Bioinformatic and integrated analysis identifies an lncRNA–miRNA–mRNA interaction mechanism in gastric adenocarcinoma

Yong Liao,Wen Cao,Kunpeng Zhang,Yang Zhou,Xin Xu,Xiaoling Zhao,Xu Yang,Jitao Wang,Shouwen Zhao,Shiyu Zhang,Longfei Yang,Dengxiang Liu,Yanpeng Tian,Weizhong Wu 한국유전학회 2021 Genes & Genomics Vol.43 No.6

Background lncRNAs–miRNAs–mRNAs networks play an important role in Gastric adenocarcinoma (GA). Identifcation of these networks provide new insight into the role of these RNAs in gastric cancer. Objectives Biological information databases were screened to characterize and examine the regulatory networks and to further investigate the potential prognostic relationship this regulation has in GA. Methods By mining The Cancer Genome Atlas (TCGA) database, we gathered information on GA-related lncRNAs, miRNAs, and mRNAs. We identifed diferentially expressed (DE) lncRNAs, miRNAs, and mRNAs using R software. The lncRNA–miRNA–mRNA interaction network was constructed and subsequent survival examination was performed. Representative genes were selected out using The Biological Networks Gene Ontology plug-in tool on Cytoscape. Additional analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms were used to screen representative genes for functional enrichment. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) were used to identify the expression of fve candidate diferential expressed RNAs. Results Information of samples from 375 cases of gastric cancer and 32 healthy cases (normal tissues) were downloaded from the TCGA database. A total of 1632 DE-mRNAs, 1008 DE-lncRNAs and 104 DE-miRNAs were identifed and screened. Among them, 65 DE-lncRNAs, 10 DE-miRNAs, and 10 DE-mRNAs form lncRNAs–miRNAs–mRNAs regulatory network. Additionally, 10 lncRNAs and 2 mRNAs were associated with the prognosis of GA. Multivariable COX analysis revealed that AC018781.1 and VCAN-AS1 were independent risk factors for GA. GO functional enrichment analysis found DE-mRNA was signifcantly enriched TERM (P<0.05). The KEGG signal regulatory network analysis found 11 signifcantly enrichment networks, the most prevailing was for the AGE-RAGE signaling pathway associated with Diabetic complications. Results of RT-qPCR was consistent with the in silico results. Conclusions The results of the present study represent a view of GA from a analysis of lncRNA, miRNA and mRNA. The network of lncRNA–miRNA–mRNA interactions revealed here may potentially further experimental studies and may help biomarker development for GA.

Transt: Fake GPS detection system based on Transformer

LongFei Li,Hyungjeong Yang(양형정),Kyungbaek Kim(김경백) Korean Institute of Information Scientists and Eng 2024 한국정보과학회 학술발표논문집 Vol.2024 No.6

Alterations of Amino Acid Level in Depressed Rat Brain

Yang, Pei,Li, Xuechun,Ni, Jian,Tian, Jingchen,Jing, Fu,Qu, Changhai,Lin, Longfei,Zhang, Hui The Korean Society of Pharmacology 2014 The Korean Journal of Physiology & Pharmacology Vol.18 No.5

Amino-acid neurotransmitter system dysfunction plays a major role in the pathophysiology of depression. Several studies have demonstrated the potential of amino acids as a source of neuro-specific biomarkers could be used in future diagnosis of depression. Only partial amino acids such as glycine and asparagine were determined from certain parts of rats' brain included hippocampi and cerebral cortex in previous studies. However, according to systematic biology, amino acids in different area of brain are interacted and interrelated. Hence, the determination of 34 amino acids through entire rats' brain was conducted in this study in order to demonstrate more possibilities for biomarkers of depression by discovering other potential amino acids in more areas of rats' brain. As a result, 4 amino acids (L-aspartic acid, L-glutamine, taurine and ${\gamma}$-amino-n-butyric acid) among 34 were typically identified as potentially primary biomarkers of depression by data statistics. Meanwhile, an antidepressant called Fluoxetine was employed to verify other potential amino acids which were not identified by data statistics. Eventually, we found L-${\alpha}$-amino-adipic acid could also become a new potentially secondary biomarker of depression after drug validation. In conclusion, we suggested that L-aspartic acid, L-glutamine, taurine, ${\gamma}$-amino-n-butyric acid and L-${\alpha}$-amino-adipic acid might become potential biomarkers for future diagnosis of depression and development of antidepressant.

Mechanism of sulfamethoxazole adsorption on wastewater-sludge-based biochar: Sludge type and modification improvement

Yongkui Yang,Yifeng Ling,Longfei Wang,Peizhe Sun,Lin Zhao,Hongyang Wang 한국화학공학회 2023 Korean Journal of Chemical Engineering Vol.40 No.5

With rapid industrialization and population growth, sewage sludge generation has increased worldwide, and it needs to be treated properly. The pyrolysis of sewage sludge into biochar provides sustainable benefits for concomitant pollutant adsorption and waste treatment. Sulfamethoxazole (SMX) antibiotics are highly prevalent in waste-water owing to their widespread utilization and low metabolic rate and removal efficiency during conventional waste-water treatment. Biochar is known to effectively remove pollutants from wastewater. However, the adsorption capacity and mechanism of SMX adsorption onto sludge-based biochar are currently unclear. Therefore, the adsorption behavior of SMX on sludge-based biochar from three sources (raw sludge, compost sludge, and digested sludge) and ZnCl2-modified biochar was investigated. Among the unmodified biochars, raw sludge-based biochar exhibited the highest adsorption capacity, followed by compost sludge-based and digested sludge-based biochar. The pore-forming effect of ZnCl2 application significantly increased the biochar specific surface area, which increased the equilibrium adsorption of SMX from 6.1 mg/g to 49.3 mg/g. The adsorption mechanisms involved electrostatic interactions, pore filling, hydrophobic interactions, hydrogen bonding, and π-π interactions. The findings of this study demonstrate the development of sewage sludge biochar and its effectiveness for the treatment of antibiotics containing wastewater.

Alterations of Amino Acid Level in Depressed Rat Brain

Pei Yang,Xuechun Li,Jian Ni,Jingchen Tian,Fu Jing,Changhai Qu,Longfei Lin,Hui Zhang 대한약리학회 2014 The Korean Journal of Physiology & Pharmacology Vol.18 No.5

Amino-acid neurotransmitter system dysfunction plays a major role in the pathophysiology ofdepression. Several studies have demonstrated the potential of amino acids as a source of neuro-specificbiomarkers could be used in future diagnosis of depression. Only partial amino acids such as glycineand asparagine were determined from certain parts of rats’ brain included hippocampi and cerebralcortex in previous studies. However, according to systematic biology, amino acids in different areaof brain are interacted and interrelated. Hence, the determination of 34 amino acids through entirerats’ brain was conducted in this study in order to demonstrate more possibilities for biomarkers ofdepression by discovering other potential amino acids in more areas of rats’ brain. As a result, 4 aminoacids (L-aspartic acid, L-glutamine, taurine and γ -amino-n-butyric acid) among 34 were typicallyidentified as potentially primary biomarkers of depression by data statistics. Meanwhile, anantidepressant called Fluoxetine was employed to verify other potential amino acids which were notidentified by data statistics. Eventually, we found L-α -amino-adipic acid could also become a newpotentially secondary biomarker of depression after drug validation. In conclusion, we suggested thatL-aspartic acid, L-glutamine, taurine, γ-amino-n-butyric acid and L-α-amino-adipic acid might becomepotential biomarkers for future diagnosis of depression and development of antidepressant.

Experimental investigation of flow characteristics around four square-cylinder arrays at subcritical Reynolds numbers

Mingyue Liu,Longfei Xiao,Lijun Yang 대한조선학회 2015 International Journal of Naval Architecture and Oc Vol.7 No.5

The Deep Draft Semi-Submersible (DDS) concepts are known for their favourable vertical motion performance. However, the DDS may experience critical Vortex-Induced Motion (VIM) stemming from the fluctuating forces on the columns. In order to investigate the current-induced excitation forces of VIM, an experimental study of flow characteristics around four square-section cylinders in a square configuration is presented. A number of column spacing ratios and array attack angles were considered to investigate the parametric influences. The results comprise flow patterns, drag and lift forces, as well as Strouhal numbers. It is shown that both the drag and lift forces acting on the cylinders are slightly different between the various L/D values, and the fluctuating forces peak at L/D = 4.14. The lift force of downstream cylinders reaches its maximum at around α = 15°. Furthermore, the flow around circularsection- cylinder arrays is also discussed in comparison with that of square cylinders.

Frequency analysis of wave run-up on vertical cylinder in transitional water depth

Deng, Yanfei,Yang, Jianmin,Xiao, Longfei,Shen, Yugao Techno-Press 2014 Ocean systems engineering Vol.4 No.3

Wave run-up is an important issue in offshore engineering, which is tightly related to the loads on the marine structures. In this study, a series of physical experiments have been performed to investigate the wave run-up around a vertical cylinder in transitional water depth. The wave run-ups of regular waves, irregular waves and focused waves have been presented and the characteristics in frequency domain have been investigated with the FFT and wavelet transform methods. This study focuses on the nonlinear features of the wave run-up and the interaction between the wave run-up and the cylinder. The results show that the nonlinear interaction between the waves and the structures might result wave run-up components of higher frequencies. The wave run-ups of the moderate irregular waves exhibit 2nd order nonlinear characteristics. For the focused waves, the incident waves are of strong nonlinearity and the wavelet coherence analysis reveals that the wave run-up at focal moment contains combined contributions from almost all the frequency components of the focused wave sequence and the contributions of frequency components up to 4th order harmonic levels are recommended to be included.

Experimental investigation of flow characteristics around four square-cylinder arrays at subcritical Reynolds numbers

Liu, Mingyue,Xiao, Longfei,Yang, Lijun The Society of Naval Architects of Korea 2015 International Journal of Naval Architecture and Oc Vol.7 No.5

The Deep Draft Semi-Submersible (DDS) concepts are known for their favourable vertical motion performance. However, the DDS may experience critical Vortex-Induced Motion (VIM) stemming from the fluctuating forces on the columns. In order to investigate the current-induced excitation forces of VIM, an experimental study of flow characteristics around four square-section cylinders in a square configuration is presented. A number of column spacing ratios and array attack angles were considered to investigate the parametric influences. The results comprise flow patterns, drag and lift forces, as well as Strouhal numbers. It is shown that both the drag and lift forces acting on the cylinders are slightly different between the various L/D values, and the fluctuating forces peak at L/D = 4.14. The lift force of downstream cylinders reaches its maximum at around ${\alpha}=15^{\circ}$. Furthermore, the flow around circular-section-cylinder arrays is also discussed in comparison with that of square cylinders.

Optimizations of Canny Edge Detection in Ghost Imaging

Guohua Wu,Dongyue Yang,Chen Chang,Longfei Yin,Bin Luo,Hong Guo 한국물리학회 2019 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.75 No.3

An optimization of the Canny edge detector’s application in ghost imaging is presented. Based on the pseudo-thermal light ghost imaging scheme with a binary object, a thin and accurate edge map can be extracted by using a Gaussian-filtering-optimized Canny edge detector. The scale of the Gaussian filter in Canny edge detection algorithm is the dominate factor in the performance of the edge detector, and can be evaluated by the bit error rate of reconstructed binary image based on the edge map. Simulation results indicate the optimal window size of Gaussian filter for ghost imaging is proportional to the full width at half maximum of the self-correlation function in the idler arm samples without any priori knowledge of the object. Experimental results show that, with an appropriate Gaussian filter, the reconstructed binary image can approach the original binary object with the minimum bit error rate, which means the edge detection result is optimal.

Displacement Interval Prediction Method for Step-like Landslides Considering Deformation State Dynamic Switching

( Linwei Li ),( Yiping Wu ),( Fasheng Miao ),( Yang Xue ),( Longfei Zhang ),( Kang Liao ),( Weifu Teng ),( Honglian Shi ) 대한지질공학회 2019 대한지질공학회 학술발표회논문집 Vol.2019 No.2

To overcome the drawbacks of previous displacement prediction models for step-like landslides, such as poor performance in predicting mutational displacement and unclear reliability of prediction results, this paper proposes a new hybrid method of landslide displacement prediction intervals. Firstly, the combination of SOM network and K-means clustering is implemented to divide the deformation states of step-like landslides into steady state and mutational state. Secondly, on the basis of expanding the mutational state samples through the comprehensive application of the engineering geology analogy method and the adaptive synthetic sampling algorithm, the random forest algorithm is used to establish an ensemble classifier for recognizing the landslide deformation states automatically. Finally, based on the Bootstrap-KELM-BPNN model, an interval prediction framework considering the dynamic switching of landslide deformation states is constructed to realize the dynamic prediction of landslide displacement. Taking Baishuihe landslide, a typical step-like landslide in the Three Gorges Reservoir Area, as an example, the dataset of XD01 monitoring point from June 2006 to December 2016 are explored to verify the effectiveness, accuracy and reliability of the proposed method.