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Descriptor-augmented machine learning for enzyme-chemical interaction predictions

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Synthetic and Systems Biotechnology 2024年第2期9卷 259-268页

作者： Yilei han Haoye Zhang Zheni Zeng Zhiyuan liu Diannan Lu Zheng liu Department of Chemical Engineering Tsinghua UniversityBeijing100084China Department of Computer Science and Technology Tsinghua UniversityBeijing100084China

Descriptors play a pivotal role in enzyme design for the greener synthesis of biochemicals,as they could characterize enzymes and chemicals from the physicochemical and evolutionary *** study examined the effects of various descriptors on the performance of Random Forest model used for enzyme-chemical relationships *** curated activity data of seven specific enzyme families from the literature and developed the pipeline for evaluation the machine learning model performance using 10-fold *** influence of protein and chemical descriptors was assessed in three scenarios,which were predicting the activity of unknown relations between known enzymes and known chemicals(new relationship evaluation),predicting the activity of novel enzymes on known chemicals(new enzyme evaluation),and predicting the activity of new chemicals on known enzymes(new chemical evaluation).The results showed that protein descriptors significantly enhanced the classification performance of model on new enzyme evaluation in three out of the seven datasets with the greatest number of enzymes,whereas chemical descriptors appear no effect.A variety of sequence-based and structure-based protein descriptors were constructed,among which the esm-2 descriptor achieved the best *** enzyme families as labels showed that descriptors could cluster proteins well,which could explain the contributions of descriptors to the machine learning *** a counterpart,in the new chemical evaluation,chemical descriptors made significant improvement in four out of the seven datasets,while protein descriptors appear no *** attempted to evaluate the generalization ability of the model by correlating the statistics of the datasets with the performance of the *** results showed that datasets with higher sequence similarity were more likely to get better results in the new enzyme evaluation and datasets with more enzymes were more likely beneficial from the protein

关键词： Enzyme-substrate interaction Enzyme design Machine learning Descriptor

Stepping forward:T-cell redirecting bispecific antibodies in cancer therapy

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Acta Pharmaceutica Sinica B 2024年第6期14卷 2361-2377页

作者： Xiaojing Qin Wenjing Ning han liu Xue liu Wenxin Luo Ningshao Xia State Key Laboratory of Vaccines for Infectious Diseases Xiang An Biomedicine LaboratorySchool of Public HealthXiamen UniversityXiamen 361102China National Institute of Diagnostics and Vaccine Development in Infectious Diseases State Key Laboratory of Molecular Vaccinology and Molecular DiagnosticsNational Innovation Platform for IndustryeEducation Integration in Vaccine Researchthe Research Unit of Frontier Technology of Structural Vaccinology of Chinese Academy of Medical SciencesXiamen UniversityXiamen 361102China

T cell-redirecting bispecific antibodies are specifically designed to bind to tumor-associated antigens,thereby engaging with CD3 on the T cell *** linkage between tumor cells and T cells actively triggers T cell activation and initiates targeted killing of the identified tumor *** antibodies have emerged as one of the most promising avenues within tumor ***,despite success in treating hematological malignancies,significant advancements in solid tumors have yet to be *** this review,we aim to address the critical challenges associated with T cellredirecting bispecific antibodies and explore novel strategies to overcome these obstacles,with the ultimate goal of expanding the application of this therapy to include solid tumors.

关键词： Bispecific antibody(BsAbs) T-cell redirecting BsAbs Tumor-associated antigens Toxicity Cytokine release syndrome Tumor microenvironment Cancer immunotherapy Combination therapy strategies

HIV Infection and Associated Factors Among Out-of-School MSM Aged 16–24 Years—6 Cities and Tianjin Municipality,China,2022–2023

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China CDC weekly 2024年第3期6卷 45-50页

作者： Hui liu Qiyu Zhu Lei Zhang Yujing liu Peng Xu Mengjie han National Center for AIDS/STD Control and Prevention Chinese Center for Disease Control and PreventionBeijingChina Chinese Association of STD and AIDS Prevention and Control BeijingChina Beijing Chaoyang Kangzhong Health and Education Center BeijingChina

What is already known about this topic?Approximately 80%of newly diagnosed human immunodeficiency virus(HIV)cases among individuals aged 15–24 years in China are attributed to out-ofschool *** is added by this report?This study presents findings on HIV prevalence and comprehensive insights into HIV service utilization,risky behaviors,and prevention knowledge among young out-of-school men who have sex with men(MSM)aged 16–24 years in *** population exhibits a disproportionately high burden of HIV,with only 51.6%of HIV cases previously *** are the implications for public health practice?HIV services should be expanded to include these key *** interventions are needed to remove barriers to regular HIV services faced by young key populations.

关键词： prevention remove expanded

Influence of powder oxidation on powder properties and formability in H13 hot-work steels processed by electron beam melting

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Journal of Iron and Steel Research International 2024年第4期31卷 924-932页

作者： Wei liu Yan Wang Li-xiong han Ying-kang Wei Hui-ping Tang Shi-feng liu School of Metallurgical Engineering Xi'an University of Architecture and TechnologyXi'an 710055ShaanxiChina School of Engineering Zhejiang University City CollegeHangzhou 310015ZhejiangChina

The oxygen content of metal powder is decisive for the recyclability of *** research on the effect of oxygen content on powder properties and material formability has practical significance for economical production with additive manufacturing while preventing the waste of ***,we deliberately oxidized the powder by baking at high temperature to increase the oxygen content in the powder and gave the calculation method of the oxygen content in the powder oxidation *** majority of oxygen element was found in the oxide particles in the powder and the oxide flm on the powder surface,which did affect the flowability of the *** is worth noting that the increase in the oxygen content does not change the phase of H13 steel,but it can promote the molten pool flow and obtain a smoother *** increase in the oxygen content in the powder is not the decisive factor for the formability and defects of the printed *** is the combined effect of the powder deformation,the increase in the oxygen content,and the impurity pollution after repeated use,which leads to the limitation of repeated utilization of the powder.

关键词： Additive manufacturing Electron beam melting H13 steel powder-Powder oxidation

Discriminative explicit instance selection for implicit discourse relation classification

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Frontiers of Computer Science 2024年第4期18卷 129-138页

作者： Wei SONG Hongfei han Xu han Miaomiao CHENG Jiefu GONG Shijin WANG Ting liu Information Engineering College Capital Normal UniversityBeijing 100048China iFLYTEK AI Research Institute Hefei 230088China Research Center for Social Computing and Information Retrieval Harbin Institute of TechnologyHarbin 150006China

Discourse relation classification is a fundamental task for discourse analysis,which is essential for understanding the structure and connection of *** discourse relation classification aims to determine the relationship between adjacent sentences and is very challenging because it lacks explicit discourse connectives as linguistic cues and sufficient annotated training *** this paper,we propose a discriminative instance selection method to construct synthetic implicit discourse relation data from easy-to-collect explicit discourse *** expanded instance consists of an argument pair and its sense *** introduce the argument pair type classification task,which aims to distinguish between implicit and explicit argument pairs and select the explicit argument pairs that are most similar to natural implicit argument pairs for data *** also propose a simple label-smoothing technique to assign robust sense labels for the selected argument *** evaluate our method on PDTB 2.0 and PDTB *** results show that our method can consistently improve the performance of the baseline model,and achieve competitive results with the state-of-the-art models.

关键词： discourse analysis PDTB discourse relation implicit discourse relation classification data expansion

Elevated CO_(2) increases soil redox potential by promoting root radial oxygen loss in paddy field

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Journal of Environmental Sciences 2024年第2期136卷 11-20页

作者： Jie Li han Zhang Wenyi Xie Cheng liu Xiaoyu liu Xuhui Zhang Lianqing Li Genxing Pan Institute of Resource Ecosystem and Environment of AgricultureNanjing Agricultural UniversityNanjing 210095China College of Agriculture Nanjing Agricultural UniversityNanjing 210095China

Soil redox potential(Eh)plays an important role in the biogeochemical cycling of soil *** its effect soil process and nutrients'availability under elevated atmospheric CO_(2) concentration and warming has seldom been ***,in this study,a field experiment was used to elucidate the effect of elevated CO_(2) concentration and warming on soil Eh,redox-sensitive elements and root radial oxygen loss(ROL).We hypothesized elevated CO_(2) and warming could alter soil Eh by promoting or inhibiting *** found that soil Eh in the rhizosphere was significantly higher than that of *** CO_(2) enhanced soil Eh by 11.5%,which corresponded to a significant decrease in soil Fe^(2+)and Mn^(2+)*** elevated CO_(2),the concentration of Fe^(2+)and Mn^(2+)decreased by 14.7%and 13.7%,*** also found that elevated CO_(2) altered rice root aerenchyma structure and promoted rice root *** elevated CO_(2),rice root ROL increased by 79.5%and 112.2%for Yangdao 6 and Changyou 5,*** had no effect on soil Eh and rice root *** warming increased the concentration of Mn^(2+)and SO_(4)^(2-)by 4.9%and 19.3%,*** was a significant interaction between elevated CO_(2) and warming on Fe^(2+)and Mn^(2+).Under elevated CO_(2),warming had no effect on the concentration of Fe^(2+)but decreased Mn^(2+)concentration *** study demonstrated that elevated atmospheric CO_(2) in the future could increase soil Eh by promoting rice root ROL,which will alter some soil nutrients'availability,such as Fe^(2+)and Mn^(2+).

关键词： Atmospheric CO_(2)enrichment Global warming Soil redox potential FACE Rice root aerenchyma

Multi-scale design of silicon/carbon composite anode materials for lithium-ion batteries:A review

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Journal of Energy Chemistry 2024年第10期97卷 30-45,I0002页

作者： liu Yang Shuaining Li Yuming Zhang Hongbo Feng Jiangpeng Li Xinyu Zhang huai Guan Long Kong Zhaohui Chen State Key Laboratory of Heavy Oil Processing China University of Petroleum-BeijingBejing 102249China State Key Laboratoryof Mesoscience and Engineering Institute of Process EngineeringChinese Academy of Sciences Beijing 100190China Institute of Flexible Electronics(IFE) Northwestern Polytechnical UniversityXi'an 710129ShaanxiChina

Silicon/carbon composites,which integrate the high lithium storage performance of silicon with the exceptional mechanical strength and conductivity of carbon,will replace the traditional graphite electrodes for high-energy lithium-ion *** strategies have been designed to synthesize silicon/carbon composites for tackling the issues of anode pulverization and poor stability in the anodes,thereby improving the lithium storage *** effect of the regulation method at each scale on the final negative electrode performance remains ***,it has not been fully clarified how the regulation methods at each scale influence the final anode *** review will categorize the materials structure into three scales:molecular scale,nanoscale,and ***,the review will examine modification methods at the molecular scale,focusing on the interfacial bonding force between silicon and ***,it will summarize various nanostructures and special shapes in the nanoscale to explore the construction of silicon/carbon ***,the review will provide an analysis of microscale control approaches,focusing on the formation of composite particle with micron size and the utilization of *** review provides a comprehensive overview of the multi-scale design of silicon/carbon composite anode materials and their optimization strategies to enhance the performance of lithium-ion batteries.

关键词： Lithium-ion batteries Silicon/carbon composites Molecular scale Nanoscale Microscale

Emerging clinical relevance of microbiome in cancer:promising biomarkers and therapeutic targets

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Protein & Cell 2024年第4期15卷 239-260页

作者： Jia-Hao Dai Xi-Rong Tan han Qiao Na liu State Key Laboratory of Oncology in South China Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangdong Provincial Clinical Research Center for CancerSun Yat-sen University Cancer CenterGuangzhou 510050China

The profound influence of microbiota in cancer initiation and progression has been under the spotlight for years,leading to numerous researches on cancer microbiome entering clinical *** promising biomarkers and therapeutic targets,the critical involvement of microbiota in cancer clinical practice has been increasingly ***,recent progress in this field is *** describe the potential of tumor-associated microbiota as effective diagnostic and prognostic biomarkers,*** addition,we highlight the relationship between microbiota and the therapeutic efficacy,toxicity,or side effects of commonly utilized treatments for cancer,including chemotherapy,radiotherapy,and *** that microbial factors influence the cancer treatment outcome,we further summarize some dominating microbial interventions and discuss the hidden risks of these *** review aims to provide an overview of the applications and advancements of microbes in cancer clinical relevance.

关键词： microbiome cancer diagnosis prognosis therapy

Effects of iron oxide on crystallization behavior and spatial distribution of spinel in stainless steel slag

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International Journal of Minerals,Metallurgy and Materials 2024年第2期31卷 292-300页

作者： Zihang Yan Qing Zhao Chengzhi han Xiaohui Mei Chengjun liu Maofa Jiang Key Laboratory for Ecological Metallurgy of Multimetallic Mineral(Ministry of Education Northeastern UniversityShenyang 110819China School of Metallurgy Northeastern UniversityShenyang 110819China

Chromium plays a vital role in stainless steel due to its ability to improve the corrosion resistance of the ***,the re-lease of chromium from stainless steel slag(SSS)during SSS stockpiling causes detrimental environmental *** prevent chromium pollution,the effects of iron oxide on crystallization behavior and spatial distribution of spinel were investigated in this *** results revealed that FeO was more conducive to the growth of spinels compared with Fe2O3 and *** were found to be mainly distrib-uted at the top and bottom of *** amount of spinel phase at the bottom decreased with the increasing FeO content,while that at the top *** average particle size of spinel in the slag with 18wt%FeO content was 12.8μ***,no notable structural changes were observed with a further increase in FeO *** other words,the spatial distribution of spinel changed when the content of iron oxide varied in the range of 8wt%to 18wt%.Finally,less spinel was found at the bottom of slag with a FeO content of 23wt%.

关键词： stainless steel slag spinel chromium waste remediation ferrous oxide