PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Single-cell transcriptome analysis reveals cellular reprogramming and changes of immune cell subsets following tetramethylpyrazine treatment in LPS-induced acute lung injury
items: Unveiling the complex double-edged sword role of exosomes in nasopharyngeal carcinoma
items: To stay or to go: resource diversity alters the dispersal behavior of sympatric cryptic marine nematodes
items: Social presence effect in language comprehension: evidence from event-related potential (ERP) research
items: Effects of tropical fruit blends on fermentative and pigmentation aspects of probiotic native cultured goat milk
items: Genome-wide analyses of the NAC transcription factor gene family in Acer palmatum provide valuable insights into the natural process of leaf senescence
items: The impact of induced stress on reactive and proactive control in depression
items: Genome-wide association study on color-image-based convolutional neural networks
items: Cloning and functional verification of Geraniol-10-Hydroxylase gene in Lonicera japonica
items: Association between maternal rectovaginal group B streptococcus and the risk of stillbirth: a meta-analysis

Single-cell transcriptome analysis reveals cellular reprogramming and changes of immune cell subsets following tetramethylpyrazine treatment in LPS-induced acute lung injury
type: item
type: AcademicArticle
description: Background Acute lung injury (ALI) is a disordered pulmonary disease characterized by acute respiratory insufficiency with tachypnea, cyanosis refractory to oxygen and diffuse alveolar infiltrates. Despite increased research into ALI, current clinical treatments lack effectiveness. Tetramethylpyrazine (TMP) has shown potential in ALI treatment, and understanding its effects on the pulmonary microenvironment and its underlying mechanisms is imperative. Methods We established a mouse model of lipopolysaccharide (LPS)-induced ALI and performed single cell RNA sequencing (scRNA-seq). Bioinformatic analyses of the immune, epithelial and endothelial cells were then performed to explore the dynamic changes of the lung tissue microenvironment. We also analyzed the effects of TMP on the cell subtypes, differential gene expression and potential regulation of transcriptional factors involved. Immunohistochemistry and enzyme-linked immunosorbent assay were performed to identify the effects of TMP on immune inflammatory response. Results We found that TMP efficiently protected against LPS-induced acute lung injury. Results of scRNA-seq showed that the cells were divided into seven major cell clusters, including immune cells, fibroblasts, endothelial cells and epithelial cells. Neither dexamethasone (Dex) nor TMP treatment showed any significant protective effects in these clusters. However, TMP treatment in the LPS-induced ALI model significantly increased follicular helper T cells and reduced CD8+ naive T cells, Vcan-positive monocytes and Siva-positive NK cells. In addition, TMP treatment increased the number of basal epithelial cells and lymphatic endothelial cells (LECs), indicating its protective effects on these cell types. Scenic analysis suggested that TMP likely mitigates LPS-induced injury in epithelial and endothelial cells by promoting FOSL1 in basal epithelial cells and JunB in LECs. Conclusions Our findings suggest that TMP appears to alleviate LPS-induced lung inj…
format: application/pdf
format: text/html
creator: Mingyan Wu
creator: Shanmei Wang
creator: Xiaolan Chen
creator: Li Shen
creator: Jurong Ding
creator: Hongbin Jiang
subject: Genetics
subject: Translational Medicine
description: doi:10.7717/peerj.18772
publisher: PeerJ Inc.
rights: © 2025 Wu et al.
abstract: Background Acute lung injury (ALI) is a disordered pulmonary disease characterized by acute respiratory insufficiency with tachypnea, cyanosis refractory to oxygen and diffuse alveolar infiltrates. Despite increased research into ALI, current clinical treatments lack effectiveness. Tetramethylpyrazine (TMP) has shown potential in ALI treatment, and understanding its effects on the pulmonary microenvironment and its underlying mechanisms is imperative. Methods We established a mouse model of lipopolysaccharide (LPS)-induced ALI and performed single cell RNA sequencing (scRNA-seq). Bioinformatic analyses of the immune, epithelial and endothelial cells were then performed to explore the dynamic changes of the lung tissue microenvironment. We also analyzed the effects of TMP on the cell subtypes, differential gene expression and potential regulation of transcriptional factors involved. Immunohistochemistry and enzyme-linked immunosorbent assay were performed to identify the effects of TMP on immune inflammatory response. Results We found that TMP efficiently protected against LPS-induced acute lung injury. Results of scRNA-seq showed that the cells were divided into seven major cell clusters, including immune cells, fibroblasts, endothelial cells and epithelial cells. Neither dexamethasone (Dex) nor TMP treatment showed any significant protective effects in these clusters. However, TMP treatment in the LPS-induced ALI model significantly increased follicular helper T cells and reduced CD8+ naive T cells, Vcan-positive monocytes and Siva-positive NK cells. In addition, TMP treatment increased the number of basal epithelial cells and lymphatic endothelial cells (LECs), indicating its protective effects on these cell types. Scenic analysis suggested that TMP likely mitigates LPS-induced injury in epithelial and endothelial cells by promoting FOSL1 in basal epithelial cells and JunB in LECs. Conclusions Our findings suggest that TMP appears to alleviate LPS-induced lung inj…
bibliographic citation: Wu et al. (2025) Single-cell transcriptome analysis reveals cellular reprogramming and changes of immune cell subsets following tetramethylpyrazine treatment in LPS-induced acute lung injury. PeerJ 13:e18772 https://doi.org/10.7717/peerj.18772
date submitted: 2024-06-10
date accepted: 2024-12-05
issued: 2025-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Mingyan
author list: Agent
  family name: Wang
  given name: Shanmei
author list: Agent
  family name: Chen
  given name: Xiaolan
author list: Agent
  family name: Shen
  given name: Li
author list: Agent
  family name: Ding
  given name: Jurong
author list: Agent
  family name: Jiang
  given name: Hongbin
doi: 10.7717/peerj.18772
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-13
copyright: © 2025 Wu et al.
attribution name: Wu et al.

Unveiling the complex double-edged sword role of exosomes in nasopharyngeal carcinoma
type: item
type: AcademicArticle
description: Nasopharyngeal carcinoma (NPC) is a malignancy arising from the epithelium of the nasopharynx. Given its late diagnosis, NPC raises serious considerations in Southeast Asia. In addition to resistance to conventional treatment that combines chemotherapy and radiation, NPC has high rates of metastasis and frequent recurrence. Exosomes are small membrane vesicles at the nanoscale that transport physiologically active compounds from their source cell and have a crucial function in signal transmission and intercellular message exchange. The exosomes detected in the tissues of NPC patients have recently emerged as a potential non-invasive liquid biopsy biomarker that plays a role in controlling the tumor pathophysiology. Here, we take a look back at what we know so far about the complex double-edged sword role of exosomes in NPC. Exosomes could serve as biomarkers and therapeutic agents, as well as the molecular mechanisms by which they promote cell growth, angiogenesis, metastasis, immunosuppression, radiation resistance, and chemotherapy resistance in NPC. Furthermore, we go over some of the difficulties and restrictions associated with exosome use. It is anticipated that this article would provide the reference for the apply of exosomes in clinical practice.
format: application/pdf
format: text/html
creator: Xueyan Huang
creator: Yuedi Tang
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Pharmacology
description: doi:10.7717/peerj.18783
publisher: PeerJ Inc.
rights: © 2025 Huang and Tang
abstract: Nasopharyngeal carcinoma (NPC) is a malignancy arising from the epithelium of the nasopharynx. Given its late diagnosis, NPC raises serious considerations in Southeast Asia. In addition to resistance to conventional treatment that combines chemotherapy and radiation, NPC has high rates of metastasis and frequent recurrence. Exosomes are small membrane vesicles at the nanoscale that transport physiologically active compounds from their source cell and have a crucial function in signal transmission and intercellular message exchange. The exosomes detected in the tissues of NPC patients have recently emerged as a potential non-invasive liquid biopsy biomarker that plays a role in controlling the tumor pathophysiology. Here, we take a look back at what we know so far about the complex double-edged sword role of exosomes in NPC. Exosomes could serve as biomarkers and therapeutic agents, as well as the molecular mechanisms by which they promote cell growth, angiogenesis, metastasis, immunosuppression, radiation resistance, and chemotherapy resistance in NPC. Furthermore, we go over some of the difficulties and restrictions associated with exosome use. It is anticipated that this article would provide the reference for the apply of exosomes in clinical practice.
bibliographic citation: Huang et al. (2025) Unveiling the complex double-edged sword role of exosomes in nasopharyngeal carcinoma. PeerJ 13:e18783 https://doi.org/10.7717/peerj.18783
date submitted: 2024-09-17
date accepted: 2024-12-09
issued: 2025-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Xueyan
author list: Agent
  family name: Tang
  given name: Yuedi
doi: 10.7717/peerj.18783
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-13
copyright: © 2025 Huang and Tang
attribution name: Huang and Tang

To stay or to go: resource diversity alters the dispersal behavior of sympatric cryptic marine nematodes
type: item
type: AcademicArticle
description: Animals can use specific environmental cues to make informed decisions about whether and where to disperse. Patch conditions are known to affect the dispersal behavior of animals, but empirical studies investigating the impact of resource diversity on the dispersal of closely related species are largely lacking. In this study, we investigated how food diversity affects the dispersal behavior of three co-occurring cryptic species of the marine bacterivorous nematode complex Litoditis marina (Pm I, Pm III and Pm IV). Using microcosms composed of a local patch (inoculation plate), a connection tube, and a distant patch (dispersal plate), we examined nematode dispersal patterns with bacteria serving as the food source. Food treatments included low-, medium-, and high-diversity bacterial mixtures of 5, 10, and 15 bacterial strains, respectively. Additionally, a single-strain food resource Escherichia coli was used as a control treatment. Both local and distant patches had either identical food treatments (‘homogeneous patches’) or E. coli in the local patches and more diverse food (low-, medium-, or high-diversity food) in distant patches (‘heterogeneous patches’). Our results show that the dispersal behavior of the cryptic species varies depending on food diversity, indicating that L. marina acquire information about their environment when making dispersal decisions. All three cryptic species tend to disperse faster toward food patches that increase fitness. Pm I and Pm IV exhibited faster dispersal toward patches with a more diverse food source, while Pm III showed similar dispersal rates toward E. coli, medium-diversity, and high-diversity food. This indicates that resource diversity can alter the dispersal behavior of cryptic species and may be an important mechanism to achieve species coexistence in the field.
format: application/pdf
format: text/html
creator: Rodgee Mae Guden
creator: Sofie Derycke
creator: Tom Moens
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.18790
publisher: PeerJ Inc.
rights: © 2025 Guden et al.
abstract: Animals can use specific environmental cues to make informed decisions about whether and where to disperse. Patch conditions are known to affect the dispersal behavior of animals, but empirical studies investigating the impact of resource diversity on the dispersal of closely related species are largely lacking. In this study, we investigated how food diversity affects the dispersal behavior of three co-occurring cryptic species of the marine bacterivorous nematode complex Litoditis marina (Pm I, Pm III and Pm IV). Using microcosms composed of a local patch (inoculation plate), a connection tube, and a distant patch (dispersal plate), we examined nematode dispersal patterns with bacteria serving as the food source. Food treatments included low-, medium-, and high-diversity bacterial mixtures of 5, 10, and 15 bacterial strains, respectively. Additionally, a single-strain food resource Escherichia coli was used as a control treatment. Both local and distant patches had either identical food treatments (‘homogeneous patches’) or E. coli in the local patches and more diverse food (low-, medium-, or high-diversity food) in distant patches (‘heterogeneous patches’). Our results show that the dispersal behavior of the cryptic species varies depending on food diversity, indicating that L. marina acquire information about their environment when making dispersal decisions. All three cryptic species tend to disperse faster toward food patches that increase fitness. Pm I and Pm IV exhibited faster dispersal toward patches with a more diverse food source, while Pm III showed similar dispersal rates toward E. coli, medium-diversity, and high-diversity food. This indicates that resource diversity can alter the dispersal behavior of cryptic species and may be an important mechanism to achieve species coexistence in the field.
bibliographic citation: Guden et al. (2025) To stay or to go: resource diversity alters the dispersal behavior of sympatric cryptic marine nematodes. PeerJ 13:e18790 https://doi.org/10.7717/peerj.18790
date submitted: 2023-06-13
date accepted: 2024-12-10
issued: 2025-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guden
  given name: Rodgee Mae
author list: Agent
  family name: Derycke
  given name: Sofie
author list: Agent
  family name: Moens
  given name: Tom
doi: 10.7717/peerj.18790
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-13
copyright: © 2025 Guden et al.
attribution name: Guden et al.

Social presence effect in language comprehension: evidence from event-related potential (ERP) research
type: item
type: AcademicArticle
description: Objective This study aimed to examine the impact of social presence on Chinese reading comprehension and associated neural responses. Methods Participants tasked with reading Chinese sentences either alone or in the presence of others and subsequently assessing the accuracy of the sentences’ meanings. Concurrently, we recorded the participants’ electrical brain responses to critical word processing. Results Behavioral results indicated no significant effect of social presence on the judgment of sentence accuracy. Electroencephalogram (EEG) results, however, revealed that reading in the presence of others elicited more pronounced left anterior negativity (LAN) components in the left front of the scalp compared to reading alone. Additionally, incorrect meanings triggered larger N400 and P600 amplitudes in the mid-parietal region than correct meanings. Conclusion Social presence intensifies early neural responses during the reading of Chinese sentences, although it does not influence semantic integration or conflict resolution. These findings support the notion that social context affects language processing.
format: application/pdf
format: text/html
creator: Teng Yu
creator: Xue Sui
creator: Yu tong Li
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.18798
publisher: PeerJ Inc.
rights: © 2025 Yu et al.
abstract: Objective This study aimed to examine the impact of social presence on Chinese reading comprehension and associated neural responses. Methods Participants tasked with reading Chinese sentences either alone or in the presence of others and subsequently assessing the accuracy of the sentences’ meanings. Concurrently, we recorded the participants’ electrical brain responses to critical word processing. Results Behavioral results indicated no significant effect of social presence on the judgment of sentence accuracy. Electroencephalogram (EEG) results, however, revealed that reading in the presence of others elicited more pronounced left anterior negativity (LAN) components in the left front of the scalp compared to reading alone. Additionally, incorrect meanings triggered larger N400 and P600 amplitudes in the mid-parietal region than correct meanings. Conclusion Social presence intensifies early neural responses during the reading of Chinese sentences, although it does not influence semantic integration or conflict resolution. These findings support the notion that social context affects language processing.
bibliographic citation: Yu et al. (2025) Social presence effect in language comprehension: evidence from event-related potential (ERP) research. PeerJ 13:e18798 https://doi.org/10.7717/peerj.18798
date submitted: 2024-07-16
date accepted: 2024-12-11
issued: 2025-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Teng
author list: Agent
  family name: Sui
  given name: Xue
author list: Agent
  family name: Li
  given name: Yu tong
doi: 10.7717/peerj.18798
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-13
copyright: ©2025 Yu et al.
attribution name: Yu et al.

Effects of tropical fruit blends on fermentative and pigmentation aspects of probiotic native cultured goat milk
type: item
type: AcademicArticle
description: Background Fruits are sources of bioactive compounds such as phenolics that bring health benefits to consumers. The addition of fruit products and microorganisms with probiotic potential in fermented goat milk can facilitate the acquisition of these benefits through diet. In this sense, the objective of this study was to evaluate the effect of incorporating a mixture of ingredients from jaboticaba (Myrciaria cauliflora), jambolana (Syzygium cumini), and mandacaru (Cereus jamacaru) fruits on fermentation parameters (pH, titratable acidity, viability of the native culture Lactiplantibacillus plantarum CNPC003 and the starter culture), associated with pigmentation (phenolic compound content and color) through experimental mixture design. Methods A simplex-centroid experimental design was conducted, comprised of seven trials totaling the addition of 30% of the fruit preparations in the final formulation of fermented milk and one control trial (without addition of preparations), with the response being the total phenolic content and the instrumental color parameter a*. Fermentations were carried out with the addition of the native culture Lactiplantibacillus plantarum CNPC003 and the starter culture Streptococcus thermophilus. Subsequently, analyses of pH, titratable acidity, viability of the native and starter cultures, total phenolic compound content, and the instrumental color parameter a* were performed. Results The final pH among trials ranged from 4.55 to 4.69, titratable acidity ranged from 0.59 to 0.64, the population of L. plantarum CNPC003 reached levels exceeding 8 log CFU/g, as did the population of Streptococcus thermophilus. The content of phenolic compounds was higher in trials T1, T5, and T7, as well as the color parameter (a*). The use of experimental mixture design contributed to the development of products with high viability of L. plantarum, high content of phenolic compounds, and a characteristic color of the added fruits, bringing benefits to consum…
format: application/pdf
format: text/html
creator: Isadora Kaline Camelo Pires de Oliveira Galdino
creator: Gabriel Monteiro da Silva
creator: Miqueas Oliveira Morais da Silva
creator: Giordanni Cabral Dantas
creator: Elainy Virgínia dos Santos Pereira
creator: Tiago Almeida de Oliveira
creator: Karina Maria Olbrich dos Santos
creator: Antonio Silvio do Egito
creator: Flávia Carolina Alonso Buriti
creator: Haíssa Roberta Cardarelli
subject: Food Science and Technology
subject: Microbiology
subject: Statistics
description: doi:10.7717/peerj.18813
publisher: PeerJ Inc.
rights: © 2025 Kaline Camelo Pires de Oliveira Galdino et al.
abstract: Background Fruits are sources of bioactive compounds such as phenolics that bring health benefits to consumers. The addition of fruit products and microorganisms with probiotic potential in fermented goat milk can facilitate the acquisition of these benefits through diet. In this sense, the objective of this study was to evaluate the effect of incorporating a mixture of ingredients from jaboticaba (Myrciaria cauliflora), jambolana (Syzygium cumini), and mandacaru (Cereus jamacaru) fruits on fermentation parameters (pH, titratable acidity, viability of the native culture Lactiplantibacillus plantarum CNPC003 and the starter culture), associated with pigmentation (phenolic compound content and color) through experimental mixture design. Methods A simplex-centroid experimental design was conducted, comprised of seven trials totaling the addition of 30% of the fruit preparations in the final formulation of fermented milk and one control trial (without addition of preparations), with the response being the total phenolic content and the instrumental color parameter a*. Fermentations were carried out with the addition of the native culture Lactiplantibacillus plantarum CNPC003 and the starter culture Streptococcus thermophilus. Subsequently, analyses of pH, titratable acidity, viability of the native and starter cultures, total phenolic compound content, and the instrumental color parameter a* were performed. Results The final pH among trials ranged from 4.55 to 4.69, titratable acidity ranged from 0.59 to 0.64, the population of L. plantarum CNPC003 reached levels exceeding 8 log CFU/g, as did the population of Streptococcus thermophilus. The content of phenolic compounds was higher in trials T1, T5, and T7, as well as the color parameter (a*). The use of experimental mixture design contributed to the development of products with high viability of L. plantarum, high content of phenolic compounds, and a characteristic color of the added fruits, bringing benefits to consum…
bibliographic citation: Oliveira Galdino et al. (2025) Effects of tropical fruit blends on fermentative and pigmentation aspects of probiotic native cultured goat milk. PeerJ 13:e18813 https://doi.org/10.7717/peerj.18813
date submitted: 2024-05-09
date accepted: 2024-12-13
issued: 2025-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oliveira Galdino
  given name: Isadora Kaline Camelo Pires de
author list: Agent
  family name: Silva
  given name: Gabriel Monteiro da
author list: Agent
  family name: Silva
  given name: Miqueas Oliveira Morais da
author list: Agent
  family name: Dantas
  given name: Giordanni Cabral
author list: Agent
  family name: Pereira
  given name: Elainy Virgínia dos Santos
author list: Agent
  family name: Oliveira
  given name: Tiago Almeida de
author list: Agent
  family name: dos Santos
  given name: Karina Maria Olbrich
author list: Agent
  family name: Egito
  given name: Antonio Silvio do
author list: Agent
  family name: Alonso Buriti
  given name: Flávia Carolina
author list: Agent
  family name: Cardarelli
  given name: Haíssa Roberta
doi: 10.7717/peerj.18813
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-13
copyright: ©2025 Kaline Camelo Pires de Oliveira Galdino et al.
attribution name: Kaline Camelo Pires de Oliveira Galdino et al.

Genome-wide analyses of the NAC transcription factor gene family in Acer palmatum provide valuable insights into the natural process of leaf senescence
type: item
type: AcademicArticle
description: Acer palmatum is a deciduous shrub or small tree. It is a popular ornamental plant because of its beautiful leaves, which change colour in autumn. This study revealed 116 ApNAC genes within the genome of A. palmatum. These genes are unevenly distributed on the 13 chromosomes of A. palmatum. An analysis of the phylogenetic tree of Arabidopsis thaliana NAC family members revealed that ApNAC proteins could be divided into 16 subgroups. A comparison of ApNAC proteins with NAC genes from other species suggested their potential involvement in evolutionary processes. Studies suggest that tandem and segmental duplications may be key drivers of the expansion of the ApNAC gene family. Analysis of the transcriptomic data and qRT‒PCR results revealed significant upregulation of most ApNAC genes during autumn leaf senescence compared with their expression levels in summer leaves. Coexpression network analysis revealed that the expression profiles of 10 ApNAC genes were significantly correlated with those of 200 other genes, most of which are involved in plant senescence processes. In conclusion, this study contributes to elucidating the theoretical foundation of the ApNAC gene family and provides a valuable basis for future investigations into the role of NAC genes in regulating leaf senescence in woody ornamental plants.
format: application/pdf
format: text/html
creator: Xin Meng
creator: Chun Feng
creator: Zhu Chen
creator: Faheem Afzal Shah
creator: Yue Zhao
creator: Yuzhi Fei
creator: Hongfei Zhao
creator: Jie Ren
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.18817
publisher: PeerJ Inc.
rights: © 2025 Meng et al.
abstract: Acer palmatum is a deciduous shrub or small tree. It is a popular ornamental plant because of its beautiful leaves, which change colour in autumn. This study revealed 116 ApNAC genes within the genome of A. palmatum. These genes are unevenly distributed on the 13 chromosomes of A. palmatum. An analysis of the phylogenetic tree of Arabidopsis thaliana NAC family members revealed that ApNAC proteins could be divided into 16 subgroups. A comparison of ApNAC proteins with NAC genes from other species suggested their potential involvement in evolutionary processes. Studies suggest that tandem and segmental duplications may be key drivers of the expansion of the ApNAC gene family. Analysis of the transcriptomic data and qRT‒PCR results revealed significant upregulation of most ApNAC genes during autumn leaf senescence compared with their expression levels in summer leaves. Coexpression network analysis revealed that the expression profiles of 10 ApNAC genes were significantly correlated with those of 200 other genes, most of which are involved in plant senescence processes. In conclusion, this study contributes to elucidating the theoretical foundation of the ApNAC gene family and provides a valuable basis for future investigations into the role of NAC genes in regulating leaf senescence in woody ornamental plants.
bibliographic citation: Meng et al. (2025) Genome-wide analyses of the NAC transcription factor gene family in Acer palmatum provide valuable insights into the natural process of leaf senescence. PeerJ 13:e18817 https://doi.org/10.7717/peerj.18817
date submitted: 2024-08-06
date accepted: 2024-12-14
issued: 2025-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Xin
author list: Agent
  family name: Feng
  given name: Chun
author list: Agent
  family name: Chen
  given name: Zhu
author list: Agent
  family name: Shah
  given name: Faheem Afzal
author list: Agent
  family name: Zhao
  given name: Yue
author list: Agent
  family name: Fei
  given name: Yuzhi
author list: Agent
  family name: Zhao
  given name: Hongfei
author list: Agent
  family name: Ren
  given name: Jie
doi: 10.7717/peerj.18817
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-13
copyright: © 2025 Meng et al.
attribution name: Meng et al.

The impact of induced stress on reactive and proactive control in depression
type: item
type: AcademicArticle
description: Background Depression, a widespread mental health issue, is often marked by impaired cognitive control, particularly in managing proactive and reactive processes. The Dual Mechanisms of Control (DMC) framework differentiates between these two modes of cognitive control: proactive control involves sustained goal maintenance, while reactive control is more stimulus-driven and transient. Stress, known to exacerbate cognitive dysfunction in depression, may influence the balance between these control processes, though the specific effects remain poorly understood. This study aimed to investigate how acute stress influences proactive and reactive control in individuals with depressive symptoms. Methods A total of 142 participants were divided into high-stress and control conditions and further categorized based on their depression levels, measured using the Beck Depression Inventory-II (BDI-II). Cognitive control was assessed using the AX-Continuous Performance Task (AX-CPT), both before and after exposure to a stress-inducing anagram task, which was designed to differentiate between high-stress and low-stress conditions. Results Participants exposed to the high-stress condition reported significantly greater stress and fatigue levels compared to the control group, validating the stress manipulation. Although the balance between reactive and proactive control, as measured by the Proactive Behavioral Index (PBI), did not show significant changes, depressive individuals in the high-stress condition exhibited a significant decline in their ability to retain contextual information, as indicated by a reduction in the d’-context index. This suggests that depressive individuals may be more prone to stress-induced difficulties in proactive control. Discussion These findings highlight the selective impact of stress on proactive cognitive control in individuals with depressive symptoms, shedding light on a potential cognitive vulnerability in depression. While the balance between r…
format: application/pdf
format: text/html
creator: Akihiro Masuyama
subject: Cognitive Disorders
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.18821
publisher: PeerJ Inc.
rights: © 2025 Masuyama
abstract: Background Depression, a widespread mental health issue, is often marked by impaired cognitive control, particularly in managing proactive and reactive processes. The Dual Mechanisms of Control (DMC) framework differentiates between these two modes of cognitive control: proactive control involves sustained goal maintenance, while reactive control is more stimulus-driven and transient. Stress, known to exacerbate cognitive dysfunction in depression, may influence the balance between these control processes, though the specific effects remain poorly understood. This study aimed to investigate how acute stress influences proactive and reactive control in individuals with depressive symptoms. Methods A total of 142 participants were divided into high-stress and control conditions and further categorized based on their depression levels, measured using the Beck Depression Inventory-II (BDI-II). Cognitive control was assessed using the AX-Continuous Performance Task (AX-CPT), both before and after exposure to a stress-inducing anagram task, which was designed to differentiate between high-stress and low-stress conditions. Results Participants exposed to the high-stress condition reported significantly greater stress and fatigue levels compared to the control group, validating the stress manipulation. Although the balance between reactive and proactive control, as measured by the Proactive Behavioral Index (PBI), did not show significant changes, depressive individuals in the high-stress condition exhibited a significant decline in their ability to retain contextual information, as indicated by a reduction in the d’-context index. This suggests that depressive individuals may be more prone to stress-induced difficulties in proactive control. Discussion These findings highlight the selective impact of stress on proactive cognitive control in individuals with depressive symptoms, shedding light on a potential cognitive vulnerability in depression. While the balance between r…
bibliographic citation: Masuyama (2025) The impact of induced stress on reactive and proactive control in depression. PeerJ 13:e18821 https://doi.org/10.7717/peerj.18821
date submitted: 2024-09-12
date accepted: 2024-12-16
issued: 2025-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Masuyama
  given name: Akihiro
doi: 10.7717/peerj.18821
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-13
copyright: © 2025 Masuyama
attribution name: Masuyama

Genome-wide association study on color-image-based convolutional neural networks
type: item
type: AcademicArticle
description: Background Convolutional neural networks have excellent modeling abilities to complex large-scale datasets and have been applied to genomics. It requires converting genotype data to image format when employing convolutional neural networks to genome-wide association studies. Existing studies converting the data into grayscale images have shown promising. However, the grayscale image may cause the loss of information of the genotype data. Methods In order to make full use of the information, we proposed a new method, color-image-based convolutional neural networks, by converting the data into color images. Results The experiments on simulation and real data show that our method outperforms the existing methods proposed by Yue and Chen for converting data into grayscale images, in which the model accuracy is improved by an average of 7.61%, and the ratio of disease risk genes is increased by an average of 18.91%. The new method has better robustness and generalized performance.
format: application/pdf
format: text/html
creator: Han-Ming Liu
creator: Zhao-Fa Liu
creator: Zi Li
creator: Cong Yu
creator: Peng-Cheng Hu
creator: Qi-Feng Liu
creator: Tai-Gui Shi
subject: Genetics
subject: Genomics
subject: Statistics
subject: Computational Science
description: doi:10.7717/peerj.18822
publisher: PeerJ Inc.
rights: © 2025 Liu et al.
abstract: Background Convolutional neural networks have excellent modeling abilities to complex large-scale datasets and have been applied to genomics. It requires converting genotype data to image format when employing convolutional neural networks to genome-wide association studies. Existing studies converting the data into grayscale images have shown promising. However, the grayscale image may cause the loss of information of the genotype data. Methods In order to make full use of the information, we proposed a new method, color-image-based convolutional neural networks, by converting the data into color images. Results The experiments on simulation and real data show that our method outperforms the existing methods proposed by Yue and Chen for converting data into grayscale images, in which the model accuracy is improved by an average of 7.61%, and the ratio of disease risk genes is increased by an average of 18.91%. The new method has better robustness and generalized performance.
bibliographic citation: Liu et al. (2025) Genome-wide association study on color-image-based convolutional neural networks. PeerJ 13:e18822 https://doi.org/10.7717/peerj.18822
date submitted: 2024-07-17
date accepted: 2024-12-16
issued: 2025-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Han-Ming
author list: Agent
  family name: Liu
  given name: Zhao-Fa
author list: Agent
  family name: Li
  given name: Zi
author list: Agent
  family name: Yu
  given name: Cong
author list: Agent
  family name: Hu
  given name: Peng-Cheng
author list: Agent
  family name: Liu
  given name: Qi-Feng
author list: Agent
  family name: Shi
  given name: Tai-Gui
doi: 10.7717/peerj.18822
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-13
copyright: © 2025 Liu et al.
attribution name: Liu et al.

Cloning and functional verification of Geraniol-10-Hydroxylase gene in Lonicera japonica
type: item
type: AcademicArticle
description: Background Geraniol 10-hydroxylase (G10H) is a cytochrome P450 monooxygenase involved in regulation, which is involved in the biosynthesis of monoterpene. However, G10H is not characterized at the enzymatic mechanism and regulatory function in Lonicera japonica. Methods and Results A gene related to the biosynthesis of monoterpenoid, geraniol 10-hydroxylase, has been cloned from the medicinal plant Lonicera japonica. The gene, LjG10H, encodes a peptide of 498 amino acids with a predicted molecular weight of 54.45 kDa. LjG10H shares a homology of 72.93–83.90% with G10H from other plants. Phylogenetic analysis suggests that the protein encoded by this gene belongs to the cytochrome P450 monooxygenase family. Tissue-specific expression analysis revealed that LjG10H is most highly expressed in flowers. Through heterologous expression in E. coli, the LjG10H protein was purified and its catalytic activity was studied. The results show that the enzyme can catalyze the hydroxylation of geraniol to 10-hydroxygeraniol. Additionally, analysis of Lonicera japonica seedlings with silenced LjG10H revealed a reduction in monoterpenoid content. Conclusions This study demonstrates that LjG10H plays an important role in the biosynthetic pathway of iridoids. This is the first article that ascribes G10H to be associated with the biosynthetic pathway of iridoid. This study provides a theoretical basis for the functional mechanism of LjG10H in regulating iridoid synthesis and provides a valuable resource for molecular breeding studies.
format: application/pdf
format: text/html
creator: Shuping Zhang
creator: Zhenhua Liu
creator: Jia Li
creator: Qian Liu
creator: Yongqing Zhang
creator: Gaobin Pu
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.18832
publisher: PeerJ Inc.
rights: © 2025 Zhang et al.
abstract: Background Geraniol 10-hydroxylase (G10H) is a cytochrome P450 monooxygenase involved in regulation, which is involved in the biosynthesis of monoterpene. However, G10H is not characterized at the enzymatic mechanism and regulatory function in Lonicera japonica. Methods and Results A gene related to the biosynthesis of monoterpenoid, geraniol 10-hydroxylase, has been cloned from the medicinal plant Lonicera japonica. The gene, LjG10H, encodes a peptide of 498 amino acids with a predicted molecular weight of 54.45 kDa. LjG10H shares a homology of 72.93–83.90% with G10H from other plants. Phylogenetic analysis suggests that the protein encoded by this gene belongs to the cytochrome P450 monooxygenase family. Tissue-specific expression analysis revealed that LjG10H is most highly expressed in flowers. Through heterologous expression in E. coli, the LjG10H protein was purified and its catalytic activity was studied. The results show that the enzyme can catalyze the hydroxylation of geraniol to 10-hydroxygeraniol. Additionally, analysis of Lonicera japonica seedlings with silenced LjG10H revealed a reduction in monoterpenoid content. Conclusions This study demonstrates that LjG10H plays an important role in the biosynthetic pathway of iridoids. This is the first article that ascribes G10H to be associated with the biosynthetic pathway of iridoid. This study provides a theoretical basis for the functional mechanism of LjG10H in regulating iridoid synthesis and provides a valuable resource for molecular breeding studies.
bibliographic citation: Zhang et al. (2025) Cloning and functional verification of Geraniol-10-Hydroxylase gene in Lonicera japonica. PeerJ 13:e18832 https://doi.org/10.7717/peerj.18832
date submitted: 2024-03-20
date accepted: 2024-12-17
issued: 2025-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Shuping
author list: Agent
  family name: Liu
  given name: Zhenhua
author list: Agent
  family name: Li
  given name: Jia
author list: Agent
  family name: Liu
  given name: Qian
author list: Agent
  family name: Zhang
  given name: Yongqing
author list: Agent
  family name: Pu
  given name: Gaobin
doi: 10.7717/peerj.18832
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-13
copyright: © 2025 Zhang et al.
attribution name: Zhang et al.

Association between maternal rectovaginal group B streptococcus and the risk of stillbirth: a meta-analysis
type: item
type: AcademicArticle
description: Background Group B streptococcus (GBS) colonization in pregnant women is associated with adverse perinatal outcomes, including stillbirth. This meta-analysis investigated the relationship between maternal rectovaginal GBS colonization and the risk of stillbirth. Methods We conducted a comprehensive literature search across several databases, including PubMed, Embase, Web of Science, Wanfang, and China National Knowledge Infrastructure, covering studies published from the inception of the database until September 9, 2024. The search focused on observational studies comparing the risk of stillbirth in pregnant women with and without rectovaginal GBS colonization. Results were summarized using odds ratios (ORs) and 95% confidence intervals (CIs), and a random-effects model was used to account for potential heterogeneity. Results A total of ten studies comprising 121,195 pregnant women were included in the analysis. The pooled results indicated no significant overall association between maternal rectovaginal GBS colonization and the risk of stillbirth (OR: 1.66, 95% CI [0.95–2.91], p = 0.08; I2 = 84%). However, sensitivity analyses revealed a significant association in studies that included intrapartum antibiotic prophylaxis (IAP) (OR: 1.36, 95% CI [1.02–1.80], p = 0.03). Subgroup analyses demonstrated a significant association between maternal rectovaginal GBS colonization and stillbirth risk in retrospective studies (OR: 2.62, p = 0.04) and in studies employing multivariate analysis (OR: 2.11, p = 0.04). Conclusions While the meta-analysis did not find a significant overall association between maternal rectovaginal GBS colonization and stillbirth, significant associations were noted under specific conditions, such as studies using IAP, retrospective designs, and multivariate analyses. Further research is needed to clarify these associations.
format: application/pdf
format: text/html
creator: Yujue Wang
creator: Jingjing Liu
creator: Jinlian Song
creator: Teng Zhang
subject: Developmental Biology
subject: Gynecology and Obstetrics
subject: Infectious Diseases
description: doi:10.7717/peerj.18834
publisher: PeerJ Inc.
rights: © 2025 Wang et al.
abstract: Background Group B streptococcus (GBS) colonization in pregnant women is associated with adverse perinatal outcomes, including stillbirth. This meta-analysis investigated the relationship between maternal rectovaginal GBS colonization and the risk of stillbirth. Methods We conducted a comprehensive literature search across several databases, including PubMed, Embase, Web of Science, Wanfang, and China National Knowledge Infrastructure, covering studies published from the inception of the database until September 9, 2024. The search focused on observational studies comparing the risk of stillbirth in pregnant women with and without rectovaginal GBS colonization. Results were summarized using odds ratios (ORs) and 95% confidence intervals (CIs), and a random-effects model was used to account for potential heterogeneity. Results A total of ten studies comprising 121,195 pregnant women were included in the analysis. The pooled results indicated no significant overall association between maternal rectovaginal GBS colonization and the risk of stillbirth (OR: 1.66, 95% CI [0.95–2.91], p = 0.08; I2 = 84%). However, sensitivity analyses revealed a significant association in studies that included intrapartum antibiotic prophylaxis (IAP) (OR: 1.36, 95% CI [1.02–1.80], p = 0.03). Subgroup analyses demonstrated a significant association between maternal rectovaginal GBS colonization and stillbirth risk in retrospective studies (OR: 2.62, p = 0.04) and in studies employing multivariate analysis (OR: 2.11, p = 0.04). Conclusions While the meta-analysis did not find a significant overall association between maternal rectovaginal GBS colonization and stillbirth, significant associations were noted under specific conditions, such as studies using IAP, retrospective designs, and multivariate analyses. Further research is needed to clarify these associations.
bibliographic citation: Wang et al. (2025) Association between maternal rectovaginal group B streptococcus and the risk of stillbirth: a meta-analysis. PeerJ 13:e18834 https://doi.org/10.7717/peerj.18834
date submitted: 2024-11-13
date accepted: 2024-12-18
issued: 2025-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wang
  given name: Yujue
author list: Agent
  family name: Liu
  given name: Jingjing
author list: Agent
  family name: Song
  given name: Jinlian
author list: Agent
  family name: Zhang
  given name: Teng
doi: 10.7717/peerj.18834
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-01-13
copyright: © 2025 Wang et al.
attribution name: Wang et al.

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