title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=162 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Prognostic value of serum Mrp 8/14 in sepsis-induced acute respiratory distress syndrome patients: a retrospective cohort study link: https://peerj.com/articles/18718 last-modified: 2024-12-13 description: BackgroundMrp 8/14 is abundantly secreted by activated neutrophils during infection and inflammation. However, its prognostic value in acute respiratory distress dyndrome (ARDS) induced by sepsis is poorly understood. Our aim was to investigate the relationship between serum Mrp 8/14 and the prognosis in sepsis-induced ARDS patients admitted to the intensive care unit (ICU).MethodsSerum Mrp 8/14 concentrations were analyzed in 118 ARDS patients induced by sepsis included in the analytical study. Patients were enrolled upon admission to the ICU of Nanjing Hospital affiliated to Nanjing Medical University. The baseline information and clinical outcomes were obtained. Patients were divided into survivor group and non-survivor group according to whether they died during ICU hospitalization.ResultsThe serum Mrp 8/14 levels were significantly increased in the non-survivor group compared to the survivor group (P < 0.05). Logistic regression analysis showed that serum Mrp 8/14, albumin and APACHE II were the independent factors for predicting the prognosis of sepsis-induced ARDS during ICU hospitalization after adjustment. Additionally, the area under the receiver operating characteristic curve for Mrp 8/14 combined with albumin was associated with ICU mortality and was higher than that of Mrp 8/14, albumin, APACHE II and Mrp 8/14 combined with APACHE II (all P < 0.05). A nomogram was constructed to predict ICU mortality and the c-indexes of predictive accuracy was 0.830 in the cohort (P < 0.05).ConclusionsThe serum Mrp 8/14 upon ICU admission in septic patients may be useful for predicting mortality in sepsis-induced ARDS patients during ICU hospitalization. creator: Caizhi Sun creator: Yongpeng Xie creator: Chenchen Zhu creator: Lei Guo creator: Bowen Xu creator: Haidong Qin creator: Xiaomin Li uri: https://doi.org/10.7717/peerj.18718 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sun et al. title: Phylogeography of the Mesa Silverside fish Chirostoma jordani (Woolman, 1894) throughout the Mexican Plateau link: https://peerj.com/articles/18256 last-modified: 2024-12-12 description: BackgroundUnderstanding the processes that influence distribution of organisms is a major goal in evolutionary biology. Speciation in freshwater fishes is mainly associated with the “island-like” model of evolution, in which the formation of land barriers between different hydrographic basins interrupts gene flow and promotes isolation. Freshwater fish therefore provide an excellent model system for macro- and micro-evolutionary studies. The Mesa Silverside, Chirostoma jordani, is one of the most widespread freshwater fish species in the Mexican Plateau, a geologically complex physiographic region with a long history of genesis, destruction and compartmentalization of hydrographic basins that has promoted the dispersal and isolation of freshwater fishes.MethodsWe used mitochondrial (Cytb and D-loop) and nuclear (first intron of the ribosomal protein S7) data and used phylogeographic and coalescent based methods to elucidate the evolutionary history of C. jordani throughout its distributional range on the Mexican Plateau.ResultsThe results obtained in the present study revealed that C. jordani consists of two main genetic groups with geographical correspondence. Clade I occur exclusively in north-western basin and shows population structure. Clade II is widely distributed across the west, central and eastern basins without population structure. The split between these two main clades was estimated at 1.4 Mya. This cladogenetic event may be associated with the allopatric process promoted by the fragmentation and compartmentalization of hydrographic basins induced by the geological and climatic history of the Mexican Plateau. creator: Isai Betancourt-Resendes creator: Rodolfo Pérez-Rodríguez creator: Kyle R. Piller creator: Omar Domínguez-Domínguez uri: https://doi.org/10.7717/peerj.18256 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Betancourt-Resendes et al. title: A polyphasic approach in the identification and biochemical characterization of Dunaliella tertiolecta with biodiesel potential from a saltern in Mauritius link: https://peerj.com/articles/18325 last-modified: 2024-12-12 description: Bioprospecting robust and oleaginous strain is crucial for the commercialization of microalgae-based biodiesel. In this study, a microalgal strain SCH18 was isolated from a solar saltern located in Mauritius. This isolate was identified as Dunaliella tertiolecta based on a polyphasic approach that combined molecular, physiological, and morphological analyses. Furthermore, the effect of different salinities on the biochemical composition and fatty acid profile of this microalga was investigated to explore its potential in producing biodiesel. Results from the growth studies showed that salinity of 1.0 M NaCl was optimal for achieving a high growth rate. Under this salt concentration, the growth rate and the doubling time were calculated as 0.39 ± 0.003 day−1 and 1.79 ± 0.01 days, respectively. In terms of biochemical composition, a substantial amount of carbohydrate (42.02 ± 5.20%), moderate amount of protein (30.35 ± 0.18%) and a low lipid content (17.81 ± 2.4%) were obtained under optimal NaCl concentration. The fatty acid analysis indicated the presence of palmitic acid, stearic acid, palmitoleic acid, oleic acid, linoleic acid, gamma, and alpha-linolenic acids, which are suitable for biodiesel synthesis. The predicted biodiesel properties were in accordance with the standard of ASTM 6751, indicating that the microalgal isolate D. tertiolecta SCH18 is a potential candidate for use in biodiesel production. creator: Kamlesh Ramdhony creator: Daneshwar Puchooa creator: Turki Kh. Faraj creator: Abdulwahed Fahad Alrefaei creator: JunFu Li creator: Rajesh Jeewon uri: https://doi.org/10.7717/peerj.18325 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ramdhony et al. title: Study of TRAF3IP3 for prognosis and immune infiltration in hepatocellular carcinoma link: https://peerj.com/articles/18538 last-modified: 2024-12-12 description: BackgroundTumor necrosis factor receptor-associated factor 3 (TRAF3)-interacting protein 3 (TRAF3IP3) expressed in various tumor cell. However, its role in hepatocellular carcinoma (HCC) was unclear. We aimed to demonstrate the relationship between TRAF3IP3 and HCC and explore the potential role of TRAF3IP3 in HCC.MethodsThe Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Genotype-Tissue Expression (GTEx), KM-Plotter, University of Alabama at Birmingham Cancer data analysis Portal (UALCAN), and Xiantao Academic Online Website were utilized for the systematic analysis of TRAF3IP3. This analysis included mRNA expression, protein expression, prognostic value, enrichment analysis, and immune cell infiltration in HCC. Subsequently, immunohistochemistry was performed to assess the expression levels of TRAF3IP3 in both cancer and non-cancer tissues of patients with HCC.ResultsAnalysis of public databases and immunohistochemical staining on 20 pairs of samples confirmed a decrease in TRAF3IP3 expression in HCC. Both the TCGA database and GSE14520 indicated that patients with high TRAF3IP3 expression had a more favorable prognosis in terms of overall survival (OS) and progression-free interval (PFI), as shown by KM curve results. Multivariate Cox regression analysis further demonstrated that high TRAF3IP3 expression was an independent protective factor for HCC prognosis (hazard ratio (HR): 0.619, 95% confidence interval (CI) [0.399–0.959]; p < 0.05). In the high TRAF3IP3 expression group, various immune response-related molecular pathways, particularly B lymphocyte-mediated pathways, were activated. The level of TRAF3IP3 expression showed a significant correlation with the presence of tumor-infiltrating CD8+ T cells. Additionally, a positive correlation was observed between immunophenoscore (IPS) and TRAF3IP3 expression. Notably, the half-maximal inhibitory concentration (IC50) of commonly used chemotherapeutic drugs, such as lapatinib and mitomycin, was inversely associated with TRAF3IP3 expression in HCC patients.ConclusionTRAF3IP3 may be as a novel and promising biomarker for prognosis prediction and immunological evaluation of HCC. creator: Xing Wang creator: Xin Gao creator: Airu Liu creator: Yan Qin creator: Zhi-Yu Ni creator: Xiao Lan Zhang uri: https://doi.org/10.7717/peerj.18538 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Wang et al. title: Variation in behaviour of native prey mediates the impact of an invasive species on plankton communities link: https://peerj.com/articles/18608 last-modified: 2024-12-12 description: Trait variation in predator populations can influence the outcome of predator-prey dynamics, with consequences for trophic dynamics and ecosystem functioning. However, the influence of prey trait variation on the impacts of predators is not well understood, especially for introduced predators where variation in prey can shape invasion outcomes. In this study, we investigated if intra-specific differences in vertical position of Daphnia influenced the impacts of the invasive zooplankton predator, Bythotrephes cederströmii, on plankton communities. Our results show that vertical position of Daphnia influenced Bythotrephes predation on smaller cladoceran species and impacts on primary production. Larger reductions in small cladoceran density and greater algal biomass were observed in mesocosms with less spatial overlap between Daphnia and Bythotrephes. These results suggest that differences in vertical position of Daphnia can alter the type and magnitude of Bythotrephes impacts in invaded systems. creator: Sarah S. Hasnain creator: Shelley E. Arnott uri: https://doi.org/10.7717/peerj.18608 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hasnain and Arnott title: ClBRN1 from Chrysanthemum lavandulifolium enhances the stress resistance of transgenic Arabidopsis link: https://peerj.com/articles/18620 last-modified: 2024-12-12 description: BackgroundChrysanthemum (Chrysanthemum×morifolium Ramat.) is a particularly important autumn perennial flower for potted plant, flower bed and border, and cut flower with high ornamental value. However, abiotic stress can affect the ornamental quality of Chrysanthemum. NAC (NAM, ATAF1-2, and CUC2) transcription factors (TFs) play an important role in regulating plant growth and development, as well as responding to abiotic stresses.MethodsIn this study, the ClBRN1 (Chrysanthemum lavandulifolium BEARSKIN gene) was isolated from the Chrysanthemum model plant C. lavandulifolium. And analyze the function of the gene through bioinformatics, subcellular localization and overexpression.ResultsBioinformatics analysis showed that the ClBRN1 gene was a member of the NAC TFs family, with a CDS (coding sequence) length of 1,080 bp and encoding 359 amino acids. The subcellular localization results found that the gene was located in the nucleus and cell membrane. Furthermore, the transgenic results in Arabidopsis thaliana showed that the gene significantly reduces plant height while improving salt and low temperature tolerance. Observation of paraffin sections of Arabidopsis stems also revealed that the secondary cell wall of overexpressing Arabidopsis stems was significantly thicker than that of wild-type. The above results indicate that the ClBRN1 gene may play an important role in regulating plant resistance to abiotic stress. This study will provide new insights for molecular breeding of resistant chrysanthemums in the future. creator: Yanxi Li creator: Wenting He creator: Yueyue Liu creator: Chendi Mei creator: Hai Wang creator: Xuebin Song uri: https://doi.org/10.7717/peerj.18620 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: The largest sauropodomorph skull from the Lower Jurassic Lufeng Formation of China link: https://peerj.com/articles/18629 last-modified: 2024-12-12 description: The Lower Jurassic Lufeng Formation of China has long been recognized for its diverse early-diverging sauropodomorph dinosaurs, with eight genera and ten species, representing more than half the Laurasian records. In this paper, we describe a new genus and species of non-sauropodan sauropodomorph, Lishulong wangi gen. et sp. nov., from Yunnan Province in southwestern China. This new taxon is represented by a partial skeleton including the skull and nine articulated cervical vertebrae, which differs from other Lufeng forms in both cranial and cervical characteristics. It bears several autapomorphies of the nasal process, the maxillary neurovascular foramen, and the cervical neural spine. Phylogenetic analysis reveals that Lishulong is an early-diverging member of the Sauropodiformes, and the sister-taxon of Yunnanosaurus. Elucidating the novel osteology of Lishulong, it possessed the largest sauropodomorph cranial material currently identified from the Lufeng Formation, not only enriches the diversity of the Lufeng dinosaur assemblage, but also enhances our understanding of the character evolution in early-diverging sauropodiforms. Furthermore, information about paleobiogeographic distributions indicates that Early Jurassic sauropodomorphs, especially Chinese taxa, have maintained multiple dispersions and exchanges within Pangaea. creator: Qian-Nan Zhang creator: Lei Jia creator: Tao Wang creator: Yu-Guang Zhang creator: Hai-Lu You uri: https://doi.org/10.7717/peerj.18629 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Preoperative 3D printing planning technology combined with orthopedic surgical robot-assisted minimally invasive screw fixation for the treatment of pelvic fractures: a retrospective study link: https://peerj.com/articles/18632 last-modified: 2024-12-12 description: ObjectiveTo explore the advantages and effectiveness of preoperative 3D printing planning technology combined with orthopedic surgical robot-assisted screw placement in the minimally invasive treatment of pelvic fractures compared to orthopedic surgical robot-assisted screw placement alone.MethodsA retrospective analysis of the clinical data of 29 patients with unstable pelvic fractures treated with orthopedic surgical robot-assisted percutaneous screw fixation from July 2021 to August 2023 was conducted. Among them, 13 patients who underwent preoperative 3D printing technology for screw planning were assigned to the experimental group, and the remaining 16 patients were assigned to the control group. All patients underwent screw fixation alone or combined with other fixation methods for fracture fixation. The application of preoperative 3D printing planning in orthopedic surgical robot operations was described. The intraoperative screw drawing time, invasive operation time, number of fluoroscopies during invasive operation, postoperative evaluation of screw accuracy, fracture healing, complications, and functional outcomes were recorded and compared between the two groups.ResultsAll patients successfully underwent surgery, with one patient in the control group experiencing numbness in the sciatic nerve innervation area. All patients were followed up for 4–15 months, with an average of 8 months, and all fractures achieved healing. The experimental group had a total of 26 screws inserted, while the control group had 30 screws. In the experimental group, the intraoperative screw drawing time was 3.0 (3.0, 3.37) min, significantly shorter than 4.0 (3.6, 4.0) min in the control group (P < 0.05). The proportion of screws not penetrating the bone postoperatively was 88.5% in the experimental group, significantly higher than 63.3% in the control group (P < 0.05). In the experimental group, the postoperative screw position, compared to the planned screw position, had an average position deviation of 3.05 ± 0.673 mm and an average spatial angle deviation of 2.22 ± 0.605°. At the last follow-up, the Majeed score was used to assess function, with the experimental group having an excellent and good rate of 84.6%, slightly higher than 75.0% in the control group, but the difference was not statistically significant (P > 0.05).ConclusionIn the treatment of pelvic fractures using screw fixation, preoperative 3D printing technology planning combined with orthopedic surgical robots, compared to orthopedic surgical robot-assisted screw placement alone, can significantly reduce intraoperative screw drawing time, decrease drawing difficulty, enhance screw placement accuracy, and does not increase invasive operation time or the number of fluoroscopies. This approach makes the surgery safer and is a method worth applying. creator: YuLong Jing creator: LiMing Chang creator: Bo Cong creator: JianHang Wang creator: MingQi Chen creator: ZhiFeng Tang creator: JingJie Luan creator: ZiYin Han creator: YangDe Liu creator: Tao Sun uri: https://doi.org/10.7717/peerj.18632 license: https://creativecommons.org/licenses/by/4.0 rights: ©2024 Jing et al. title: Exploration of key mechanisms underlying the therapeutic effects of AMD3100 on attenuating lipopolysaccharide-induced acute lung injury in mice link: https://peerj.com/articles/18698 last-modified: 2024-12-12 description: ContextAMD3100, a CXCR4 antagonist, has beneficial effects immaculate in the treatment of acute lung injury (ALI).ObjectiveALI is a severe inflammatory condition associated with poor prognosis and limited treatment options. AMD3100, has therapeutic effects that reduce ALI. Our study explored the regulatory mechanisms of AMD3100 in alleviating the injury of lipopolysaccharide (LPS)-induced ALI in mice.Materials and MethodsMale ICR mice were randomly divided into control, LPS-treated, AMD3100-treated, and LPS + AMD3100-treatment groups. The histological changes of lung tissues from different groups were evaluated using hematoxylin and eosin staining. Lung injury was measured by ELISA and lung wet/dry ratio. Moreover, lung tissues from the four groups were subjected to transcriptome sequencing followed by differential expression, functional enrichment, protein-protein interaction (PPI) networks, and transcription factor analyses. The validation of mRNAs and protein levels were conducted with qRT-PCR and ELISA.ResultsHematoxylin and eosin staining combined with the concentration of IL-1 and IL1-β and lung wet/dry ratios revealed that AMD3100 reduced the level of LPS-induced lung injury. Analysis of the transcriptome sequencing data identified 294 differentially expressed genes in the LPS-induced ALI mouse model. Based on the PPI network and module analysis, hub targets of AMD3100, such as Cxcl10 and Cxcl9, were identified in module 1, and hub targets, such as Cxcl12 and Cxcl1, were identified in module 2. Cxcl10 and Cxcl9 are involved in the Toll-like receptor signaling pathway, and Cxcl12 and Cxcl1 arae enriched in the nuclear factor-kappa B signaling pathway. Cxcl19, Cxcl10, and Cxcl1 are targeted by transcription factors like NF-κB. The validation of mRNAs and protein levels conducted by PCR and ELISA supported our transcriptome data.ConclusionsOur findings indicate that AMD3100 may exhibit a therapeutic effect on LPS-induced ALI in mice by modulating multiple chemokines to inhibit the Toll-like receptor/nuclear factor-kappa B signaling pathway. creator: Zhou Lv creator: Bohan Zhang creator: Hui Zhang creator: Yanfei Mao creator: Qihong Yu creator: Wenwen Dong uri: https://doi.org/10.7717/peerj.18698 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Lv et al. title: Habitual tea consumption is associated with a lower prevalence of kidney stone disease in postmenopausal women link: https://peerj.com/articles/18639 last-modified: 2024-12-11 description: BackgroundMenopause is associated with an increased risk of kidney stone disease (KSD). However, for postmenopausal women, how to avoid KSD has rarely been studied. The aim of this study was to explore whether drinking tea is associated with a reduction in the prevalence of KSD in postmenopausal women.MethodsWe collected 11,484 postmenopausal women from the Taiwan Biobank, and used questionnaires to obtain information on tea drinking, KSD, and comorbidities. The participants were divided into two groups according to habitual tea consumption: tea-drinking and non-tea-drinking groups. The association between habitual tea consumption and KSD was examined by logistic regression analysis.ResultsThere were 2,035 postmenopausal women in the tea-drinking group and 9,449 postmenopausal women in the non-tea-drinking group. The mean age of all participants was 61 years. Compared to the non-tea-drinking group, the tea-drinking group had a significantly lower prevalence of KSD (7% vs. 5%). The odds ratio (OR) of KSD was lower in those who habitually drank tea than in those who did not (OR = 0.78; 95% confidence interval [CI] [0.63 to 0.96]) after adjusting for confounders. Moreover, postmenopausal women with a daily intake of two cups of tea or more had a 30% reduced risk of KSD compared to those who did not habitually drink tea (OR = 0.71, 95% CI [0.56 to 0.90]).ConclusionsOur results suggest that habitual tea drinking may be associated with a reduction in the prevalence of KSD in postmenopausal women. Further studies are warranted to investigate the protective effect of tea on the development of KSD. creator: Kuan-Hsien Wu creator: Jia-In Lee creator: Yung-Chin Lee creator: Jung-Tsung Shen creator: Hsun-Shuan Wang creator: Yao-Hsuan Tsao creator: Yi-Hsuan Wu creator: Shu-Pin Huang creator: Szu-Chia Chen creator: Jhen-Hao Jhan creator: Jiun-Hung Geng uri: https://doi.org/10.7717/peerj.18639 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Wu et al.