title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=626 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Ability of combined soluble urokinase plasminogen activator receptor to predict preventable emergency attendance in older patients in Japan: a prospective pilot study link: https://peerj.com/articles/14322 last-modified: 2022-11-04 description: Soluble urokinase plasminogen activator receptor (suPAR) is a strong and nonspecific inflammatory biomarker that reflects various immunologic reactions, organ damage, and risk of mortality in the general population. Although prior research in acute medical patients showed that an elevation in suPAR is related to intensive care unit admission and risk of readmission and mortality, no studies have focused on the predictive value of suPAR for preventable emergency attendance (PEA). This study aims to evaluate the predictive value of suPAR, which consists of a combination of white blood cell count (WBC), C-reactive protein (CRP), and the National Early Warning Score (NEWS), for PEA in older patients (>65 years) without trauma who presented to the emergency department (ED). This single-center prospective pilot study was conducted in the ED of the Association of EISEIKAI Medical and Healthcare Corporation Minamitama Hospital, in Hachiouji City, Tokyo, Japan, from September 16, 2020, to June 21, 2022. The study included all patients without trauma aged 65 years or older who were living in their home or a facility and presented to the ED when medical professionals decided an emergency consultation was required. Discrimination was assessed by plotting the receiver-operating characteristic (ROC) curve and calculating the area under the ROC curve (AUC). During the study period, 49 eligible older patients were included, and thirteen (26.5%) PEA cases were detected. The median suPAR was significantly lower in the PEA group than in the non-PEA group (p < 0.05). For suPAR, the AUC for the prediction of PEA was 0.678 (95% CI 0.499–0.842, p < 0.05), and there was no significant difference from other variables as follows: 0.801 (95% CI 0.673–0.906, p < 0.001) for WBC, 0.833 (95% CI 0.717–0.934, p < 0.001) for CRP, and 0.693 (95% CI 0.495–0.862, p < 0.05) for NEWS. Furthermore, the AUC for predicting PEA was 0.867 (95% CI 0.741–0.959, p < 0.001) for suPAR + WBC + CRP + NEWS, which was significantly higher than that of the original suPAR (p < 0.01). The cutoff values, sensitivity, specificity, and odds ratio of suPAR and suPAR + WBC + CRP + NEWS were 7.5 and 22.88, 80.6% and 83.3%, 53.8% and 76.9%, and 4.83 and 16.67, respectively. This study has several limitations. First, this was pilot study, and we included a small number of older patients. Second, the COVID-19 pandemic occurred during the study period, so that there may be selection bias in the study population. Third, our hospital is a secondary emergency medical institution, and as such, we did not treat very fatal cases, which could be another cause of selection bias. Our single-center study has demonstrated the moderate utility of the combined suPAR as a triage tool for predicting PEA in older patients without trauma receiving home medical care. Before introducing suPAR to the prehospital setting, evidence from multicenter studies is needed. creator: Toshiya Mitsunaga creator: Yuhei Ohtaki creator: Wataru Yajima creator: Kei Sugiura creator: Yutaka Seki creator: Kunihiro Mashiko creator: Masahiko Uzura creator: Satoshi Takeda uri: https://doi.org/10.7717/peerj.14322 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mitsunaga et al. title: Cigarette smoking induces the activation of RIP2/caspase-12/NF-κB axis in oral squamous cell carcinoma link: https://peerj.com/articles/14330 last-modified: 2022-11-04 description: Cigarette smoking is one of the major risk factors for the occurrence and progression of oral squamous cell carcinoma (OSCC). Receptor-interacting protein 2 (RIP2) has been involved in mucosal immunity and homeostasis via a positive regulation of nuclear factor κB (NF-κB) transcription factor activity. Caspase-12 can bind to RIP2 and dampen mucosal immunity. However, the roles of RIP2/NF-κB and caspase-12 in OSCC induced by cigarette smoking remain unknown. Herein, we investigated the effects of cigarette smoking on the RIP2/NF-κB and caspase-12 in human OSCC tissues and OSCC cell lines (HSC-3). We first observed that RIP2 mediated NF-κB activation and caspase-12 upregulation in OSCC patients with cigarette smoking and cigarette smoke extract (CSE)-treated HSC-3 cells, respectively. Moreover, we confirmed that the downregulation of RIP2 by siRNA resulted in the reduction of caspase-12 expression and NF-κB activity in the presence of CSE treatment in vitro. In summary, our results indicated that cigarette smoking induced the activation of the RIP2/caspase-12/NF-κB axis and it played an important role in the development of OSCC. The RIP2/caspase-12/NF-κB axis could be a target for OSCC prevention and treatment in the future. creator: Yajie Qian creator: Wenmei Wang creator: Deyan Chen creator: Yanan Zhu creator: Yong Wang creator: Xiang Wang uri: https://doi.org/10.7717/peerj.14330 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Qian et al. title: Ecological roles of secondary metabolites of Saposhnikovia divaricata in adaptation to drought stress link: https://peerj.com/articles/14336 last-modified: 2022-11-04 description: Saposhnikovia divaricata is a traditional Chinese herb that mainly grows in arid grasslands and strongly adapts to various stresses. Drought is not only a major abiotic stress factor but also a typical feature conducive to producing high-quality medicinal material. The present study investigated by treating S. divaricata plants with polyethylene glycol (PEG-6000). Ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) identified 146 compounds from the roots of S. divaricata, among which seven primary metabolites and 28 secondary metabolites showed significant changes after drought treatment. UV-Vis spectrophotometer detected the activity of antioxidant enzymes and the content of superoxide anion (O2−.) and malondialdehyde (MDA). The differential primary metabolites revealed that drought promotes glycolysis, reducing primary metabolism and enhancing secondary metabolism. Meanwhile, the differential secondary metabolites showed an increase in the content of compounds upstream of the secondary metabolic pathway, and other glycosides and increased that of the corresponding aglycones. The activities of antioxidant enzymes and the content of O2−. and MDA shown different changes duing the drought treatment. These observations indicate that drought promotes the biosynthesis and transformation of the secondary metabolites and activity of antioxidant enzymes, improving plant adaptability. The present study also analyzed a few primary and secondary metabolites of S. divaricata under different degrees and durations of drought and speculated on the metabolic pathways in an arid environment. The findings indicate the biological nature, diversity, and complexity of secondary metabolites and the mechanisms of plant adaptation to ecological stress. creator: Sisi Cao creator: Lei Shi creator: Ying Shen creator: Luwen He creator: Xiangcai Meng uri: https://doi.org/10.7717/peerj.14336 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Cao et al. title: Evaluation and characterization of indigenous rice (Oryza sativa L.) landraces resistant to brown planthopper Nilaparvata lugens (Stål.) biotype 4 link: https://peerj.com/articles/14360 last-modified: 2022-11-04 description: Evaluation and identification of resistant donors for brown planthopper (BPH) Nilaparvata lugens (Stål.), an economically important insect pest of rice, is a continuous process to develop new resistant rice varieties. However, several rice landraces of north-eastern India are not yet characterized for BPH resistance. In the present study, a set of 218 rice landraces were screened in both greenhouse and open-field conditions for three consecutive years, and thereafter forty selected promising entries were explored to evaluate their phenotypic and genotypic reactions against BPH biotype 4. Based on phenotypic evaluations, five landraces were identified as resistant, while 31 were moderately resistant, and grouped under the major cluster I and II, respectively, in a circular dendrogram. Antixenosis and antibiosis studies of these landraces divulged that, compared to the susceptible check variety, resistant landraces exhibited the lowest feeding rate, survival, and nymphal and adult settling, but higher frequency of unhatched eggs of BPH. Un-infested resistant landraces registered higher levels of ascorbic acid, oxalic acid and crude silica, however, elevated levels of total free amino acid, potassium and crude silica were observed under BPH herbivory. The present study focuses on identifying new donors having BPH resistance resources which could be useful in genomic studies for the development of BPH biotype 4 resistant rice varieties. creator: Debashis Roy creator: Abhisek Biswas creator: Sukamal Sarkar creator: Gautam Chakraborty creator: Ahmed Gaber creator: Mohamed I. Kobeasy creator: Akbar Hossain uri: https://doi.org/10.7717/peerj.14360 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Roy et al. title: Relationship between body composition and bone mass in normal-weight and overweight adolescents link: https://peerj.com/articles/14108 last-modified: 2022-11-03 description: Adolescence is a period characterized by large accumulation of bone mass. Body composition is an important determinant of bone mass. This study aimed to assess the relationship of bone mass with lean mass (LM) and fat mass (FM) in normal-weight and overweight adolescents with consideration of sex, sexual maturation and physical activity covariates. A total of 118 adolescents (60 girls and 58 boys) aged between 10 and 14 years participated in the study. Individuals were classified as normal weight or overweight according to body mass index. Bone mineral density (BMD), bone mineral content (BMC), LM, and FM were measured by dual-energy X-ray absorptiometry. In normal-weight adolescents, LM (β = 0.725, p < 0.001) and FM (β = 0.185, p = 0.019) were associated with lumbar spine BMC, whereas in overweight adolescents only LM (β = 0.736, p < 0.001) was associated with lumbar spine BMC. Furthermore, in the normal-weight group, FM and LM were associated with total body less head BMD (LM, β = 0.792, p < 0.001; FM, β = 0.257, p = 0.007) and lumbar spine BMD (LM, β = 0.553, p < 0.001; FM, β = 0.199, p < 0.035). In the overweight group, only LM was associated with total body less head BMD (β = 0.682, p < 0.001) and lumbar spine BMD (β = 0.528, p < 0.001). LM was the main predictor of bone mass in normal-weight and overweight adolescents. FM was associated with bone mass in normal-weight adolescents only. LM may be considered an important and useful marker in adolescents, when investigating bone health in this population. Activities that promote LM gain to reduce the risk of bone fractures and diseases in adulthood are recommended. creator: Mateus Augusto Bim creator: André de Araujo Pinto creator: Hector Cris Colares de Angelo creator: Isadora Gonzaga creator: Adriana Coutinho de Azevedo Guimarães creator: Érico Pereira Gomes Felden creator: Wellington Roberto Gomes de Carvalho creator: Karen Hind creator: Andreia Pelegrini uri: https://doi.org/10.7717/peerj.14108 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bim et al. title: The impact of aging and physical training on angiogenesis in the musculoskeletal system link: https://peerj.com/articles/14228 last-modified: 2022-11-03 description: Angiogenesis is the physiological process of capillary growth. It is strictly regulated by the balanced activity of agents that promote the formation of capillaries (pro-angiogenic factors) on the one hand and inhibit their growth on the other hand (anti-angiogenic factors). Capillary rarefaction and insufficient angiogenesis are some of the main causes that limit blood flow during aging, whereas physical training is a potent non-pharmacological method to intensify capillary growth in the musculoskeletal system. The main purpose of this study is to present the current state of knowledge concerning the key signalling molecules implicated in the regulation of skeletal muscle and bone angiogenesis during aging and physical training. creator: Magdalena Zmudzka creator: Jerzy A. Zoladz creator: Joanna Majerczak uri: https://doi.org/10.7717/peerj.14228 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zmudzka et al. title: Differences in leaf and root litter decomposition in tropical montane rainforests are mediated by soil microorganisms not by decomposer microarthropods link: https://peerj.com/articles/14264 last-modified: 2022-11-03 description: BackgroundPlant litter decomposition is a key process in carbon and nutrient cycling. Among the factors determining litter decomposition rates, the role of soil biota in the decomposition of different plant litter types and its modification by variations in climatic conditions is not well understood.MethodsIn this study, we used litterbags with different mesh sizes (45 µm, 1 mm and 4 mm) to investigate the effect of microorganisms and decomposer microarthropods on leaf and root litter decomposition along an altitudinal gradient of tropical montane rainforests in Ecuador. We examined decomposition rates, litter C and N concentrations, microbial biomass and activity, as well as decomposer microarthropod abundance over one year of exposure at three different altitudes (1,000, 2,000 and 3,000 m).ResultsLeaf litter mass loss did not differ between the 1,000 and 2,000 m sites, while root litter mass loss decreased with increasing altitude. Changes in microbial biomass and activity paralleled the changes in litter decomposition rates. Access of microarthropods to litterbags only increased root litter mass loss significantly at 3,000 m. The results suggest that the impacts of climatic conditions differentially affect the decomposition of leaf and root litter, and these modifications are modulated by the quality of the local litter material. The findings also highlight litter quality as the dominant force structuring detritivore communities. Overall, the results support the view that microorganisms mostly drive decomposition processes in tropical montane rainforests with soil microarthropods playing a more important role in decomposing low-quality litter material. creator: Laura M. Sánchez-Galindo creator: Dorothee Sandmann creator: Franca Marian creator: Tobias Lauermann creator: Mark Maraun creator: Stefan Scheu uri: https://doi.org/10.7717/peerj.14264 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sánchez-Galindo et al. title: Diagnostic performance of circulating tumor DNA as a minimally invasive biomarker for hepatocellular carcinoma: a systematic review and meta-analysis link: https://peerj.com/articles/14303 last-modified: 2022-11-03 description: PurposeThis study aimed to assess the diagnostic performance of circulating tumor DNA (ctDNA) in hepatocellular carcinoma (HCC).Materials and MethodsWe enrolled all relevant studies published up to 5 January 2022. Three primary subgroups were investigated: qualitative or quantitative ctDNA analyses, combined alpha-fetoprotein (AFP), and ctDNA assay. In addition to the three primary subgroups, we also evaluated the diagnostic value of methylated SEPTIN9 (mSEPT9), which has been studied extensively in the diagnosis of hepatocellular carcinoma. After a search based on four primary databases, we used a bivariate linear mixed model to analyze the pooled sensitivity (SEN), specificity (SPE), positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR). We also plotted hierarchical summary receiver operating characteristics (HSROC) and utilized lambda as well as the area under the curve (AUC) to create summary receiver operating characteristic (SROC) curves to estimate the diagnostic value of ctDNA.ResultsA total of 59 qualified articles with 9,766 subjects were incorporated into our meta-analysis. The integrated SEN, SPE, and DOR in the qualitative studies were 0.50 (95% CI [0.43–0.56]), 0.90 (95% CI [0.86–0.93]), and 8.72 (95% CI [6.18–12.32]), respectively, yielding an AUC of 0.78 and lambda of 1.93 (95% CI [1.56–2.33]). For quantitative studies, the corresponding values were 0.69 (95% CI [0.63–0.74]), 0.84 (95% CI [0.77–0.89]), 11.88 (95% CI [7.78–18.12]), 0.81, and 2.32 (95% CI [1.96–2.69]), respectively. Six studies were included to evaluate the SETP9 methylation, which yielded an AUC of 0.86, a SEN of 0.80 (95% CI [0.71–0.87]), and a SPE of 0.77 (95% CI [0.68–0.85]). Likewise, ctDNA concentration yielded an AUC of 0.73, with a SEN of 0.63 (95% CI [0.56–0.70]) and a SPE of 0.86 (95% CI [0.74–0.93]). AFP combined with ctDNA assay resulted in an AUC of 0.89, with a SEN of 0.82 (95% CI [0.77–0.86]) and a SPE of 0.84 (95% CI [0.76–0.90]).ConclusionThis study shows that circulating tumor DNA, particularly mSEPT9, shows promising diagnostic potential in HCC; however, it is not enough to diagnose HCC independently, and ctDNA combined with conventional assays such as AFP can effectively improve diagnostic performance. creator: Jia Jie Li creator: Yanqing Lv creator: Huifan Ji uri: https://doi.org/10.7717/peerj.14303 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: Comparison of epiphytic and intestinal bacterial communities in freshwater snails (Bellamya aeruginosa) living on submerged plants link: https://peerj.com/articles/14318 last-modified: 2022-11-03 description: The combination of submerged plants and snails can combat eutrophication of freshwater systems by suppressing algal growth and assimilating nutrients. By consuming epiphytes, snails can benefit the growth of submerged plants. However, the efficiency of this phytoremediation strategy may depend on the microbes associated with the plants and snails. In this study, we compared the epiphytic bacterial communities on submerged plants (Vallisneria natans and Cabomba caroliniana) and intestinal bacterial communities of a snail, Bellamya aeruginosa, found on these plants using 16S rRNA gene sequencing. Epiphytic bacterial communities were similar between the two plant species and snails shared a high proportion of snail intestinal bacterial OTUs (75%) and genera (85%) with plants they grazed on. However, significant variations of Bray-Curtis distances differentiated epiphytic and intestinal bacterial communities. In addition, between the top 50 genera shared by intestinal and epiphytic bacterial communities, more Spearman correlations were detected within bacterial communities associated with snails than between communities associated with plants (190 vs. 143), and the correlations in epiphytic bacterial networks were more concentrated on certain genera, indicating they possessed distinct bacterial networks. This suggests the bacterial communities associated with snails do not depend strongly on the plant they graze on, which may be important for better understanding the role of snails in aquatic eco-restoration. creator: Fucai Liu creator: Kejun Li uri: https://doi.org/10.7717/peerj.14318 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu and Li title: Publication delays and associated factors in ophthalmology journals link: https://peerj.com/articles/14331 last-modified: 2022-11-03 description: IntroductionThis study aimed to evaluate the publication delays and correlative factors of peer-reviewed ophthalmology journals.MethodsThe ophthalmology journals listed in the Journal Citation Report 2020 were retrieved from the Web of Science database. The first original research article of each journal issue from January to December 2020 was extracted, and its submission, final revision, acceptance, and publication dates were obtained. Information on impact factors, advance online publication (AOP) status, open access (OA) rate and acceptance rate in 2020 was also collected. The correlations between publication delays and potential associated factors were analyzed.ResultsA total of 58 ophthalmology journals were included and information on 685 articles was collected. The median times from submission to acceptance, from acceptance to publication, and from submission to publication were 118.0 (IQR, 74.0–185.0) days, 31.0 (IQR, 15.0–64.0) days, and 161.0 (IQR, 111.0–232.0) days, respectively. A higher impact factor was correlated with shorter delays of acceptance and publication (P < 0.05). There was a positive correlation between acceptance rates and publication delays (r = 0.726, P = 0.007). Forty-seven (81.03%) journals provided AOP. There was no statistically significant difference for impact factors and publication delays between journal with and without AOP (all P > 0.05). No correlation between OA rate and publication delays or impact factors was detected (all P > 0.05).ConclusionsJournals with higher impact factors and lower acceptance rates tend to have quicker publication processes. No significant associations were detected between publication delays and AOP or OA rate. creator: Yinglin Yu creator: Wei Li creator: Chaoqun Xu creator: Yuan Tan creator: Weining Zhu creator: Bowen Zhang creator: Yingshi Zou creator: Leyi Hu creator: Guangming Jin creator: Zhenzhen Liu uri: https://doi.org/10.7717/peerj.14331 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yu et al.