bluuebunny/crossref_metadata_2025_split huggingface dataset:
A prognostic nomogram in AFP-negative hepatocellular carcinoma based on LASSO Cox regression
Authors: Zhou Dong dong , Liu Xiao li , Wang Xin hui , Yan Feng na , Wang Peng , Yan Hui wen , Jiang Yu yong , Yang Zhi yun 
Published: August 2020

Abstract
PurposeHepatocellular carcinoma (HCC) patients with alpha-fetoprotein (AFP)-negative (<8.78 ng/mL) have special clinicopathologic characteristics and prognosis. The aim of this study was to apply a new method to establish and validate a new model for predicting the prognosis of HCC patients with AFP-negative.Materials and MethodsA total of 410 AFP-negative patients with clinical diagnosed with HCC as a primary cohort; 148 AFP-negative HCC patients as an independent validation cohort. In primary cohort, independent factors for overall survival (OS) by LASSO Cox regression were all contained into the nomogram1; by univariate and multivariate Cox hazard analysis were all contained into the nomogram2. Nomograms performance and discriminative power were assessed with concordance index (C-index) values, area under curve (AUC), Calibration curve and decision curve analyses (DCA). The results were validated in the validation cohort.ResultsThe C-index of nomogram1was 0.708 (95%CI: 0.673-0.743), which was superior to nomogram2 (0.706) and traditional modes (0.606-0.629). The AUC of nomogram1 was 0.736 (95%CI: 0.690-0.778). In the validation cohort, the nomogram1 still gave good discrimination (C-index: 0.752, 95%CI: 0.691-0.813; AUC: 0.784, 95%CI: 0.709-0.847) and good calibration. The calibration curve for probability of OS showed good homogeneity between prediction by nomogram1 and actual observation. DCA demonstrated that nomogram1 was clinically useful. Moreover, patients were divided into three distinct risk groups for OS by the nomogram1: low-risk group, middle-risk group and high-risk group, respectively.ConclusionsNovel nomogram based on LASSO Cox regression presents more accurate and useful prognostic prediction for patients with AFP-negative HCC. This model could help AFP-negative HCC facilitate a personalized prognostic evaluation.
Seamless Data Analysis, Visualizations and Sharing: Perspective from IRRI’s Rainfed Rice Breeding Program
Authors: Hussain Waseem , Bhosale Sankalp , Catolos Margaret , Anumalla Mahender , Khanna Apurva , Cruz Ma Teresa Sta. , Ramos Joie 
Published: August 2020

Abstract
Phenotypic data analysis is a key component in crop breeding to extract meaningful insights from data in making better breeding decisions. Each year the rainfed rice breeding (RRB) program at IRRI conducts trials in the national agricultural research and extension systems (NARES) network-partner sites across South Asia, Southeast Asia and Africa. Analyzing the data from the network trials and sharing the results with the partners in the best possible format is a daunting task. It is crucial to demystify data analysis to the NARES partners for making better breeding decisions. Here, we provide an overview of how RRB program at IRRI has leveraged R computational power with open-source resource tools like R Markdown, plotly , LaTeX and HTML to develop a unique data analysis workflow and redesigned it to a reproducible document for better interpretation, visualization and seamlessly sharing with partners. The generated report is the state-of-the-art implementation of analysis workflow and outputs either in text, tables or graphics in a unified way as one document. The analysis is highly reproducible and can be regenerated based at any time. The plots are built with enhanced dynamic and interactive visualizations to aid in better understanding and extract information with ease. Tables are highly interactive and manageable rendering liberty to be exported within the document in numerous formats. The source code and demo data set for download and use is available at https://github.com/whussain2/Analysis-pipeline . Conclusively, the analysis workflow and document we presented is not limited to IRRI’s RRB program but is applicable to any organization or institute with full-fledged breeding programs.
Dynamic Changes in the Rhizosphere Bacterial Community in Monoculture and Intercropped Corn and Soybean During Various Crop Growth Stages
Authors: Li Han , Luo Luyun , Tang Bin , Guo Huanle , Cao Zhongyang , Zeng Qiang , Chen Songlin , Chen Zhihui 
Published: August 2020

Abstract
Although rhizosphere microorganisms have been studied for a long time, rhizosphere microbial communities based on monoculture and intercropped soybean and corn have rarely been studied. To define the effect of crop monoculture and intercropping on soil physicochemical properties and rhizosphere microbial communities, field experiments were conducted using corn and soybean cultivars at five different crop growth stages. The pH and soil organic matter (SOM) were the key factors affecting crop rhizosphere soil microorganisms. The content of available phosphorus(AP) in the intercropped soybean/corn soil samples was higher than that in the monoculture soil samples at five different growth stages.The content of available cadmium(ACd) in monoculture soybean rhizosphere soil samples decreased and then increased, but the intercropped soybean soil samples indicated an opposite trend.Proteobacteria, Chloroﬂexi, Acidobacteria, Actinobacteria, and Firmicutes were the dominant phyla in the soybean and cornrhizosphere soil samples. Crops of the same plant species showed little difference in the bacterial community diversity under the two planting modes. The results showed that the cadmium content in cadmium-polluted soil could be reduced by the soybean/corn intercropping system. The crop rhizosphere bacterial community is not only regulated by the crop itself but also influenced by the planting pattern.
LncRNA LEF1-AS1/LEF1/FUT8 Axis Mediates Colorectal Cancer Progression by Regulating α1, 6-Fucosylation via Wnt/β-Catenin Pathway
Authors: Qi Yu , Shan Yujia , Li Shuangda , Huang Yiran , Guo Yanru , Huang Tong , Jia Li 
Published: August 2020

Abstract
Background: Fucosylation alteration is involved in several steps of human cancer pathogenesis. Dysregulated long noncoding RNA (lncRNA) often leads to malignancy in colorectal cancer (CRC). Methods: Differential levels of LEF1-AS1, LEF1 and FUT8 are analyzed by qRT-PCR and western blot. Chip, RIP, EMSA and luciferase reporter assay confirm the direct interaction among LEF1-AS1, MLL1, H3K4me3, LEF1 and FUT8. Functionally, CRC cell proliferation, proliferation, migration and invasion are analyzed by CCK8 assay, colony formation assay, transwell assay and flow cytometry. The xenografts nude mice models, lung metastasis and liver metatstasis are established to determine the effect of LEF1-AS1/LEF1/FUT8 axis on CRC progression in vivo.Results: Here, we identify that LEF1-AS1 and LEF1 are higher in CRC tissues than that in adjacent tissues, as well as upregulated in CRC cell lines than that in normal colorectal cells. Altered levels of LEF1-AS1 modulate LEF1 expression, while altered LEF1 could not regulate LEF1-AS1. LEF1-AS1 recruits MLL1 to the promoter region of LEF1, induces H3K4me3 methylation modification and mediates LEF1 transcription. Furthermore, α1-6 fucosyltransferase FUT8 is overexpressed in CRC tissues and positively correlated to LEF1. FUT8 is a direct target of transcription factor LEF1, which regulates FUT8 level. Altered FUT8 also regulates the core fucosylation of CRC cells, and LEF1-AS1 mediates FUT8 level through activation of Wnt/β-catenin/LEF1 pathway, thereby resulting in β-catenin nuclear translocation. In addition, LEF1-AS1 mediates the proliferation, migration and invasion of CRC cells in vitro. LEF1-AS1 silence hinders the tumorigenesis, liver and lung metastasis of SW620 cells in vivo, while overexpressed FUT8 abolishes the suppressive impact of LEF1-AS1 repression on the biological behavior of SW620 cells. Conclusion: Our studies uncovered a novel mechanism for constitutive LEF1-AS1/LEF1/FUT8 axis in CRC progression by regulating α1, 6-fucosylation via Wnt/β-catenin pathway, and consequently, as a potential therapeutic target in CRC.
Irradiation-Induced Polyploidy Giant Cancer Cells Mediate Tumor Cell Repopulation via Neosis
Authors: Zhang Zhengxiang , He Sijia , Xiao Feng , Cheng Jin , Wang Yiwei , Zhao Minghui , Zhao Yucui , Li Chuanyuan , Huang Qian 
Published: August 2020

Abstract
Background Tumor repopulation generally describes the phenomenon that residual tumor cells surviving therapies tenaciously proliferate and reestablish the tumor, presenting an embarrassing plight for cancer treatment. However, the cellular and molecular mechanisms underlying this process remains poorly understood. In this study, we proposed polyploidy giant cancer cells (PGCCs)-mediated and neosis-based tumor repopulation after radiotherapy.Methods The formation of PGCCs after irradiation was examined in vitro and in vivo. The demise of X-ray irradiated cells was detected by flow cytometry, clonogenic cell survival assay and transmission electron microscopy. Western blot was used to test cell proliferation and death related protein expression level of these irradiated cells. Time lapse microscopy was adopted to observe the destiny of PGCCs. The property of these PGCCs was identified by TUNEL assay, Brdu chasing assay, western blot, immunocytochemical and immunofluorescence staining. The relationship of HMGB1 with PGCCs-derived tumor repopulation was conducted via HMGB1 chemical inhibitors. Finally, animal model was used to verify the formation of PGCCs, and the relevance of HMGB1 in this process was investigated by immunohistochemical staining.Results The majority of PGCCs induced by irradiation move towards cell demise, whereas some of them intriguingly possessed proliferative property. Utilizing time-lapse microscopy and single-cell cloning assay, we observed that neosis derived from those PGCCs with proliferative capacity contributed to tumor cell repopulation after irradiation. Using the conditioned media collected from dying tumor cells to perform single-cell cloning assay, we unexpectedly demonstrated that HMGB1 released from dying tumor cells participated the process of neosis-based tumor repopulation. In irradiation treated animal tumor bearing model, the expression level of HMGB1 increased after irradiation compare with non-irradiated group. Moreover, some PGCCs presented high HMGB1 expression. Interestingly, we also observed that the proliferation potential of PGCCs varied. Some PGCCs proliferated at early stage, while some PGCCs proliferated at late stage.Conclusion X-ray irradiation could induce the formation of PGCCs, which could move towards both cell death and survival; irradiation-generating PGCCs mediated tumor cell repopulation after irradiation via neosis; HMGB1 released from dying cells stimulated the process of neosis and participated in tumor repopulation after irradiation.
CircCDKN2B-AS1 Interacts with IMP3 to Stabilize Hexokinase 2 mRNA and Facilitate Cervical Squamous Cell Carcinoma Aerobic Glycolysis Progression
Authors: Zhang Yanan , Zhao Lu , Yang Shizhou , Cen Yixuan , Zhu Tingjia , Wang Lingfang , Xia Lili , Liu Yuwan , Zou Jian , Xu Junfen , Li Yang , Cheng Xiaodong , Lu Weiguo , Wang Xinyu , Xie Xing 
Published: August 2020

Abstract
Background: Circular RNAs(circRNAs) have been reported to play key roles in the development of various cancers. However, the biological function and clinical significance of most circRNAs are still elusive. The purpose of this study is to explore the function and mechanism of a certain circRNA named circCDKN2B-AS1 in cervical cancer development, and its potential value in clinic. Methods: The qRT-PCR array was conducted to verify the expression level of circCDKN2B-AS1. CCK8 assay, transwell assay, and FCM were undertaken to detect cellular proliferation, migration, and apoptosis, respectively. Seahorse XFe 96 analyzer was used to measure the glycolysis metabolism level. RNA pulldown, RIP, actinomycin-D adding assay and Western Blot were used to screen and elucidate the potential mechanisms. BALB/c nude mice and zebrafish embryo（AB,WT） were used as animal models to investigate tumorigenesis capability.18FDG-microPET/CT was used to detect the glucose metabolism level of subcutaneous tumor in nude mice. Results: CircCDKN2B-AS1, circular isoform of lncRNA CDKN2B-AS1, was upregulated in cervical cancer and precancer tissues. We found that circCDKN2B-AS1 associated with IMP3 protein depending on a specific binding site and regulated the stability of Hexokinase 2(HK2) mRNA, the rate-limiting enzyme of aerobic glycolysis pathway. The expression level of circCDKN2B-AS1 fated the binding of IMP3 to 3’UTR of HK2 mRNA, consequently affects cell malignant phenotypes and aerobic glycolysis of cervical cancer in vitro and in vivo. Mutant circCDKN2B-AS1 lacking of the IMP3 binding site didn’t have such effects. Utilizing an inhibitory peptide to block the interaction between circCDKN2B-AS1 and IMP3 protein impeded the binding of IMP3 to 3’UTR of HK2 mRNA and suppressed aerobic glycolysis in cervical cancer cells.Conclusions: Our findings demonstrate that circCDKN2B-AS1 facilitates aerobic glycolysis by sponging IMP3 protein to stabilize HK2 mRNA, consequently promotes malignant phenotypes in cervical cancer, which may provide a potential approach for cervical cancer therapeutics.
Hypoxia-Autophagy Axis Induces VEGFA by Peritoneal Mesothelial Cells to Promote Gastric Cancer Peritoneal Metastasis Through an Integrin α5-Fibronectin Pathway
Authors: Wang Xiaoxun , Che Xiaofang , Yu Yang , Cheng Yu , Bai Ming , Yang Zichang , Guo Qiqiang , Xie Xiaochen , Li Danni , Guo Min , Hou Kezuo , Guo Wendong , Qu Xiujuan , Cao Liu 
Published: August 2020

Abstract
Background: Peritoneal metastasis (PM) is an important pathological process in the progression of gastric cancer (GC). The metastatic potential of tumor and stromal cells is governed by hypoxia, which is a key molecular feature of the tumor microenvironment. Mesothelial cells also participate in this complex and dynamic process. However, the molecular mechanisms underlying the hypoxia-driven mesothelial-tumor interactions that promote peritoneal metastasis of GC remain unclear.Methods: We determined the hypoxic microenvironment in PM of nude mice by immunohistochemical analysis and screened VEGFA by human growth factor array kit. The crosstalk mediated by VEGFA between peritoneal mesothelial cells (PMCs) and GC cells was determined in GC cells incubated with conditioned medium prepared from hypoxia-treated PMCs. The association between VEGFR1 and integrin α5 and fibronectin in GC cells was enriched using Gene Set Enrichment Analysis and KEGG pathway enrichment analysis. In vitro and xenograft mouse models were used to evaluate the impact of VEGFA/VEGFR1 on gastric cancer peritoneal metastasis. Confocal microscopy and immunoprecipitation were performed to determine the effect of hypoxia-induced autophagy.Results: Here we report that in the PMCs of the hypoxic microenvironment, SIRT1 is degraded via the autophagic lysosomal pathway, leading to increased acetylation of HIF-1α and secretion of VEGFA. Under hypoxic conditions, VEGFA derived from PMCs acts on VEGFR1 of GC cells, resulting in p-ERK/p-JNK pathway activation, increased integrin α5 and fibronectin expression, and promotion of PM.Conclusions: Our findings have elucidated the mechanisms by which PMCs promote PM in GC in hypoxic environments. This study also provides a theoretical basis for considering autophagic pathways or VEGFA as potential therapeutic targets to treat PM in GC.
Circular RNA MCTP2 Inhibits Cisplatin Resistance in Gastric Cancer by miR-99a-5p-Mediated Induction of MTMR3 Expression
Authors: Sun Guangli , Li Zheng , He Zhongyuan , Wang Weizhi , Wang Sen , Zhang Xing , Cao Jiacheng , Xu Penghui , Wang Haixiao , Huang Xiaoxu , Xia Yiwen , Lv Jialun , Xuan Zhe , Jiang Tianlu , Fang Lang , Yang Jing , Zhang Diancai , Xu Hao , Xu Zekuan 
Published: August 2020

Abstract
Background: Cisplatin (CDDP) is the first-line chemotherapy for gastric cancer (GC). Poor prognosis of GC patients is partially due to development of CDDP resistance. Circular RNAs (circRNAs) are a subclass of non-coding RNAs that function as microRNA (miRNA) sponges. The role of circRNAs in CDDP resistance in GC has not been evaluated. Methods: RNA-sequencing was used to identify the differentially expressed circRNAs between the CDDP-resistant and CDDP-sensitive GC cells. qRT-PCR was used to detect the expression of circMCTP2 in GC tissues. The effects of circMCTP2 on CDDP resistance were investigated in vitro and in vivo. Pull-down assays and Luciferase reporter assays were performed to confirm the interaction among circMCTP2, miR-99a-5p, and myotubularin related protein 3 (MTMR3). The protein expression levels of MTMR3 were detected by western blotting. Autophagy was evaluated by confocal microscopy and transmission electron microscopy (TEM).Results: CircMCTP2 was found to be downregulated in the CDDP-resistant GC cells and tissues as compared to that of the CDDP-sensitive ones. A high level of circMCTP2 was found to be a favorable factor for the prognosis of patients with GC. CircMCTP2 inhibited cell proliferation and autophagy while promoting apoptosis of CDDP-resistant GC cells in response to CDDP treatment. CircMCTP2 upregulated MTMR3 by sponging miR-99a-5p, and knockdown of MTMR3 could reverse the effects of circMCTP2 on CDDP resistance and autophagy of GC cells. Conclusions: CircMCTP2 sensitizes GC to CDDP through the upregulation of MTMR3 by sponging miR-99a-5p. Overexpression of CircMCTP2 could be a new therapeutic strategy for counteracting CDDP resistance in GC.
Determinant of Practice of Birth Preparedness and Complication Readiness Plan Among Pregnant Women at Debretabor, North west Ethiopia: A Community Based Cross Sectional Study.
Authors: Negash Berhan Tsegaye 
Published: August 2020

Abstract
Background: Nearly all of maternal deaths in the world occurred in sub-Saharan African countries. As Ethiopian demographic health survey report, there were 412 maternal deaths per 100,000 live births in 2016. Delays in decision to seek and receive care are the main causes of these deaths. Birth preparedness and complication readiness plan has been globally endorsed pivotal strategy to decrease these delays. Therefore, this study was aimed to assess the level of practice and factors associated with practice of birth preparedness plan among pregnant women. Methods: Community based cross-sectional study was done among 356 pregnant women selected by simple random sampling technique from July 1-30/2017 in Debretabor town. We selected samples by simple random sampling technique. Data were collected using interview administered questionnaire. Then, we coded, cleaned and entered data through Epidata version 3.1. Finally, exported and analyzed by SPSS. Logistic regression analysis was done to identify association between explanatory variables and practice of birth preparedness and complication plan. An adjusted odds ratio with 95% confidence interval and p-value less than 0.05 was computed to determine the level of significance in multi-variable logistic regression model.Results: Prevalence of birth preparedness and complication readiness plan was 73.9% in this study. primary education status (AOR=3.2,95%CI,1.3-7.8) and secondary educational status (AOR=4.1,95%CI,1.6-10.3), Primigravida (AOR=4.7,95%CI,1.9-11.3), partner involvement in birth preparedness and complication readiness plan (AOR=3.4,95%CI,1.9-6.1), initiating antenatal care in first trimester and media exposure (AOR=1.9,95%CI,1.0-3.3) were significantly associated factors with birth preparedness and complication readiness plan in this study. Conclusions: Level of practice of birth preparedness and complication readiness plan was high in the current study. Higher education status, early ante-natal care initiation, partner involvement in birth preparedness and exposure to media were the factors associated with practice of birth preparedness and complication readiness. Therefore, emphasize on continues education through media, design educational curriculum which should include birth preparedness plan, increase partner participation in birth preparedness and complication readiness plan. Furthermore, early initiation of antenatal care is mandatory.
Status of Disrespectful and Abusive Maternity Care Among Women who Delivered in Hospitals of Sidama zone, South Ethiopia, in 2019.
Authors: Negash Berhan Tsegaye , Yoseph Amanuel 
Published: August 2020

Abstract
Background: Disrespectful and abusive maternity care is occurred at various degree at health institutions across many countries including Ethiopia. Consequently, maternal mortality remains high in Ethiopia. Despite its importance, information is scarce about disrespect and abusive care. Hence, this study aimed to assesses magnitude and factors associated with disrespectful and abusive maternity care during child birth in public health facilities of Sidama zone, South Ethiopia. Methods: Facility based cross-sectional study was conducted in sidama zone public health institutions from February 1-30, 2019. We have applied purposive sampling method for selection of health institutions. In addition, study participants were selected by systematic random sampling technique. Data were collected using checklist and exist interview administered questionnaire. Then, we coded, cleaned and entered data through Epidata version 3.1. Finally, exported and analyzed by SPSS. Logistic regression analysis was done to identify association between explanatory variables and disrespectful and abusive care. An adjusted odds ratio with 95% confidence interval and p-value less than 0.05 was computed to determine the level of significance.Result: From a total of 577 study participants, only 548 study participants have participated in this study making a response rate of 95%. Magnitude of disrespect and abuse maternity care was 46.9% [95%CI: 42.8-51]. Marital status of single (AOR= 2.6, 95% CI=1.8-6.67), four and more births (AOR=4.67,95%CI:1.6-12.8), instrumental delivery (AOR=2.63,95% CI,1.0-6.6), and care provision by female birth attendants (AOR=1.7,95%CI,1.1-2.7) were factors positively associated with disrespect and abusive maternity care during childbirth. Conclusion: Magnitude of disrespect and abusive maternity care is high in this study. Instrumental delivery, female health care provider and four and above deliveries and single marital status were factors associated with disrespect and abuse care. Therefore, government facilities should national health strategies and policies should focus on respectful maternity care. It is also recommended to give intensive training on respectful maternity care especially in public hospitals by involving more female health care provider. Promotion of family planning service can be used as alternative method of reduction of reduction of disrespect and abusive maternal care indirectly.