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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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A Neural-network-based Alternative Scheme to Include Nonhydrostatic Processes in an Atmospheric Dynamical Core

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Advances in Atmospheric Sciences 2024年第6期41卷 1083-1099,I0002,I0003页

作者： Yang xia Bin WANG lijuan li li liU Jianghao li li DONG Shiming XU Yiyuan li Wenwen xia Wenyu HUANG Juanjuan liU Yong WANG Hongbo liU Ye PU Yujun HE Kun xia Ministry of Education Key Laboratory for Earth System Modeling and Department of Earth System ScienceTsinghua UniversityBeijing 100084China State Key Laboratory of Numerical Modeling for Atmospheric Sciences and Geophysical Fluid Dynamics Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China Innovation Group 311020008 Southern Marine Science and Engineering Guangdong LaboratoryZhuhai 519000China Shanghai Ecological Forecasting and Remote Sensing Center Shanghai 200030China Key Laboratory of Earth System Modeling and Prediction China Meteorological AdministrationBeijing 100081China College of Ocean Sciences University of Chinese Academy of SciencesBeijing 100049China

Here,a nonhydrostatic alternative scheme(NAS)is proposed for the grey zone where the nonhydrostatic impact on the atmosphere is evident but not large enough to justify the necessity to include an implicit nonhydrostatic solver in an atmospheric dynamical *** NAS is designed to replace this solver,which can be incorporated into any hydrostatic models so that existing well-developed hydrostatic models can effectively serve for a longer *** advances in machine learning(ML)provide a potential tool for capturing the main complicated nonlinear-nonhydrostatic *** this study,an ML approach called a neural network(NN)was adopted to select leading input features and develop the *** NNs were trained and evaluated with 12-day simulation results of dry baroclinic-wave tests by the Weather Research and Forecasting(WRF)*** forward time difference of the nonhydrostatic tendency was used as the target variable,and the five selected features were the nonhydrostatic tendency at the last time step,and four hydrostatic variables at the current step including geopotential height,pressure in two different forms,and potential temperature,***,a practical NAS was developed with these features and trained layer by layer at a 20-km horizontal resolution,which can accurately reproduce the temporal variation and vertical distribution of the nonhydrostatic *** by the NN-based NAS,the improved hydrostatic solver at different horizontal resolutions can run stably for at least one month and effectively reduce most of the nonhydrostatic errors in terms of system bias,anomaly root-mean-square error,and the error of the wave spatial pattern,which proves the feasibility and superiority of this scheme.

关键词： neural network nonhydrostatic alternative scheme atmospheric model dynamical core

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CNT array-induced nanobubble assembly,nanodisk fabrication and enhanced spectral detection of CNT bundle density

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Nano Research 2024年第8期17卷 7737-7745页

作者： Zhiyuan xia Ziming Ye Bo Zhao Tingsong Zhang Qi Wang Kun Chen Meng li xiaobing Kong Yu-qing Zheng Enzheng Shi Yuanyuan Shang Anyuan Cao School of Materials Science and Engineering Peking UniversityBeijing 100871China School of Integrated Circuits Peking UniversityBeijing 100871China School of Physics and Microelectronics Zhengzhou UniversityZhengzhou 450001China School of Engineering Westlake UniversityHangzhou 310024China

Alignment,functionalization and detection of carbon nanotube(CNT)bundles are vital processes for utilizing this onedimensional nanomaterial in ***,we report a polymer-assisted wet shearing method to acquire super-aligned craterpatterned CNT arrays by nanobubble(NB)self-assembly with a"migrate and aggregation"mechanism and use craters to controllably mold even-sized nanodisks periodically along CNT bundles with tunable *** green,low-cost method can be extended to diverse substrates and fabricate different *** an example,the Ag-nanodisk-patterned CNT arrays are utilized as substrates of surface-enhanced Raman scattering(SERS)for rhodamine 6G(R6G)and methylene blue(MB)in which a linear correlation is found between the SERS intensity and the CNT bundle density due to the periodic distribution of hot spots,enabling a spectral detection of CNT bundles and their densities by conventional dye *** from routine morphological characterization,this spectral method possesses an enhanced accuracy and a detection range of 0.1–2μm^(–1),showing its uniqueness in the detection of CNT bundle density since the intensity of traditional spectral merely relates to the quantity of CNTs,exhibiting its potential in future CNT-bundle-based electronics.

关键词： CNT arrays nanobubbles self-assembly nanodisks surface-enhanced Raman scattering(SERS)

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Distribution of paired immunoglobulin-like receptor B in the nervous system related to regeneration difficulties after unilateral lumbar spinal cord injury

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Neural Regeneration Research 2015年第7期10卷 1139-1146页

作者： Wan-shu Peng Chao Qi Hong Zhang Mei-ling Gao Hong Wang Fei Ren xia-qing li Department of Pathophysiology Shanxi Medical University

Paired immunoglobulin-like receptor B（Pir B） is a functional receptor of myelin-associated inhibitors for axonal regeneration and synaptic plasticity in the central nervous system, and thus suppresses nerve regeneration. The regulatory effect of Pir B on injured nerves has received a lot of attention. To better understand nerve regeneration inability after spinal cord injury, this study aimed to investigate the distribution of Pir B（via immunofluorescence） in the central nervous system and peripheral nervous system 10 days after injury. Immunoreactivity for Pir B increased in the dorsal root ganglia, sciatic nerves, and spinal cord segments. In the dorsal root ganglia and sciatic nerves, Pir B was mainly distributed along neuronal and axonal membranes. Pir B was found to exhibit a diffuse, intricate distribution in the dorsal and ventral regions. Immunoreactivity for Pir B was enhanced in some cortical neurons located in the bilateral precentral gyri. Overall, the findings suggest a pattern of Pir B immunoreactivity in the nervous system after unilateral spinal transection injury, and also indicate that Pir B may suppress repair after injury.

关键词： nerve regeneration paired immunoglobulin-like receptor B myelin inhibitory factor spinal cord injury peripheral nervous system central nervous system cerebral cortex dorsal root ganglion neural regeneration

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Classification of complete 3-dimensional self-shrinkers in the Euclidean space R^(4)

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Science China Mathematics 2024年第4期67卷 873-882页

作者： qing-Ming Cheng Zhi li Guoxin Wei Department of Applied Mathematics Faculty of ScienceFukuoka UniversityFukuoka 814-0180Japan College of Mathematics and Information Science Henan Normal UniversityXinxiang 453007China School of Mathematical Sciences South China Normal UniversityGuangzhou 510631China

In this paper,we completely classify 3-dimensional complete self-shrinkers with the constant norm S of the second fundamental form and the constant f3in the Euclidean space R^(4),where hij’s are components of the sec... 详细信息

关键词： mean curvature ow self-shrinker the generalized maximum principle

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Potential of arbuscular mycorrhizal fungi for soil health:A review

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Pedosphere 2024年第2期34卷 279-288页

作者： Junling ZHANG Ruotong ZHAO xia li Jiangzhou ZHANG College of Resources and Environmental Sciences National Academy of Agriculture Green DevelopmentKey Laboratory of Plant-Soil InteractionsMinistry of EducationChina Agricultural UniversityBeijing 100193China College of Agronomy and life Science Shanxi Datong UniversityDatong 037009China College of Resources and Environment/International Magnesium Institute Fujian Agriculture and Forestry UniversityFuzhou 350002China

Soil health is an important component of“One Health”.Soils provide habitat to diverse and abundant *** microbial diversity and functions is essential for building healthy soils towards sustainable *** mycorrhizal fungi(AMF)form potentially symbiotic associations with approximately 80%of land plant species that are well recognized for carbon flux and nutrient *** addition to disentangling the signaling pathways and regulatory mechanisms between the two partners,recent advances in hyphosphere research highlight some emerging roles of AMF and associated microbes in the delivery of soil *** paper reviews the contribution of AMF to soil health in agroecosystems,with a major focus on recent progress in the contribution of hyphosphere microbiome to nutrient cycling,carbon sequestration,and soil *** hyphosphere microbiome and fungal stimulants open avenues for developing new fertilizer formulas to promote AMF *** practice,developing AMF-friendly management strategies will have long-term positive effects on sustainable agriculture aiming at simultaneously providing food security,increasing resource use efficiency,and maintaining environment integrity.

关键词： arbuscular mycorrhizal fungi-friendly management strategies carbon sequestration hyphosphere microbiome nutrient cycling soil aggregation soilfunctions

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Highly efficient expression of human extracellular superoxide dismutase(rhEcSOD)with ultraviolet-B-induced damage-resistance activity in transgenic silkworm cocoons

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Insect Science 2024年第4期31卷 1150-1164页

作者： Feng Wang Ri-Yuan Wang De-Bin Zhong Ping Zhao qing-You xia Integrative Science Center of Germplasm Creation in Western China(CHONGqing)Science City Biological Science Research CenterSouthwest UniversityChongqingChina Century Legend Biotechnology Research Institute(Chongqing)Co. Ltd.ChongqingChina

Extracellular superoxide dismutase(EcSOD)protects tissues from oxidative stress,and thus is considered as a therapeutic agent for many diseases such as atherosclerosis,hypertension,and ***,cost-effective production of bioactive recombinant human EcSOD(rhEcSOD)remains a ***,we developed an efficient strategy for producing active rhEcSOD by transgenic *** was successfully synthesized as homodimers and homotetramers in the middle silk gland and spun into the cocoons with a concentration of 9.48±0.21 mg/*** of rhEcSOD from the cocoons could be conveniently achieved with a purity of 99.50%and a yield of 3.5±0.5 mg/***,N-glycosylation at the only site of N89 in rhEcSOD with 10 types were *** purified rhEcSOD gained the potent enzymatic activity of 4162±293 U/mg after Cu/Zn ions *** importantly,rhEcSOD was capable of penetrating and accumulating in the nuclei of cells to maintain cell morphology and attenuate ultraviolet B-induced cell apoptosis by eliminating reactive oxygen species and inhibiting the C-Jun N-terminal kinase signaling *** results demonstrated that the transgenic silkworm could successfully produce rhEcSOD with enzymatic and biological activities for biomedical applications.

关键词： antioxidant human extracellular superoxide dismutase recombinant expression silkworm silk gland

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Optimal Virtual Battery Model for Aggregating Storage-like Resources with Network Constraints

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CSEE Journal of Power and Energy Systems 2024年第4期10卷 1843-1847页

作者： Zhenfei Tan Ao Yu Haiwang Zhong xianfeng Zhang qing xia Chongqing Kang Department of Electrical Engineering and Sichuan Energy Internet Research Institute Tsinghua UniversityBeijing 100084China Science and Technology Institute of China Three Gorges Corporation Hubei 430010China

A virtual battery(VB)provides a succinct interface for aggregating distributed storage-like resources(SLR)to interact with a utility-level *** overcome the drawbacks of existing VB models,including conservatism and neglecting network constraints,this paper optimizes the power and energy parameters of VB to enlarge its flexibility *** optimal VB is identified by a robust optimization problem with decision-dependent *** algorithm based on the Benders decomposition is developed to solve this *** proposed method yields the largest VB satisfying constraints of both network and *** studies verify the superiority of the optimal VB in terms of security guarantee and less conservatism.

关键词： Aggregation decision-dependent uncertainty flexibility robust optimization virtual battery

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Clarifying the relationship and analyzing the influential factors of bronchial asthma in children with attention-deficit hyperactivity disorder

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World Journal of Psychiatry 2024年第4期14卷 513-522页

作者： Gui-xia Wang xiao-Ying Xu Xi-qing Wu Department of Infectious Diseases Dongying People’s HospitalDongying 257000Shandong ProvinceChina Department of Children's Health Dongying People’s HospitalDongying 257000Shandong ProvinceChina Department of Children's Health Shengli Oilfield Central HospitalDongying 257000Shandong ProvinceChina

BACKGROUND Bronchial asthma is closely related to the occurrence of attention-deficit hyperactivity disorder(ADHD)in children,which can easily have adverse effects on children’s learning and social *** have shown that childhood asthma can increase the risk of ADHD and the core symptoms of *** with children with ADHD alone,children with asthma and ADHD are more likely to show high levels of hyperactivity,hyperactive-impulsive and other externalizing behaviors and anxiety in clinical practice and have more symptoms of somatization and emotional *** To explore the relationship between ADHD in children and bronchial asthma and to analyze its influencing *** This retrospective cohort study was conducted at Dongying People's Hospital from September 2018 to August *** diagnosed with ADHD at this hospital were selected as the ADHD group,while healthy children without ADHD who underwent physical examinations during the same period served as the control *** and parental data were collected for all participating children,and multivariate logistic regression analysis was employed to identify risk factors for comorbid asthma in children with *** differences were detected between the ADHD group and the control group in terms of family history ofasthma and allergic diseases, maternal complications during pregnancy, maternal use of asthma and allergymedications during pregnancy, maternal anxiety and depression during pregnancy, and parental relationshipstatus (P < 0.05). Out of the 183 children in the ADHD group, 25 had comorbid asthma, resulting in a comorbidityrate of 13.66% (25/183), compared to the comorbidity rate of 2.91% (16/549) among the 549 children in the controlgroup. The difference in the asthma comorbidity rate between the two groups was statistically significant (P <0.05). The results of the multivariate logistic regression analysis indicated that family history of asthma

关键词： Attention-deficit hyperactivity disorder Children Bronchial asthma Risk factors Anxiety Depression

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TaSRO1 interacts with TaVP1 to modulate seed dormancy and pre-harvest sprouting resistance in wheat

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Journal of Integrative Plant Biology 2024年第1期66卷 36-53页

作者： Shupeng liu li li Wenlong Wang Guangmin xia Shuwei liu Key Laboratory of Plant Development and Environmental Adaptation Biology Ministry of EducationSchool of Life ScienceShandong UniversityQingdao 266237China

Dormancy is an adaptive trait which prevents seeds from germinating under unfavorable environmental *** with weak dormancy undergo pre-harvest sprouting(PHS)which decreases grain yield and *** the genetic mechanisms that regulate seed dormancy and resistance to PHS is crucial for ensuring global food *** this study,we illustrated the function and molecular mechanism of TaSRO1 in the regulation of seed dormancy and PHS resistance by suppressing *** tasro1 mutants exhibited strong seed dormancy and enhanced resistance to PHS,whereas the mutants of tavp1 displayed weak *** evidence has shown that TaVP1 is epistatic to *** evidence has shown that TaSRO1 interacts with TaVP1 and represses the transcriptional activation of the PHS resistance genes TaPHS1 and ***,TaSRO1 undermines the synergistic activation of TaVP1 and TaABI5 in PHS resistance ***,we highlight the great potential of tasro1 alleles for breeding elite wheat cultivars that are resistant to PHS.

关键词： wheat seed dormancy pre-harvest sprouting(PHS) ABA signaling vivipary

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