bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly Efficient Biosynthesis of Indole-3-acetic acid by Enterobacter xiangfangensis BHW6
Authors: Zhang Bi-Xian , Wang Ying-Ying , Hu Xiaomei 
Published: August 2020

Abstract
Background: Indole-3-acetic acid (IAA) plays an important role in the growth and development of plants. Various bacteria in the rhizosphere are capable to produce IAA that acts as a signaling molecule for the communication between plants and microbes to promote the plant growth. Due to the low IAA content and various interfering analogs, it is difficult to detect and isolate IAA from microbial secondary metabolites. Results: A predominant strain with a remarkable capability to secrete IAA was identified as Enterobacter xiangfangensis BHW6 based on 16S rRNA gene sequence, the determination of average nucleotide identity (ANI) and digital DDH (dDDH). The maximum IAA content (134-1129 μg/mL) was found with the addition of 0.2-15 g/L of L-tryptophan at pH 5 for 6 days, which was 4-40 fold higher than that in the absence of L-tryptophan. The highest yield of IAA was obtained at the stationary phase of bacterial growth. An acidic culture medium was preferred for the IAA biosynthesis of the strain. The strain was tolerant and stable to produce IAA in the presence 2.5%-5% (w/v) of NaCl. IAA was then isolated through column chromatography with a mobile phase of hexane/ethyl acetate (1/2, v/v) and characterized by 1H Nuclear Magnetic Resonance (1H NMR). Conclusions: A remarkable IAA production was obtained from E. xiangfangensis BHW6 that was tryptophan–dependent. According to genomic analysis, the ipdC gene coding for the key enzyme (indole-3-pyruvate decarboxylase) was identified indicating that IAA biosynthesis was mainly through the indole-3-pyruvia acid (IPyA) pathway, which was further confirmed by intermediate assay. E. xiangfangensis BHW6 with an important economic value has great prospect in agricultural and industrial application.
Choosing the best embryogenesis medium in carrot by data mining technology
Authors: Ziarani Masoumeh Fallah , Tohidfar Masoud , Mirjalili Mohammah Hosein , Gavlighi Hassan Ahmadi , Hesami Mohsen 
Published: August 2020

Abstract
Plant cell, tissue and organ culture (PCTOC) is extensively used to propagate faster and more plants, to produce virus-free plants, and secondary metabolites production as well. This requires the optimization of PCTOC conditions for each plant and final aim. Optimizing the micropropagation is time-consuming and costly, because it is different from the plant and even for each variety. In addition requires the optimization of the concentration and type of hormone and the type of explants for each variety in the stages of callogenesis, embryogenesis, shooting and rooting. Hence, today researchers have used Data Mining with using an artificial neural network (ANN) to predict the best conditions for tissue culture and saved time and money considerably. In this research, radial basis function (RBF) model was used to predict the best conditions for carrot tissue culture and the results showed that the highest and the least sensitivity were related to variety and percentage of Agar in liter, respectively. The results prediction of the RBF model showed that the percentage of embryogenesis was 62.5%, but the percentage of embryogenesis in laboratory obtain 75%. The results showed that the RBF model is a good model to predict the results.
Sum of High-Risk Gene Mutation (SHGM): A Novel Attempt to Assist Differential Diagnosis for Adrenocortical Carcinoma with Benign Adenoma, Based Detection of Mutations of Nine Target Genes.
Authors: Zheng Guo-Yang , Zhang Xue-Bin , Li Han-Zhong , Zhang Yu-Shi , Deng Jian-Hua , Wu Xing-Cheng 
Published: August 2020

Abstract
Background
There has been no research on applying gene detection to differential diagnosis of adrenocortical carcinoma (ACC). We attempted to explore a novel auxiliary method for differential diagnosis between ACC with benign adrenocortical adenoma (ACA), based on mutations of target genes in tissues.
Methods
Nine genes were chosen as target genes, including TP53, CTNNB1, ARMC5, PRKAR1A, ZNRF3, RB1, APC, MEN1 and RPL22. Exons capture and sequencing of target genes were performed in 98 cases of tissue samples by using FastTarget technology, including 41 ACC tissues, 32 ACA tissues and 25 normal adrenal gland tissues. Significant mutations were detected and identified, and the clinical information was collected, for further comparative analysis and application to assist differential diagnosis of ACC.
Results
We identified 132 significant gene mutations and 227 significant mutation sites in 37 ACC tissues, much more than ACA and normal adrenal gland tissues. Mutation rates of 6 genes in ACC tissues were obviously higher than ACA tissues, including ZNRF3, ARMC5, TP53, APC, RB1, and PRKAR1A, which were regarded as high-risk genes. The sum of mutated high-risk genes detected in each sample was denominated sum of high-risk gene mutation (SHGM), and the rates of SHGM > 0 and SHGM > 1 in ACC tissues were 73.0% and 62.2% respectively, which were both obviously higher than those in ACA tissues, with significant statistic differences. Especially for the 8 cases of ACC with diameter < 5 cm, SHGM > 0 and SHGM > 1 were found in 6 samples (75%) and 4 samples (50%), respectively. However, no relevance was found between SHGM and clinical characteristics of ACC.
Conclusions
We identified 6 high-risk genes in ACC tissues, of which the mutation rates in ACC tissues were significantly higher than those in ACA or normal adrenal gland tissues. The sum of mutated high-risk genes detected in ACC tissues was denominated SHGM, which was potential to assist the differential diagnosis of ACC with ACA, especially for the small-size ACC.
Combination of Circulating Cell-Free DNA and Metabolic Tumor Burden to Distinguish Non-Small Cell Lung Cancer from Tuberculosis
Authors: Zheng Wen-qiang , Zhang Puhong , Quan Bin , Gao Guang-jian , Chen Qing , Dai Yun-hai , Zhai Jian 
Published: August 2020

Abstract
Background: Non-small cell lung (NSCLC) holds high mortality owing to the difficulty to early detection from other lung mass, such as tuberculosis. This study evaluates the clinical value of the combination of circulating cell-free DNA (cfDNA) quantification and metabolic tumor burden to distinguish NSCLC from tuberculosis. Methods: A total of 149 NSCLC patients, 151 tuberculosis patients and 150 healthy controls were included. Quantifying serum cfDNA fragments from ALU (115 bp) gene by RT-PCR. Metabolic tumor burden (SUV-Maxa) values were detected by preoperative the 18F-fluorodeoxyglucose positron emission tomography (18F-FDG PET/CT). A549 cell, NCI–H460 cell, NSCLC and tuberculosis mice model were used to elucidate the specific mechanism. Results: Serum cfDNA levels and SUV-Maxa were higher in NSCLC patients than those in healthy controls and those in tuberculosis. Meanwhile, mice models showed the similar discovery. In addition, obvious correlations of cfDNA and metabolic tumor burden were only existed in NSCLC patients and mice model, rather than tuberculosis and control. Moreover, the combination of cfDNA and metabolic tumor burden displayed better effect to distinguish NSCLC from tuberculosis than alone use. Mechanistically, upregulated Glucose transporter 1 (GLU1) increased necroptosis-induce cfDNA rise by FasL/caspase 8/caspase 3 pathway and promoted metabolic tumor burden in NSCLC. Conclusions: The combination of cfDNA and metabolic tumor burden displayed better effect to distinguish NSCLC from tuberculosis, owing to upregulated GLU1 increased cfDNA levels by FasL/caspase 8/caspase 3 pathways and promoted metabolic tumor burden in NSCLC.
Transcriptomic and Metabolomic Profiling Reveal the p53-Dependent Benzeneacetic Acid Attenuation of Silica-Induced Epithelial–Mesenchymal Transition in Human Bronchial Epithelial Cells
Authors: Zhou Meiling , Ju Zhao , Jin Jing , Pan Huiji , Ding Ping , Huang Ruixue 
Published: August 2020

Abstract
Background: Silica exposure underlies the development of silicosis, one of the most serious occupational hazards worldwide. We aimed to explore the interaction of the silica-induced epithelial–mesenchymal transition (EMT)-related transcripts with the cellular metabolism regulated by p53.Methods: We knocked out p53 using CRISPR/Cas9 in the human bronchial epithelial (HBE) cell line. The transcriptomic and metabolomic analyses and integrative omics were conducted using microarrays, GC-MS, and MetaboAnalyst, respectively. Results: Fifty-two mRNAs showed significantly altered expression in the HBE p53-KO cells post-silica exposure. A total of 42 metabolites were putatively involved in p53-dependent silica-mediated HBE cell dysfunction. Through integrated data analysis, we obtained five significant p53-dependent metabolic pathways including phenylalanine, glyoxylate, dicarboxylate, and linoleic acid metabolism, and the citrate cycle. Through metabolite screening, we further identified that benzeneacetic acid, a key regulation metabolite in the phenylalanine metabolic pathway, attenuated the silica-induced EMT in HBE cells ina p53-dependent manner. Interestingly, despite the extensive p53-related published literature, the clinical translation of these studies remains unsubstantial. Conclusions: Our study offers new insights into the molecular mechanisms by which epithelial cells respond to silica exposure and provide fresh perspective and direction for future clinical biomarker research and potential clinically sustainable and translatable role of p53.
LncRNA CBR3-AS1 Regulates of Breast Cancer Drug Sensitivity as a Competing Endogenous RNA Through the JNK1/MEK4‑Mediated MAPK Signal Pathway
Authors: Zhang Ming , Wang Yan , Jiang Longyang , Song Xinyue , Zheng Ang , Gao Hua , Wei Minjie , Zhao Lin 
Published: August 2020

Abstract
Background: Adriamycin (ADR) resistance is one of the main obstacles to improve the clinical prognosis of breast cancer (BRCA) patients. Long non-coding RNAs (lncRNAs) can regulate cell behavior, but the role of these RNAs in anti ADR of BRCA remains unclear. Here we aim to investigate the imbalance of a particular long noncoding RNA, lncRNA CBR3 antisense RNA 1 (CBR3-AS1), and its role in ADR resistance.Methods: Microarray analysis of ADR-resistant BRCA cells was performed to identify CBR3-AS1. CCK8 assay and colony formation assay were used to detect the sensitivity of BRCA cells to ADR. Dual-luciferase reporter, RNA pull down, IHC and Western blot were used to verify the relationship between CBR3-AS1, miRNA and target genes. In vivo, the effect of CBR3-AS1 on BRCA resistance was observed by xenograft tumor model. The role of CBR3-AS1 in influencing ADR sensitivity was verified by clinical BRCA specimens, TCGA, CCLE, and GDSC databases.Results: Here, we found that lncRNA CBR3-AS1 was significantly increased in BRCA tissues and was closely correlated with poor prognosis. CBR3-AS1 overexpression promoted ADR resistance in BRCA cells in vitro and in vivo. Mechanistically, we identified that CBR3-AS1 functioned as a competitive endogenous RNA by acting as a molecular sponge of miR-25-3p. MEK4 and JNK1 of MAPK pathway were the direct downstream proteins of CBR3-AS1 / miR-25-3p axis in BRCA cells.Conclusions: In summary, our findings demonstrate that CBR3-AS1 plays a critical role in the chemotherapy resistance of BRCA by mediating the miR-25-3p, MEK4/JNK1 regulatory axis. The potential of CBR3-AS1 as an oncogene and therapeutic biomarker of BRCA was identified.
Drone-Assisted Aerial Surveys of Large Animals in Siberian Winter Forests
Authors: Atuchin Victor , Prosekov Alexander , Vesnina Anna , Kuznetsov Alexander 
Published: August 2020

Abstract
There are two main reasons for monitoring the population of forest animals. First of all, regular surveys reveal the real state of biodiversity. Second, they guarantee a prompt response to any negative environmental factor that affects the animal population and make it possible to eliminate the threat before any permanent damage has been done. The research objective was to study the potential of drone planes equipped with thermal infrared imaging cameras. Drone planes proved effective in covering large areas, while thermal infrared cameras provided accurate statistics in the harsh winter conditions of Siberia. The research featured the population of the European elk (Alces alces), which is gradually deteriorating due to poaching and deforestation. The surveyed territory included the Salair State Nature Reserve in the Kemerovo Region, or Kuzbass (Russia). The authors developed an effective methodology for processing the data obtained from drone-mounted thermal infrared cameras. The research provided reliable results concerning the changes in the elk population on the territory in question. The use of drone planes proved an effective means of ungulate animal survey on large areas of Siberian winter forests.
Cardiac Helical Function
Authors: Trainini Jorge , Lowenstein Jorge , Beraudo Mario , Wernicke Mario , Llabata Vicente Mora , Lowenstein-Haber Diego , Trainini Alejandro , Costa Francesc Carreras 
Published: August 2020

Abstract
Background. The aim of this study was to investigate: a) the starts and ends of the myocardial band; b) the slippage between the band segments, when performing both torsion and ventricular detorsion, implies that there should be an antifriction mechanism that avoids dissipating the energy; c) the electrical activation of the endocardial and epicardial bands and secondarily understand ventricular twist and the mechanism of active suction during the diastolic isovolumic phase. Methods. They were used: a) Ten young-bovine hearts (800-1000 g) and seven human hearts (one embrión, 4 g; one 10 years, 250 g and five adult, 300 g/average); b) five patients with no structural cardiac abnormalities and normal QRS complexes underwent three-dimensional endoepicardial electroanatomic mapping. Results. We have found in all the bovine and human hearts studied a nucleus (fulcrum) underlying the right trigone, whose osseus, chondroid or tendinous histological structure depends on the specimen analyzed. All the hearts studied presented myocardial attachment to the rigid structure of the fulcrum. Hyaluronic acid was found in the cleavage planes between the myocardial bundles.Endo-epicardial mapping demonstrates an electrical activation sequence in the area of the apex loop in agreement with the synchronic contraction of the descending and ascending band segments, consistent with the mechanism of ventricular twist. The late activation of the ascending band segment is consistent with its persistent contraction during the initial period of the isovolumic diastolic phase (the basis of the suction mechanism). Conclusions. The finding of the fulcrum gives support to the spiral myocardial band being the point of fixation that allows the helicoidal torsion. The hyaluronic acid would act as a lubricant and provide great resistance to mechanical pressures. This study explains the ventricular twist and the active suction mechanism during the isovolumic diastolic and early ventricular filling phases.Trial. This work does not correspond to a trial
A Genomic-Clinicopathologic Nomogram for the Preoperative Prediction of Lymph Node Metastasis in Gastric Cancer
Authors: Zhong Xin , Xuan Feichao , Qian Yun , Pan Junhai , Wang Suihan , Chen Wenchao , Lin Tianyu , Zhu Hepan , Wang Xianfa , Wang Guanyu 
Published: August 2020

Abstract
Background: Preoperative evaluation of the lymph node (LN) state is of pivotal significance for therapy strategy decisions in gastric cancer (GC) patients. However, there is lack of noninvasive method that can identify such status preoperatively. We aimed at developing a genomic biosignature based model to forecast the possibility of LN metastasis in GC patients.Methods: We employed the RNA profile retrieving strategy and conducted RNA expression profiling in a large GC cohort (GSE62254, n = 300) from Gene Expression Ominus (GEO). In the exploratory stage, 300 GC patients from GSE62254 were involved and the differentially expressed RNAs (DERs) for LN-status were determined using R software. The GC samples in GSE62254 were randomly divided into a learning set (n = 210) and a verification set (n = 90). By performing the Least absolute shrinkage and selection operator (LASSO) regression approach, a set of 23-RNA signature was established and the signature based nomogram was subsequently built for distinguishing LN condition. The diagnostic effectiveness of this model was assessed, as well as the clinical performance subsequently assessed using the decision curve analysis (DCA). Metascape was used for bioinformatic analysis of the DERsResults: Based on this genomic signature, we established a nomogram which robustly distinguished LN status in the learning (AUC = 0.916, 95% CI 0.833–0.999) and verification sets (AUC = 0.775, 95% CI 0.647–0.903). DCA demonstrated the clinical value of this nomogram. Functional enrichment analysis of the DERs was conducted using bioinformatics methods which posited that these DERs were involved with several lymphangiogenesis-correlated cascades.Conclusions: Here, we present a genomic signature based nomogram that integrates the 23-RNA biosignature based scores and Lauren classification. This model can be readily utilized to estimate the possibility of LN metastasis with good performance in GC. The uncovering of the DERs reveals the prospective biogenesis of LN metastasis in GC.
miRNA-101 Regulates Filamentogenesis During Migration and Invasion of Cervical Cancer Cells
Authors: Zhang Ping , Wudu Muli , Huang Zi-Qi , Liu Yang , Erken Abuliaizezi , Lin Chen 
Published: August 2020

Abstract
Background: miRNAs play critical roles in cervical cancer (CC) progression. miRNA-101 is a tumour suppressor in several cancers. The aim of this study was to investigate the in vitro and in vivo effect of miRNA-101 on the biological behaviour of CC cells by analysing the formation of filamentous pseudopodia.Methods: Quantitative reverse-transcription-polymerase chain reaction was performed to analyse miRNA-101 expression in CC cells before and after its transfection. Cell counting kit-8, transwell migration, and wound healing assays were performed to investigate the effect of miRNA-101 on the malignant behaviour of CC cells in vitro. The impact of miRNA-101 on filopodia initiation in CC cells was investigated via scanning electron microscopy and TRITC-labelled phalloidin staining evaluation. In vivo analysis was performed using a nude mouse model of CC, established via subcutaneous tumour transplantation, to validate the role of miRNA-101 on CC malignant behaviour. One-way ANOVA with Fisher’s least significant difference post hoc test and t-test were used to evaluate statistical significance of differences between groups.Results: miRNA-101 was significantly downregulated in CC cell lines. Overexpression of miRNA-101 inhibited the malignant behaviours of CC cells in vitro, while it inhibited the formation of filopodia in CC cells. Similar results were observed using immunofluorescence and confocal microscopy.Conclusions: These results indicate that miRNA-101 inhibits CC migration and invasion. The present findings, combined with future research, will help provide a theoretical basis and novel insight for the clinical management of CC.
Effect of Ca+2 on P. aeruginasa and B. cereus metabolites
Authors: Kahraman Hüseyin , Keskin Zeliş Budak 
Published: August 2020

Abstract
Background: The effects of Ca+2 on virulence and some parameters were tried to be analyzed in this study. P. aeruginosa and B. cereus were used as Gram (-) bacteria as a control and Gram (+) bacteria as a control. Both bacteria are soil bacteria. Results: Amylase; P. aeruginosa is 102% increase in 0.1 M Ca+2 concentrations and B. cereus caused an increase in 123%. Biofilm P. aeruginosa; 200% increase in 0.1 M Ca+2 concentrations. B. cereus caused a 252% increase in the presence of 0.15 M Ca+2. Las B; in accordance with B. cereus, Las B activity decreased 1.7 times more than with P. aeruginosa. H2O2; P. aeruginosa increased by 60% resistance. B. cereus caused only a 3% increase. Protease in P. aeruginosa increase of 220%. B. cereus caused a 548% increase. Pyorubin, a pigment, caused an increase in the presence of Ca+2. However, these increases are not seen as significant increases.Conclusion: In this study; the effect of Ca+2 on protease, amylase, LasB elastolytic assay, H2O2, pyorubin and biofilm was investigated in a 24 hour time. In the study we have conducted here, the effect of Ca+2 meat on the production of some secondary metabolites on Gram (-) P. aeruginosa and Gram (+) B. cereus was investigated for the first time. As a result, although there are many different related studies, they are not comparative as in ours. Therefore, our study has progressed in a different direction and it is a first in its field.
An Empirical Analysis of Policy Barriers Related to Trade Costs for Exporters
Authors: Noureen Shabana , Mahmood Zafar 
Published: August 2020

Abstract
The trade costs imposed by numerous policy and non-policy barriers on exporters are still considered an impediment in their export growth rate. Thus, this paper aims to measure over-year trends in total trade costs and trends in trade costs related to policy barriers. Further, to find out which trade cost-policy barriers are high. The research found that total trade costs have a decreasing trend for the rest of the world while developing countries like Pakistan have the lowest rate of a declining trend. Trade cost estimates associated with tariff barriers show a declining trend, whereas trade costs related to non-tariff barriers are on the rise as compared to developed countries. The results further reveal that higher trade costs are among the major factors that have rendered especially developing countries’ exports uncompetitive in world markets.JEL codes: F1, F10, F13, F14
Impact of Variety Type and Irrigation on Technical Efficiency of Potato Farmers: The Case of Terai Region of Nepal
Authors: Adhikari Surya Prasad , Ghimire Yuga Nath , Timsina Krishna Prasad , Gairhe Samaya 
Published: August 2020

Abstract
The national average potato productivity is far below as compared to other neighbouring countries due to several production constraints. Variety and irrigation are the important factors to increase production. The aim of this study is to find the technical efficiency of potato production and to estimate the impact of variety type and irrigation on technical efficiency. A multistage random sampling procedure was employed to select 300 potato farmers from three districts of Nepal. The study used a stochastic frontier production function model to find the production elasticity coefficients of inputs, determinants of efficiency, and technical efficiency of potato farmers. Results showed that variety type and irrigation have a significant positive impact on the technical efficiency of potato production. Nepalese improved varieties adopter farmers were more efficient (73%) than Indian (66%) and local (59%) potato varieties. Likewise, Irrigated potato farming has higher efficiency (71%) than rainfed potato (61%) farming. The mean technical efficiency value of potato farmers was 69 per cent and farmers can increase it with better use of available resources. It is suggested that use of improved potato varieties and irrigation application along with proper amounts of inputs used help to improve technical efficiency of potato farmers.