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Phylogenomic conflict analyses in the apple genus Malus *** widespread hybridization and allopolyploidy driving diversification,with insights into the complex biogeographic history in the Northern Hemisphere

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Journal of Integrative Plant Biology 2022年第5期64卷 1020-1043页

作者： Bin-Bin Liu Chen Ren Myounghai Kwak Richard GJHodel Chao Xu Jian He Wen-Bin Zhou Chien-Hsun Huang Hong Ma guan-ze qian De-Yuan Hong Jun Wen State Key Laboratory of Systematic and Evolutionary Botany Institute of Botanythe Chinese Academy of SciencesBeijing 100093China Department of Botany National Museum of Natural HistorySmithsonian InstitutionPO Box 37012Washington 20013–7012DCUSA Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical GardenThe Chinese Academy of SciencesGuangzhou 510650China guangdong Provincial Key Laboratory of Applied Botany South China Botanical GardenThe Chinese Academy of SciencesGuangzhou 510650China National Institute of Biological Resources Incheon 22689South Korea School of Ecology and Nature Conservation Beijing Forestry UniversityBeijing 100083China Department of Plant and Microbial Biology North Carolina State UniversityRaleigh 27965NCUSA State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200433China Department of Biology Huck Institutes of the Life SciencesPennsylvania State University510D Mueller LaboratoryUniversity ParkPennsylvania 16802USA College of Life Sciences Liaocheng UniversityLiaocheng 252059China

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting *** this study,785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato,an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy *** nuclear phylogeny recovered the monophyly of Malus s.l.(including Docynia);however,the genus was supported to be biphyletic in the plastid *** ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear *** conflict analysis demonstrated that ILS,hybridization,and allopolyploidy could explain the widespread nuclear gene tree *** deep hybridization event(Malus doumeri)and one recent event(Malus coronaria)were detected in Malus ***,our historical biogeographic analysis integrating living and fossil data supported a widespread East Asianwestern North American origin of Malus *** the Eocene,followed by several extinction and dispersal events in the Northern *** also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.

关键词： deep genome skimming genomic discordance historical biogeography massive extinction reticulate evolution single-copy nuclear genes

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Fairness in machine learning: definition, testing,debugging, and application

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Science China(Information Sciences) 2024年第9期67卷 41-61页

作者： Xuanqi GAO Chao SHEN Weipeng JIANG Chenhao LIN qian LI qian WANG Qi LI Xiaohong guan Faculty of Electronic and Information Engineering Xi'an Jiaotong University School of Cyber Science and Engineering Wuhan University Institute for Network Sciences and Cyberspace Tsinghua University

In recent years, artificial intelligence technology has been widely used in many fields, such as computer vision, natural language processing and autonomous driving. Machine learning algorithms, as the core technique of AI, have significantly facilitated people's lives. However, underlying fairness issues in machine learning systems can pose risks to individual fairness and social security. Studying fairness definitions, sources of problems, and testing and debugging methods of fairness can help ensure the fairness of machine learning systems and promote the wide application of artificial intelligence technology in various fields. This paper introduces relevant definitions of machine learning fairness and analyzes the sources of fairness problems. Besides, it provides guidance on fairness testing and debugging methods and summarizes popular datasets. This paper also discusses the technical advancements in machine learning fairness and highlights future challenges in this area.

关键词： artificial intelligence security machine learning security machine learning fairness model testing model debugging

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Partial aging can counter-intuitively couple with sulfidation to improve the reactive durability of zerovalent iron

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Frontiers of Environmental Science & Engineering 2024年第2期18卷 1-11页

作者： Yiwei Liu Kaili Gu Jinhua Zhang Jinxiang Li Jieshu qian Jinyou Shen Xiaohong guan Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing 210094China School of Ecological and Environmental Sciences East China Normal UniversityShanghai 200241China

Sulfated zero-valent iron(SZVI)has shown promising applications in wastewater ***,the rapid decline in the reactivity of SZVI with time limits its real *** mediate this problem,partial aging was proposed to improve the reactive durability of *** Cr(VI)as the target contaminant,we found that the aged ZVI(AZVI)gradually lost reactivity as aging time increased from 0.5 to 2 ***-intuitively,the partially aged SZVI(ASZVI)showed greater reactivity than SZVI when exposed to oxygenated water for a period ranging from 0.5 to 14 *** addition,the ASZVI with 0.5 d of aging time(ASZVI-0.5)not only maintained reactivity in successive runs but also increased the Cr(VI)removal capacity from 9.1 mg/g by SZVI to 19.1 mg/g by *** analysis further revealed that the electron transfer from the Fe0 core to the shell was mediated by the conductive FeS and FeS2 in the subshell of ***,the lepidocrocite and magnetite on the surface of ASZVI facilitated Cr(VI)adsorption and subsequent electron transfer for Cr(VI)***,the iron(hydr)oxide shell could retain the conductive FeS and FeS2 in the subshell,allowing ASZVI to reduce Cr(VI)efficiently and *** general,partial aging can enhance the reactive durability of ZVI when coupled with sulfidation and this synergistic effect will be beneficial to the application of SZVI-based technology for wastewater treatment.

关键词： zerovalent iron Sulfidation Partial aging Interface reconstruction Electron transfer

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Simulation of gas-solids heat transfer in cyclone pyrolyzer using CFD-DEM model

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Particuology 2024年第2期85卷 155-166页

作者： Nan Zhang Xueer Pan Jingxuan Yang qian Liu Wenhao Lian Xiao Du Zhonglin Zhang Xiaogang Hao Guoqing guan College of Chemical Engineering and Technology Taiyuan University of TechnologyTaiyuan030024China School of Chemistry and Chemical Engineering North University of ChinaTaiyuan030051China Shanxi Jinke Technology Service Company Limited Taiyuan030000China Labraory of Eey onveron Engineerng Institute f Rgional Innvation(RI)Hosaki Univerty3-BunkychoHiroak036-8561Japan

Fast heat transfer in the pyrolyzer can increase the yield of pyrolysis gas and tar,and improve the quality of *** with the downer pyrolyzer,the cyclone pyrolyzer can simultaneously achieve high solids holdup and violent turbulence,and correspondingly faster heat *** this work,the heat transfer behavior in the cyclone pyrolyzer is specifically studied using the computational fluid dynamics-discrete element *** simulation results reveal that the gas-solids heat convection contributes mainly to the heat transfer process,and the heat radiation and conduction are relatively small and almost negligible,*** with the downer pyrolyzer under the same operating conditions,the heating rate is significantly increased in the cyclone *** analyzing the flow characteristics in the cyclone pyrolyzer,it is found that the region of high convective heat transfer rate coincides with that of natural cyclone ***,the final coal temperature increases with the increase of gas velocity and exists a maximum *** results can offer some qualitative understanding of the heat transfer behavior in the cyclone pyrolyzer.

关键词： Cyclone pyrolyzer Rapidly heating Heat convection Natural cyclone length CFD-DEM

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Evolution exploration and structure prediction of Keggin-type group IVB metal-oxo clusters

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Chinese Chemical Letters 2024年第5期35卷 487-492页

作者： Run-Han Li Tian-Yi Dang Wei guan Jiang Liu Ya-qian Lan Zhong-Min Su School of Chemistry South China Normal UniversityGuangzhou 510006China Institute of Functional Material Chemistry Faculty of ChemistryNortheast Normal UniversityChangchun 130024China Institute of Theoretical Chemistry Jilin UniversityChangchun 130023China

The fascinating chemical structure and broad application prospect of Keggin-type polyoxometalates(POMs)have attracted many chemists to explore and discover *** the traditional Keggin,larger metal atomic radius,higher metal coordinated numbers,lower metal valence states and other features allow the group IVB metal-based Keggin(IVB-Keggin)more space and unknown in terms of structure and ***,density functional theory(DFT)calculations were performed to explore the influences including cores,shells,caps,and terminal ligands,et *** IVB-Keggin,and analyze the possibility of novel structure *** the perspective of multi-layer onion-like clusters,molecular energy level,host-guest interaction energy,surface charge and covalent bond polarity can be further adjusted to achieve the oriented design of functional *** insights are expected to provide theoretical support for experimental synthesis,opening a new perspective to understand the growth of Keggin.

关键词： Keggin Metal-oxo clusters Group IVB Onion pattern DFT

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Immunoglobulin G-mediated food intolerance and metabolic syndrome influence the occurrence of reflux esophagitis in Helicobacter pylori-infected patients

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World Journal of Gastroenterology 2024年第8期30卷 855-862页

作者： Li-Hui Wang Bin-Bin Su Sheng-Shu Wang guan-Chao Sun Kun-Ming Lv Yi Li Hui Shi qian-qian Chen College Chinese PLA General HospitalBeijing 100853China Department of Gastroenterology Second Medical Center of Chinese PLA General HospitalBeijing 100853China Institute of Geriatrics The 2nd Medical CenterBeijing Key Laboratory of Aging and GeriatricsNational Clinical Research Center for Geriatrics DiseasesSecond Medical Center of Chinese PLA General HospitalBeijing 100853China Department of Gastroenterology First Medical Center of Chinese PLA General HospitalBeijing 100853China

BACKGROUND Reflux esophagitis has an increasing prevalence and complex and diverse *** its risk factors is crucial to understanding the etiology,prevention,and management of the *** occurrence of reflux esophagitis may be associated with food reactions,Helicobacter pylori(***)infection,and metabolic *** To investigate the risk factors for reflux esophagitis and analyze the effects of immunoglobulin(Ig)G-mediated food intolerance,*** infection,and metabolic syndrome on reflux *** Outpatients attending the Second Medical Center of the PLA General Hospital between 2017 and 2021 were retrospectively *** patients’basic information,test results,gastroscopy results,*** test results,and IgG-mediated food intolerance results were *** logistic regression analysis was used to analyze risk factors for reflux *** mediation analysis was used to evaluate the effects of IgG-mediated food intolerance and metabolic syndrome on *** infection affecting reflux *** A total of 7954 outpatients were included;the prevalence of reflux esophagitis,IgG-mediated food intolerance,*** infection,and metabolic syndrome were 20.84%,61.77%,35.91%,and 60.15%,*** analysis showed that the independent risk factors for reflux esophagitis included IgG-mediated food intolerance(OR=1.688,95%CI:1.497-1.903,P<0.00001)and metabolic syndrome(OR=1.165,95%CI:1.030-1.317,P=0.01484),and the independent protective factor for reflux esophagitis was *** infection(OR=0.400,95%CI:0.351-0.456,P<0.00001).IgG-mediated food intolerance had a partially positive mediating effect on *** infection as it was associated with reduced occurrence of reflux esophagitis(P=0.0200).Metabolic syndrome had a partially negative mediating effect on *** infection and reduced the occurrence of reflux esophagitis(P=0.0220).CONCLUSION Patients with IgG-mediated food intol

关键词： Gastroesophageal reflux Esophagitis Food intolerance Metabolic syndrome Helicobacter pylori Chemokines

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Genome-wide identification of the pectate lyase(PEL)gene family members in Malvaceae,and their contribution to cotton fiber quality

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Journal of Integrative Agriculture 2024年第10期23卷 3264-3282页

作者： qian Deng zeyu Dong zequan Chen Zhuolin Shi Ting Zhao Xueying guan Yan Hu Lei Fang Zhejiang Provincial Key Laboratory of Crop Genetic Resources the Advanced Seed InstituteCollege of Agriculture andBiotechnologyZhejiang UniversityHangzhou 300058China Hainan Institute Zhejiang UniversitySanya 572025China

Pectin is a major constituent of the plant cell *** lyase(PEL,EC 4.***.2.2)uses anti-β-elimination chemistry to cleave theα-1,4 glycosidic linkage in the homogalacturonan region of ***,limited information is available on the comprehensive and evolutionary analysis of PELs in the *** this study,we identified 597PEL genes from 10 Malvaceae *** and motif analyses revealed that these PELs are classified into six subfamilies:Clades I,II,III,IV,Va,and *** two largest subfamilies,Clades I and II,contained 237 and222 PEL members,*** members of Clades Va and Vb only contained four or five motifs,far fewer than the other *** duplication analysis showed that segmental duplication played a crucial role in the expansion of the PEL gene family in Gossypium *** PELs from Clades I,IV,Va,and Vb were expressed during the fiber elongation stage,but nearly all PEL genes from Clades II and III showed no expression in any of the investigated fiber developmental *** further performed single-gene haplotype association analysis in 2,*** accessions and 229 *** ***,14 PELs were significantly associated with fiber length and strength traits in *** with superior fiber quality,while only eight GhPEL genes were found to be significantly associated with fiber quality traits in *** findings provide important information for further evolutionary and functional research on the PEL gene family members and their potential use for fiber quality improvement in cotton.

关键词： Malvaceae pectate lyase(PEL) Gossypium species fiber quality

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Inferring the Effects of Protein Variants on Protein-Protein Interactions with Interpretable Transformer Representations

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Research 2024年第2期2023卷 473-489页

作者： Zhe Liu Wei qian Wenxiang Cai Weichen Song Weidi Wang Dhruba Tara Maharjan Wenhong Cheng Jue Chen Han Wang Dong Xu guan Ning Lin Shanghai Mental Health Center Shanghai Jiao Tong University School of MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina Shanghai Key Laboratory of Psychotic Disorders ShanghaiChina School of Information Science and Technology Institute of Computational BiologyNortheast Normal UniversityChangchunChina Department of Electrical Engineering and Computer Science University of MissouriColumbiaMO 65211USA Christopher S.Bond Life Sciences Center University of MissouriColumbiaMO 65211USA

Identifying pathogenetic variants and inferring their impact on protein-protein interactions sheds light on their functional consequences on *** by the availability of experimental data on the consequences of protein interaction,most existing methods focus on building models to predict changes in protein binding ***,we introduced MIPPI,an end-to-end,interpretable transformer-based deep learning model that learns features directly from sequences by leveraging the interaction data from *** was specifically trained to determine the types of variant impact(increasing,decreasing,disrupting,and no effect)on protein-protein *** demonstrate the accuracy of MIPPI and provide interpretation through the analysis of learned attention weights,which exhibit correlations with the amino acids interacting with the ***,we showed the practicality of MIPPI in prioritizing de novo mutations associated with complex neurodevelopmental disorders and the potential to determine the pathogenic and driving ***,we experimentally validated the functional impact of several variants identified in patients with such ***,MIPPI emerges as a versatile,robust,and interpretable model,capable of effectively predicting mutation impacts on protein-protein interactions and facilitating the discovery of clinically actionable variants.

关键词： consequences weights versatile

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Advances in the treatment of diabetic peripheral neuropathy by modulating gut microbiota with traditional Chinese medicine

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World Journal of Diabetes 2024年第8期15卷 1712-1716页

作者： Ye-Yao Li Rui-qian guan Zhi-Bo Hong Yao-Lei Wang Li-Min Pan Department of Endocrinology The Second Affiliated Hospital of Heilongjiang University of Chinese MedicineHarbin 150001Heilongjiang ProvinceChina Department of Tuina The Second Affiliated Hospital of Heilongjiang University of Chinese MedicineHarbin 150001Heilongjiang ProvinceChina

Diabetic peripheral neuropathy(DPN)is one of the strongest risk factors for diabetic foot ulcers(neuropathic ulcerations)and the existing ulcers may further deteriorate due to the damage to sensory ***,the resulting numbness in the limbs causes difficulty in discovering these ulcerations in a short *** is associated with gut microbiota *** Chinese medicine(TCM)compounds such as Shenqi Dihuang Decoction,Huangkui Capsules and Qidi Tangshen Granules can reduce the clinical symptoms of diabetic nephropathy by modulating gut *** current review discusses whether TCM compounds can reduce the risk of DPN by improving gut microbiota.

关键词： Diabetes Peripheral neuropathy Traditional Chinese medicine Gut microbiota Diabetic foot ulcer Treatment

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IQGAP3 promotes the progression of glioma as an immune and prognostic marker

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Oncology Research 2024年第4期32卷 659-678页

作者： XIAOFENG GAO JUANJUAN GE XUZHENG GAO NA MEI YANTING SU SHIGANG SHAN WENBIN qian JIANGHENG guan ZHENWANG ZHANG LONG WANG Hubei Provincial Key Laboratory of Diabetic Cardiovascular Diseases Xianning Medical CollegeHubei University of Science and TechnologyXianning437100China School of Stomatology and Ophthalmology Xianning Medical CollegeHubei University of Science and TechnologyXianning437100China School of Basic Medical Sciences Xianning Medical CollegeHubei University of Science and TechnologyHubei University of Science and TechnologyXianning437100China School of Pharmacy Xianning Medical CollegeHubei University of Science and TechnologyXianning437100China Department of Neurosurgery The General Hospital of Chinese PLA Central Theater CommandWuhan430070China

Background:IQGAP3 plays a crucial role in regulating cell proliferation,division,and cytoskeletal *** expression of IQGAP3 has been linked to various tumors,but its function in glioma is not well ***:Various methods,including genetic differential analysis,single-cell analysis,ROC curve analysis,Cox regression,Kaplan-Meier analysis,and enrichment analysis,were employed to analyze the expression patterns,diagnostic potential,prognostic implications,and biological processes involving IQGAP3 in normal and tumor *** impact of IQGAP3 on immune infiltration and the immune microenvironment in gliomas was evaluated using ***,the cBioPortal database was used to analyze copy number variations and mutation sites of *** validation was also performed to assess the effects of IQGAP3 on glioma cells and explore underlying ***:High IQGAP3 expression in gliomas is associated with an unfavorable prognosis,particularly in wild-type IDH and 1p/19q non-codeleted *** analysis revealed that IQGAP3 is involved in regulating the cell cycle,PI3K/AKT signaling,p53 signaling,and PLK1-related ***,IQGAP3 expression may be closely related to the immunosuppressive microenvironment of ***-K88742110 and LY-303511 are potential drugs for targeting IQGAP3 in anti-glioma *** vitro experiments showed that downregulation of IQGAP3 inhibits the proliferation and migration of glioma cells,with the PLK1/PI3K/AKT pathway potentially playing a crucial role in IQGAP3-mediated glioma ***:IQGAP3 shows promise as a valuable biomarker for diagnosis,prognosis,and immunotherapeutic strategies in gliomas.

关键词： IQGAP3 Tumor immune infiltration Prognosis Glioma Biomarker

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