title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=145 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Social presence effect in language comprehension: evidence from event-related potential (ERP) research link: https://peerj.com/articles/18798 last-modified: 2025-01-13 description: ObjectiveThis study aimed to examine the impact of social presence on Chinese reading comprehension and associated neural responses.MethodsParticipants 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.ResultsBehavioral 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.ConclusionSocial 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. creator: Teng Yu creator: Xue Sui creator: Yu tong Li uri: https://doi.org/10.7717/peerj.18798 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Yu et al. title: Effects of tropical fruit blends on fermentative and pigmentation aspects of probiotic native cultured goat milk link: https://peerj.com/articles/18813 last-modified: 2025-01-13 description: BackgroundFruits 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.MethodsA 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.ResultsThe 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 consumer health. 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 uri: https://doi.org/10.7717/peerj.18813 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Kaline Camelo Pires de Oliveira Galdino et al. title: Genome-wide analyses of the NAC transcription factor gene family in Acer palmatum provide valuable insights into the natural process of leaf senescence link: https://peerj.com/articles/18817 last-modified: 2025-01-13 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. 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 uri: https://doi.org/10.7717/peerj.18817 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Meng et al. title: The impact of induced stress on reactive and proactive control in depression link: https://peerj.com/articles/18821 last-modified: 2025-01-13 description: BackgroundDepression, 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.MethodsA 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.ResultsParticipants 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.DiscussionThese 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 reactive and proactive control remained stable, the impaired retention of contextual information post-stress points to a specific deficit in proactive control. This could have implications for targeted cognitive interventions, such as cognitive control training, aimed at enhancing resilience against stress in depressive populations. Future research should explore the long-term effects of stress on cognitive control, particularly in clinically diagnosed individuals. creator: Akihiro Masuyama uri: https://doi.org/10.7717/peerj.18821 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Masuyama title: Genome-wide association study on color-image-based convolutional neural networks link: https://peerj.com/articles/18822 last-modified: 2025-01-13 description: BackgroundConvolutional 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.MethodsIn 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.ResultsThe 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. 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 uri: https://doi.org/10.7717/peerj.18822 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Liu et al. title: Cloning and functional verification of Geraniol-10-Hydroxylase gene in Lonicera japonica link: https://peerj.com/articles/18832 last-modified: 2025-01-13 description: BackgroundGeraniol 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 ResultsA 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.ConclusionsThis 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. creator: Shuping Zhang creator: Zhenhua Liu creator: Jia Li creator: Qian Liu creator: Yongqing Zhang creator: Gaobin Pu uri: https://doi.org/10.7717/peerj.18832 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Zhang et al. title: Association between maternal rectovaginal group B streptococcus and the risk of stillbirth: a meta-analysis link: https://peerj.com/articles/18834 last-modified: 2025-01-13 description: BackgroundGroup 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.MethodsWe 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.ResultsA 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).ConclusionsWhile 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. creator: Yujue Wang creator: Jingjing Liu creator: Jinlian Song creator: Teng Zhang uri: https://doi.org/10.7717/peerj.18834 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Wang et al. title: Treatment options for Achilles tendinopathy: a scoping review of preclinical studies link: https://peerj.com/articles/18143 last-modified: 2025-01-10 description: BackgroundAchilles tendinopathy (AT) management can be difficult, given the paucity of effective treatment options and the degenerative nature of the condition. Innovative therapies for Achilles tendinopathy are therefore direly needed. New therapeutic developments predominantly begin with preclinical animal and in vitro studies to understand the effects at the molecular level and to evaluate toxicity. Despite the publication of many preclinical studies, a comprehensive, quality-assessed review of the basic molecular mechanisms in Achilles tendinopathy is lacking.ObjectivesThis scoping review aims to summarize the literature regarding in vitro and in vivo animal studies examining AT treatments and evaluate their effect on tendon properties. Also, a quality assessment of the included animal studies is done. We provide a comprehensive insight into the current state of preclinical AT treatment research which may guide preclinical researchers in future research.Eligibility criteriaTreatment options of Achilles tendinopathy in chemically or mechanically induced in vivo or in vitro Achilles tendinopathy models, reporting biomechanical, histological, and/or biochemical outcomes were included.Sources of evidenceA systematically conducted scoping review was performed in PubMed, Embase.com, Clarivate Analytics/Web of Science, and the Wiley/Cochrane Library. Studies up to May 4, 2023 were included.Charting MethodsData from the included articles were extracted and categorized inductively in tables by one reviewer. The risk-of-bias quality assessment of the included animal studies is done with Systematic Review Centre for Laboratory Animal Experimentation risk-of-bias tool.ResultsA total of 98 studies is included, which investigated 65 different treatment options. 80% of studies reported significant improvement in the Achilles tendon characteristics after treatment. The main results were; maximum load and stiffness improvement; fibre structure recovered and less inflammation was observed; collagen I fibrils increased, collagen III fibrils decreased, and fewer inflammatory cells were observed after treatment. However, 65.4% to 92.5% of the studies had an uncertain to high risk of bias according to the risk-of-bias tool of the Systematic Review Centre for Laboratory Animal Experimentation.ConclusionsDespite promising preclinical treatment outcomes, translation to clinical practice lags behind. This may be due to the poor face validity of animal models, heterogeneity in Achilles tendinopathy induction, and low quality of the included studies. Preclinical treatments that improved the biomechanical, histological, and biochemical tendon properties may be interesting for clinical trial investigation. Future efforts should focus on developing standardized preclinical Achilles tendinopathy models, improving reporting standards to minimize risk of bias, and facilitating translation to clinical practice. creator: Nathanael Opoku Agyeman-Prempeh creator: Huub Maas creator: George L. Burchell creator: Neal L. Millar creator: Maarten H. Moen creator: Theodoor Henri Smit uri: https://doi.org/10.7717/peerj.18143 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Agyeman-Prempeh et al. title: Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation link: https://peerj.com/articles/18515 last-modified: 2025-01-10 description: Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting significant challenges to downstream analysis and inference. To address this issue, we have developed Virseqimprover, a computational pipeline that can extend assembled contigs to complete or nearly complete genomes while maintaining extension quality. Virseqimprover first examines whether there is any chimeric sequence based on read coverage, breaks the sequence into segments if there is, then extends the longest segment with uniform depth of coverage, and repeats these procedures until the sequence cannot be extended. Finally, Virseqimprover annotates the gene content of the resulting sequence. Results show that Virseqimprover has good performances on correcting and extending viral contigs to their full lengths, hence can be a useful tool to improve the completeness and minimize the assembly errors of viral contigs. Both a web server and a conda package for Virseqimprover are provided to the research community free of charge. creator: Haoqiu Song creator: Saima Sultana Tithi creator: Connor Brown creator: Frank O. Aylward creator: Roderick Jensen creator: Liqing Zhang uri: https://doi.org/10.7717/peerj.18515 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Song et al. title: Soil polluted system shapes endophytic fungi communities associated with Arundo donax: a field experiment link: https://peerj.com/articles/18789 last-modified: 2025-01-10 description: With the expansion of the mining industry, environmental pollution from microelements (MP) and red mud (RM) has become a pressing issue. While bioremediation offers a cost-effective and sustainable solution, plant growth in these polluted environments remains difficult. Arundo donax is one of the few plants capable of surviving in RM-affected soils. To identify endophytic fungi that support A. donax in different contaminated environments and to inform future research combining mycorrhizal techniques with hyperaccumulator plants, we conducted a field experiment. The study compared endophytic fungal communities in A. donax grown in uncontaminated, MP soils contaminated with cadmium (Cd), arsenic (As), and lead (Pb), and RM-contaminated soils. Our findings showed that soil nutrient profiles differed by contamination type, with Cd concentrations in MP soils exceeding national pollution standards (GB 15168-2018) and RM soils characterized by high aluminum (Al), iron (Fe), and alkalinity. There were significant differences in the endophytic fungal community structures across the three soil types (p < 0.001). Co-occurrence network analysis revealed that endophytic fungi in MP soils exhibited competitive niche dynamics, whereas fungi in RM soils tended to share niches. Notably, Pleosporales sp., which accounted for 18% of the relative abundance in RM soils, was identified as a dominant and beneficial endophyte, making it a promising candidate for future bioremediation efforts. This study provides valuable insights into the role of endophytic fungi in phytoremediation and highlights their potential as resources for improving plant-microbe interactions in contaminated environments. creator: Xiaohui Wang creator: Yao Wang creator: Yingqiang Sun creator: Keyi Wang creator: Junbo Yang creator: Danjuan Zeng creator: Ling Mo creator: Jianxiong Liao creator: Qianshu Peng creator: Yu Yao creator: Gaozhong Pu uri: https://doi.org/10.7717/peerj.18789 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Wang et al.