title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=456 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Prediction of PM2.5 concentration based on the CEEMDAN-RLMD-BiLSTM-LEC model link: https://peerj.com/articles/15931 last-modified: 2023-08-28 description: Air quality has emerged as a critical concern in recent years, with the concentration of PM2.5 recognized as a vital index for assessing it. The accuracy of predicting PM2.5 concentrations holds significant value for effective air quality monitoring and management. In response to this, a combined model comprising CEEMDAN-RLMD-BiLSTM-LEC has been introduced, analyzed, and compared against various other models. The combined decomposition method effectively underlines the fundamental characteristics of the data compared to individual decomposition techniques. Additionally, local error correction (LEC) efficiently addresses the issue of prediction errors induced by excessive disturbances. The empirical results of nine steps indicate that the combined CEEMDAN-RLMD-BiLSTM-LEC model outperforms single prediction models such as RLMD and CEEMDAN, reducing MAE, RMSE, and SAMPE by 36.16%, 28.63%, 45.27% and 16.31%, 6.15%, 37.76%, respectively. Moreover, the inclusion of LEC in the model further diminishes MAE, RMSE, and SMAPE by 20.69%, 7.15%, and 44.65%, respectively, exhibiting commendable performance in generalization experiments. These findings demonstrate that the combined CEEMDAN-RLMD-BiLSTM-LEC model offers high predictive accuracy and robustness, effectively handling noisy data predictions and severe local variations. With its wide applicability, this model emerges as a potent tool for addressing various related challenges in the field. creator: Qiao Guo creator: Haoyu Zhang creator: Yuhao Zhang creator: Xuchu Jiang uri: https://doi.org/10.7717/peerj.15931 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Guo et al. title: Diversity analysis of Populus euphratica endophytic bacteria in Tarim River Basin, China link: https://peerj.com/articles/15934 last-modified: 2023-08-28 description: The bacterial diversity in Populus euphratica stem storage liquid samples grown in Shaya County and Yuli County of the Tarim River Basin was investigated. A culture-dependent (dilution spread plate method) and culture-independent method (PCR-RFLP technique) were used to identify the endophytic bacteria community structure and composition in P. euphratica in Tarim River Basin. Sixty-six bacterial strains were isolated from P. euphratica stem storage liquid samples on three agar media. The 16S rDNA gene was amplified and sequenced using bacterial universal primers. Phylogenetic analysis showed that the 66 strains belonged to three phyla (Firmicutes, Actinomycetes, and Gamma-Proteobacteria) and included 16 genera and 29 species. Among them, Pseudomonas (27.27%) and Bacillus (19.69%) were the dominant isolates. CGM-17 was a potentially new species of Pantoea. Restriction fragment length polymorphism of 16S rDNA gene amplified by polymerase chain reaction (PCR-RFLP) revealed 48 operational taxonomic units (OTUs). Phylogenetic analysis indicated that the 48 OTUs belonged to Firmicutes, Actinobacteria, Proteobacteria (α-, β-, γ-subgroup), Bacteroidetes, and Verrucomicrobia. Gamma-Proteobacteria was the dominant group, similarly to the culture-dependent method, accounting for 53% of the entire bacterial clone library. Our results indicate that P. euphratica endophytic bacteria diversity in the Tarim River Basin was rich, and the resources of endophytic bacteria were high. They provide valuable reference data and species resources for screening indigenous and functional strains of endophytic bacteria in P. euphratica. creator: Gang Cheng creator: Yan Cheng creator: Erkin Rahman uri: https://doi.org/10.7717/peerj.15934 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Cheng et al. title: Identification of Zip8-correlated hub genes in pulmonary hypertension by informatic analysis link: https://peerj.com/articles/15939 last-modified: 2023-08-28 description: BackgroundPulmonary hypertension (PH) is a syndrome characterized by marked remodeling of the pulmonary vasculature and increased pulmonary vascular resistance, ultimately leading to right heart failure and even death. The localization of Zrt/Irt-like Protein 8 (ZIP8, a metal ion transporter, encoded by SLC39A8) was abundantly in microvasculature endothelium and its pivotal role in the lung has been demonstrated. However, the role of Zip8 in PH remains unclear.MethodsBioinformatics analysis was employed to identify SLC39A8 expression patterns and differentially expressed genes (DEGs) between PH patients and normal controls (NC), based on four datasets (GSE24988, GSE113439, GSE117261, and GSE15197) from the Biotechnology Gene Expression Omnibus (NCBI GEO) database. Gene set enrichment analysis (GSEA) was performed to analyze signaling pathways enriched for DEGs. Hub genes were identified by cytoHubba analysis in Cytoscape. Reverse transcriptase-polymerase chain reaction was used to validate SLC39A8 and its correlated metabolic DEGs expression in PH (SU5416/Hypoxia) mice.ResultsSLC39A8 expression was downregulated in PH patients, and this expression pattern was validated in PH (SU5416/Hypoxia) mouse lung tissue. SLC39A8-correlated genes were mainly enriched in the metabolic pathways. Within these SLC39A8-correlated genes, 202 SLC39A8-correlated metabolic genes were screened out, and seven genes were identified as SLC39A8-correlated metabolic hub genes. The expression patterns of hub genes were analyzed between PH patients and controls and further validated in PH mice. Finally, four genes (Fasn, Nsdhl, Acat2, and Acly) were downregulated in PH mice. However, there were no significant differences in the expression of the other three hub genes between PH mice and controls. Of the four genes, Fasn and Acly are key enzymes in fatty acids synthesis, Nsdhl is involved in cholesterol synthesis, and Acat2 is implicated in cholesterol metabolic transformation. Taken together, these results provide novel insight into the role of Zip8 in PH. creator: FanRong Zhao creator: Yujing Chen creator: Yuliang Xie creator: Shuang Kong creator: LiaoFan Song creator: Hanfei Li creator: Chao Guo creator: Yanyan Yin creator: Weifang Zhang creator: Tiantian Zhu uri: https://doi.org/10.7717/peerj.15939 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhao et al. title: Self-assembly of Hyaluronic Acid-Cu-Quercetin flavonoid nanoparticles: synergistic chemotherapy to target tumors link: https://peerj.com/articles/15942 last-modified: 2023-08-28 description: BackgroundIn this study, a natural compound quercetin (Qu) was investigated for its various antitumor effects. However, due to its poor water solubility and low bioavailability, its clinical application is limited. To overcome this constraint, a modification was to Qu, which resulted in the creation of novel flavonoid self-assembling nanoparticles (HCQ NPs).MethodsHCQ NPs were synthesized by a self-assembly method and characterized using transmission electron microscopy, the Malvern Zetasizer instrument, X-ray photoelectron spectroscopy (XPS), the ultraviolet-visible spectrophotometric method (UV-vis), Fourier transform infrared (FITR) and inductively coupled plasma mass spectrometry. Extracellular, methylene blue spectrophotometric analysis was used to determine the ability of HCQ NPs to react with different concentrations of H2O2 to form hydroxyl radicals (•OH). Intracellular, DCFH-DA staining was used to detect the ability of HCQ NPs to react with H2O2 to generate reactive oxygen species. Flow cytometry was used to detect the uptake of HCQ NPs by MDA-MB-231 cells at different time points. The biocompatibility of HCQ NPs was evaluated using the Cell Counting Kit-8 (CCK-8) assay. Calcein AM/PI double staining and the CCK-8 assay were used to evaluate the synergistic antitumor effect of HCQ NPs and H2O2.ResultsHCQ NPs showed uniformly sized analogous spherical shapes with a hydrodynamic diameter of 55.36 ± 0.27 nm. XPS revealed that Cu was mainly present as Cu2+ in the HCQ NPs. UV−vis absorption spectrum of the characteristic peak of HCQ NPs was located at 296 nm. Similarly, FTIR spectroscopy revealed a complex formation of Qu and Cu2+ that substantially changed the wavenumber of the 4-position C = O characteristic absorption peak. Based on the proportion of Qu and Cu2+ (1:2), the total drug loading of Qu and Cu2+ in the HCQ NPs for therapeutic purposes was calculated to be 9%. Methylene blue spectrophotometric analysis of •OH indicated that Cu can lead to the generation of •OH by triggering Fenton-like reactions. HCQ NPs rapidly accumulated in MDA-MB-231 cells with the extension of time, and the maximum accumulation concentration was reached at about 0.5 h. Calcein AM/PI double staining and CCK-8 revealed synergistic antitumor effects of HCQ NPs including the chemotherapeutic effect of Qu and chemodynamic therapy by Cu2+ in a simulated tumor microenvironment. HCQ NPs demonstrated very low toxicity in LO2 cells in the biocompatibility experiment.ConclusionThis study show cases a new method of creating self-assembled flavonoid HCQ NPs that show great for fighting cancer. creator: Hanxun Yue creator: Xuan Zhao creator: Qin Yong creator: Min Shi creator: Xiaofeng Jiang creator: Yating Zhang creator: Xian Yu uri: https://doi.org/10.7717/peerj.15942 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yue et al. title: Ophthalmic nurses’ knowledge, attitude, and practice toward venous thromboembolic prevention: a dual-center cross-sectional survey link: https://peerj.com/articles/15947 last-modified: 2023-08-28 description: BackgroundVenous thromboembolism (VTE) is a severe preventable complication among ophthalmic surgical patients. The knowledge, attitude, and practice (KAP) of nurses play a key role in effective VTE prevention. However, little is known about the KAP of ophthalmic nurses’ VTE prevention. This study aimed to examine the level of KAP toward VTE prevention among Chinese ophthalmic nurses and to investigate the influencing factors of their VTE practice.MethodsA total of 610 ophthalmic nurses from 17 cities in Hunan and Zhejiang Provinces, China, participated in this study. Data was collected via the Sojump online platform from March to April 2021. A self-administered VTE questionnaire was developed to assess nurses’ KAP toward VTE prevention. Multiple linear regression analysis was used to analyze the influencing factors of ophthalmic nurses’ VTE prevention practice.ResultsThe scores (correct rates) of ophthalmic nurses’ knowledge, attitude, and practice were 103.87 ± 20.50 (76.4%), 21.96 ± 2.72, and 48.96 ± 11.23 (81.6%), respectively. The three lowest-scored knowledge items were related to VTE complications, physical prevention, and risk assessment. The three lowest-scored attitude items were related to nurses’ training, VTE risk, and patient education. The three lowest-scored practice items were related to the assessment scale, VTE assessment, and patient education. Nurses’ knowledge, attitude, and practice were significantly correlated with each other. Multiple linear regression analysis showed that Hunan Province (B = 2.77, p = 0.006), general hospital (B = 2.97, p = 0.009), outpatient department (B = 3.93, p = 0.021), inpatient department (B = 2.50, p = 0.001), previous VTE prevention training (B = 3.46, p < 0.001), VTE prevention management in hospital (B = 4.93, p < 0.001), better knowledge (B = 0.04, p = 0.038), and positive attitude towards VTE prevention (B = 1.35, p < 0.001) were all significantly and positively associated with higher practice scores in VTE prevention.ConclusionsOur study provided a comprehensive understanding of the ophthalmic nurses’ knowledge, attitude, and practice in VTE prevention, as well as identified specific items in each dimension for improvement. In addition, our study showed multiple factors were associated with ophthalmic nurses’ practice in VTE prevention, including environmental factors, training and management, knowledge and attitudes toward VTE prevention. Our findings provide important implications and guidance for future intervention programs to improve the ophthalmic nurses’ knowledge, attitude, and practice in VTE prevention. creator: Xiaoxi Zhou creator: Minhui Dai creator: Lingyu Sun creator: Chunyan Li creator: Wendi Xiang creator: Yaoyao Lin creator: Dandan Jiang uri: https://doi.org/10.7717/peerj.15947 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhou et al. title: Comprehensive transcriptional analysis of pig facial skin development link: https://peerj.com/articles/15955 last-modified: 2023-08-28 description: BackgroundSkin development is a complex process that is influenced by many factors. Pig skin is used as an ideal material for xenografts because it is more anatomically and physiologically similar to human skin. It has been shown that the skin development of different pig breeds is different, and some Chinese pig breeds have the characteristics of skin thickness and facial skin folds, but the specific regulatory mechanism of this skin development is not yet clear.MethodsIn this study, the facial skin of Chenghua sows in the four developmental stages of postnatal Day 3 (D3) , Day 90 (D90) , Day 180 (D180), and Year 3 (Y3) were used as experimental materials, and RNA sequencing (RNA–seq) analysis was used to explore the changes in RNA expression in skin development at the four developmental stages, determine the differentially expressed messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), and perform functional analysis of related genes by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses.ResultsA pairwise comparison of the four developmental stages identified several differentially expressed genes (DEGs) and found that the number of differentially expressed RNAs (DE RNAs) increased with increasing developmental time intervals. Elastin (ELN) is an important component of the skin. Its content affects the relaxation of the epidermis and dermal connection, and its expression is continuously downregulated during the four developmental stages. The functions of DEGs at different developmental stages were examined by performing GO and KEGG analyses, and the GO terms and enrichment pathways of mRNAs, lncRNAs, miRNAs, and circRNAs highly overlapped, among which the PPAR signaling pathway, a classical pathway for skin development, was enriched by DEGs of D3 vs. D180, D90 vs. D180 and D180 vs. Y3. In addition, we constructed lncRNA-miRNA-mRNA and circRNA-miRNA interaction networks and found genes that may be associated with skin development, but their interactions need further study.ConclusionsWe identified a number of genes associated with skin development, performed functional analyses on some important DEGs and constructed interaction networks that facilitate further studies of skin development. creator: Yujing Li creator: Rui Shi creator: Rong Yuan creator: Yanzhi Jiang uri: https://doi.org/10.7717/peerj.15955 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Lanspora dorisauae, a new marine fungus from rocky shores in Taiwan link: https://peerj.com/articles/15958 last-modified: 2023-08-28 description: This article reports a new marine fungus, Lanspora dorisauae (Phomatosporales, Sordariomycetes, Ascomycota), on trapped wood collected in coastal sites of Taiwan. This new fungus was subjected to a morphological examination and a phylogenetic study based on a combined analysis of the 18S, 28S, ITS rDNA, TEF1-α and RPB2 genes. Lanspora dorisauae is characterized by dark-coloured ascomata with a short neck, periphysate ostioles, subclavate, deliquescing asci without an apical ring, presence of wide paraphyses, striated wall ascospores with crown-like appendages on one pole of the ascospores. Phylogenetically, L. dorisauae grouped with Lanspora coronata (type species) with strong support. Lanspora coronata lacks paraphyses and appendages occur on both ends of the ascospores, while paraphyses are present and ascospore appendage is unipolar in L. dorisauae. Lanspora cylindrospora formed a sister clade with L. coronata and L. dorisauae, but it significantly differs in morphology with the latter two species in having cylindrical asci with an apical J- ring, smooth ascospore wall and no ascospore appendages, and may be better referred to a new genus. Lanspora, together with Phomatospora and Tenuimurus, belong to the Phomatosporaceae, Phomatosporales. Phomatospora berkeleyi should be sequenced to test the validity of the order Phomatosporales and the family Phomatosporaceae. creator: Ka-Lai Pang creator: Sheng-Yu Guo creator: Ami Shaumi creator: Satinee Suetrong creator: Anupong Klaysuban creator: Michael W. L. Chiang creator: E. B. Gareth Jones uri: https://doi.org/10.7717/peerj.15958 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Pang et al. title: Seed bio-priming with beneficial Trichoderma harzianum alleviates cold stress in maize link: https://peerj.com/articles/15644 last-modified: 2023-08-25 description: Maize is one of the major crops in the world and the most productive member of the Gramineae family. Since cold stress affects the germination, growth, and productivity of corn seeds, the present study aimed to investigate the effect of seed biopriming with Trichoderma harzianum on the tolerance of two genotypes of maize seedlings to cold stress. This study was conducted in triplicates in factorial experiment with a complete randomized block design (CRBD). The study was conducted in the greenhouse and laboratory of the University of Mohaghegh Ardabili, Ardabil, Iran. Experimental factors include two cultivars (AR68 cold-resistant and KSC703 cold-sensitive maize cultivars), four pretreatment levels (control, biopriming with T. harzianum, exogenous T. harzianum, and hydropriming), and two levels of cold stress (control and cold at 5 °C) in a hydroponic culture medium. The present study showed that maize leaves’ establishment rate and maximum fluorescence (Fm) are affected by triple effects (C*, P*, S). The highest establishment (99.66%) and Fm (994 units) rates were observed in the KP3 control treatment. Moreover, among the pretreatments, the highest (0.476 days) and the lowest (0.182 days) establishment rates were related to P0 and P3 treatments, respectively. Cultivar A showed higher chlorophyll a and b, carotenoid content, and establishment rate compared to cultivar K in both optimal and cold conditions. The highest root dry weight (11.84 units) was obtained in cultivar A with P3 pretreatment. The pretreatments with T. harzianum increased physiological parameters and seedling emergence of maize under cold and optimal stress conditions. Pretreatment and cultivar improved catalase activity in roots and leaves. Higher leaf and root catalase activity was observed in the roots and leaves of cultivar K compared to cultivar A. The cold treatment significantly differed in peroxidase activity from the control treatment. Cultivar K showed higher catalase activity than cultivar A. The main effects of pretreatment and cold on polyphenol oxidase activity and proline content showed the highest polyphenol oxidase activity and proline content in hydropriming (H) treatment. Cold treatment also showed higher polyphenol oxidase activity and proline content than cold-free conditions. creator: Mehdi Afrouz creator: R Z. Sayyed creator: Bahman Fazeli-Nasab creator: Ramin Piri creator: WaleedHassan Almalki creator: Betty Natalie Fitriatin uri: https://doi.org/10.7717/peerj.15644 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Afrouz et al. title: Characterization of endoplasmic reticulum-associated degradation in the human fungal pathogen Candida albicans link: https://peerj.com/articles/15897 last-modified: 2023-08-25 description: BackgroundCandida albicans is the most prevalent human fungal pathogen. In immunocompromised individuals, C. albicans can cause serious systemic disease, and patients infected with drug-resistant isolates have few treatment options. The ubiquitin-proteasome system has not been thoroughly characterized in C. albicans. Research from other organisms has shown ubiquitination is important for protein quality control and regulated protein degradation at the endoplasmic reticulum (ER) via ER-associated protein degradation (ERAD).MethodsHere we perform the first characterization, to our knowledge, of ERAD in a human fungal pathogen. We generated functional knockouts of C. albicans genes encoding three proteins predicted to play roles in ERAD, the ubiquitin ligases Hrd1 and Doa10 and the ubiquitin-conjugating enzyme Ubc7. We assessed the fitness of each mutant in the presence of proteotoxic stress, and we used quantitative tandem mass tag mass spectrometry to characterize proteomic alterations in yeast lacking each gene.ResultsConsistent with a role in protein quality control, yeast lacking proteins thought to contribute to ERAD displayed hypersensitivity to proteotoxic stress. Furthermore, each mutant displayed distinct proteomic profiles, revealing potential physiological ERAD substrates, co-factors, and compensatory stress response factors. Among candidate ERAD substrates are enzymes contributing to ergosterol synthesis, a known therapeutic vulnerability of C. albicans. Together, our results provide the first description of ERAD function in C. albicans, and, to our knowledge, any pathogenic fungus. creator: Ellen M. Doss creator: Joshua M. Moore creator: Bryce H. Harman creator: Emma H. Doud creator: Eric M. Rubenstein creator: Douglas A. Bernstein uri: https://doi.org/10.7717/peerj.15897 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Doss et al. title: NEAL: an open-source tool for audio annotation link: https://peerj.com/articles/15913 last-modified: 2023-08-25 description: Passive acoustic monitoring is used widely in ecology, biodiversity, and conservation studies. Data sets collected via acoustic monitoring are often extremely large and built to be processed automatically using artificial intelligence and machine learning models, which aim to replicate the work of domain experts. These models, being supervised learning algorithms, need to be trained on high quality annotations produced by experts. Since the experts are often resource-limited, a cost-effective process for annotating audio is needed to get maximal use out of the data. We present an open-source interactive audio data annotation tool, NEAL (Nature+Energy Audio Labeller). Built using R and the associated Shiny framework, the tool provides a reactive environment where users can quickly annotate audio files and adjust settings that automatically change the corresponding elements of the user interface. The app has been designed with the goal of having both expert birders and citizen scientists contribute to acoustic annotation projects. The popularity and flexibility of R programming in bioacoustics means that the Shiny app can be modified for other bird labelling data sets, or even to generic audio labelling tasks. We demonstrate the app by labelling data collected from wind farm sites across Ireland. creator: Anthony Gibbons creator: Ian Donohue creator: Courtney Gorman creator: Emma King creator: Andrew Parnell uri: https://doi.org/10.7717/peerj.15913 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gibbons et al.