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Supervised Capacity Preserving Mapping: A Clustering Guided Visualization Method for scRNAseq data [article]

Zhiqian Zhai, Yu Leo Lei, Rongrong Wang, Yuying Xie
2021 bioRxiv   pre-print
The rapid development of scRNA-seq technologies enables us to explore the transcriptome at the cell level in a large scale. Recently, various computational methods have been developed to analyze the scRNAseq data such as clustering and visualization. However, current visualization methods including t-SNE and UMAP are challenged by the limited accuracy of rendering the geometic relationship of populations with distinct functional states. Most visualization methods are unsupervised, leaving out
more » ... formation from the clustering results or given labels. This leads to the inaccurate depiction of the distances between the bona fide functional states. In particular, UMAP and t-SNE are not optimal to preserve the global geometric structure. They may result in a contradiction that clusters with near distance in the embedded dimensions are in fact further away in the original dimensions. Besides, UMAP and t-SNE cannot track the variance of clusters. Through the embedding of t-SNE and UMAP, the variance of a cluster is not only associated with the true variance but also is proportional to the sample size. We present supCPM, a robust supervised visualization method, which separates different clusters, preserves global structure, and tracks the cluster variance. Compared with six visualization methods using synthetic and real datasets, supCPM shows improved performance than other methods in preserving the global geometric structure and data variance. Overall, supCPM provides an enhanced visualization pipeline to assist the interpretation of functional transition and accurately depict population segregation.
doi:10.1101/2021.06.18.448900 fatcat:2x4huacxrjhx5mypqkyi2pomfm

Main Quality Traits Analysis and Evaluation of Potato Germplasms

Ruixia Xie, Xiaochuan Zhang, Linke Wu, Zhiqian Guo, Guohui Zhang, Bangqiang Yu
2021 Molecular Plant Breeding  
Yu (2018) evaluated and analyzed the contents of reducing sugar, soluble sugar and starch as well as the color difference and texture traits of tuber and whole powder from 119 germplasm materials with  ...  varieties such as whole powder, fried slices, fried strips or cooking can be selected, mainly based on low reducing sugar and high dry matter, while referring to other agronomic and quality traits (Yu  ... 
doi:10.5376/mpb.2021.12.0028 fatcat:4kjnpp754vdb3ma2ylsusnl2tq

Impact of Public Education and Regional Economic Growth in China: A Shadow-Price Perspective

Zhiqian Yu, Ning Zhu, Tomas Baležentis
2017 Sustainability  
The aforementioned result has been termed "recession in the middle region" by China's educational authorities and is consistent with Yu [22] .  ...  Author Contributions: Zhiqian Yu analyzed the data and completed the draft; Ning Zhu and Tomas Baležentis designed the methodology.  ... 
doi:10.3390/su9081333 fatcat:p2q2sz46frfv7nc34xavtzdtqa

Accelerated Testing with Multiple Failure Modes under Several Temperature Conditions

Zongyue Yu, Zhiqian Ren, Junyong Tao, Xun Chen
2014 Mathematical Problems in Engineering  
A complicated device may have multiple failure modes, and some of the failure modes are sensitive to low temperatures. To assess the reliability of a product with multiple failure modes, this paper presents an accelerated testing in which both of the high temperatures and the low temperatures are applied. Firstly, an acceleration model based on the Arrhenius model but accounting for the influence of both the high temperatures and low temperatures is proposed. Accordingly, an accelerated testing
more » ... plan including both the high temperatures and low temperatures is designed, and a statistical analysis method is developed. The reliability function of the product with multiple failure modes under variable working conditions is given by the proposed statistical analysis method. Finally, a numerical example is studied to illustrate the proposed accelerated testing. The results show that the proposed accelerated testing is rather efficient.
doi:10.1155/2014/839042 fatcat:f6z2jm6frfd4zksig4iot2ifs4

Final Energy Consumption Trends and Drivers in Czech Republic and Latvia

Zhiqian Yu, Dalia Streimikiene, Tomas Balezentis, Rimantas Dapkus, Radislav Jovovic, Veselin Draskovic
2017 Amfiteatru Economic  
This paper analyses the trends of final energy consumption in Latvia and Czech Republic. Analysis of final energy consumption during 2000-2013 period indicated the main driving forces of final energy consumption during and after world financial crisis of 2008. The paper aimed to evaluate the impact of economic activity and other factors on final energy consumption. The decomposition of the final energy consumption is assessed by analyzing effect of different drivers by the main end-users sector
more » ... (industry, transport, households, agriculture, services), activity, demography, lifestyles, structural effects, energy savings etc. The results show that the reduction in final energy consumption in most EU members states before and after year 2008 can be related to the decline in energy intensities within endusers sectors. At the same time, the increase in final energy intensity after the year 2008 is attributed to expansion of energy demand sectors. Comparison of final energy consumption trends and drivers in Latvia and Czech Republic indicated that Czech Republic implemented more policies and measures in industry and tertiary sector and this provided for final energy consumption decreased and huge energy savings in these sectors.
doaj:2eb70267ecbf4c65bdcabb7b827ead8e fatcat:zbtl3wrvhrbfljwcj4dfxasay4

Linking Activation of Microglia and Peripheral Monocytic Cells to the Pathophysiology of Psychiatric Disorders

Yuta Takahashi, Zhiqian Yu, Mai Sakai, Hiroaki Tomita
2016 Frontiers in Cellular Neuroscience  
Yu et al. (2015) investigated the effects of lithium on two cell types: monocyte-derived dendritic cells treated with lithium and microglia separated from lithiumtreated mice.  ...  Copyright © 2016 Takahashi, Yu, Sakai and Tomita. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).  ... 
doi:10.3389/fncel.2016.00144 pmid:27375431 pmcid:PMC4891983 fatcat:c3c6fhstkrby5by7n7yh3omdxy

Enhanced IMP3 Expression Activates NF-кB Pathway and Promotes Renal Cell Carcinoma Progression

Xuelian Pei, Muhan Li, Jun Zhan, Yu Yu, Xiaofan Wei, Lizhao Guan, Hakan Aydin, Paul Elson, Ming Zhou, Huiying He, Hongquan Zhang, Zhiqian Zhang
2015 PLoS ONE  
Insulin-like growth factor 2 mRNA binding protein 3 (IMP3) is expressed in metastatic and a subset of primary renal cell carcinoma (RCC). However, the role of IMP3 in RCC progression was poorly understood. We aim to uncover the mechanism of IMP3 in regulating clear cell RCC (CCRCC) progression and validate the prognostic significance of IMP3 in localized CCRCC. Methods Caki-1 cells stably overexpressing IMP3 and Achn cells with knockdown of IMP3 were analyzed for cell migration and invasion by
more » ... ranswell assay. RNA-seq was used to profile gene expression in IMP3-expressing Caki-1 cells. A cohort of 469 localized CCRCC patients were examined for IMP3 expression by immunohistochemistry using tumor tissue array. Results IMP3 promoted Caki-1 cell migration and invasion, whereas knockdown of IMP3 by RNAi inhibited Achn cell migration and invasion. Enhanced IMP3 expression activated NF-кB pathway and through which, it functioned in promoting the RCC cell migration. IMP3 expression in localized CCRCC was found to be associated with higher nuclear grade, higher T stage, necrosis and sarcomatoid differentiation (p< 0.001). Enhanced IMP3 expression was correlated with shorter recurrence-free and overall survivals. Multivariable analysis validated IMP3 as an independent prognostic factor for localized CCRCC patients.
doi:10.1371/journal.pone.0124338 pmid:25919292 pmcid:PMC4412497 fatcat:x4rg674z6nfwhmt7nh35ctyce4

Substation area joint defensive protection strategy based on distributed cooperative all-in-one device

Fanrong WEI, Mengqi YU, Zhiqian BO, Kun YU, Jingguang HUANG
2016 Journal of Modern Power Systems and Clean Energy  
Integration of primary and secondary devices are impelled by the development of smart grid. Based on the ideology of primary and secondary device integration, an all-in-one device and its concept, configuration and function are proposed. Then, an all-in-one device framework of distributed substation area protection is proposed. Point-topoint model and virtual local area network (VLAN) based network-to-network model are adopted in this framework. The dual redundancy on hardware and software
more » ... is realized by modularization and protection information mirroring storage/overwriting. Considering the fact that the sampling, logic judgment and information sharing processes of protection may fail in atrocious conditions, a distributed cooperative all-in-one device cluster based substation area joint defensive protection strategy is proposed. The adaptability of sectional component failure in secondary system is strengthened by reusing module function, setting value mirroring storage and dynamic load balancing computing ability to constitute strong intelligent outdoor secondary device integrated network. Finally, the simulation examples based on EPOCHS which consider various system failure conditions are presented to verify the validity and rationality of the proposed architecture and strategy.
doi:10.1007/s40565-016-0207-6 fatcat:ljwc4a7e65hgxjnuhnxrdfi2wi


2017 Journal of Business Economics and Management  
Acknowledgement Zhiqian Yu gratefully acknowledges financial support from the Youth Talents Project of Guangdong Province (2015WQNCX122) and the Youth Academic Team Project at Guangzhou University (201602XSTD  ...  Zhiqian YU is an Assistant Professor of Economics at School of Economics and Statistics, Guangzhou University.  ... 
doi:10.3846/16111699.2017.1322633 fatcat:t4vhllb7hjhfneaw6kjfrkgrni

Microglial Gene Expression Alterations in the Brains of Patients with Psychiatric Disorders

Mai Sakai, Yuta Takahashi, Zhiqian Yu, Hiroaki Tomita
2016 Advances in Neuroimmune Biology  
As recent studies have shown that microglia play a key role in inflammation and immunological challenges as well as have broader roles in synaptic modulation in the brain, studies on psychiatric disorders have increasingly focused on microglia. Microglial abnormalities have consistently been observed in psychiatric postmortem brain studies, including altered microglial activation and changes in the protein and mRNA expression levels of microglial marker molecules, such as major
more » ... y complex, class II, DR (HLA-DR), complement receptor type 3 (CD11b), ionized calcium binding adaptor molecule 1 (IBA-1), macrosialin (CD68) and glucose transporter type 5 (GLUT5). Microglial abnormalities have also been observed in positron emission tomography (PET) studies. Recent advances in omics-based microglial gene expression profiling of psychiatric brains may elucidate microglial involvement in the pathogeneses of psychiatric disorders. In the present paper, we review the current status of research on expression profiling of microglia-relevant molecules in psychiatric postmortem and imaging studies and we discuss future research directions.
doi:10.3233/nib-160110 fatcat:ufdfxer5vbgg7lfvgbhkco6tre

The essential role of PRAK in tumor metastasis and its therapeutic potential

Yuqing Wang, Wei Wang, Haoming Wu, Yu Zhou, Xiaodan Qin, Yan Wang, Jia Wu, Xiu-Yuan Sun, Yan Yang, Hui Xu, Xiaoping Qian, Xuewen Pang (+4 others)
2021 Nature Communications  
AbstractMetastasis is the leading cause of cancer-related death. Despite the recent advancements in cancer treatment, there is currently no approved therapy for metastasis. The present study reveals a potent and selective activity of PRAK in the regulation of tumor metastasis. While showing no apparent effect on the growth of primary breast cancers or subcutaneously inoculated tumor lines, Prak deficiency abrogates lung metastases in PyMT mice or mice receiving intravenous injection of tumor
more » ... ls. Consistently, PRAK expression is closely associated with metastatic risk in human cancers. Further analysis indicates that loss of function of PRAK leads to a pronounced inhibition of HIF-1α protein synthesis, possibly due to reduced mTORC1 activities. Notably, pharmacological inactivation of PRAK with a clinically relevant inhibitor recapitulates the anti-metastatic effect of Prak depletion, highlighting the therapeutic potential of targeting PRAK in the control of metastasis.
doi:10.1038/s41467-021-21993-9 pmid:33741957 fatcat:x57enxcivnepdpqhfb7yt4m2zq

Plasma-Activated Saline Promotes Antibiotic Treatment of Systemic Methicillin-Resistant Staphylococcus aureus Infection

Lu Yang, Gulimire Niyazi, Yu Qi, Zhiqian Yao, Lingling Huang, Zifeng Wang, Li Guo, Dingxin Liu
2021 Antibiotics  
Systemic infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are life-threatening due to their strong multidrug resistance, especially since the biofilms formed by MRSA are more difficult to inactivate by antibiotics, causing long term recurrence of infection. Plasma-activated saline (PAS), a derived form of cold atmospheric-pressure plasma, can effectively inactivate bacteria and cancer cells and has been applied to sterilization and cancer treatment. Previous studies have
more » ... emonstrated that the pretreatment of MRSA with PAS could promote the action of antibiotics. Here, the PAS was used as an antibiotic adjuvant to promote the inactivation of MRSA biofilms by rifampicin and vancomycin, and the combined treatment reduced approximately 6.0-log10 MRSA cells in biofilms. The plasma-activated saline and rifampicin synergistically and effectively reduced the systemic infection in the murine model. The histochemical analysis and the blood hematological and biochemical test demonstrated that the combined treatment with plasma-activated saline and rifampicin improved the blood hematological and biochemical parameters of infected mice by reducing the infection. Therefore, PAS based on plasma technology represents a new strategy for the treatment of infectious disease caused by multidrug-resistant bacteria and alleviating antibiotic resistance.
doi:10.3390/antibiotics10081018 fatcat:ez6xc5svwrgq7b45uknibngio4

How does corporate social responsibility impact banking efficiency: a case in China

Ning Zhu, Jelena Stjepcevic, Tomas Baležentis, Zhiqian Yu, Bing Wang
2017 E & M Ekonomie a Management  
Abstract HOW DOES CORPORATE SOCIAL RESPONSIBILITY IMPACT BANKING EFFICIENCY: A CASE IN CHINA Ning Zhu, Jelena Stjepcevic, Tomas Baležentis, Zhiqian Yu, Bing Wang Much of the earlier literature was  ... 
doi:10.15240/tul/001/2017-4-006 fatcat:zqadhijw4ffqfodcbmxfskqrcy

Cardamonin Inhibits Metastasis of Lewis Lung Carcinoma Cells by Decreasing mTOR Activity

Pei-Guang Niu, Yu-Xuan Zhang, Dao-Hua Shi, Ying Liu, Yao-Yao Chen, Jie Deng, Zhiqian Zhang
2015 PLoS ONE  
The mammalian target of rapamycin (mTOR) regulates the motility and invasion of cancer cells. Cardamonin is a chalcone that exhibits anti-tumor activity. The previous study had proved that the anti-tumor effect of cardamonin was associated with mTOR inhibition. In the present study, the anti-metastatic effect of cardamonin and its underlying molecule mechanisms were investigated on the highly metastatic Lewis lung carcinoma (LLC) cells. The proliferation, invasion and migration of LLC cells
more » ... measured by MTT, transwell and wound healing assays, respectively. The expression and activation of mTOR-and adhesion-related proteins were assessed by Western blotting. The in vivo effect of cardamonin on the metastasis of the LLC cells was investigated by a mouse model. Treated with cardamonin, the proliferation, invasion and migration of LLC cells were significantly inhibited. The expression of Snail was decreased by cardamonin, while that of E-cadherin was increased. In addition, cardamonin inhibited the activation of mTOR and its downstream target ribosomal S6 kinase 1 (S6K1). Furthermore, the tumor growth and its lung metastasis were inhibited by cardamonin in C57BL/6 mice. It indicated that cardamonin inhibited the invasion and metastasis of LLC cells through inhibiting mTOR. The metastasis inhibitory effect of cardamonin was correlated with down-regulation of Snail and up-regulation of E-cadherin.
doi:10.1371/journal.pone.0127778 pmid:25996501 pmcid:PMC4440626 fatcat:67omxmybv5b7beza2yikwkotqa

Experience of therapeutic plasma exchange in rheumatic diseases: Albumin may be a suitable substitute for plasma

Zhiqian Bai, Yu Chen, Lingli Dong
2021 Archives of Rheumatology  
In this study, we aimed to assess the value of therapeutic plasma exchange (TPE) in the treatment of rheumatic diseases and compare the safety of different replacement fluids used in TPE. A total of 727 TPE procedures in 285 patients (57 males, 228 females; mean age: 39.7±15.4 years; range, 13 to 79 years) with rheumatic diseases between January 2011 and February 2019 were retrospectively analyzed. Data including demographic and clinical characteristics of the patients were recorded. Treatment
more » ... esponse to TPE and adverse events were evaluated in all patients. Indications for TPE included 13 different disorders, with the majority being systemic lupus erythematosus (up to 50%). The mean number of TPE sessions was 2.55±1.00 per patient and the mean exchange plasma volume was 2,270±256 mL per session. Combined plasma and albumin was the most frequently used replacement fluid (69.5%), followed by albumin and plasma in 20.5% and 10.0% of episodes, respectively. Up to 73.7% (210/285) patients achieved clinical improvement after TPE treatment. Adverse events occurred in 15.1% (110/727) of all the procedures, and allergic reaction (34.5%) was the most common event. The overall incidence rate of complication was similar among the three types of replacement fluids (p=0.214). Based on our study results, TPE is an invasive, but safe, useful and, sometimes, essential tool with an acceptable risk/benefit ratio for most rheumatic diseases. Albumin can be used as a feasible substitute for plasma in case of shortage of blood resources.
doi:10.46497/archrheumatol.2021.8447 pmid:34870172 pmcid:PMC8612486 fatcat:lfoxuzzkmzbevad7lscfuoru3e
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