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Advancements in prokaryotic systematics and the role of bergey's International Society for Microbial Systematics in addressing challenges in the meta-data era

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National Science Review 2024年第7期11卷 292-304页

作者： Jian-Yu Jiao Rashidin Abdugheni Dao-Feng Zhang Iftikhar Ahmed Mukhtiar Ali Maria Chuvochina Svetlana N.Dedysh Xiuzhu Dong Markus G?ker brian P.Hedlund Philip Hugenholtz Kamlesh Jangid Shuang-Jiang Liu Edward R.b.Moore Manik Prabhu Narsing Rao Aharon Oren Ramon Rossello-Mora bhagwan Narayan Rekadwad Nimaichand Salam Wensheng Shu Iain C.Sutcliffe Wee Fei Aaron Teo Martha E.Trujillo Stephanus N.Venter william b.whitman.guopin. zhao Wen-Jun Li State Key Laboratory of biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) School of Life Sciences Sun Yat-Sen University State Key Laboratory of Desert and Oasis Ecology Key Laboratory of Ecological Safety and Sustainable Development in Arid LandsXinjiang Institute of Ecology and Geography Chinese Academy of Sciences Jiangsu Province Engineering Research Center for Marine bio-resources Sustainable Utilization&College of Oceanography Hohai University National Culture Collection of Pakistan(NCCP) Land Resources Research Institute(LRRI) National Agricultural Research Centre(NARC) The University of Queensland School of Chemistry and Molecular Biosciences Australian Centre for Ecogenomics Winogradsky Institute of Microbiology Research Center of BiotechnologyRussian Academy of Sciences State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures School of Life Sciences University of Nevada Nevada Institute of Personalized Medicine University of Nevada bioenergy Group MACS Collection of Microorganisms Agharkar Research Institute State Key Laboratory of Microbial Technology Shandong University Department of Infectious Disease Institute for Biomedicine and Culture Collection University of Gothenburg(CCUG) Institute for BiomedicineSahlgrenska AcademyUniversity of Gothenburg Instituto de Ciencias Aplicadas Facultad de Ingeniería Universidad Autónoma de Chile The Alexander Silberman Institute of Life Sciences The Edmond J.Safra Campus The Hebrew University of Jerusalem Marine Microbiology Group Department of Animal and Microbial Biodiversity Mediterranean Institute for Advanced Studies(IMEDEA CSIC-UIB) MicrobeAI Lab Division of Microbiology and Biotechnology Yenepoya Research Centre Yenepoya(Deemed to be University) National Agri-Food biotechnology Institute Institute of Ecological Science Sch

Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic *** transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, bergey's Manual of Systematics of Archaea and bacteria(bMSAb) and bergey's International Society for Microbial Systematics(bISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of bMSAb and bISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of bISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.

关键词： prokaryotic systematics bergey's Manual of Systematics of Archaea and bacteria (bMSAb) bergey's International Society for Microbial Systematics (bISMiS) meta-data era

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Generalized time-dependent generator coordinate method for induced fission dynamics

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Frontiers of physics 2024年第4期19卷 1-12页

作者： b.Li D.Vretenar T.Nikšić J.zhao P.W.zhao J.Meng State Key Laboratory of Nuclear Physics and Technology School of PhysicsPeking UniversityBeijing 100871China Physics Department Faculty of ScienceUniversity of Zagreb10000 ZagrebCroatia Center for Circuits and Systems Peng Cheng LaboratoryShenzhen 518055China

The generalized time-dependent generator coordinate method(TD-GCM)is extended to include pairing *** correlated GCM nuclear wave function is expressed in terms of time-dependent generator states and weight *** particle–hole channel of the effective interaction is determined by a Hamiltonian derived from an energy density functional,while pairing is treated dynamically in the standard bCS approximation with time-dependent pairing tensor and single-particle occupation *** the inclusion of pairing correlations,various time-dependent phenomena in open-shell nuclei can be described more *** model is applied to the description of saddle-to-scission dynamics of induced *** generalized TD-GCM charge yields and total kinetic energy distribution for the fission of 240Pu,are compared to those obtained using the standard time-dependent density functional theory(TD-DFT)approach,and with available data.

关键词： nuclear density functional theory generator coordinate method fission dynamics

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H-and J-aggregation of conjugated small molecules in organic solar cells

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Journal of Energy Chemistry 2024年第6期93卷 174-192,I0005页

作者： Qiaoqiao zhao Feng He State Key Laboratory of biobased Material and Green Papermaking Qilu University of TechnologyShandong Academy of SciencesJinan 250353ShangdongChina Shenzhen Grubbs Institute and Department of Chemistry Southern University of Science and TechnologyShenzhen 518055GuangdongChina Guangdong Provincial Key Laboratory of Catalysis Southern University of Science and TechnologyShenzhen 518055GuangdongChina

As H-and J-aggregation receive more and more attention in the research of organic solar cells(OSCs),especially in small molecular systems,deep understanding of aggregation behavior is needed to guide the design of conjugated small molecular structure and the fabrication process of OSC *** this end,this review is ***,the review firstly introduced the basic information about H-and J-aggregation of conjugated small molecules in ***,the characteristics of H-and J-aggregation and the methods to identify them were ***,it reviewed the research progress of H-and J-aggregation of conjugated small molecules in OSCs,including the factors influencing H-and J-aggregation in thin film and the effects of H-and J-aggregation on OPV performance.

关键词： H-aggregation J-aggregation Organic solar cells Small molecules Efficiency Stability

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Cortical Organoid-on-a-Chip with Physiological Hypoxia for Investigating Tanshinone IIA-Induced Neural Differentiation

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Research 2024年第3期2023卷 457-468页

作者： Yue Zhi Yujuan Zhu Jinglin Wang Junqi zhao Yuanjin zhao Department of Rheumatology and Immunology Nanjing Drum Tower HospitalClinical Medical College of Traditional Chinese and Western MedicineNanjing University of Chinese MedicineNanjing210023China State Key Laboratory of bioelectronics School of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096China Shenzhen Research Institute Southeast UniversityShenzhen518038China

Cortical organoids represent cutting-edge models for mimic human brain development during the early and even middle stage of pregnancy, while they often fail to recreate the complex microenvironmental factors, such as physiological hypoxia. Herein, to recapitulate fetal brain development, we propose a novel cortical organoid-on-a-chip with physiological hypoxia and further explore the effects of tanshinone IIA (Tan IIA) in neural differentiation. The microfluidic chip was designed with a micropillar array for the controlled and efficient generation of cortical organoids. With low oxygen, the generated cortical organoids could recapitulate key aspects of early-gestational human brain development. Compared to organoids in normoxic culturing condition, the promoted neurogenesis, synaptogenesis and neuronal maturation were observed in the present microsystem, suggesting the significance of physiological hypoxia in cortical development. based on this model, we have found that Chinese herbal drug Tan IIA could promote neural differentiation and maturation, indicating its potential therapeutic effects on neurodevelopmental disorders as well as congenital neuropsychiatric diseases. These results indicate that the proposed biomimetic cortical organoid-on-a-chip model with physiological hypoxia can offer a promising platform to simulate prenatal environment, explore brain development, and screen natural neuroactive components.

关键词： promoted herbal cutting

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THE EXISTENCE OF PSEUDOHARMONIC MAPS FOR SMALL HORIZONTAL ENERGY

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Acta Mathematica Scientia 2024年第5期44卷 1955-1964页

作者： biqiang zhao Shanghai Center for Mathematical Sciences Fudan UniversityShanghai200433China

In this paper,we consider pseudoharmonic heat flow with small initial horizontal energy and give the existence of pseudoharmonic maps from closed pseudo-Hermitian manifolds into closed Riemannian manifolds.

关键词： pseudoharmonic map pseudoharmonic heat flow small horizontal energy

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HDPairFinder:A data processing platform for hydrogen/deuterium isotopic labeling-based nontargeted analysis of trace-level amino-containing chemicals in environmental water

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Journal of Environmental Sciences 2024年第2期136卷 583-593页

作者： Tingting zhao Kristin Carroll Caley b.Craven Nicholas J.P.Wawryk Shipei Xing Jian Guo Xing-Fang Li Tao Huan Department of Chemistry Faculty of ScienceUniversity of British ColumbiaVancouver Campus2036 Main MallVancouverBritish ColumbiaV6T 1Z1Canada Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlberta T6G 2G3Canada

The combination of hydrogen/deuterium(H/D)formaldehyde-based isotopic methyl labeling with solid-phase extraction and high-performance liquid chromatography–high resolution mass spectrometry(HPLC-HRMS)is a powerful analytical solution for nontargeted analysis of trace-level amino-containing chemicals in water *** the huge amount of chemical information generated in HPLC-HRMS analysis,identifying all possible H/Dlabeled amino chemicals presents a significant challenge in data *** address this,we designed a streamlined data processing pipeline that can automatically extract H/D-labeled amino chemicals from the raw HPLC-HRMS data with high accuracy and ***,we developed a cross-correlation algorithm to correct the retention time shift resulting from deuterium isotopic effects,which enables reliable pairing of H-and D-labeled ***,we implemented several bioinformatic solutions to remove false chemical features generated by in-source fragmentation,salt adduction,and natural13C ***,we used a data mining strategy to construct the AMINES library that consists of over 38,000 structure-disjointed primary and secondary amines to facilitate putative compound ***,we integrated these modules into a freely available R program,*** rationale of each module was justified and its performance tested using experimental H/D-labeled chemical standards and authentic water *** further demonstrated the application of HDPairFinder to effectively extract N-containing contaminants,thus enabling the monitoring of changes of primary and secondary N-compounds in authentic water *** is a reliable bioinformatic tool for rapid processing of H/D isotopic methyl labeling-based nontargeted analysis of water samples,and will facilitate a better understanding of N-containing chemical compounds in water.

关键词： Isotope labeling Nontargeted analysis Reactive N-compounds HPLC-HRMS Source water

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Trajectory of COVID-19 response and management strategy in China:scientific rationale driven strategy adjustments

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Frontiers of Medicine 2024年第1期18卷 19-30页

作者： Zeyu Zhang Yue Yan Lina zhao Yizhou bian Ning zhao You Wu Dahai zhao Zongjiu Zhang Institute for Hospital Management Tsinghua UniversityBeijing100084China School of Medicine Tsinghua UniversityBeijing100084China School of International and Public Affairs Shanghai Jiao Tong UniversityShanghai200030China Yale University-Shanghai Jiao Tong University Joint Center for Health Policy Shanghai Jiao Tong UniversityShanghai200030China

The pneumonia caused by novel coronavirus SARS-CoV-2 infection in early December 2019,which was later named coronavirus disease 2019(COVID-19)by the World Health Organization(WHO),rapidly spread across the *** has made extraordinary efforts to this unprecedented pandemic,put its response and control at a very high level of infectious disease management(Category b but with measures for Category A),given top priority to the people and their lives,and balanced the pandemic control and socio-economic *** more than three years’fighting against this disease,China downgraded the management of COVID-19 to Category b infectious disease on January 8,2023 and the WHO declared the end of public health emergency on May 5,***,the ending of pandemic does not mean that the disease is no longer a health *** against COVID-19 from China and the whole world should be learned to prepare well for the future public health *** article gives a systematic review of the trajectory of COVID-19 development in China,summarizes the critical policy arrangements and provides evidence for the adjustment during policy making process,so as to share experiences with international community and contribute to the global health for all humanity.

关键词： COVID-19 public health response and control strategy science-based policy making

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Recent advances in small-scale hydrogel-based robots for adaptive biomedical applications

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Nano Research 2024年第2期17卷 649-662页

作者： Mingzhe Nie Qilong zhao Xuemin Du Institute of biomedical&Health Engineering Shenzhen Institute of Advanced Technology(SIAT)Chinese Academy of Sciences(CAS)Shenzhen 518055China

Small-scale robots,ranging in size from micrometers to centimeters,have gained significant attention in the biomedical ***,conventional small-scale robots made of rigid materials encounter challenges in adapting themselves to the soft tissues and complicated environments of human *** to the rigid counterpart,small-scale hydrogel-based robots hold great promises due to their tissue-like low modulus,outstanding biocompatibility and accessible stimuli-responsive *** attributes offer small-scale hydrogel-based robots with multimodal locomotion and reinforced functions,further enhancing the adaptability in manipulation and tasks execution for various biomedical *** this review,we present recent advances in small-scale hydrogel-based *** first summarize the design principles of small-scale hydrogel-based robots including materials,fabrication techniques and manipulation strategies,then highlighting their upgraded functions and adaptive biomedical ***,we discuss existing challenges and future perspectives for small-scale hydrogel-based robots.

关键词： small-scale robot hydrogel locomotion multi-function adaptability

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Pr-Tb synergistic strengthening on coercivity of Nd-Ce-Fe-b magnets grain boundary diffused with Pr-Tb-Al-Ga alloys

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Journal of Rare Earths 2024年第9期42卷 1704-1709,I0003页

作者： Ruifang Song Hang zhao Haibo Feng Institute of Functional Materials Central Iron&Steel Research InstituteBeijing100081China

Sintered Nd-Ce-Fe-b magnets were grain boundary diffused(GbDed) with Pr_(x)Tb_(80-x)Al_(10)Ga_(10)(at%)(x=0,20,40,60,80) *** effect of Pr/Tb content in diffusion source on magnetic properties,microstructure and elements distribution of GbDed magnets was *** Pr is used to substitute for 75% Tb in diffusion source,Tb consumption per unit coercivity improvement of GbDed magnet reduces by 77%,compared with the Tb_(80)Al_(10)Ga_(10) diffused *** element diffuses into magnets and then forms Tb-rich shell with high magneto-crystalline anisotropy field surrounding main phase grains,resulting in substantial coercivity *** with low melting point diffuses deeply along liquid grain boundary phase during GbD *** can eliminate some sharp defects of main phase grains and make grain boundaries smooth,which provides diffusion channels for further diffusion of Tb ***,there are more diffusion channels for Tb and less Tb enriched at surface region,making Tb diffuse more deeply and improving Tb utilization *** method significantly improves the coercivity,and realizes the green,efficient and high-quality utilization of heavy rare earth(HRE)elements.

关键词： Grain boundary diffusion Rare earths Microstructure Synergistic strengthening

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cKbET:assessing goodness of batch effect correction for single-cell RNA-seq

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Frontiers of Computer Science 2024年第1期18卷 215-228页

作者： Yameng zhao Yin GUO Limin LI School of Mathematics and Statistics Xi’an Jiaotong UniversityXi’an 710049China

Single-cell RNA sequencing reveals the gene structure and gene expression status of a single cell,which can reflect the heterogeneity between ***,batch effects caused by non-biological factors may hinder data integration and downstream *** the batch effect can be evaluated by visualizing the data,which actually is subjective and *** this work,we propose a quantitative method cKbET,which considers the batch and cell type information *** cKbET method accesses batch effects by comparing the global and local fraction of cells of different batches in different cell *** verify the performance of our cKbET method on simulated and real biological data *** experimental results show that our cKbET method is superior to existing methods in most *** general,our cKbET method can detect batch effect with either balanced or unbalanced cell types,and thus evaluate batch correction methods.

关键词： single-cell RNA-seq dataset b batch effect assessment cKbET method

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