title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=398 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identification and validation of key genes associated with pathogenesis and prognosis of gastric cancer link: https://peerj.com/articles/16243 last-modified: 2023-10-16 description: BackgroundGastric cancer (GC) is the fourth leading cause of cancer-related death worldwide. However, the precise mechanisms and specific biomarkers of GC have not been fully elucidated. We therefore sought to identify and validate the genes associated with GC.MethodsRNA sequencing was performed on gastric tissue specimens from 10 cases each of non-atrophic gastritis (NAG), intestinal metaplasia (IM), and GC. Validation of gene expression was conducted through immunohistochemistry (IHC) staining. The Kaplan–Meier Plotter database was utilized to screen genes associated with prognosis, while protein–protein interaction analysis was conducted to identify hub genes.ResultsIn GC-IM, the differentially expressed genes (DEGs) were predominantly enriched in pathways related to ECM-receptor interaction, focal adhesion, PI3K-Akt pathway, and pathways in cancer. Conversely, in IM-NAG, the DEGs were primarily enriched in pathways associated with fat digestion and absorption, pancreatic secretion, and retinol metabolism. IHC staining revealed elevated expression levels of KLK7 and KLK10 in GC. Specifically, KLK7 expression was found to be correlated with differentiation (P = 0.025) and depth of invasion (P = 0.007) in GC, while both KLK7 and KLK10 were associated with the overall survival (P < 0.05). Furthermore, a total of ten hub genes from DEGs in GC-NAG (COL6A2, COL1A1, COL4A1, COL1A2, SPARC, COL4A2, FN1, PCOLCE, SERPINH1, LAMB1) and five hub genes in IM-NAG (SI, DPP4, CLCA1, MEP1A, OLFM4) were demonstrated to have a significant correlation with the prognosis of GC.ConclusionsThe present study successfully identified and validated crucial genes associated with GC, providing valuable insights into the underlying mechanisms of this disease. The findings of this study have the potential to inform clinical practice. creator: Ai Li creator: Yan Li creator: Yueyue Li creator: Mingming Zhang creator: Hong Zhang creator: Feixue Chen uri: https://doi.org/10.7717/peerj.16243 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Developing a semi-pelagic trawl to capture redfish in the Gulf of St. Lawrence, Canada link: https://peerj.com/articles/16244 last-modified: 2023-10-16 description: In this study, we developed a semi-pelagic trawl to target redfish (Sebastes spp.) and potentially reduce the capture of bycatch species and seabed impacts in the Gulf of St. Lawrence, Canada. The new trawl used an innovative technique connecting the upper bridles of the trawl to the warps, anterior of the trawl doors, leading to the trawl system being fished off the seabed. Such a technique can be used to match the heights of redfish as they move above the seabed during their diurnal cycle while allowing bycatch species related to the seabed to escape under the trawl. A 1:10 scale model of the trawl was constructed and evaluated in a flume tank to optimize the rigging and then a full-scale trawl was constructed for sea trials. Two field experiments subsequently evaluated the trawl at sea. The first field experiment concentrated on the experimental trawl’s operation and video observations of redfish behaviour in the trawl mouth and its effect on trawl entry. The second field experiment concentrated on a small-scale preliminary test on the catch of redfish and bycatch species when the trawl was on or off the seabed. Capture results, though preliminary, indicate that redfish can be targeted commercially with a semi-pelagic trawl, though some redfish will escape under the trawl. Additionally, results suggest that the catches of bycatch species may be reduced. In conclusion, this study suggests that a semi-pelagic trawl could be considered an effective technique to harvest redfish sustainably. creator: Vang Y. Nguyen creator: Shannon M. Bayse creator: Paul D. Winger creator: Harold DeLouche creator: George Legge uri: https://doi.org/10.7717/peerj.16244 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Nguyen et al. title: The transcriptome of the entomopathogenic fungus Culicinomyces clavisporus contains an ortholog of the insecticidal ribotoxin Hirsutellin link: https://peerj.com/articles/16259 last-modified: 2023-10-16 description: The entomopathogenic fungus Culicinomyces clavisporus is known to infect and kill mosquito larvae and therefore has been seen as a potential biological control agent against disease vector mosquitoes. Whereas most fungal entomopathogens infect hosts by penetrating the external cuticle, C. clavisporus initiates infection through ingestion (per os). This unique infection strategy suggests that the C. clavisporus genome may be mined for novel pathogenicity factors with potential for vector control. To this end, an Isoseq-based transcriptome analysis was initiated, and resulted in a total of 3,512,145 sequences, with an average length of 1,732 bp. Transcripts assembly and annotation suggested that the C. clavisporus transcriptome lacked the cuticle-degrading proteins that have been associated with other entomopathogenic fungi, supporting the per os pathogenicity process. Furthermore, mining of the sequence data unexpectedly revealed C. clavisporus transcripts homologous to the Hirsutellin toxin. Comparative sequence analyses indicated that the C. clavisporus Hirsutellin predicted protein has retained the canonical molecular features that have been associated with the ribotoxic and insecticidal properties of the original toxin isolated from Hirsutella thompsonii. The identification of an Hirsutellin ortholog in C. clavisporus was supported by phylogenetic analyses demonstrating that Culicinomyces and Hirsutella were closely related genera in the Ophiocordycipitaceae family. Validation of the mosquitocidal activity of this novel C. clavisporus protein has yet to be performed but may help position Hirsutellin orthologs as prime candidates for the development of alternative biocontrol approaches complementing the current toolbox of vector mosquito management strategies. creator: Dana Foresman creator: Aurélien Tartar uri: https://doi.org/10.7717/peerj.16259 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Foresman and Tartar title: Effect of 8-week frequency-specific electrical muscle stimulation combined with resistance exercise training on muscle mass, strength, and body composition in men and women: a feasibility and safety study link: https://peerj.com/articles/16303 last-modified: 2023-10-16 description: In recent years, electrical muscle stimulation (EMS) devices have been developed as a complementary training technique that is novel, attractive, and time-saving for physical fitness and rehabilitation. While it is known that EMS training can improve muscle mass and strength, most studies have focused on the elderly or specific patient populations. The aim of this study was to investigate the effects of frequency-specific EMS combined with resistance exercise training for 8 weeks on muscle mass, strength, power, body composition, and parameters related to exercise fatigue. Additionally, we aimed to evaluate the feasibility and safety of EMS as an exercise aid to improve body composition. We recruited 14 male and 14 female subjects who were randomly assigned to two groups with gender parity (seven male and seven female/group): (1) no EMS group (age: 21.6 ± 1.7; height: 168.8 ± 11.8 cm; weight: 64.2 ± 14.4 kg) and (2) daily EMS group (age: 21.8 ± 2.0; height: 167.8 ± 9.9 cm; weight: 68.5 ± 15.5 kg). The two groups of subjects were very similar with no significant difference. Blood biochemical routine analysis was performed every 4 weeks from pre-intervention to post-intervention, and body composition, muscle strength, and explosive power were evaluated 8 weeks before and after the intervention. We also performed an exercise challenge analysis of fatigue biochemical indicators after 8 weeks of intervention. Our results showed that resistance exercise training combined with daily EMS significantly improved muscle mass (p = 0.002) and strength (left, p = 0.007; right, p = 0.002) and significantly reduced body fat (p < 0.001) than the no EMS group. However, there was no significant advantage for biochemical parameters of fatigue and lower body power. In summary, our study demonstrates that 8 weeks of continuous resistance training combined with daily upper body, lower body, and abdominal EMS training can significantly improve muscle mass and upper body muscle strength performance, as well as significantly reduce body fat percentage in healthy subjects. creator: Mon-Chien Lee creator: Chin-Shan Ho creator: Yi-Ju Hsu creator: Ming-Fang Wu creator: Chi-Chang Huang uri: https://doi.org/10.7717/peerj.16303 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Lee et al. title: Macrophage polarization in tissue fibrosis link: https://peerj.com/articles/16092 last-modified: 2023-10-13 description: Fibrosis can occur in all major organs with relentless progress, ultimately leading to organ failure and potentially death. Unfortunately, current clinical treatments cannot prevent or reverse tissue fibrosis. Thus, new and effective antifibrotic therapeutics are urgently needed. In recent years, a growing body of research shows that macrophages are involved in fibrosis. Macrophages are highly heterogeneous, polarizing into different phenotypes. Some studies have found that regulating macrophage polarization can inhibit the development of inflammation and cancer. However, the exact mechanism of macrophage polarization in different tissue fibrosis has not been fully elucidated. This review will discuss the major signaling pathways relevant to macrophage-driven fibrosis and profibrotic macrophage polarization, the role of macrophage polarization in fibrosis of lung, kidney, liver, skin, and heart, potential therapeutics targets, and investigational drugs currently in development, and hopefully, provide a useful review for the future treatment of fibrosis. creator: Huidan Yang creator: Hao Cheng creator: Rongrong Dai creator: Lili Shang creator: Xiaoying Zhang creator: Hongyan Wen uri: https://doi.org/10.7717/peerj.16092 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yang et al. title: Comprehensive study of serine/arginine-rich (SR) gene family in rice: characterization, evolution and expression analysis link: https://peerj.com/articles/16193 last-modified: 2023-10-13 description: As important regulators of alternative splicing (AS) events, serine/arginine (SR)-rich proteins play indispensable roles in the growth and development of organisms. Until now, the study of SR genes has been lacking in plants. In the current study, we performed genome-wide analysis on the SR gene family in rice. A total of 24 OsSR genes were phylogenetically classified into seven groups, corresponding to seven subfamilies. The OsSR genes’ structures, distribution of conserved domains, and protein tertiary structure of OsSR were conserved within each subfamily. The synteny analysis revealed that segmental duplication events were critical for the expansion of OsSR gene family. Moreover, interspecific synteny revealed the distribution of orthologous SR gene pairs between rice and Arabidopsis, sorghum, wheat, and maize. Among all OsSR genes, 14 genes exhibited NAGNAG acceptors, and only four OsSR genes had AS events on the NAGNAG acceptors. Furthermore, the distinct tissue-specific expression patterns of OsSR genes showed that these genes may function in different developmental stages in rice. The AS patterns on the same OsSR gene were variable among the root, stem, leaf, and grains at different filling stages, and some isoforms could only be detected in one or a few of tested tissues. Meanwhile, our results showed that the expression of some OsSR genes changed dramatically under ABA, GA, salt, drought, cold or heat treatment, which were related to the wide distribution of corresponding cis-elements in their promoter regions, suggesting their specific roles in stress and hormone response. This research facilitates our understanding of SR gene family in rice and provides clues for further exploration of the function of OsSR genes. creator: Rui Gao creator: Yingying Lu creator: Nan Wu creator: Hui Liu creator: Xiaoli Jin uri: https://doi.org/10.7717/peerj.16193 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gao et al. title: A contrast-enhanced CT-based whole-spleen radiomics signature for early prediction of oxaliplatin-related thrombocytopenia in patients with gastrointestinal malignancies: a retrospective study link: https://peerj.com/articles/16230 last-modified: 2023-10-13 description: BackgroundThrombocytopenia is a common adverse event of oxaliplatin-based chemotherapy. Grade 2 or higher oxaliplatin-related thrombocytopenia may result in dose reduction, discontinuation or delay initiation of chemotherapy and may adversely affect the therapeutic efficacy and even overall survival of patients. Early recognition of patients at risk of developing grade 2 or higher thrombocytopenia is critical. However, to date there is no well-established method to early identify patients at high risk. The aims of this study were to develop and validate a contrast-enhanced CT-based whole-spleen radiomics signature for early prediction of grade 2 or higher thrombocytopenia in patients with gastrointestinal malignancies treated with oxaliplatin-based chemotherapy and to explore the incremental value of combining the radiomics signature and conventional clinical factors for risk prediction.MethodsA total of 119 patients with gastrointestinal malignancies receiving oxaliplatin-based chemotherapy from March 2017 to December 2020 were retrospectively included and randomly divided into a training cohort (n = 85) and a validation cohort (n = 34). Grade 2 or higher thrombocytopenia occurred in 26.1% of patients (22 and nine patients in the training and validation cohort, respectively) with a median time interval of 101 days from the start of chemotherapy. The whole-spleen radiomics features were extracted on the portal venous phase of the first follow-up CT images. The least absolute shrinkage and selection operator (LASSO) algorithm was applied to select radiomics features and to build the radiomics signature for the prediction of grade 2 or higher thrombocytopenia. A clinical model that included clinical factors only and a clinical-radiomics model that incorporated clinical factors and radiomics signature were constructed. The performances of both models were evaluated and compared in the training, validation and the whole cohorts.ResultsThe radiomics signature yielded favorable performance in predicting grade 2 or higher thrombocytopenia, with the area under the curve (AUC), sensitivity and specificity being 0.865, 81.8% and 84.1% in the training cohort and 0.747, 77.8% and 80.0% in the validation cohort. The AUCs of the clinical-radiomics model in the training and validation cohorts reached 0.913 (95% CI [0.720–0.935]) and 0.867 (95% CI [0.727–1.000]), greater than the AUCs of the clinical model. Integrated discrimination improvement (IDI) index showed that incorporating radiomic signature into conventional clinical factors significantly improved the predictive accuracy by 17.0% (95% CI [4.9%–29.1%], p = 0.006) in the whole cohort.ConclusionsContrast-enhanced CT-based whole-spleen radiomics signature might serve as an early predictor for grade 2 or higher thrombocytopenia during oxaliplatin-based chemotherapy in patients with gastrointestinal malignancies and provide incremental value over conventional clinical factors. creator: Yuhong Dai creator: Yiqi Cheng creator: Ziling Zhou creator: Zhen Li creator: Yan Luo creator: Hong Qiu uri: https://doi.org/10.7717/peerj.16230 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Dai et al. title: A review on the relationship between Arachidonic acid 15-Lipoxygenase (ALOX15) and diabetes mellitus link: https://peerj.com/articles/16239 last-modified: 2023-10-13 description: Arachidonic acid 15-lipoxygenase (ALOX15), as one of the lipoxygenase family, is mainly responsible for catalyzing the oxidation of various fatty acids to produce a variety of lipid components, contributing to the pathophysiological processes of various immune and inflammatory diseases. Studies have shown that ALOX15 and its related products are widely distributed in human tissues and related to multiple diseases such as liver, cardiovascular, cerebrovascular diseases, diabetes mellitus and other diseases. Diabetes mellitus (DM), the disease studied in this article, is a metabolic disease characterized by a chronic increase in blood glucose levels, which is significantly related to inflammation, oxidative stress, ferroptosis and other mechanisms, and it has a high incidence in the population, accompanied by a variety of complications. Figuring out how ALOX15 is involved in DM is critical to understanding its role in diseases. Therefore, ALOX15 inhibitors or combination therapy containing inhibitors may deliver a novel research direction for the treatment of DM and its complications. This article aims to review the biological effect and the possible function of ALOX15 in the pathogenesis of DM. creator: Kaiying He creator: Xiaochun Zhou creator: Hongxuan Du creator: Jing Zhao creator: Rongrong Deng creator: Jianqin Wang uri: https://doi.org/10.7717/peerj.16239 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 He et al. title: Prognostic value of serum phosphate levels in sepsis: a systematic review and meta-analysis link: https://peerj.com/articles/16241 last-modified: 2023-10-13 description: BackgroundThere remain controversies over the conclusion of different serum phosphate levels as prognostic predictors of sepsis patients. As such, this study investigated the association between different serum phosphate and the prognosis of sepsis.MethodsData from PubMed, Embase, Cochrane Library, and Web of Science were systematically retrieved from the inception of databases to June 1, 2023 and independently screened and extracted by two authors. Binary variables in the study were estimated as relative risk ratio (RR) and 95% confidence interval (CI), and continuous variables were estimated as mean and standard deviation. The Newcastle-Ottawa Scale (NOS) was employed to evaluate the quality of the included studies, and subgroup analysis and sensitivity analysis were performed for all outcomes to explore the sources of heterogeneity.ResultsTen studies were included in this study including 38,320 patients with sepsis or septic shock. Against normal serum phosphate levels, a high serum phosphate level was associated with an elevated all-cause mortality risk (RR = 1.46; 95% CI [1.22–1.74]; P = 0.000) and prolonged Intensive Care Unit (ICU) length of stay (LOS) (WMD = 0.63; 95% CI [0.27–0.98]; P = 0.001). However, there was no significant difference in the in-hospital LOS (WMD = 0.22; 95% CI [−0.61–1.05]; P = 0.609). A low serum phosphate level was not significantly associated with the all-cause mortality risk (RR = 0.97; 95% CI [0.86–1.09]; P = 0.588), ICU LOS (WMD = −0.23; 95% CI [−0.75–0.29]; P = 0.394) and in-hospital LOS (WMD = −0.62; 95% CI [−1.72–0.49]; P = 0.274).ConclusionSepsis patients with high serum phosphate levels before therapeutic interventions were associated with a significant increase in the all-cause mortality risk, prolonged ICU LOS, and no significant difference in in-hospital LOS. Sepsis patients with low serum phosphate levels before interventions may have a reduced risk of all-cause mortality, shorter ICU LOS, and in-hospital LOS, but the results were not statistically significant. creator: Shengfeng Wei creator: Yunhan Li creator: Chunhua Zhang creator: Xiangjian Guo creator: Xinmeng Liang creator: Yanmei Huang creator: Fan Zhang creator: Jihong Li creator: Qiangqiang Liu uri: https://doi.org/10.7717/peerj.16241 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wei et al. title: Effect of vascular endothelial growth factor 165 on dopamine level in the retinas of guinea pigs with form-deprivation myopia link: https://peerj.com/articles/16255 last-modified: 2023-10-13 description: BackgroundMyopia is the most common refractive error because excessive increase in the axial length of a myopic eye leads to the thinning of the posterior scleral pole and can cause serious complications resulting in blindness. Thus, myopia has become a great concern worldwide. Dopamine (DA) plays a role in the development of myopia. Moreover, in Parkinson’s disease, it has been proved that vascular endothelial growth factor 165 (VEGF165) can promote the survival and recovery of DA neurons, resulting in increased DA secretion in the striatum, thereby treating neuropathy. Therefore, we speculate that VEGF165 can also promote the release of DA in the retina to inhibit the occurrence and development of myopia. We aimed to investigate the effect of VEGF165 on DA levels in the retinas of guinea pigs with form-deprivation myopia (FDM) and the effects of DA on myopia prevention and control.MethodsHealthy 3-week-old pigmented guinea pigs were randomly divided into blank, FDM, phosphate buffer saline (PBS), 1, 5, and 10 ng groups. The FDM model was established by covering the right eye continuously with a translucent latex balloon pullover for 14 days. The pigs in the PBS, 1, 5, and 10 ng groups were injected with PBS buffer and 1, 5, and 10 ng of VEGF165 recombinant human protein, respectively, in the vitreous of the right eye before masking. The refractive error and axial length were measured before and after modeling. All retinas were used for biomolecular analyses after 14 days.ResultsWe found that the intravitreal injection of VEGF165 elevated DA levels in the retina and was effective in slowing the progression of myopia, and 1 ng of VEGF165 was the most effective. Moreover, the number of vascular endothelial cell nuclei in the 1 ng group was lower than that in the other VEGF165 groups.ConclusionsOur data suggest that VEGF165 has a promoting effect on DA in the retinas of guinea pigs with FDM, potentially controlling the development of myopia. creator: Ruiting Sun creator: Qingsheng Peng creator: Fengyi Zhang creator: Honglian Gao creator: Tong Li creator: Lei Wang creator: Lei Zhang uri: https://doi.org/10.7717/peerj.16255 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Sun et al.