
author list: Agent
  family name: Ruan
  given name: Liming
doi: 10.7717/peerj.17376
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-05-20
copyright: ©2024 Liu et al.
attribution name: Liu et al.

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