title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1202 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Impact of breast surgery on survival of patients with stage IV breast cancer: a SEER population-based propensity score matching analysis link: https://peerj.com/articles/8694 last-modified: 2020-03-18 description: BackgroundBreast surgery for stage IV breast cancer remains controversial. The aim of this study was to investigate the impact of breast surgery on survival of stage IV breast cancer patients based on the Surveillance, Epidemiology, and End Results (SEER) database from 2010 to 2015.MethodsIn total, 13,034 patients were selected and divided into surgery and non-surgery groups. Univariate and multivariable analyses were conducted to determine factors related to survival. Propensity score matching method was utilized to achieve balanced covariates across different groups. One-to-one (1:1) PSM was conducted to construct a matched sample consisting of pairs of surgery and non-surgery subjects. Breast cancer-specific survival (BCSS) and overall survival (OS) of the two groups were assessed by Kaplan–Meier plots and Cox proportional hazard regression models. Stratified analysis according to different variables was also performed.ResultsPatients treated with breast surgery were more likely to be younger, smaller tumor size, more advanced nodal status, higher histology grade and higher proportion of bone-only metastasis. Those who received chemotherapy and radiotherapy also tended to be treated with surgery. After adjustment for potential confounders, breast surgery group exhibited a better survival both in BCSS (HR = 0.557, 95% CI [0.523–0.594], p < 0.001) and OS (HR = 0.571, 95% CI [0.537–0.607], p < 0.001). After propensity score matching, the surgery and non-surgery group consisted of 2,269 patients respectively. The median survival time was 43 months for the surgery group and 27 months for the non-surgery group. Kaplan–Meier curves indicated that breast surgery could clearly improve both the BCSS and OS for patients with stage IV breast cancer. On multivariate analysis, surgery group was associated with a better survival compared with the non-surgery group (BCSS: HR = 0.542, 95% CI [0.499–0.589], p < 0.001; OS: HR = 0.555, 95% CI [0.512–0.601], p < 0.001). Furthermore, this survival advantage persisted in all subgroups irrespective of age, race, tumor size, nodal status, histology grade, molecular subtype, chemotherapy status, radiotherapy status or status of distant metastasis.ConclusionOur study provided additional evidence that patients with stage IV breast cancer could benefit from breast surgery and it might play a more important role in multimodality therapy. creator: Yuxiang Lin creator: Kaiyan Huang creator: Qiang Zeng creator: Jie Zhang creator: Chuangui Song uri: https://doi.org/10.7717/peerj.8694 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lin et al. title: The relationship between propagule pressure and establishment success in alien bird populations: a re-analysis of Moulton & Cropper (2019) link: https://peerj.com/articles/8766 last-modified: 2020-03-18 description: A recent analysis by Moulton & Cropper (2019) of a global dataset on alien bird population introductions claims to find no evidence that establishment success is a function of the size of the founding population. Here, we re-analyse Moulton & Cropper’s data and show that this conclusion is based on flawed statistical methods—their data in fact confirm a strong positive relationship between founding population size and establishment success. We also refute several non-statistical arguments against the likelihood of such an effect presented by Moulton & Cropper. We conclude that a core tenet of population biology—that small populations are more prone to extinction—applies to alien populations beyond their native geographic range limits as much as to native populations within them. creator: Tim M. Blackburn creator: Phillip Cassey creator: Julie L. Lockwood creator: Richard P. Duncan uri: https://doi.org/10.7717/peerj.8766 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Blackburn et al. title: Predictive value of CONUT score combined with serum CA199 levels in postoperative survival of patients with pancreatic ductal adenocarcinoma: a retrospective study link: https://peerj.com/articles/8811 last-modified: 2020-03-18 description: BackgroundThe preoperative controlling nutritional status (CONUT) score and serum carbohydrate antigen 199 (CA199) levels are individually correlated with the prognosis of pancreatic ductal adenocarcinoma (PDAC). The objective of this study aimed to investigate the efficacy of CONUT score and CA199 (CONUT-CA199) combination in predicting the prognosis of PDAC patients undergoing radical surgery.MethodsWe retrospectively analyzed the preoperative CONUT scores and serum CA199 levels of 294 patients with PDAC who underwent radical resection at the Affiliated Hospital of Southwest Medical University between March 2012 and July 2019. Patients were divided into four groups on the basis of their preoperative CONUT scores and serum CA199 levels: CONUTlow/CA199low (1), CONUTlow/CA199high (2), CONUThigh/CA199low (3) and CONUThigh/CA199high (4). The prognostic effects were compared among the groups.ResultsCONUThigh was more frequent in patients with positive peripancreatic infiltration and Clavien–Dindo classification of ≥IIIa (P < 0.001). Kaplan–Meier analysis revealed obvious difference in overall survival (OS) and recurrence-free survival (RFS) among patients with PDAC having CONUT-CA199 scores of 1, 2, 3 and 4 (P < 0.001). Peripancreatic infiltration, lymph node metastasis, pTNM stage, CONUT score, serum CA199 levels and CONUT-CA199 classification were found to be the independent prognostic factors for OS and RFS in multivariate analyses. In time-dependent receiver operating characteristic (ROC) analyses, the area of the CONUT-CA199 score under the ROC curve (AUC) was higher than that of the preoperative CONUT score or serum CA199 levels for the prediction of OS and RFS.ConclusionCONUT-CA199 classification may be more effective in predicting the postoperative prognosis of PDAC patients. creator: Ankang Wang creator: Bo Sun creator: Min Wang creator: Hao Shi creator: Zhiwei Huang creator: Tao He creator: Qiu Li creator: Jiaqi Deng creator: Wenguang Fu creator: Yu Jiang uri: https://doi.org/10.7717/peerj.8811 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Wang et al. title: Transcription levels and prognostic significance of the NFI family members in human cancers link: https://peerj.com/articles/8816 last-modified: 2020-03-18 description: BackgroundThe nuclear factor I (NFI) is a family of transcription factors consisting of four distinct but closely related genes, NFIA, NFIB, NFIC and NFIX, which are important in the development of various tissues and organs in mammals. Recent study results have shown that NFI family may play a critical role in the progression of various human tumors and have been identified as key tumor suppressors and oncogenes for many cancers. However, the expression levels and distinctive prognostic values of the NFI family remain poorly explored in most cancers.Materials and MethodsIn the present study, the differences in mRNA expression of the NFI family in various cancers were investigated using the Oncomine and TCGA databases, and the mRNA expression, genetic alteration and DNA methylation of the NFI family members in various cancers were examined using cBioPortal for Cancer Genomics. In addition, the prognostic significance of the NFI family was assessed in multiple cancers using the Kaplan–Meier plotter (KM plotter) and SurvExpress databases.ResultsThe mRNA expression levels in the NFI family were significantly downregulated in most cancers compared with normal tissues and DNA hypermethylation might downregulate the NFI family expression. Although NFIX expression was not downregulated in kidney, colorectal and prostate cancers. Furthermore, NFIB expression was upregulated in gastric cancer. Further survival analyses based on the KM plotter and SurvExpress databases showed dysregulations of the NFI genes were significantly correlated with survival outcomes in breast, lung, and head and neck cancers. Decreased expression levels of NFIA, NFIB and NFIC were associated with poor overall survival (OS) in head and neck cancer. Low mRNA expression of NFIA and NFIB was significantly associated with OS and first progression in lung adenocarcinoma, but not in lung squamous cell carcinoma. In addition, potential correlations between NFI family members and survival outcomes were also observed in liver, esophageal, kidney and cervical cancer.ConclusionThe results from the present study indicated certain members of the NFI family could be promising therapeutic targets and novel prognostic biomarkers for human cancers. creator: Yuexian Li creator: Cheng Sun creator: Yonggang Tan creator: Lin Li creator: Heying Zhang creator: Yusi Liang creator: Juan Zeng creator: Huawei Zou uri: https://doi.org/10.7717/peerj.8816 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: Identification of a three-m6A related gene risk score model as a potential prognostic biomarker in clear cell renal cell carcinoma link: https://peerj.com/articles/8827 last-modified: 2020-03-18 description: BackgroundClear cell renal cell carcinoma (ccRCC) is one of the most prevalent malignancies worldwide, N6-methyladenosine (m6A) has been shown to play important roles in regulating gene expression and phenotypes in both health and disease. Here, our purpose is to construct a m6A-regulrator-based risk score (RS) for prediction of the prognosis of ccRCC.MethodsWe used clinical and expression data of m6A related genes from The Cancer Genome Atlas (TCGA) dataset and the Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression analysis to develop an RS to predict survival of patients with ccRCC, and analyzed correlations between RS and other clinical indicators such as age, grade and stage. Validation of this RS was then engaged in another cohort, E-MTAB-1980 from the ArrayExpress dataset. Finally, we used quantitative real-time PCR to analyze the expression profile of genes consists of the RS.ResultsA three-gene RS including METTL3, METTL14 and HNRNPA2B1 which can predict overall survival (OS) of ccRCC patients from TCGA. After applying this RS into the validation cohort from Arrayexpress, we found that it successfully reproduced the result; furthermore, the results of PCR validation were in line with our analysis.ConclusionTo sum up, our study has identified an RS composed of m6A related genes that may predict the prognosis of ccRCC patients, which might be helpful for future therapeutic strategies. Our results call for further experimental studies for validations. creator: Yiqiao Zhao creator: Zijia Tao creator: Xiaonan Chen uri: https://doi.org/10.7717/peerj.8827 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhao et al. title: ARF family identification in Tamarix chinensis reveals the salt responsive expression of TcARF6 targeted by miR167 link: https://peerj.com/articles/8829 last-modified: 2020-03-18 description: Auxin response factors (ARFs) are important transcription factors (TFs) that are differentially expressed in response to various abiotic stresses. The important roles of ARFs and small RNA-ARF pathways in mediating plant growth and stress responses have emerged in several recent studies. However, no studies on the involvement of ARFs in tamarisk trees, which are resistant to salinity, have been conducted. In this study, systematic analysis revealed 12 TcARF genes belonging to five different groups in Tamarix chinensis. The microRNA response elements of miR160, which belongs to group I and miR167, which belongs to group III, were conserved in terms of their location and sequence. Moreover, digital gene expression profiles suggested that a potential miR167 target gene, TcARF6, was rapidly expressed in response to salt stress. Cloning of TcARF6 revealed that TcARF6 could be an activation TF with a glutamine-rich region and expression pattern analysis revealed that the expression of TcARF6 was significantly downregulated specifically in the roots. A significant negative correlation in the expression pattern of tch-miR167/TcARF6 indicated that this module may play a key role in the response to salt stress. Overall, these results provide basic information on the posttranscriptional regulation of TcARF6 for future investigations of the T. chinensis salt-stress response. creator: Youju Ye creator: Jianwen Wang creator: Wei Wang creator: Li-an Xu uri: https://doi.org/10.7717/peerj.8829 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ye et al. title: Trypophobia as an urbanized emotion: comparative research in ethnic minority regions of China link: https://peerj.com/articles/8837 last-modified: 2020-03-18 description: Trypophobia is a strong emotion of disgust evoked by clusters of holes or round objects (e.g., lotus seed pod). It has become increasingly popular and been studied since 2010s, mainly in the West and Japan. Considering this, trypophobia might be a modern emotion, and hence urbanization possibly plays key roles in trypophobia. To address this issue, we compared the degree of trypophobia between urban and less urban people in China. In an experiment, we asked participants about their degree of discomfort from trypophobic images. The results showed that trypophobia occurred in both groups, although the effect size was larger in urban than less urban people. Moreover, post-experimental interviews and post-hoc analyses revealed that older people in less urban area did not experience as much trypophobia. Our findings suggest that trypophobia links to urbanization and age-related properties. creator: Siqi Zhu creator: Kyoshiro Sasaki creator: Yue Jiang creator: Kun Qian creator: Yuki Yamada uri: https://doi.org/10.7717/peerj.8837 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhu et al. title: Non-ambulatory children with cerebral palsy: effects of four months of static and dynamic standing exercise on passive range of motion and spasticity in the hip link: https://peerj.com/articles/8561 last-modified: 2020-03-17 description: PurposeThe aim of this study was to compare the effects of four months of two types of structured training regimes, static standing (StS) versus dynamic standing (DyS), on passive range of motion (PROM) and spasticity in the hip among non-ambulatory children with cerebral palsy.MethodTwenty non-ambulatory children with cerebral palsy participated in an exercise intervention study with a crossover design. During StS, the Non-ambulatory children with cerebral palsy were encouraged to exercise according to standard care recommendations, including daily supported StS for 30–90 min. During DyS, daily exercise for at least 30 min at a speed between 30 and 50 rpm in an Innowalk (Made for movement, Norway) was recommended. We assessed adaptive effects from the exercise programs through PROM in the hip assessed with a handheld goniometer, and spasticity in the hip assessed with the Modified Ashworth Scale before and after 30 min of StS or DyS. A trained physiotherapist performed the assessments. The exercise test and exercise training were performed in the children’s habitual environment. Non-parametric statistics were used and each leg was used as its own control.ResultPROM increased in all directions after 30 min (p < 0.001), and after four months of exercise training (p < 0.001) of DyS. Thirty minutes of DyS lowered the spasticity in the muscles around the hip (p < 0.001) more than 30 min of StS (p < 0.001).ConclusionThirty minutes of DyS increased PROM and decreased spasticity among non-ambulatory children with CP. Four months of DyS increased PROM but did not decrease spasticity. These results can help inform individualised standing recommendations. creator: Åsa B. Tornberg creator: Katarina Lauruschkus uri: https://doi.org/10.7717/peerj.8561 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tornberg and Lauruschkus title: Overexpression of Myo1e promotes albumin endocytosis by mouse glomerular podocytes mediated by Dynamin link: https://peerj.com/articles/8599 last-modified: 2020-03-17 description: BackgroundAs a fundamental process internalizing molecules from the plasma membrane, endocytosis plays a crucial role in podocyte biology. Our previous study has identified that overexpression of Myole may enhance podocyte endocytosis. However, its potential mechanism has been not well understand. Thus, we aimed to analyze whether albumin endocytosis by mouse glomerular podocytes is dependent on Myo1e expression. Also, we aimed to elucidate whether the underlying mechanism is mediated by Dynamin.MethodsFirstly, mouse podocyte cells (MPC5) were treated with different concentrations of FITC-bovine serum albumin (BSA). The fluorescence intensity and cell viability were detected by flow cytometry and MTT assays, respectively. Afterwards, the optimal concentration of FITC-BSA was determined. Secondly, MPC5 cells were treated with Myole overexpression or knockdown. Cell morphology was observed under microscope. Immunofluorescence assay was used to determine the expression of F-actin. The protein expression of nephrin and podocin was detected by western blot. Flow cytometry was used to detect MPC5 cell apoptosis with annexin V. Finally, MPC5 cells were treated with Myole overexpression and/or Dynasore (a GTPase inhibitor of Dynamin). The fluorescence intensity was detected using flow cytometry assay.ResultsMPC5 endocytosis BSA was elevated with a concentration-dependent manner. MTT results showed that MPC5 cell viability was inhibited with a concentration-dependent manner. Myo1e overexpression promoted podocyte endocytic FITC-BSA, which was contrary to its knockdown. Under microscope, after inhibition of Myo1e, podocyte foot process fusion was observed. Myo1e overexpression promoted the expression of cytoskeleton F-actin and podocyte-specific molecules (nephrin and podocin) in podocyte endocytic FITC-BSA. Furthermore, we found that Myo1e promoted the apoptosis of podocytes. Dynasore attenuated the increase in endocytosis of FITC-BSA induced by Myo1e overexpression, suggesting that podocytes might mediate albumin endocytosis via Myo1e-Dynamin-Albumin.ConclusionOur findings revealed that overexpression of Myo1e promotes albumin endocytosis in mouse glomerular podocyte endocytic albumin mediated by Dynamin. creator: Huijun Shen creator: Yu Bao creator: Chunyue Feng creator: Haidong Fu creator: Jianhua Mao uri: https://doi.org/10.7717/peerj.8599 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Shen et al. title: The role of age, sex, anthropometry, and body composition as determinants of physical fitness in nonobese children aged 6–12 link: https://peerj.com/articles/8657 last-modified: 2020-03-17 description: PurposeThe determinants of physical fitness in children have been given limited attention. In particular, the relative role of chronological age, sex, anthropometry, and body composition in physical fitness of children has been barely investigated. This cross-sectional study investigated determinants of physical fitness using a set of predictive variables including, in addition to chronological age and sex, a large panel of anthropometric measurements as well as body composition. The study was carried out in a convenience sample of children aged 6–12 participating in a summer camp.MethodsOne-hundred-ninety-three children (128 males) fulfilled all requirements and entered analysis. Health-related physical fitness components (speed, muscular power and balance) were explored by means of field tests, namely the 30-m dash test for running speed, the standing long jump and the seated chest pass test for lower limbs and upper body muscular power, respectively, and the flamingo balance test for static balance. Determinants of physical fitness were investigated by regression analysis using chronological age, sex, anthropometry, and body composition in a hierarchical approach. To minimize the expected effect of collinearity in predictor variables, an original statistical approach using Random Forests analysis was adopted.ResultsAge predicted 45.2%, 43.6%, 35.6% and 25.6%; and sex 9.5%, 10.7%, 6.3% and 2.0% of variance in the 30-m dash, seated chest pass, standing long jump, and flamingo balance test, respectively. Anthropometry and body composition explained a limited or no percentage of variance. The adjusted R2 (root mean square error) was 0.61 (0.31 s), 0.45 (0.32 m), 0.58 (0.15 m) and 0.41 (0.75 logs) for the 30-m dash, seated chest pass, standing long jump, and flamingo balance test, respectively making these models useful when physical fitness tests are not feasible.ConclusionsWe highlighted the respective role of chronological age, sex, anthropometry, and body composition in physical fitness of children in the wide age range 6–12 years. Data confirm and expand on previous literature by showing with a strictly conservative statistical approach that chronological age is a main determinant of physical fitness of both boys and girls, sex playing a limited role. The role of anthropometry was even less important, and no role was found for body composition. These findings should be considered when planning/implementing motor development or physical education programs. creator: Chiara Milanese creator: Marco Sandri creator: Valentina Cavedon creator: Carlo Zancanaro uri: https://doi.org/10.7717/peerj.8657 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Milanese et al.