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Developing ChatGPT for biology and medicine: a complete review of biomedical question answering

Biophysics Reports 2024年第3期10卷 152-171页

作者： qing li Lei li Yu li Department of Computer Science and Engineering the Chinese University of Hong Kong

ChatGPT explores a strategic blueprint of question answering(QA) to deliver medical diagnoses, treatment recommendations, and other healthcare support. This is achieved through the increasing incorporation of medical domain data via natural language processing(NLP) and multimodal paradigms. By transitioning the distribution of text, images, videos, and other modalities from the general domain to the medical domain, these techniques have accelerated the progress of medical domain question answering(MDQA). They bridge the gap between human natural language and sophisticated medical domain knowledge or expert-provided manual annotations, handling large-scale, diverse, unbalanced, or even unlabeled data analysis scenarios in medical contexts. Central to our focus is the utilization of language models and multimodal paradigms for medical question answering, aiming to guide the research community in selecting appropriate mechanisms for their specific medical research *** tasks such as unimodal-related question answering, reading comprehension, reasoning, diagnosis, relation extraction, probability modeling, and others, as well as multimodal-related tasks like vision question answering, image captioning, cross-modal retrieval, report summarization, and generation, are discussed in detail. Each section delves into the intricate specifics of the respective method under consideration. This paper highlights the structures and advancements of medical domain explorations against general domain methods, emphasizing their applications across different tasks and datasets. It also outlines current challenges and opportunities for future medical domain research,paving the way for continued innovation and application in this rapidly evolving field. This comprehensive review serves not only as an academic resource but also delineates the course for future probes and utilization in the field of medical question answering.

关键词： ChatGPT Medical question answering Nature language processing Multimodal paradigms Large language models

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Characterization of Mutations in Genes Related to Rifampicin and Isoniazid Resistance in Multidrug-resistant Mycobacterium tuberculosis Strains from Hangzhou,China

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Biomedical and Environmental Sciences 2023年第9期36卷 869-873页

作者： HUANG Yin Yan XIE li WU Yi Fei JIA qing Jun CHENG qing lin li qing Chun AI li Yun BAI Xue Xin Department of TB Control and Prevention Hangzhou Center for Disease Control and PreventionHangzhou 310021ZhejiangChina

Tuberculosis(TB),caused by the Mycobacterium tuberculosis complex(MTBC),is the 13^(th)leading cause of death and the second leading cause of infectious killer after COVID-19(above HIV and AIDS),according to the World Health Organization's 2022 Global TB *** 2021,10.6 million people were diagnosed with a new episode of TB and 1.6 million people died as a result.

关键词： tuberculosis death Mycobacterium

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An update on the function and regulation of methylerythritol phosphate and mevalonate pathways and their evolutionary dynamics

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Journal of Integrative Plant Biology 2021年第7期63卷 1211-1226页

作者： Xiaojun Pu Xiumei Dong qing li Zexi Chen li liu State Key Laboratory of Biocatalysis and Enzyme Engineering Hubei Collaborative Innovation Center for Green Transformation of BioResourcesHubei Key Laboratory of Industrial BiotechnologySchool of Life SciencesHubei UniversityWuhan 434200China Key Laboratory for Economic Plants and Biotechnology Kunming Institute of Botanythe Chinese Academy of Sciencesand Yunnan Key Laboratory for Wild Plant ResourcesKunming 650201China School of life Sciences Yunnan UniversityKunming 650091China University of the Chinese Academy of Sciences Beijing 100049China

Isoprenoids are among the largest and most chemically diverse classes of organic compounds in nature and are involved in the processes of photosynthesis, respiration, growth, development,and plant responses to stress. The basic building block units for isoprenoid synthesis-isopentenyl diphosphate and its isomer dimethylallyl diphosphate-are generated by the mevalonate (MVA) and methylerythritol phosphate(MEP) pathways. Here, we summarize recent advances on the roles of the MEP and MVA pathways in plant growth, development and stress responses, and attempt to define the underlying gene networks that orchestrate the MEP and MVA pathways in response to developmental or environmental *** phylogenomic analysis, we also provide a new perspective on the evolution of the plant isoprenoid pathway. We conclude that the presence of the MVA pathway in plants may be associated with the transition from aquatic to subaerial and terrestrial environments, as lineages for its core components are absent in green algae. The emergence of the MVA pathway has acted as a key evolutionary event in plants that facilitated land colonization and subsequent embryo development, as well as adaptation to new and varied environments.

关键词： evolutionary innovation MEP pathway MVA pathway retrograde signaling stress

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Ectopic Expression of FaDREB2 Enhances Osmotic Tolerance in Paper Mulberry

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Journal of Integrative Plant Biology 2011年第12期53卷 951-960页

作者： Mei-Ru li Yan li Hong-qing li Guo-Jiang Wu Key Laboratory of Plant Resources Conservation and Sustainable Utilization South China Botanical Garden Chinese Academy of Sciences Guangzhou 510650 China Xinjiang University Urumqi 830046 China Guangdong Provincial Key Lab of Biotechnology for Plant Development South China Normal University Guangzhou 510631 China

Dehydration-responsive element binding （DREB） proteins are a subfamily of AP2/ERF transcription factors that have been shown to improve tolerance to osmotic stresses in plants. To improve the osmotic stress tolerance of paper mulberry （Broussonetia papyrifera L. Vent）, an economically important tree, we transformed it with a plasmid carrying tall fescue （Festuca arundinacea Schreb） FaDREB2 under the control of CaMV 35S. The ectopic expression of FaDREB2 did not cause growth retardation, and the paper mulberry seedlings expressing FaDREB2 showed higher salt and drought tolerance than wild-type plants （WT）. After 13 d of withholding water, or 15 d in the presence of 250 mM NaCI, all the WT plants died, while the plants expressing FaDREB2 survived. The FaDREB2 transgenic plants had higher leaf water and chlorophyll contents, accumulated more proline and soluble sugars, and had less membrane damage than the WT plants under high salt and water-deficient conditions. Taken together, the results indicate the feasibility of improving tolerance to multiple environmental stresses in paper mulberry seedlings via genetic engineering, by introducing FaDREB2, which promotes the increased accumulation of osmolytes （soluble sugars and proline）, to counter osmotic stresses caused by abiotic factors.

关键词： FaDREB2 Broussonetia papyrifera paper mulberry salt tolerance drought tolerance

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A Cultural Study of Chinese American Women's Self-Identification and Education

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Frontiers of Education in China 2010年第2期5卷 186-196页

作者： qing li Department of Cultural Foundations of Education Syracuse UniversityNY 13244USA

This qualitative research aims to investigate the process of how Chinese American women develop their identities while growing up in the United States as daughters of Chinese ***,the author explores the following questions:How do Chinese American women come to identify themselves as Chinese American,and act this identity in their everyday lives?How does the process of self-identification interact with their interpretations of how they are perceived and recognized?How do they incorporate educational messages from their family and schooling into their own understandings of the social world they live in?How have their understandings of their identity changed along the path with their encountering different social contexts and institutions?Through collecting personal accounts by interviews,the researcher intends to unravel the intersectionality of race,class,gender,and ethnicity,and illustrate how that would affect these Chinese American women's educational experience and life outcomes accordingly.

关键词： Chinese American immigrant minority race/ethnicity identity

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Synchronization and Control of Halo-Chaos in Beam Transport Network with Small World Topology

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Communications in Theoretical Physics 2007年第4期47卷 752-758页

作者： liU Qiang FANG Jin-qing li Yong China Institute of Atomic Energy P.O. Box 275-81 Beijing 102413 China

The synchronous conditions of two kinds of the small-world （SW） network are studied. The small world topology can affect on dynamical behaviors of the beam transport network （BTN） largely, if the BTN is constructed with the SW topology, the global linear coupling and special linear feedback can realize the synchronization control of beam halo-chaos as well as periodic state in the BTN with the SW topology, respectively. This important result can provide an effective way for the experimental study and the engineering design of the BTN in the high-current accelerator driven radioactive clean nuclear power systems, and may have potential use in prospective applications for halo-chaos secure communication.

关键词： beam halo-chaos synchronization control small-world network beam transport network global linear coupling special linear feedback

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Formation mechanism and modeling of surface waviness in incremental sheet forming

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Frontiers of Mechanical Engineering 2022年第2期17卷 129-143页

作者： Kai HAN Xiaoqiang li Yanle li Peng XU Yong li qing li Dongsheng li School of Mechanical Engineering and Automation Beihang UniversityBeijing 100083China Beijing Institute of Aeronautical Materials Beijing 100095China School of Mechanical Engineering Shandong UniversityJinan 250061China Key Laboratory of High Efficiency and Clean Mechanical Manufacture Ministry of EducationJinan 250061China Materials Science Branch of Chinalco Research Institute Chinalco Materials Application Research Institute Co.Ltd.Beijing 102209China

mproving and controlling surface quality has always been a challenge for incremental sheet forming (ISF), whereas the generation mechanism of waviness surface is still unknown, which impedes the widely application of ISF in the industrial field. In this paper, the formation mechanism and the prediction of waviness are both investigated through experiments, numerical simulation, and theoretical analysis. Based on a verified finite element model, the waviness topography is predicted numerically for the first time, and its generation is attributed to the residual bending deformation through deformation history analysis. For more efficient engineering application, a theoretical model for waviness height is proposed based on the generation mechanism, using a modified strain function considering deformation modes. This work is favorable for the perfection of formation mechanism and control of surface quality in ISF.

关键词： surface waviness incremental sheet forming numerical simulation formation mechanism deformation history

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Feedback Learning Based Dead Write Termination for Energy Efficient STT-RAM Caches

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Chinese Journal of Electronics 2017年第3期26卷 460-467页

作者： SHEN Fanfan HE Yanxiang ZHANG Jun JIANG Nan li qing'an li Jianhua Computer School Wuhan University State Key Laboratory of Software Engineering Wuhan University School of Computer and Information Hefei University of Technology

Spin-torque transfer RAM(STT-RAM) is a promising candidate to replace SRAM for larger Last level cache(LLC). However, it has long write latency and high write energy which diminish the benefit of adopting STT-RAM caches. A common observation for LLC is that a large number of cache blocks have never been referenced again before they are evicted. The write operations for these blocks, which we call dead writes, can be eliminated without incurring subsequent cache misses. To address this issue, a quantitative scheme called Feedback learning based dead write termination(FLDWT) is proposed to improve energy efficiency and performance of STT-RAM based LLC. FLDWT dynamically learns the block access behavior by using data reuse distance and data access frequency, and then classifies the blocks into dead blocks and live blocks. FLDWT terminates dead write block requests and improves the estimation accuracy via feedback information. Compared with STT-RAM baseline in the lastlevel caches, experimental results show that our scheme achieves energy reduction by 44.6% and performance improvement by 12% on average with negligible overhead.

关键词： Dead blocks Energy efficiency Spintransfer torque RAM(STT-RAM) Last level cache(LLC)

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Existing form and effect of zirconium in pure Mg,Mg-Yb,and Mg-Zn-Yb alloys

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Rare Metals 2009年第3期28卷 289-296页

作者： YU Wenbin HE Hong li Chunmei li qing liU Zhiyi QIN Bing School of Materials Science and Engineering Southwest University Chongqing 400715 China School of Materials Science and Engineering Central South University Changsha 410083 China

The existing form and grain refining effects of small zirconium addition in pure Mg, Mg-Yb and Mg-Zn binary alloys, and Mg-Zn-Yb ternary alloy （ZK60-Yb） were investigated. The results show that Zr element exists mainly in single and cluster particles of pure α-Zr or Zn-Zr compounds inside grains and at grain boundaries. Only the particles located in the interior of grains can act as the nucleus for α-Mg growth and effectively promote the formation of fine equiaxed grains. The broken and dispersed Zr-rich particles produced during the hot extrusion process can form nebulous banded structure in which these fine particles may act as obstacles to dislocation motion in wrought magnesium alloys.

关键词： magnesium alloys zirconium grain refinement microstructure ytterbium

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DFT Investigation on the Enantioselectivity of Olefin Carboacylation Catalyzed by a Rh(Ⅰ) Complex

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Chinese Journal of Structural Chemistry 2020年第4期39卷 630-642页

作者： CHENG Xue-li li li-qing HAN Yin-Feng TAN qing-Long XIA Qi-Ying School of Chemistry and Chemical Engineering Taishan UniversityTai’an 271000China School of Chemistry Chemical Engineering and MaterialsZaozhuang UniversityZaozhuang 277160China School of Chemistry and Chemical Engineering Linyi UniversityLinyi 276005China

The C-C bond activation and recyclization of benzocyclobutenone to poly-fused rings catalyzed by the[Rh(R,S-L)]+complex producing the R,S-,S,R-,R,R-and S,S-product were investigated systematically at the BP86/6-31G(d,p)level in gas phase and THF,and the R,S-and S,R-reaction pathways were revisited at the M062X/6-31G(d,p)level in *** computational results reveal that THF only marginally alters the free-energy barriers,but elevates the relative energies of all *** BP86 functional testifies that in both gas phase and THF,the activation of strained C-C bonds bears relatively low free-energy barriers,and the rate-determining steps of S,R-and R,R-channels are different from those of R,S-and S,*** BP86 functional also predicts that the R,S-channel is energetically most favorable in gas phase,but the S,R-product is dominant in *** change of NPA charges can mirror the variation of molecular structures to elucidate reaction mechanisms.

关键词： benzocyclobutenone carboacylation enantioselectivity BP86 M06-2X

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