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| 1 | Towards better analysis of machine learning models:A visual analytics perspective显示文摘Interactive model analysis,the process of understanding,diagnosing,and refining a machine learning model with the help of interactive visualization,is very important for users to efficiently solve real-world artificial intelligence and data mining problems.Dramatic advances in big data analytics have led to a wide variety of interactive model analysis tasks.In this paper,we present a comprehensive analysis and interpretation of this rapidly developing area.Specifically,we classify the relevant work into three categories:understanding,diagnosis,and refinement.Each category is exemplified by recent influential work.Possible future research opportunities are also explored and discussed. | Shixia Liu Xiting Wang Mengchen Liu Jun Zhu | 2017 | Visual Informatics2017，1，1： | 9 |
| 2 | Artemisinin Biosynthesis in Non-glandular Trichome Cells of Artemisia annua显示文摘Artemisinin-based combination therapy(ACT)forms the first line of malaria treatment.However,the yield fluctuation of artemisinin has remained an unsolved problem in meeting the global demand for ACT.This problem is mainly caused by the glandular trichome(GT)-specific biosynthesis of artemisinin in all currently used Artemisia annua cultivars.Here,we report that non-GT cells of self-pollinated inbred A.annua plants can express the artemisinin biosynthetic pathway.Gene expression analysis demonstrated the transcription of six known pathway genes in GT-free leaves and calli of inbred A.annua plants.LC-qTOF-MS/MS analysis showed that these two types of GT-free materials produce artemisinin,artemisinic acid,and arteannuin B.Detailed IR-MALDESI image profiling revealed that these three metabolites and dihydroartemisinin are localized in non-GT cells of leaves of inbred A.annua plants.Moreover,we employed all the above approaches to examine artemisinin biosynthesis in the reported XL annua glandless(gl)mutant.The resulting data demonstrated that leaves of regenerated gl plantlets biosynthesize artemisinin.Codectively,these findings not only add new knowledge leading to a revision of the current dogma of artemisinin biosynthesis inannua but also may expedite innovation of novel metabolic engineering approaches for high and stable production of artemisinin in the future. | Rika Judd M.Caleb Bagley Mingzhuo Li Yue Zhu Caiyan Lei Seyit Yuzuak Mans Ekelof Gaobin Pu Xiting Zhao David C.Muddiman De-Yu Xie | 2019 | Molecular Plant2019，12，5： | 5 |
| 3 | The integration of transcriptomic and transgenic analyses reveals the involvement of the SA response pathway in the defense of chrysanthemum against the necrotrophic fungus Alternaria sp.显示文摘Chrysanthemum morifolium cv.‘Huaihuang’has ornamental,edible,medicinal,and tea product uses.However,its field growth,yield,and quality are negatively affected by black spot disease caused by Alternaria sp.(Strain:HQJH10092301;GenBank accession number:KF688111).In this study,we transcriptionally and transgenically characterized a new cultivar,‘Huaiju 2#’(Henan Traditional Chinese Medicine Plant Cultivar identification number:2016002),which was bred from‘Huaihuang’and shows resistance to Alternaria sp.Numerous‘Huaiju 2#’plants were inoculated with Alternaria sp.for three or five days.Metabolic analysis showed increases in both salicylic acid(SA)and jasmonic acid(JA)in infected plants compared to the control.Protein activity analysis also revealed a significant increase in defense enzyme activities in infected plants.RNA-Seq of plants infected for 3 or 5 days produced a total of 58.6 GB of clean reads.Among these reads,16,550 and 13,559 differentially expressed genes(DEGs)were identified in Cm_3 dpi(sample from 3 days post-inoculation labeled as Cm_3 dpi)and Cm_5 dpi(sample from 5 days post-inoculation labeled as Cm_5 dpi),respectively,compared with their controls(Cm_0 d:a mixture samples from 0 d(before inoculation)and those treated with sterile distilled water at 3 dpi and 5 dpi).Gene annotation and cluster analysis of the DEGs revealed a variety of defense responses to Alternaria sp.infection,which were characterized by increases in resistance(R)proteins and the reactive oxygen species(ROS),Ca2+,mitogen-activated protein kinase(MAPK),and JA signaling pathways.In particular,SA signaling was highly responsive to Alternaria sp.infection.The qPCR analysis of 12 DEG candidates supported their differential expression characterized by using the RNA-Seq data.One candidate was CmNPR1(nonexpressor of pathogenesis-related gene 1),an important positive regulator of SA in systemic acquired resistance(SAR).Overexpression of CmNPR1 in‘Huaiju 2#’increased the resistance of transgenic plants to black spot.These findings indicate that the SA response pathway is likely involved in the defense of‘Huaiju 2#’against Alternaria sp.pathogens. | Xiting Zhao Lingyu Song Liwei Jiang Yuting Zhu Qinghui Gao Dandan Wang Jing Xie Meng Lv Ping Liu Mingjun Li | 2020 | Horticulture Research2020，7，1： | 3 |
| 4 | Engineering the viscoelasticity of gelatin methacryloyl(GelMA)hydrogels via small“dynamic bridges”to regulate BMSC behaviors for osteochondral regeneration显示文摘The dynamic extracellular matrix(ECM)constantly affects the behaviors of cells.To mimic the dynamics of ECM with controllable stiffness and energy dissipation,this study proposes a strategy in which a small molecule,3,4-dihydroxybenzaldehyde(DB),was used as fast'dynamic bridges'to construct viscoelastic gelatin methacryloyl(GelMA)-based hydrogels.The storage modulus and loss modulus of hydrogels were independently adjusted by the covalent crosslinking density and by the number of dynamic bonds.The hydrogels exhibited self-healing property,injectability,excellent adhesion and mechanical properties.Moreover,the in vitro results revealed that the viscous dissipation of hydrogels favored the spreading,proliferation,osteogenesis and chondrogenesis of bone marrow mesenchymal stem cells(BMSCs),but suppressed their adipogenesis.RNA-sequencing and immunofluorescence suggested that the viscous dissipation of hydrogels activated Yes-associated protein(YAP)by stabilizing integrinβ1,and further promoted nuclear translocation of smad2/3 andβ-catenin to enhance chondrogenesis and osteogenesis.As a result,the viscoelastic GelMA hydrogels with highest loss modulus showed best effect in cartilage and subchondral bone repair.Taken together,findings from this study reveal an effective strategy to fabricate viscoelastic hydrogels for modulating the interactions between cells and dynamic ECM to promote tissue regeneration. | Changjiang Liu Qifan Yu Zhangqin Yuan Qianping Guo Xiting Liao Feng Han Tao Feng Guoping Liu Runze Zhao Zhuang Zhu Haijiao Mao Caihong Zhu Bin Li | 2023 | Bioactive Materials2023，，7： | 1 |
| 5 | Evaluating the Public Perceptions of Nuclear Power in China:Evidence from a Contingent Valuation Survey显示文摘 | Chuanwang Sun Xiting Zhu | 2014 | Energy Policy2014，，6： | 1 |
| 6 | Changes of Relevant Indexes of Photosynthetic Pigment and Nitrogen Metabolism in Leaves of Chrysanthemum morifolium Ramat. ‘Huaibai' after TAV-free显示文摘[Objective]The paper was to explore effects of Tomato aspermy virus(TAV)-free on chlorophyll content and nitrogen metabolism of Chrysanthemum morifolium Ramat. ‘Huaibai',in order to provide a theoretical basis for field popularization and application of TAV-free‘Huai bai'plantlets. [Method]With previously acquired TAV-free test-tube plantlets of‘Huaibai'as the experimental materials and its ordinary test-tube plantlets as the control(CK),chlorophyll content and some indexes related to nitrogen metabolism in leaves were determined during subculture.[Result]During subculture,the contents of chlorophyll a and chlorophyll b in leaves of CK and TAV-free‘Huaibai'test-tube plantlets increased with the subculture days. Both realized the largest increase at the 22^(th) day of subculture,and their increase amplitudes were 5. 24% and 41. 69%,respectively. Compared with CK,the chlorophyll a and chlorophyll b contents of TAV-free test-tube plantlets increased at the same time point of subculture,with significant difference(P < 0. 05) or extremely significant difference(P<0. 01). Furthermore,the nitrate reductase(NR) activity,free proline and soluble protein contents of TAV-free‘Huaibai'were all significantly higher than those of CK,and the highest increase amplitudes were 27. 99%(subculture for 22 d),28. 10%(subculture for 22 d) and 5. 89%(subculture for 38 d),respectively.[Conclusion]TAV-free could effectively improve chlorophyll content and nitrogen metabolism level of‘Huaibai',and was conducive to its growth and development. | Zhao Xiting Liu Ke Zhu Yuting Wang Zhaoyang Zhou Yingyuan Fan Zijian Jiang Liwei Li Mingjun | 2016 | Plant Diseases and Pests2016，7，4： | 0 |
| 7 | Effects of drying methods on the structure and emulsifying capacity of egg yolk lecithin显示文摘The purpose of this study was to investigate the effects of different drying methods,including ultrasonic vacuum drying,vacuum drying,vacuum freeze-drying,hot-air drying and spray drying,on the structure and emulsifying capacity of egg yolk lecithin based on Raman spectra.The results showed that ultrasonic vacuum drying and spray drying can induce the vibration of C-N bonds in the polar O-C-C-N^(+)head skeleton of egg yolk lecithin.The shift of the peak attributed to the C-N bond from 717 cm^(−1)to 774 and 772 cm^(−1)indicated that the vibration of some C-N bonds in the O-C-C-N^(+)skeleton had transformed from gauche to trans.Ultrasonic vacuum drying exerted the most intense effect on the C-C skeleton of egg yolk lecithin,with the greatest vibration peaks at 1062 cm^(−1),1128 cm^(−1),and 1097 cm^(−1)in the Raman spectra of egg yolks.Specifically,it relieved gauche vibration and strengthened trans vibration in the C-C skeleton.Hence,the I_(gauche)/I_(trans)ratio of the egg yolk lecithin processed through ultrasonic vacuum drying decreased.Ultrasonic vacuum drying and spray drying decreased the I_(2850)/I_(2878)ratio of the vibration peak of C-H bonds in the lipid chains of egg yolk lecithin.The weakening of the symmetric stretching vibration of the C-H bond and the strengthening of antisymmetric stretching vibration indicated that orderliness among the molecular chains of lipid bilayer membranes had increased,whereas liquidity had decreased.The emulsifying capacities were highly significantly different among various egg yolk lecithin samples,in which the highest emulsifying capacity(49.58 m^(2)/g)was shown for the egg yolk lecithin prepared through vacuum freeze-drying,and ultrasonic vacuum drying produced the lowest emulsifying capacity(14.77 m^(2)/g).This study demonstrated that ultrasonic vacuum drying and spray drying drastically affected the structure of egg yolk lecithin.The appropriate drying method can be selected based on sample volume and production situation. | Xiting Bai Jiaqi Gao Yu Yang Wenxue Zhu Jinling Fan | 2020 | International Journal of Agricultural and Biological Engineering2020，13，4： | 0 |
| 8 | Ex utero intrapartum therapy in infants with congenital diaphragmatic hernia:a propensity score matching analysis显示文摘Objective Previous studies have shown that ex utero intrapartum therapy(EXIT)is safe and feasible for newborns with congenital diaphragmatic hernia(CDH).This study reports our experience with EXIT in fetuses with CDH in an attempt to explore the efficacy of EXIT on the survival rate of this population.Methods A retrospective analysis of the clinical data of 116 children with CDH was conducted.The children were assigned to EXIT and non-EXIT groups.Propensity score matching(PSM)toward clinical data was performed,and the clinical characteristics and outcomes were compared.Taking survival at discharge as the main outcome,logistic regression analysis was carried out to explore the efficacy of EXIT on survival.Results During the study period,30 of 116 children received EXIT.After PSM,the survival rates of the EXIT group and the non-EXIT group were 82.76%(24/29)and 48.28%(14/29),respectively(p=0.006).EXIT(OR=0.083,95%CI=0.013to 0.525,p=0.008),liver herniation(OR=16.955,95%CI=2.342 to 122.767,p=0.005),and gestational age at diagnosis(OR=0.662,95%CI=0.497 to 0.881,p=0.005)were independent mortality-related risk factors of all children with CDH.Ninety-nine of 116 children underwent surgery.After PSM,the postoperative survival rates of the EXIT group and non-EXIT group were 84.6%(22/26)and 76.9%(20/26),respectively(p=0.754).Liver herniation(OR=10.451,95%CI=1.641 to 66.544,p=0.013)and gestational age at diagnosis(OR=0.736,95%CI=0.577 to 0.938,p=0.013)were independent mortality-related risk factors of children after surgery.Conclusion EXIT can be performed safely for selected prenatally diagnosed CDH neonates with potentially better survival and does not cause more maternal complications compared with traditional cesarean section. | Yunlong Zhao Ying Wang Chao Liu Yulin Jiang Yandong Wei Hua Meng Shan Jian Xiting Zhu Lijian Pei Xiaochen Bai Feng Feng Yan Lv Xiya Zhou Qingwei Qi Jingna Li Lishuang Ma | 2022 | World Journal of Pediatric Surgery2022，5，4： | 0 |
| 9 | Activity Gel Analysis of Endopeptidases in Rose Petals显示文摘Poor resolution for the identification of endopeptidase(EP) activity in activity gel assays is a critical issue in the analysis of the postharvest physiology of rose petals. In this paper, major factors influencing EP activity gel assays were evaluated. The results showed that a phosphate(NaH_2PO_4/Na_2HPO_4) buffer favors the detection of clear EP bands, as compared to Tris–HCl buffer. Removal of salts and pigments with Sephadex G-25 columns was vital to the measurement of EP activity in rose petal extracts. For optimal resolution of bands, we show that before electrophoresis,samples should be treated for 10 min at 40 °C. Additionally, electrophoresis should be done in 12% SDS–PAGE co-polymerized with 0.15%(w/v) gelatin. After electrophoresis, the optimal incubation temperature and pH are 42 °C and 7.0, respectively. Using our optimized assay, Rh-EP1,Rh-EP2, Rh-EP3, three proteases with molecular masses of 200, 123.5, and 97.4 kD, respectively, were detected in rose petals. Experiments using EP class-specific inhibitors revealed that Rh-EP2 and Rh-EP3 were both serine proteases, while Rh-EP1 was a metalloprotease. In this study, we also measured changes in EP activity during flower opening, senescence, and water deficit stress(WDS) using our optimized activity gel assay,and found that Rh-EP3 may be more relevant to senescence in roses compared with Rh-EP1 or Rh-EP2. Changes occurring to EPs after WDS were similar to those during the period from flower opening to senescence, and Rh-EP3 activities were greatly increased by WDS treatment. Collectively, our results suggest that significant increases in Rh-EPs activities, especially increases in Rh-EP3 activity, may contribute to the flower senescence induced under WDS treatment. | ZHAO Xiting ZHANG Changqing ZHU Yuting LI Tianzhong GAO Junping | 2016 | Horticultural Plant Journal2016，2，2： | 0 |
| 10 | Network Pharmacology-based Strategy for Predicting Active Ingredients and Potential Targets of Cuscutae semen and Lycii fructus in Spermatogenic Dysfunction显示文摘Background:Traditional Chinese Medicine(TCM)Cuscutae semen(SC,Tusizi from Cuscuta chinensis Lam.)and Lycii fructus(FL,Gouqi from Lycium barbarum L.),are also used as a herb pair(SC-FL)to treat various ailments,including spermatogenic dysfunction(SD),a disease responsible for low fertility in males.Objective:Herein,we will further determine the bioactive components,component targets and partial molecular mechanisms of the herb pair for the treatment of SD.Methods:We employed the traditional Chinese medicine systems pharmacology database in combination with Ultra high performance liquid chromatography(UHPLC)analysis to analyze the active ingredients of the SC-FL herbal pair and explore its possible targets and underlying mechanism in treatment of spermatogenic dysfunction(SD).Moreover,we used a Sprague-Dawley rat model,generated by using glucosides of Tripterygium wilfordii(GTW),to evaluate the effect of SC-FL and the underlying mechanism on SD and reliability of certain key targets and pathways obtained from the pharmacology analysis.Results:We identified 56 active ingredients in SC-LF affecting 41 overlapping gene signals that influenced SD treatment outcomes.262 Gene Ontology(GO)terms and 170 pathways were yielded under analyses of Gene Ontology,Kyoto Encyclopedia of Gene and Genome pathway from which we predicted that cell proliferation and apoptosis were the primary biological processes(BP)involved in the treatment of SD by SC-LF.The results showed that SC-FL treatment significantly improved the testicular organ coefficient along with sperm count and motility,while reduced testicular damage and testicular tissue cell apoptosis in SD model.Mechanistically,SC-FL significantly upregulated the expression levels of anti-apoptotic proteins AR and BCL2 and downregulated those of pro-apoptotic proteins BAD,BAX,cleaved caspase 3,and CASP3.Conclusion:Collectively,these results indicated that SC-FL elicited a protective effect by potentially regulating apoptosis,thus suggesting that it will represent an effective reagent for male infertility. | Jianxiong Ma Siqi Guan Yutian Zhu Lei Dong Xiting Wang Wangqiang Chen Caifei Ding Bodong Lv Hongxuan Tong | 2022 | Clinical Complementary Medicine and Pharmacology2022，2，4： | 0 |
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