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| 1 | Causal Inference显示文摘Causal inference is a powerful modeling tool for explanatory analysis,which might enable current machine learning to become explainable.How to marry causal inference with machine learning to develop explainable artificial intelligence(XAI)algorithms is one of key steps toward to the artificial intelligence 2.0.With the aim of bringing knowledge of causal inference to scholars of machine learning and artificial intelligence,we invited researchers working on causal inference to write this survey from different aspects of causal inference.This survey includes the following sections:“Estimating average treatment effect:A brief review and beyond”from Dr.Kun Kuang,“Attribution problems in counterfactual inference”from Prof.Lian Li,“The Yule–Simpson paradox and the surrogate paradox”from Prof.Zhi Geng,“Causal potential theory”from Prof.Lei Xu,“Discovering causal information from observational data”from Prof.Kun Zhang,“Formal argumentation in causal reasoning and explanation”from Profs.Beishui Liao and Huaxin Huang,“Causal inference with complex experiments”from Prof.Peng Ding,“Instrumental variables and negative controls for observational studies”from Prof.Wang Miao,and“Causal inference with interference”from Dr.Zhichao Jiang. | Kun Kuang Lian Li Zhi Geng Lei Xu Kun Zhang Beishui Liao Huaxin Huang Peng Ding Wang Miao Zhichao Jiang | 2020 | Engineering2020，6，3： | 8 |
| 2 | Roles of low?density lipoproteinreceptor?related protein 1 in tumors显示文摘Low-density lipoprotein receptor-related protein 1(LRP1,also known as CD91),a multifunctional endocytic and cell signaling receptor,is widely expressed on the surface of multiple cell types such as hepatocytes,fibroblasts,neurons,astrocytes,macrophages,smooth muscle cells,and malignant cells.Emerging in vitro and in vivo evidence demonstrates that LRP1 is critically involved in many processes that drive tumorigenesis and tumor progression.For example,LRP1 not only promotes tumor cell migration and invasion by regulating matrix metalloproteinase(MMP)-2and MMP-9 expression and functions but also inhibits cell apoptosis by regulating the insulin receptor,the serine/threonine protein kinase signaling pathway,and the expression of Caspase-3.LRPI-mediated phosphorylation of the extracellular signal-regulated kinase pathway and c-jun N-terminal kinase are also involved in tumor cell proliferation and invasion.In addition,LRP1 has been shown to be down-regulated by microRNA-205 and methylation of LRP1CpG islands.Furthermore,a novel fusion gene,LRP1-SNRNP25,promotes osteosarcoma cell invasion and migration.Only by understanding the mechanisms of these effects can we develop novel diagnostic and therapeutic strategies for cancers mediated by LRP1. | Peipei Xing Zhichao Liao Zhiwu Ren Jun Zhao Fengju Song Guowen Wang Kexin Chen Jilong Yang | 2016 | Chinese Journal of Cancer2016，35，1： | 4 |
| 3 | Influence of hydraulic retention time on behavior of antibiotics and antibiotic resistance genes in aerobic granular reactor treating biogas slurry显示文摘The behavior of antibiotics and the corresponding resistance genes in aerobic granular reactors for treating biogas slurry under different hydraulic retention times (10.7 h, Rl;8 h, R2) was investigated in this study. The results indicated that the hydraulic retention time could affect the effluent concentrations and removal efficiencies of sulfonamides. The average removal rates of tetracyclines, fluoroquinolones, and sulfonamides were 63%, 46%, and 90% in Rl, and 62%, 46%, and 86% in R2, respectively. Although the removal efficiencies of tetracyclines and fluoroquinolones were similar in both reactors, the respective accumulated concentrations of tetracyclines and fluoroquinolones in R1 were 7.00 and 11.15μg/g SS, which were lower than those in R2 (8.92 and 13.37μg/g SS, respectively). The difference in the relative abundance of target antibiotic resistance genes between both reactors was not significant, yet the average relative abundances of all target resistance genes in R1 were higher than those in R2 after 45 days of operation. The results of this study suggested that a longer hydraulic retention time could enhance the antibiotic removal ability of aerobic granular sludge, yet it may also increase the risk of surplus sludge utilization from a resistance genes point of view. | Jie Liao Chaoxiang Liu Lin Liu Jie Li Hongyong Fan Jiaqi Ye Zhichao Zeng | 2019 | Frontiers of Environmental Science & Engineering2019，13，3： | 2 |
| 4 | The prognostic significance of non-sentinel lymph node metastasis in cutaneous and acral melanoma patients—A multicenter retrospective study显示文摘Background:Whether non-sentinel lymph node(SLN)-positive melanoma patients can benefit from completion lymph node dissection(CLND)is still unclear.The current study was performed to identify the prognostic role of nonSLN status in SLN-positive melanoma and to investigate the predictive factors of non-SLN metastasis in acral and cutaneous melanoma patients.Methods:The records of 328 SLN-positive melanoma patients who underwent radical surgery at four cancer centers from September 2009 to August 2017 were reviewed.Clinicopathological data including age,gender,Clark level,Breslow index,ulceration,the number of positive SLNs,non-SLN status,and adjuvant therapy were included for survival analyses.Patients were followed up until death or June 30,2019.Multivariable logistic regression modeling was performed to identify factors associated with non-SLN positivity.Log-rank analysis and Cox regression analysis were used to identify the prognostic factors for disease-free survival(DFS)and overall survival(OS).Results:Among all enrolled patients,220(67.1%)had acral melanoma and 108(32.9%)had cutaneous melanoma.The 5-year DFS and OS rate of the entire cohort was 31.5%and 54.1%,respectively.More than 1 positive SLNs were found in 123(37.5%)patients.Positive non-SLNs were found in 99(30.2%)patients.Patients with positive non-SLNs had significantly worse DFS and OS(log-rank P<0.001).Non-SLN status(P=0.003),number of positive SLNs(P=0.016),and adjuvant therapy(P=0.025)were independent prognostic factors for DFS,while non-SLN status(P=0.002),the Breslow index(P=0.027),Clark level(P=0.006),ulceration(P=0.004),number of positive SLNs(P=0.001),and adjuvant therapy(P=0.007)were independent prognostic factors for OS.The Breslow index(P=0.020),Clark level(P=0.012),and number of positive SLNs(P=0.031)were independently related to positive non-SLNs and could be used to develop more personalized surgical strategy.Conclusions:Non-SLN-positive melanoma patients had worse DFS and OS even after immediate CLND than those with non-SLN-negative melanoma.The Breslow index,Clark level,and number of positive SLNs were independent predictive factors for non-SLN status. | Wei Sun Yu Xu JiLong Yang ZhiChao Liao Tao Li Kai Huang Poulam Patel WangJun Yan Yong Chen | 2020 | Cancer Communications2020，40，11： | 2 |
| 5 | Clinicopathological features of pseudomyogenic hemangioendothelioma and precision therapy based on whole exome sequencing显示文摘Dear Editor Pseudomyogenic hemangioendothelioma(PHE)is a newly recognized subtype of hemangioendothelioma characterized by the presence of fibrohistiocytic and myoid cells arranged in a fibroma-like or dermatofibroma-like pattern[1].This rare type of tumor was first named by Hornick and Fletcher[2]and categorized as the novel soft tissue tumor classification system of the World Health Organization in 2013[3].Prior to this,it was referred to as fibroma-like variant of epithelioid sarcoma(ES)and epithelioid sarcoma-like hemangioendothelioma[4]. | Junqiang Wei Zhichao Liao Gang Zhao Nazmun Nahar Chao Zhang Jia Lu Yun Yang Jilong Yang | 2020 | Cancer Communications2020，40，4： | 2 |
| 6 | The Combined Effects of Celecoxib and Minocycline Hydrochloride on Inhibiting the Osseous Metastasis of Breast Cancer in Nude Mice显示文摘 | Niu Guangfeng Liao Zhichao Cai Lin | 2008 | Cancer Biotherapy & Radiopharmaceuticals2008，4，23： | 1 |
| 7 | Three-dimensional multiphase modeling of a proton exchange membrane electrolysis cell with a new interdigitated-jet hole flow field显示文摘The flow field structure on the bipolar plate significantly affects the performance of the proton exchange membrane electrolysis cell(PEMEC).This paper proposes a new interdigitated-jet hole flow field(JHFF)design to improve the uniformities of liquid saturation,temperature,and current density distributions.The common single-path serpentine flow field(SSFF)and interdigitated flow field(IFF)are used as comparative references to constitute three PEMEC cases.An advanced numerical model has been established to simulate the performance of the PEMEC using CFD software.The results show that,due to the perpendicular mainstream and the pressure difference,the JHFF enhances the mass and heat transfer inside the porous electrode by introducing strong forced convection,which promotes gas removal underneath the ribs and cooling.Compared with the comparative flow fields,the uniformities of liquid saturation,temperature,and current density distributions by using the JHFF at the anode side are increased by 19.1%,53.2%,and 40.4%,respectively.Further,mainly owing to the largest conductive area,the PEMEC with the JHFF has superior polarization performance,which is 8.05%higher than the PEMEC with the SSFF. | WANG XueYe WANG ZhiMing FENG YuanCheng XU Chao CHEN ZhiChao LIAO ZhiRong JU Xing | 2022 | Science China(Technological Sciences)2022，65，5： | 1 |
| 8 | Water‐absorption characteristics of organic–inorganic composite superabsorbent polymers and its effect on summer maize root growth显示文摘 | Zhou Bo Liao Renkuan Li Yunkai Gu Tao Yang Peiling Feng Ji Xing Weimin Zou Zhichao | 2012 | J. Appl. Polym. Sci2012，，2： | 1 |
| 9 | The Jasmine(Jasminum sambac)Genome Provides Insight into the Biosynthesis of Flower Fragrances and Jasmonates显示文摘Jasminum sambac(jasmine flower),a world-renowned plant appreciated for its exceptional flower fragrance,is of cultural and economic importance.However,the genetic basis of its fragrance is largely unknown.Here,we present the first de novo genome assembly of J.sambac with 550.12 Mb(scaffold N50=40.10 Mb)assembled into 13 pseudochromosomes.Terpene synthase(TPS)genes associated with flower fragrance are considerably amplified in the form of gene clusters through tandem duplications in the genome.Gene clusters within the salicylic acid/benzoic acid/theobromine(SABATH)and benzylalcohol O-acetyltransferase/anthocyanin O-hydroxycinnamoyltransferases/anthranilate N-hydroxycinnamoyl/benzoyltransferase/deacetylvindoline 4-O-acetyltransferase(BAHD)superfamilies were identified to be related to the biosynthesis of phenylpropanoid/benzenoid compounds.Several key genes involved in jasmonate biosynthesis were duplicated,causing an increase in copy numbers.In addition,multi-omics analyses identified various aromatic compounds and many genes involved in fragrance biosynthesis pathways.Furthermore,the roles of JsTPS3 in b-ocimene biosynthesis,as well as JsAOC1 and JsAOS in jasmonic acid biosynthesis,were functionally validated.The genome assembled in this study for J.sambac offers a basic genetic resource for studying floral scent and jasmonate biosynthesis,and provides a foundation for functional genomic research and variety improvements in Jasminum. | Gang Chen Salma Mostafa Zhaogeng Lu Ran Du Jiawen Cui Yun Wang Qinggang Liao Jinkai Lu Xinyu Mao Bang Chang Quan Gan Li Wang Zhichao Jia Xiulian Yang Yingfang Zhu Jianbin Yan Biao Jin | 2023 | Genomics, Proteomics & Bioinformatics2023，21，1： | 0 |
| 10 | The efficacies and biomarker investigations of antiprogrammed death-1 (anti-PD-1)-based therapies for metastatic bone and soft tissue sarcoma显示文摘Objective:Sarcomas are a group of rare malignancies with various subtypes.Patients with metastatic sarcoma who have failed traditional treatments can possibly achieve better prognoses from using novel therapies,including anti-programmed death-1(PD-1)-based therapies.Methods:We retrospectively analyzed clinical data of 24 metastatic sarcoma patients from June 15,2016 to December 30,2019.These patients mainly received angiogenesis inhibitors combined with anti-PD-1 therapy after they became resistant to traditional treatments.Furthermore,8 patients underwent panel DNA and whole transcript sequencing.Results:Six patients received 2 cycles of anti-PD-1 therapy and were included in the safety evaluation only group.The median follow-up time was 5.77 months.The median progression-free survival was 7.59 months,the overall response rate was 16.7%and the disease control rate was 55.6%.Based on whole exome and transcript sequencing data,there was no association between TMB,TNB,MSI,HLA-LOH,and PD-L1 expressions and sarcoma types with clinical responses.Immunotherapy efficacy and bioinformatics analyses indicated higher intratumoral heterogeneity(ITH)in progressive disease(PD)patients and lower ITH in partial response(PR)and stable disease patients.A higher percentage of immune cell infiltration,especially monocytes,was observed in PR patients.Active stromal gene expression was increased in PD patients but decreased in PR patients.Enrichment analysis revealed that an increased TGF-βsignaling pathway was reversely correlated with anti-PD-1 efficacy,while a decreased inflammatory response signaling pathway was positively correlated with anti-PD-1 efficacy.Conclusions:Our study showed PD-1 inhibitors combined with anti-angiogenesis agents were effective and well-tolerated.ITH,monocyte ratio,stroma subtypes,and the status of immune-associated signaling pathways may be related with anti-PD-1 based therapy. | Jia Lu Ting Li Zhichao Liao Hui Yu Yongtian Zhao Haixiao Wu Zhiwu Ren Jun Zhao Ruwei Xing Sheng Teng Yun Yang Xiangchun Li Kexin Chen Jonathan Trent Jilong Yang | 2022 | Cancer Biology & Medicine2022，19，6： | 0 |
| 11 | Clinical study of apatinib in the treatment of stage IV osteogenic sarcoma after failure of chemotherapy显示文摘Objective:To analyze the efficacy and safety o f apatinib in the treatment of stage IV osteogenic sarcoma after chemotherapy failure through a single-arm,prospective,and open clinical phase II study.Methods:Information on 34 patients with stage IV osteogenic sarcoma treated with apatinib after failure o f chemotherapy in Tianjin Medical University Cancer Institute and Hospital between September 2015 and December 2019 was collected and analyzed.The participants included 23 males and 11 females,with an average age of 35.24 years(11-73 years).The objective response rate(ORR),disease control rate(DCR),progression-free survival(PFS),PFS rate(PFR),and overall survival(OS)were evaluated.The treatmentrelated adverse events(AEs)and safety of apatinib were also evaluated.Results:O f the 34 patients,33 were able to be evaluated for efficacy.One patient received apatinib treatment for less than one cycle;therefore,only safety analysis was performed.The 12-week clinical evaluation showed that 2 patients had a partial response(PR),24 patients had stable disease(SD),and 7 patients had progressive disease(PD).The ORR,DCR,and PFR at 12 weeks were 6.06%(2/33),78.79%(26/33),and 82%,respectively.By the end of the follow-up,6 patients had SD(18.18%,6/33),27 patients had PD(81.82%,27/33),and 15 patients died because of disease progression(45.45%,15/33).The ORR was 0(0/33),the DCR was 18.18%(6/33),and the median PFS(mPFS)was 7.89 months(95%Cl:4.56-11.21).The median OS(mOS)was 17.61 months(95%Cl:10.85-24.37).The most common treatment-related AEs were hand-foot syndrome(35.29%,12/34),proteinuria(32.35%,11/34),and hypertension(32.35%,11/34). | Zhichao Liao Ting Li Chao Zhang Xinyue Liu Ruwei Xing Sheng Teng Yun Yang Gang Zhao Xu Bai Jun Zhao Jilong Yang | 2020 | Cancer Biology & Medicine2020，17，2： | 0 |
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