title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=460 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: EXOSC10 is a novel hepatocellular carcinoma prognostic biomarker: a comprehensive bioinformatics analysis and experiment verification link: https://peerj.com/articles/15860 last-modified: 2023-09-08 description: BackgroundHepatocellular carcinoma (HCC) is a common malignant tumor. There are few studies on EXOSC10 (exosome component 10) in HCC; however, the importance of EXOSC10 for HCC remains unclear.MethodsIn the study, the prognosis value of EXOSC10 and the immune correlation were explored by bioinformatics. The expression of EXOSC10 was verified by tissue samples from clinical patients and in vitro experiment (liver cancer cell lines HepG2, MHCC97H and Huh-7; normal human liver cell line LO2). Immunohistochemistry (IHC) was used to detect EXOSC10 protein expression in clinical tissue from HCC. Huh-7 cells with siEXOSC10 were constructed using lipofectamine 3000. Cell counting kit 8 (CCK-8) and colony formation were used to test cell proliferation. The wound healing and transwell were used to analyze the cell migration capacity. Mitochondrial membrane potential, Hoechst 33342 dye, and flow cytometer were used to detect the change in cell apoptosis, respectively. Differential expression genes (DEGs) analysis and gene set enrichment analysis (GSEA) were used to investigate the potential mechanism of EXOSC10 and were verified by western blotting.ResultsEXOSC10 was highly expressed in tissues from patients with HCC and was an independent prognostic factor for overall survival (OS) in HCC. Increased expression of EXOSC10 was significantly related to histological grade, T stage, and pathological stage. Multivariate analysis indicated that the high expression level of EXOSC10 was correlated with poor overall survival (OS) in HCC. GO and GSEA analysis showed enrichment of the cell cycle and p53-related signaling pathway. Immune analysis showed that EXOSC10 expression was a significant positive correlation with immune infiltration in HCC. In vitro experiments, cell proliferation and migration were inhibited by the elimination of EXOSC10. Furthermore, the elimination of EXOSC10 induced cell apoptosis, suppressed PARP, N-cadherin and Bcl-2 protein expression levels, while increasing Bax, p21, p53, p-p53, and E-cadherin protein expression levels.ConclusionsEXOSC10 had a predictive value for the prognosis of HCC and may regulate the progression of HCC through the p53-related signaling pathway. creator: Zhi-Yong Meng creator: Yu-Chun Fan creator: Chao-Sheng Zhang creator: Lin-Li Zhang creator: Tong Wu creator: Min-Yu Nong creator: Tian Wang creator: Chuang Chen creator: Li-He Jiang uri: https://doi.org/10.7717/peerj.15860 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Meng et al. title: Dieting alleviates hyperuricemia and organ injuries in uricase-deficient rats via down-regulating cell cycle pathway link: https://peerj.com/articles/15999 last-modified: 2023-09-08 description: Dieting is a basic treatment for lowering hyperuricemia. Here, we aimed to determine the optimal amount of dietary food that lowers serum uric acid (SUA) without modifying the dietary ingredients in rats. Increased SUA was found in food-deprived 45-day-old uricase-deficient rats (Kunming-DY rats), and the optimal amount of dietary food (75% dietary intake) to lower SUA was established by controlling the amount of food given daily from 25% to 100% for 2 weeks. In addition to lowering SUA by approximately 22.5 ± 20.5%, the optimal amount of dietary food given for 2 weeks inhibited urine uric acid excretion, lowered the uric acid content in multiple organs, improved renal function, lowered serum triglyceride, alleviated organ injuries (e.g., liver, kidney and intestinal tract) at the histological level, and down-regulated the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway of the cell cycle (ko04110). Taken together, these results demonstrate that 75% dietary food effectively lowers the SUA level without modifying dietary ingredients and alleviates the injuries resulting from uricase deficiency or hyperuricemia, the mechanism of which is associated with the down-regulation of the cell cycle pathway. creator: Yun Yu creator: Xulian Wan creator: Dan Li creator: Yalin Qi creator: Ning Li creator: Guangyun Luo creator: Hua Yin creator: Lei Wang creator: Wan Qin creator: Yongkun Li creator: Lvyu Li creator: Weigang Duan uri: https://doi.org/10.7717/peerj.15999 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yu et al. title: Predictors of one-year mortality following hip fracture surgery in elderly link: https://peerj.com/articles/16008 last-modified: 2023-09-08 description: BackgroundUnderstanding mortality risk factors is critical to reducing mortality among elderly hip fracture patients. To investigate the effects of admission and post-operative levels of distribution width of red blood cells (RDW), albumin, and RDW/albumin (RA) ratio on predicting 1-year mortality following hip fracture surgery.MethodsA retrospective study was conducted on 275 elderly patients who underwent hip fracture surgery in a tertiary hospital between January 2018 and January 2022. Deaths within one year of hip fracture were defined as the deceased group. The survivors were defined as those who survived for at least one year. The relationship between admission and post-operative levels of RDW, albumin, RA, and mortality within one year after hip surgery was assessed statistically, including binary logistic regression analysis. The study also assessed other factors related to mortality.ResultsOne-year mortality was 34.7%. There was a 3.03-year (95% CI [1.32–4.75]) difference between the deceased (79.55 ± 8.36 years) and survivors (82.58 ± 7.41 years) (p < 0.001). In the deceased group, the mean hemoglobin (HGB) values at admission (p = 0.022) and post-operative (p = 0.04) were significantly lower. RDW values at admission (p = 0.001) and post-op (p = 0.001) were significantly lower in the survivor group. The mean albumin values at admission (p < 0.001) and post-operative (p < 0.001) in the survivor group were significantly higher than in the deceased group. A significant difference was found between the survivor group and the deceased group in terms of mean RA ratio at admission and post-operative (p < 0.001). Based on binary logistic regression analysis, presence of chronic obstructive pulmonary disease (COPD) (OR 3.73, 95% CI [1.8–7.76]), RDW (OR 1.78, 95% CI [1.48–2.14]), and albumin (OR 0.81, 95% CI [0.75–0.87]), values at admission were found to be independent predictors of 1-year mortality in elderly patients with hip fracture.ConclusionBased on this study, presence of COPD, higher RDW, and lower albumin levels at admission were independent predictors of 1-year mortality following hip fracture surgery in the elderly. creator: Mehmet Özel creator: Mustafa Altıntaş creator: Ali Cankut Tatlıparmak uri: https://doi.org/10.7717/peerj.16008 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Özel et al. title: Retrospective study: risk assessment model for osteoporosis—a detailed exploration involving 4,552 Shanghai dwellers link: https://peerj.com/articles/16017 last-modified: 2023-09-08 description: BackgroundOsteoporosis, a prevalent orthopedic issue, significantly influences patients’ quality of life and results in considerable financial burden. The objective of this study was to develop and validate a clinical prediction model for osteoporosis risk, utilizing computer algorithms and demographic data.MethodIn this research, a total of 4,552 residents from Shanghai were retrospectively included. LASSO regression analysis was executed on the sample’s basic characteristics, and logistic regression was employed for analyzing clinical characteristics and building a predictive model. The model’s diagnostic capacity for predicting osteoporosis risk was assessed using R software and computer algorithms.ResultsThe predictive nomogram model for bone loss risk, derived from the LASSO analysis, comprised factors including BMI, TC, TG, HDL, Gender, Age, Education, Income, Sleep, Alcohol Consumption, and Diabetes. The nomogram prediction model demonstrated impressive discriminative capability, with a C-index of 0.908 (training set), 0.908 (validation set), and 0.910 (entire cohort). The area under the ROC curve (AUC) of the model was 0.909 (training set), 0.903 (validation set), and applicable to the entire cohort. The decision curve analysis further corroborated that the model could efficiently predict the risk of bone loss in patients.ConclusionThe nomogram, based on essential demographic and health factors (Body Mass Index, Total Cholesterol, Triglycerides, High-Density Lipoprotein, Gender, Age, Education, Income, Sleep, Alcohol Consumption, and Diabetes), offered accurate predictions for the risk of bone loss within the studied population. creator: Dan Han creator: Zhongcheng Fan creator: Yi-sheng Chen creator: Zichao Xue creator: Zhenwei Yang creator: Danping Liu creator: Rong Zhou creator: Hong Yuan uri: https://doi.org/10.7717/peerj.16017 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Han et al. title: Cross species/genera transferability of simple sequence repeat markers, genetic diversity and population structure analysis in gladiolus (Gladiolus × grandiflorus L.) genotypes link: https://peerj.com/articles/15820 last-modified: 2023-09-07 description: BackgroundGenetic analysis of gladiolus germplasm using simple sequence repeat (SSR) markers is largely missing due to scarce genomic information. Hence, microsatellites identified for related genera or species may be utilized to understand the genetic diversity and assess genetic relationships among cultivated gladiolus varieties.MethodsIn the present investigation, we screened 26 genomic SSRs (Gladiolus palustris, Crocus sativus, Herbertia zebrina, Sysirinchium micranthum), 14 chloroplast SSRs (Gladiolus spp., chloroplast DNA regions) and 25 Iris Expressed Sequence Tags (ESTs) derived SSRs across the 84 gladiolus (Gladiolus × grandiflorus L.) genotypes. Polymorphic markers detected from amplified SSRs were used to calculate genetic diversity estimates, analyze population structure, cluster analysis and principal coordinate analysis (PCoA).ResultsA total of 41 SSRs showed reproducible amplification pattern among the selected gladiolus cultivars. Among these, 17 highly polymorphic SSRs revealed a total of 58 polymorphic alleles ranging from two to six with an average of 3.41 alleles per marker. Polymorphic information content (PIC) values ranged from 0.11 to 0.71 with an average value of 0.48. A total of 4 SSRs were selectively neutral based on the Ewens–Watterson test. Hence, 66.66% of Gladiolus palustris, 48% of Iris spp. EST, 71.42% of Crocus sativus SSRs showed cross-transferability among the gladiolus genotypes. Analysis of genetic structure of 84 gladiolus genotypes revealed two subpopulations; 35 genotypes were assigned to subpopulation 1, 37 to subpopulation 2 and the remaining 12 genotypes could not be attributed to either subpopulation. Analysis of molecular variance indicated maximum variance (53.59%) among individuals within subpopulations, whereas 36.55% of variation among individuals within the total population. The least variation (9.86%) was noticed between two subpopulations. Moderate (FST = 0.10) genetic differentiation between two subpopulations was observed. The grouping pattern of population structure was consistent with the unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on simple matching dissimilarity coefficient and PCoA.ConclusionSSR markers from the present study can be utilized for cultivar identification, conservation and sustainable utilization of gladiolus genotypes for crop improvement. Genetic relationships assessed among the genotypes of respective clusters may assist the breeders in selecting desirable parents for crossing. creator: Varun Hiremath creator: Kanwar Pal Singh creator: Neelu Jain creator: Kishan Swaroop creator: Pradeep Kumar Jain creator: Sapna Panwar creator: Nivedita Sinha uri: https://doi.org/10.7717/peerj.15820 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hiremath et al. title: Body size and trophic level increase with latitude, and decrease in the deep-sea and Antarctica, for marine fish species link: https://peerj.com/articles/15880 last-modified: 2023-09-07 description: The functional traits of species depend both on species’ evolutionary characteristics and their local environmental conditions and opportunities. The temperature-size rule (TSR), gill-oxygen limitation theory (GOLT), and temperature constraint hypothesis (TCH) have been proposed to explain the gradients of body size and trophic level of marine species. However, how functional traits vary both with latitude and depth have not been quantified at a global scale for any marine taxon. We compared the latitudinal gradients of trophic level and maximum body size of 5,619 marine fish from modelled species ranges, based on (1) three body size ranges, <30, 30–100, and >100 cm, and (2) four trophic levels, <2.20, 2.20–2.80, 2.81–3.70, >3.70. These were parsed into 5° latitudinal intervals in four depth zones: whole water column, 0–200, 201–1,000, and 1,001–6,000 m. We described the relationship between latitudinal gradients of functional traits and salinity, sea surface and near seabed temperatures, and dissolved oxygen. We found mean body sizes and mean trophic levels of marine fish were smaller and lower in the warmer latitudes, and larger and higher respectively in the high latitudes except for the Southern Ocean (Antarctica). Fish species with trophic levels ≤2.80 were dominant in warmer and absent in colder environments. We attribute these differences in body size and trophic level between polar regions to the greater environmental heterogeneity of the Arctic compared to Antarctica. We suggest that fish species’ mean maximum body size declined with depth because of decreased dissolved oxygen. These results support the TSR, GOLT and TCH hypotheses respectively. Thus, at the global scale, temperature and oxygen are primary factors affecting marine fishes’ biogeography and biological traits. creator: Han-Yang Lin creator: Mark John Costello uri: https://doi.org/10.7717/peerj.15880 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Lin and Costello title: Relationship between catheter related cerebrospinal fluid infections and systemic immune-inflammation index link: https://peerj.com/articles/15905 last-modified: 2023-09-07 description: BackgroundThis study investigated the relationship between the systemic immune inflammation index (SII) and catheter-related infections and their effects on prognosis in pediatric patients.MethodsA total of 56 pediatric patients diagnosed with ventriculoperitoneal (V-P) shunt infection between January 2017 and October 2019 were included. V-P shunt infection diagnosis was made based on clinical findings. All cerebrospinal fluid (CSF) samples were subjected to direct microscopic examination and culture. Protein, glucose, and sodium levels in CSF, CSF leukocytes, and hematological and biochemical parameters were measured.ResultsFifty-six patients with growth in CSF culture were included in this study. 55.4% of the cases were female and 44.6% male. V-P shunt was detected in 82.1% of the cases and external ventricular drainage (EVD) catheter-related infection in 17.9%. The CSF/blood glucose ratio was significantly lower (p = 0.046), and SII was significantly increased (p = 0.002) in non-coagulase-negative staphylococci.ConclusionsEarly and appropriate antibiotic therapy reduces morbidity and mortality in catheter-related infections. However, it is important to start empirical antibiotherapy until culture results are expected. Therefore, further research on the estimation of possible factors is needed. creator: Sebnem Nergiz creator: Pinar Aydin Ozturk uri: https://doi.org/10.7717/peerj.15905 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Nergiz and Aydin Ozturk title: Identification and expression analysis of the small auxin-up RNA (SAUR) gene family in Lycium ruthenicum link: https://peerj.com/articles/15941 last-modified: 2023-09-07 description: The plant hormone auxin regulates numerous aspects of plant growth and development, and small auxin-up RNA (SAUR) is the largest family of early auxin response genes in higher plants. SAUR has been implicated in the regulation of multiple biological processes. However, no comprehensive analysis of SAUR genes has been reported in Lycium ruthenicum. L. ruthenicum is a thorny shrub with very pronounced salt and drought tolerance, and studies have shown that stem thorns are related to drought tolerance in L. ruthenicum. In this study, the identification, phylogenetic analysis, and conserved motif prediction of SAUR genes were extensively explored. Furthermore, the tissue expression patterns of selected SAUR genes were assayed with quantitative real-time polymerase chain reaction (RT-qPCR). A total of 33 putative LrSAURs were identified and divided into three clusters in a phylogenetic tree of L. ruthenicum. MEME analysis identified 10 motifs in L. ruthenicum, and the results suggested that motif 1 and motif 3 were widely distributed. Analyzing the transcriptome data of stem thorns at four developmental stages indicated that LrSAURs were differentially expressed in L. ruthenicum, and could be divided into six expression patterns. The RT-qPCR analysis of 21 genes showed that LrSAUR2, LrSAUR8, LrSAUR9, LrSAUR11, LrSAUR12, and LrSAUR19 were mainly expressed in stems and stem thorns, and may be related to stem thorn development. creator: Jing Hu creator: Qiushi Yu creator: Shengxiu Jiang creator: Xiaoke Hu creator: Xuemin Li creator: Zhongchao Liu uri: https://doi.org/10.7717/peerj.15941 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hu et al. title: The evolution of SARS-CoV-2 and the COVID-19 pandemic link: https://peerj.com/articles/15990 last-modified: 2023-09-07 description: Scientists have made great efforts to understand the evolution of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) to provide crucial information to public health experts on strategies to control this viral pathogen. The pandemic of the coronavirus disease that began in 2019, COVID-19, lasted nearly three years, and nearly all countries have set different epidemic prevention policies for this virus. The continuous evolution of SARS-CoV-2 alters its pathogenicity and infectivity in human hosts, thus the policy and treatments have been continually adjusted. Based on our previous study on the dynamics of binding ability prediction between the COVID-19 spike protein and human ACE2, the present study mined over 10 million sequences and epidemiological data of SARS-CoV-2 during 2020-2022 to understand the evolutionary path of SARS-CoV-2. We analyzed and predicted the mutation rates of the whole genome and main proteins of SARS-CoV-2 from different populations to understand the adaptive relationship between humans and COVID-19. Our study identified a correlation of the mutation rates from each protein of SARS-CoV-2 and various human populations. Overall, this analysis provides a scientific basis for developing data-driven strategies to confront human pathogens. creator: Yuanfang Si creator: Weidong Wu creator: Xia Xue creator: Xiangdong Sun creator: Yaping Qin creator: Ya Li creator: Chunjing Qiu creator: Yingying Li creator: Ziran Zhuo creator: Yang Mi creator: Pengyuan Zheng uri: https://doi.org/10.7717/peerj.15990 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Si et al. title: Head lice: impact of COVID-19 and slow recovery of prevalence in Cambridgeshire, UK link: https://peerj.com/articles/16001 last-modified: 2023-09-07 description: Following school closures and changes in contact behavior of children and adults a reduced head louse prevalence has been reported from across the globe. In parallel, sales of treatments were observed to fall, partly because of supply problems of some products following the pandemic, but this did not appear to result in more cases of infestation. Surveys of schools in and around Cambridge, UK, found that infestation rates were significantly reduced particularly in city schools compared with similar surveys conducted before the COVID-19 pandemic. Contrary to expectation the number of cases in schools has only risen slowly since schools returned to normal full time working in 2022–2023. creator: Ian F. Burgess creator: Elizabeth R. Brunton creator: Mark N. Burgess uri: https://doi.org/10.7717/peerj.16001 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Burgess et al.