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| 1 | Speciation with gene flow via cycles of isolation and migration:insights from multiple mangrove taxa显示文摘Allopatric speciation requiring an unbroken period of geographical isolation has been the standard model of neo-Darwinism. While doubts have been repeatedly raised, strict allopatry without any gene flow remains a plausible mechanism in most cases. To rigorously reject strict allopatry, genomic sequences superimposed on the geological records of a well-delineated geographical barrier are necessary. The Strait of Malacca,narrowly connecting the Pacific and Indian Ocean coasts, serves at different times either as a geographical barrier or a conduit of gene flow for coastal/marine species. We surveyed 1700 plants from 29 populations of 5 common mangrove species by large-scale DNA sequencing and added several whole-genome assemblies. Speciation between the two oceans is driven by cycles of isolation and gene flow due to the fluctuations in sea level leading to the opening/closing of the Strait to ocean currents. Because the time required for speciation in mangroves is longer than the isolation phases, speciation in these mangroves has proceeded through many cycles of mixing-isolation-mixing, or MIM, cycles. The MIM mechanism, by relaxing the condition of no gene flow, can promote speciation in many more geographical features than strict allopatry can. Finally, the MIM mechanism of speciation is also efficient, potentially yielding mn(m > 1) species after n cycles. | Ziwen He Xinnian Li Ming Yang Xinfeng Wang Cairong Zhong Norman C.Duke Chung-I Wu Suhua Shi | 2019 | National Science Review2019，6，2： | 14 |
| 2 | Molecular heterogeneity of anti-PD-1/PD-L1 immunotherapy efficacy is correlated with tumor immune microenvironment in East Asian patients with non-small cell lung cancer显示文摘Objective:The aim of this study was to investigate how the tumor immune microenvironment differs regarding tumor genomics,as well as its impact on prognoses and responses to immunotherapy in East Asian patients with non-small cell lung cancer(NSCLC).Methods:We performed an integrated analysis using publicly available data to identify associations between anti-programmed death 1(PD-1)/programmed death-ligand 1(PD-L1)immunotherapy efficacy and classic driver oncogene mutations in East Asian NSCLC patients.Four pooled and clinical cohort analyses were used to correlate driver oncogene mutation status and tumor microenvironment based on PD-L1 and CD8+tumor-infiltrating lymphocytes(TILs).Immune infiltrating patterns were also established for genomic NSCLC subgroups using the CIBERSORT algorithm.Results:Based on East Asian NSCLC patients,TIDE analyses revealed that for anti-PD-1/PD-L1 immunotherapy,epidermal growth factor receptor(EGFR)-mutant and anaplastic lymphoma kinase(ALK)-rearranged tumors yielded inferior responses;however,although Kirsten rat sarcoma viral oncogene homolog(KRAS)-mutant tumors responded better,the difference was not statistically significant(EGFR:P=0.037;ALK:P<0.001;KRAS:P=0.701).Pooled and clinical cohort analyses demonstrated tumor immune microenvironment heterogeneities correlated with oncogenic patterns.The results showed remarkably higher PD-L1-and TIL-positive KRAS-mutant tumors,suggesting KRAS mutations may drive an inflammatory phenotype with adaptive immune resistance.However,the EGFR-mutant or ALK-rearranged groups showed a remarkably higher proportion of PD-L1-/TIL-tumors,suggesting an uninflamed phenotype with immunological ignorance.Notably,similar to triple wild-type NSCLC tumors,EGFR L858R-mutant tumors positively correlated with an inflammatory phenotype,suggesting responsiveness to anti-PD-1/PD-L1 immunotherapy(P<0.05).Furthermore,the CIBERSORT algorithm results revealed that EGFR-mutant and ALK-rearranged tumors were characterized by an enriched resting memory CD4+T cell population(P<0.001),as well as a lack of CD8+T cells(P<0.01),and activated memory CD4+T cells(P=0.001).Conclusions:Our study highlighted the complex relationships between immune heterogeneity and immunotherapeutic responses in East Asian NSCLC patients regarding oncogenic dependence. | Runsen Jin Chengming Liu Sufei Zheng Xinfeng Wang Xiaoli Feng Hecheng Li Nan Sun Jie He | 2020 | Cancer Biology & Medicine2020，17，3： | 10 |
| 3 | KRAS-G12D mutation drives immune suppression and the primary resistance of anti-PD-1/PD-L1 immunotherapy in non-small cell lung cancer显示文摘Background:Although immune checkpoint inhibitors(ICIs)against programmed cell death protein 1(PD-1)and its ligand PD-L1 have demonstrated potency towards treating patients with non-small cell lung carcinoma(NSCLC),the potential association between Kirsten rat sarcoma viral oncogene homolog(KRAS)oncogene substitutions and the efficacy of ICIs remains unclear.In this study,we aimed to find point mutations in the KRAS gene resistant to ICIs and elucidate resistance mechanism.Methods:The association between KRAS variant status and the efficacy of ICIs was explored with a clinical cohort(n=74),and confirmed with a mouse model.In addition,the tumor immune microenvironment(TIME)of KRASmutant NSCLC,such as CD8+tumor-infiltrating lymphocytes(TILs)and PD-L1 level,was investigated.Cell lines expressing classic KRAS substitutions were used to explore signaling pathway activation involved in the formation of TIME.Furthermore,interventions that improved TIME were developed to increase responsiveness to ICIs.Results:We observed the inferior efficacy of ICIs in KRAS-G12D-mutant NSCLC.Based upon transcriptome data and immunostaining results from KRAS-mutant NSCLC,KRAS-G12D point mutation negatively correlated with PD-L1 level and secretion of chemokines CXCL10/CXCL11 that led to a decrease in CD8+TILs,which in turn yielded an immunosuppressive TIME.The analysis of cell lines overexpressing classic KRAS substitutions further revealed that KRAS-G12D mutation suppressed PD-L1 level via the P70S6K/PI3K/AKT axis and reduced CXCL10/CXCL11 levels by down-regulating high mobility group protein A2(HMGA2)level.Notably,paclitaxel,a chemotherapeutic agent,upregulated HMGA2 level,and in turn,stimulated the secretion of CXCL10/CXCL11.Moreover,PD-L1 blockade combined with paclitaxel significantly suppressed tumor growth compared with PD-L1 inhibitor monotherapy in a mouse model with KRAS-G12D-mutant lung adenocarcinoma.Further analyses revealed that the combined treatment significantly enhanced the recruitment of CD8+TILs via the up-regulation of CXCL10/CXCL11 levels.Results of clinical study also revealed the superior efficacy of chemo-immunotherapy in patients with KRAS-G12D-mutant NSCLC compared with ICI monotherapy.Conclusions:Our study elucidated the molecular mechanism by which KRASG12D mutation drives immunosuppression and enhances resistance of ICIs in NSCLC.Importantly,our findings demonstrate that ICIs in combination with chemotherapy may be more effective in patients with KRAS-G12D-mutant NSCLC. | Chengming Liu Sufei Zheng Zhanyu Wang Sihui Wang Xinfeng Wang Lu Yang Haiyan Xu Zheng Cao Xiaoli Feng Qi Xue Yan Wang Nan Sun Jie He | 2022 | Cancer Communications2022，42，9： | 4 |
| 4 | Liquid biopsy for esophageal cancer: Is detection of circulating cell-free DNA as a biomarker feasible?显示文摘Esophageal cancer(EC)is a common cancer and is histopathologically classified into esophageal squamous cell carcinoma and esophageal adenocarcinoma.EC is a worldwide public health issue because of late diagnosis and lack of effective therapy.In contrast to standard tumor biopsies,liquid biopsies are emerging as a tool which is minimally invasive that can complement or even substitute more classical approaches.Specifically,cell-free DNA(cfDNA)has shown promise in cancer-related clinical applications.Indeed,cfDNA has been shown to be an effective circulating biomarker for non-invasive cancer diagnosis and monitoring of cancer patients.Although the clinical application of cfDNA has been reported on other cancers,few studies have evaluated its use in EC.Here,we review this relevant literature and discuss limitations and advantages of its application in the diagnosis and monitoring of EC. | Zuyang Yuan Xinfeng Wang Xiao Geng Yin Li Juwei Mu Fengwei Tan Qi Xue Shugeng Gao Jie He | 2021 | Cancer Communications2021，41，1： | 4 |
| 5 | Genes and speciation: is it time to abandon the biological species concept?显示文摘The biological species concept(BSC)is the cornerstone of neo-Darwinian thinking.In BSC,species do not exchange genes e让her during or after speciation.However,as gene flow during speciation is increasingly being reported in a substantial literature,让seems time to reassess the revered;but often doubted;BSC.Contrary to the common perception;BSC should expect substantial gene flow at the onset of speciation,not least because geographical isolation develops gradually.Although BSC does not stipulate how speciation begins,it does require a sustained period of isolation for speciation to complete its course.Evidence against BSC must demonstrate that the observed gene flow does not merely occur at the onset of speciation but continues until its completion.Importantly^recent genomic analyses cannot reject this more realistic version of BSC;although future analyses may still prove让wrong.The ultimate acceptance or rejection of BSC is not merely about a historical debate;rather,it is about the fundamental nature of species-are species(and,hence;divergent adaptations)driven by a relatively small number of genes,or by thousands of them?Many levels ofbiology,ranging from taxonomy to biodiversity;depend on this resolution. | Xinfeng Wang Ziwen He Suhua Shi Chung-I Wu | 2020 | National Science Review2020，7，8： | 3 |
| 6 | Natural ecological water demand in the lower Heihe River显示文摘The ecological environment in the lower Heihe River has been deteriorating due to large water consump-tion in the upper and middle reaches,and less available water downstream.To restore the ecological environment in the lower Heihe River,the ecological water demand should be guaranteed.The natural vegetation area in the lower Heihe River was first obtained through the inter-pretation of remote sensing images taken in 1998.Based on the analysis for the Quota of the natural ecological water demand in the lower Heihe River and the deter-mination of the natural ecological water demand calcula-tion method,the ecological water demand in the lower Heihe Riverwascalculated.Finally,thenatural ecological water demand in the lower Heihe River under the current situation was calculated with the groundwater storage volume change method,Aweliyongrufe method and the measured water volume method.In comparison,the nat-ural ecological water demand in the lower Heihe River is 3.91–4.056108 m^(3). | Xinfeng FU Hongmou HE Xiaohui JIANG Shengtian YANG Guoqing WANG | 2008 | Frontiers of Environmental Science & Engineering2008，2，1： | 3 |
| 7 | Fast Converging Estimator for Covariance Matrix Structure of Compound-Gaussian Clutter显示文摘 | JIAN Tao HE You SU Feng PING Dianfa GU Xinfeng | 2010 | Chinese Journal of Electronics2010，19，3： | 2 |
| 8 | Preparation of lead carbonate from spent lead paste via chemical conversion显示文摘 | Xinfeng Zhu Jiakuan Yang Linxia Gao Jianwen Liu Danni Yang Xiaojuan Sun Wei Zhang Qin Wang Lei Li Dongsheng He R. Vasant Kumar | 2013 | Hydrometallurgy2013，，： | 1 |
| 9 | Novel Range-SpreadTarget Detectors in Non-Gaussian Clutter 显示文摘 | You He Tao Jian Changwen Qu Xinfeng Gu | 2010 | IEEE Transactions onAerospace Electronic Systems2010，46，3： | 1 |
| 10 | A novel recurrence-associated metabolic prognostic model for risk stratification and therapeutic response prediction in patients with stage Ⅰ lung adenocarcinoma显示文摘Objective:The proportion of patients with stageⅠlung adenocarcinoma(LUAD)has dramatically increased with the prevalence of low-dose computed tomography use for screening.Up to 30%of patients with stageⅠLUAD experience recurrence within 5 years after curative surgery.A robust risk stratification tool is urgently needed to identify patients who might benefit from adjuvant treatment.Methods:In this first investigation of the relationship between metabolic reprogramming and recurrence in stageⅠLUAD,we developed a recurrence-associated metabolic signature(RAMS).This RAMS was based on metabolism-associated genes to predict cancer relapse and overall prognoses of patients with stageⅠLUAD.The clinical significance and immune landscapes of the signature were comprehensively analyzed.Results:Based on a gene expression profile from the GSE31210 database,functional enrichment analysis revealed a significant difference in metabolic reprogramming that distinguished patients with stageⅠLUAD with relapse from those without relapse.We then identified a metabolic signature(i.e.,RAMS)represented by 2 genes(ACADM and RPS8)significantly related to recurrence-free survival and overall survival times of patients with stageⅠLUAD using transcriptome data analysis of a training set.The training set was well validated in a test set.The discriminatory power of the 2 gene metabolic signature was further validated using protein values in an additional independent cohort.The results indicated a clear association between a high risk score and a very poor patient prognosis.Stratification analysis and multivariate Cox regression analysis showed that the RAMS was an independent prognostic factor.We also found that the risk score was positively correlated with inflammatory response,the antigen-presenting process,and the expression levels of many immunosuppressive checkpoint molecules(e.g.,PD-L1,PD-L2,B7-H3,galectin-9,and FGL-1).These results suggested that high risk patients had immune response suppression.Further analysis revealed that anti-PD-1/PD-L1 immunotherapy did not have significant benefits for high risk patients.However,the patients could respond better to chemotherapy.Conclusions:This study is the first to highlight the relationship between metabolic reprogramming and recurrence in stageⅠLUAD,and is the first to also develop a clinically feasible signature.This signature may be a powerful prognostic tool and help further optimize the cancer therapy paradigm. | Chengming Liu Sihui Wang Sufei Zheng Xinfeng Wang Jianbin Huang Yuanyuan Lei Shuangshuang Mao Xiaoli Feng Nan Sun Jie He | 2021 | Cancer Biology & Medicine2021，18，3： | 1 |
| 11 | DDoS Defense Algorithm Based on Multi-Segment Timeout Technology显示文摘Through the analysis to the DDoS(distributed denial of service) attack, it will conclude that at different time segments, the arrive rate of normal SYN (Synchronization) package are similar, while the abnormal packages are different with the normal ones. Toward this situation a DDoS defense algorithm based on multi-segment timeout technology is presented, more than one timeout segment are set to control the net flow. Experiment results show that in the case of little flow, multi-segment timeout has the ability dynamic defense, so the system performance is improved and the system has high response rate. | DU Ruizhong YANG Xiaohui MA Xiaoxue HE Xinfeng | 2006 | Wuhan University Journal of Natural Sciences2006，11，6： | 1 |
| 12 | Iterative methods for solving a system of variational inclusions involving H-η-monotone operators in Banach spaces显示文摘 | Lou Jian He Xinfeng He Zhen | 2008 | Computers Math Appl2008，55，： | 1 |
| 13 | Iterative methods for solving a system of variational inclusions involving H-η-monotone operators in Banach spaces显示文摘 | HOU Jian HE Xinfeng HE Zhen | 2008 | Computers & Mathematics with Applications2008，55，： | 1 |
| 14 | Leaching of spent lead acid battery paste components by sodium citrate and acetic acid 显示文摘 | Zhu Xinfeng He Xiong Yang Jiakuan | 2013 | Journal of Hazardous Materials2013，250，15： | 1 |
| 15 | Leaching of spent lead acid battery paste components by sodium citrate and acetic acid 显示文摘 | Zhu Xinfeng He Xiong Yang Jiakuan | 2013 | Journal of Hazardous Materials2013，，15： | 1 |
| 16 | Leaching of spent lead acid battery paste components by sodium citrate and acetic acid显示文摘 | Xinfeng Zhu Xiong He Jiakuan Yang Linxia Gao Jianwen Liu Danni Yang Xiaojuan Sun Wei Zhang Qin Wang R Vasant Kumar | 2013 | Journal of Hazardous Materials2013，，： | 1 |
| 17 | Characteristics of a new photosynthetic bacterial strain for hydrogen production and its application in wastewater treatment显示文摘 | Yongzhen Tao Yanling He Yongqiang Wu Fanghua Liu Xinfeng Li Wenming Zong Zhihua Zhou | 2008 | International Journal of Hydrogen Energy2008，，3： | 1 |
| 18 | Leaching of spent lead acid battery paste components by sodium citrate and acetic acid显示文摘 | Xinfeng Zhu Xiong He Jiakuan Yang Linxia Gao Jianwen Liu Danni Yang Xiaojuan Sun Wei Zhang Qin Wang R Vasant Kumar | 2013 | Journal of Hazardous Materials2013，，： | 1 |
| 19 | Single-cell analysis reveals the potential mechanisms of pyrotinib resistance in non-small cell lung cancer显示文摘Dear Editor,Lung cancer still remains the leading cause of cancer death worldwide,80-90%of which are non-small cell lung cancer(NSCLC).In 2-3%of NSCLC patients,mutations in human epidermal growth factor receptor 2(HER2)have been identified as oncogenic drivers.However,HER2 has been poorly reported as a therapeutic target for advanced NSCLC despite of the outstanding improvements in breast cancer receiving HER2-targeting regimens. | Xinfeng Wang Yuan Li Runsen Jin Sufei Zheng Yuejun Luo Peng Wu Zhanyu Wang Yuxin Yao Nan Sun Jie He | 2023 | Signal Transduction and Targeted Therapy2023，8，2： | 0 |
| 20 | Relationship between White-partridge Feather Trait and SLC45A2 Polymorphism in Wenchang Chicken显示文摘[Objective]The paper was to study the inheritance of white-partridge feather trait in Wenchang chicken and identify the related genetic variation,so as to provide references for the utilization of white-partridge population of Wenchang chicken and molecular marker-assisted selection of white-partridge feather trait.[Method]The inheritance of white-partridge feather trait was studied by reciprocal cross test.SLC45A2 was selected as a candidate gene based on the genetic characteristics of white-partridge feather and results of previous researches.The variation in the exon domain of SLC45A2 gene was analyzed by re-sequencing method.The relationship between missense mutation/nonsense mutation in the exon domain and white-partridge feather trait was verified.[Result]Reciprocal cross test showed that white-partridge feather trait was associated recessive inheritance compared with yellow-partridge feather.The amplification results indicated that there were five SNPs in SLC45A2 gene,in which three were located in exon domain,including two missense mutations(c.a74g and c.gll54c)and one synonymous mutation(c.c561t).The missense mutation was verified with Wenchang chicken Bawang chicken,Qingyuan partridge chicken,Xinghua chicken and red jungle fowl as materials.The results demonstrated that c.g1154c locus of SLC45A2 gene was completely linked with white-partridge feather trait.[Conclusion]The trait of white-partridge feathers showed recessive inheritance and c.g1154c locus might be the causation. | He Yiping Chen Jie Gao Xinfeng Xu Jiguo | 2020 | Animal Husbandry and Feed Science2020，12，3： | 0 |
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