Multi-scale and Interactive Visual Analysis of Public Bicycle System

( Xiaoying Shi ),( Yang Wang ),( Fanshun Lv ),( Xiaohang Yang ),( Qiming Fang ),( Li Zhang ) 한국인터넷정보학회 2019 KSII Transactions on Internet and Information Syst Vol.13 No.6

Public bicycle system (PBS) is a new emerging and popular mode of public transportation. PBS data can be adopted to analyze human movement patterns. Previous work usually focused on specific scales, and the relationships between different levels of hierarchies are ignored. In this paper, we introduce a multi-scale and interactive visual analytics system to investigate human cycling movement and PBS usage condition. The system supports level-of-detail explorative analysis of spatio-temporal characteristics in PBS. Visual views are designed from global, regional and microcosmic scales. For the regional scale, a bicycle network is constructed to model PBS data, and an flow-based community detection algorithm is applied on the bicycle network to determine station clusters. In contrast to the previous used Louvain algorithm, our method avoids producing super-communities and generates better results. We provide two cases to demonstrate how our system can help analysts explore the overall cycling condition in the city and spatio-temporal aggregation of stations.

Construction of a resequencing-based high-density genetic map for grape using an interspecific population (Vitis amurensis × Vitis vinifera)

Shi Guangli,Sun Dan,Wang Zhenxing,Liu Xiaoying,Guo Jianhui,Zhang Susu,Zhao Ying,Ai Jun 한국원예학회 2022 Horticulture, Environment, and Biotechnology Vol.63 No.4

A high-density genetic map is a prerequisite for marker-assisted selection of crop species. Here, we developed a high-density genetic map of Vitis using 92 F1 progeny derived from the cross between two wine grape cultivars, ‘Shuanghong’ and ‘Italian Riesling’. Whole genome resequencing (WGS) technology was used to generate SNP markers for the map. The map consisted of 1351 recombination bin markers (210,873 SNPs), distributed on 19 linkage groups (LGs), with an average distance of 0.65 cM between adjacent bin markers and a map distance of 860.46 cM. The high levels of uniform coverage and collinearity between the 19 LGs and the grape reference genome indicated that the map is of high quality and can serve as a powerful platform for evaluating grapevines and deciphering the genetic mechanism of important economic and agronomic traits. Our findings will facilitate the process of mapping quantitative trait loci (QTL) that control important horticultural and economic traits of grape.

Efficient starvation therapy with three-pathway blocking in combination with PTT/CDT for TME reversal and tumor apoptosis

Mengchao Ding,Xiaoying Kong,Weiyan Chen,Lei Yan,He Huang,Zunzhou Lv,Peng Jiang,Ali Mu,Congcong Huang,Jinsheng Shi 한국공업화학회 2022 Journal of Industrial and Engineering Chemistry Vol.110 No.-

Single cancer starvation therapy (ST) strategy can’t achieve satisfactory anti-tumor effect, mainly due tothe diversified nutritional sources of tumor cells. Herein, CuS@Axitinib-SiO2@2-Deoxy-D-glucose(2-DG)-CaCO3-RGD nanoparticles (CADCR NPs) were prepared for three-pathway blocking for efficient starvationtherapy as well as reinforced photothermal therapy (PTT) and chemodynamic therapy (CDT). AfterCADCR NPs were targeted to tumor cells, CaCO3 was ruptured in the acidic environment, releasingCa2+ to chelate glutamine and cutting off the glutamine metabolic pathway of the tumor. 2-DG was alsoreleased from mesoporous SiO2 and restrained the glycolytic pathway of tumor cells. In addition, underthe thermal stimulus of near-infrared irradiation, axitinib was released from CuS NPs, which inhibited theproliferation of tumor blood vessels, ultimately inhibiting the aerobic respiratory pathway of tumor cells. Interestingly, CADCR NPs also showed potential to reshape the tumor microenvironment (TME) and promotedthe transformation of macrophages from M2 to M1 type, increasing the expression of CD8+ T cellsin the tumor site. In conclusion, CADCR NPs achieve severe tumor starvation by simultaneously interferingwith three energy metabolic pathways, and further enhance tumor treatment with the aid of PTT,CDT, and TME improvement, which exhibits great potential for clinical cancer therapy.

Experimental study on the consolidation of saturated silty clay subjected to cyclic thermal loading

Bai, Bing,Shi, Xiaoying Techno-Press 2017 Geomechanics & engineering Vol.12 No.4

The objective of this paper is to experimentally study the consolidation of saturated silty clay subjected to repeated heating-cooling cycles using a modified temperature-controlled triaxial apparatus. Focus is placed on the influence of the water content, confining pressure, and magnitudes and number of thermal loading cycles. The experimental results show that the thermally induced pore pressure increases with increasing water content and magnitude of thermal loading in undrained conditions. After isothermal consolidation at an elevated temperature, the pore pressure continues to decrease and gradually falls below zero during undrained cooling, and the maximum negative pore pressure increases as the water content decreases or the magnitude of thermal loading increases. During isothermal consolidation at ambient temperature after one heating-cooling cycle, the pore pressure begins to rise due to water absorption and finally stabilizes at approximately zero. As the number of thermal loading cycles increases, the thermally induced pore pressure shows a degrading trend, which seems to be more apparent under a higher confining pressure. Overall, the specimens tested show an obvious volume reduction at the completion of a series of heating-cooling cycles, indicating a notable irreversible thermal consolidation deformation.

Cloning and expression of a wild eggplant cytochrome P450 gene, StoCYP77A2, involved in plant resistance to Verticillium dahliae

Liu Yang,Ce Shi,Xiaoying Mu,Chao Liu,Ke Shi,Wen-jiao Zhu,Qing Yang 한국식물생명공학회 2015 Plant biotechnology reports Vol.9 No.4

Plant P450s play an important role in plant response to environmental stimuli, especially to pathogen challenge, besides leading to the biosynthesis of secondary metabolites. In this work, a Verticillium dahliae-induced cDNA sequence was cloned from wild eggplant Solanum torvum and designated StoCYP77A2. StoCYP77A2 encodes a 511-amino acid peptide that shows sequence homology to the plant CYP77 family. StoCYP77A2 is expressed in a tissue-specific manner with the highest expression level in stem. The expression level of StoCYP77A2 was increased in wild eggplants which were infected with Verticillium dahlia. We expressed StoCYP77A2 in V. dahliae-sensitive tobacco, and the transgenic tobacco plants were more resistant to V. dahliae infection than the wild type. Protein extraction of transgenic tobacco showed strong antifungal activity against V. dahliae, indicating that StoCYP77A2 may be involved in the synthesis of some antimicrobial compounds. These results suggest that StoCYP77A2 plays a role in plant defense to V. dahliae infection.

Research of 3D image processing of VR technology in medicine based on DNN

Gong ZhaoZhe,Li XiaoDong,Shi XiaoYing,Liu Geng,Chen Bin 한국인터넷정보학회 2022 KSII Transactions on Internet and Information Syst Vol.16 No.5

According to a survey published in an authoritative journal in January 2020, the globalincidence rate of mental illness is 8.3% for men and 10.6% for women, which indicates thatmental illness has become a globally recognized obstacle. Therefore, specific psychotherapy including mental illness will become an important research topic. It is very effective forpatients with special mental diseases, such as mental illness, to reduce their mental reaction byexposure therapy; the system uses the virtual reality system of medical images processed by learningalgorithm to reproduce the effect of virtual reality exposure method of the high scene of transparent ladder. Compared with the old invasive exposure scene, the results show that theimprovement of both conditions has obvious effect, and the effect of human treatment underthe two conditions is not good. There are obvious differences, which show that virtual reality model will gradually replace the on-the-spot feeling. Finally, with more and more researchers have put forward a variety of other virtual reality image processing models, the research of image processing has gradually become more and more interested.

Visual Analysis of Deep Q-network

( Dewen Seng ),( Jiaming Zhang ),( Xiaoying Shi ) 한국인터넷정보학회 2021 KSII Transactions on Internet and Information Syst Vol.15 No.3

In recent years, deep reinforcement learning (DRL) models are enjoying great interest as their success in a variety of challenging tasks. Deep Q-Network (DQN) is a widely used deep reinforcement learning model, which trains an intelligent agent that executes optimal actions while interacting with an environment. This model is well known for its ability to surpass skilled human players across many Atari 2600 games. Although DQN has achieved excellent performance in practice, there lacks a clear understanding of why the model works. In this paper, we present a visual analytics system for understanding deep Q-network in a non-blind matter. Based on the stored data generated from the training and testing process, four coordinated views are designed to expose the internal execution mechanism of DQN from different perspectives. We report the system performance and demonstrate its effectiveness through two case studies. By using our system, users can learn the relationship between states and Q-values, the function of convolutional layers, the strategies learned by DQN and the rationality of decisions made by the agent.

Significantly enhanced antifouling and separation capabilities of PVDF membrane by synergy of semi-interpenetrating polymer and TiO2 gel nanoparticles

Yongdi Ma,Xi Chen,Shuai Wang,Hualin Dong,Xiaoying Zhai,Xin Shi,Jianzu Wang,Rujiang Ma,Wangqing Zhang 한국공업화학회 2022 Journal of Industrial and Engineering Chemistry Vol.108 No.-

PVDF membrane has strong hydrophobicity and low anti-pollution performance, greatly limiting its practicalapplication. These drawbacks have been successfully overcome by designing and then preparing amembrane with a semi-interpenetrating polymer (semi-IPN) of PVDF/poly(acrylic acid) (PAA) as themembrane matrix, TiO2 nanoparticles as functional components and F127 as pore-forming agent. Thesemi-IPN was prepared by copolymerizing acrylic acid with N,N methyl acrylamide in the presence ofPVDF, and the TiO2 gel nanoparticles were in situ formed in the membrane-forming process. The propertiesof the composite membrane were significantly affected by the semi-IPN, F127 and TiO2. By adjustingthe membrane structure with the semi-IPN, F127 and TiO2 nanoparticles, we prepared a composite membranewith a water contact angle of 40, a BSA rejection ratio of 87.5% and a water flux of 802.5 L/m2/h/bar. After a simple UV irradiation, the water flux of this composite membrane rose to 1030 L/m2/h/bar,without any rejection decline. The membrane contaminated by humic acid could recover the water fluxup to above 95.3% of its original value by a single UV irradiation, showing a very good antifouling performance. In addition, the composite membrane also exhibited a very strong pollution resistance and separationperformance for bovine serum albumin and oil-water emulsion. All in all, based on the synergy ofthe semi-IPN and the evenly dispersed TiO2 nanoparticles, the prepared composite membrane exhibitedexcellent comprehensive properties and demonstrated a great potential for various separationapplications.

Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques

Santra, Sampa,Tomaras, Georgia D.,Warrier, Ranjit,Nicely, Nathan I.,Liao, Hua-Xin,Pollara, Justin,Liu, Pinghuang,Alam, S. Munir,Zhang, Ruijun,Cocklin, Sarah L.,Shen, Xiaoying,Duffy, Ryan,Xia, Shi-Mao Public Library of Science 2015 PLoS pathogens Vol.11 No.8

<▼1><P>HIV-1 mucosal transmission begins with virus or virus-infected cells moving through mucus across mucosal epithelium to infect CD4<SUP>+</SUP> T cells. Although broadly neutralizing antibodies (bnAbs) are the type of HIV-1 antibodies that are most likely protective, they are not induced with current vaccine candidates. In contrast, antibodies that do not neutralize primary HIV-1 strains in the TZM-bl infection assay are readily induced by current vaccine candidates and have also been implicated as secondary correlates of decreased HIV-1 risk in the RV144 vaccine efficacy trial. Here, we have studied the capacity of anti-Env monoclonal antibodies (mAbs) against either the immunodominant region of gp41 (7B2 IgG1), the first constant region of gp120 (A32 IgG1), or the third variable loop (V3) of gp120 (CH22 IgG1) to modulate <I>in vivo</I> rectal mucosal transmission of a high-dose simian-human immunodeficiency virus (SHIV-BaL) in rhesus macaques. 7B2 IgG1 or A32 IgG1, each containing mutations to enhance Fc function, was administered passively to rhesus macaques but afforded no protection against productive clinical infection while the positive control antibody CH22 IgG1 prevented infection in 4 of 6 animals. Enumeration of transmitted/founder (T/F) viruses revealed that passive infusion of each of the three antibodies significantly reduced the number of T/F genomes. Thus, some antibodies that bind HIV-1 Env but fail to neutralize virus in traditional neutralization assays may limit the number of T/F viruses involved in transmission without leading to enhancement of viral infection. For one of these mAbs, gp41 mAb 7B2, we provide the first co-crystal structure in complex with a common cyclical loop motif demonstrated to be critical for infection by other retroviruses.</P></▼1><▼2><P><B>Author Summary</B></P><P>Antibodies specifically recognize antigenic sites on pathogens and can mediate multiple antiviral functions through engagement of effector cells via their Fc region. Current HIV-1 vaccine candidates induce polyclonal antibody responses with multiple antiviral functions, but do not induce broadly neutralizing antibodies. An improved understanding of whether certain types of non-neutralizing HIV-1 specific antibodies can individually protect against HIV-1 infection may facilitate vaccine development. Here, we test whether non-neutralizing antibodies with multiple antiviral functions mediated through FcR engagement and recognition of virus particles or virus-infected cells can limit infection, despite lacking classical virus neutralization activity. In a passive antibody infusion-rhesus macaque challenge model, we tested the ability of non-neutralizing monoclonal antibodies to limit virus acquisition. We demonstrate that two different types of non-neutralizing antibodies, one that recognizes both virus particles and infected cells (7B2) and another that recognizes only infected cells (A32) were capable of decreasing the number of transmitted founder viruses. Further, we provide the structure of 7B2 in complex with the gp41 cyclical loop motif, a motif critical for entry. These findings provide insights into the role that antibodies with antiviral properties, including virion capture and FcR mediated effector function, may play in protecting against HIV-1 acquisition.</P></▼2>