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Generic Interpretable Reaction Condition Predictions with Open Reaction Condition Datasets and Unsupervised Learning of Reaction Center

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Research 2024年第2期2023卷 773-794页

作者： Xiaorui Wang Chang-Yu hsieh Xiaodan Yin Jike Wang Yuquan Li Yafeng Deng Dejun Jiang Zhenxing Wu Hongyan Du Hongming Chen Yun Li Huanxiang Liu Yuwei Wang Pei Luo Tingjun Hou Xiaojun Yao Dr.Neher's Biophysics Laboratory for lnnovative Drug Discovery State Key Laboratory of Quality Research in Chinese MedicineMacao Institute for Applied Research in Medicine and HealthMacao University of Science and TechnologyMacao999078China innovation Institute for Artificial Intelligence in Medicine of Zhejiang University College of Pharmaceutical SciencesZhejiang UniversityHangzhou310058China Faculty of Applied Sciences Macao Polytechnic UniversityMacao999078China College of Chemistry and Chemical Engineering Lanzhou UniversityLanzhou730000China Carbon Silicon AI Technology Co. LtdHangzhouZhejiang 310018China Center of Chemistry and Chemical Biology Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangzhou 510530China College of Pharmacy Shaanxi University of Chinese MedicineXianyangShaanxi712044China

Effective synthesis planning powered by deep learning(DL)can significantly accelerate the discovery of new drugs and ***,most DL-assisted synthesis planning methods offer either none or very limited capability to recommend suitable reaction conditions(RCs)for their reaction ***,the prediction of RCs with a DL framework is hindered by several factors,including:(a)lack of a standardized dataset for benchmarking,(b)lack of a general prediction model with powerful representation,and(c)lack of *** address these issues,we first created 2 standardized RC datasets covering a broad range of reaction classes and then proposed a powerful and interpretable Transformer-based RC predictor named *** careful design of the model architecture,pretraining method,and training strategy,Parrot improved the overall top-3 prediction accuracy on catalysis,solvents,and other reagents by as much as 13.44%,compared to the best previous model on a newly curated ***,the mean absolute error of the predicted temperatures was reduced by about 4℃.Furthermore,Parrot manifests strong generalization capacity with superior cross-chemical-space prediction *** analysis indicates that Parrot effectively captures crucial chemical information and exhibits a high level of interpretability in the prediction of *** proposed model Parrot exemplifies how modern neural network architecture when appropriately pretrained can be versatile in making reliable,generalizable,and interpretable recommendation for RCs even when the underlying training dataset may still be limited in diversity.

关键词： versatile absolute generalization

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Enhancing Generic Reaction Yield Prediction through Reaction Condition-Based Contrastive Learning

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Research 2024年第3期 685-702页

作者： Xiaodan Yin Chang-Yu hsieh Xiaorui Wang Zhenxing Wu Qing Ye Honglei Bao Yafeng Deng Hongming Chen Pei Luo Huanxiang Liu Tingjun Hou Xiaojun Yao Dr.Neher’s Biophysics Laboratory for Innovative Drug Discovery State Key Laboratory of Quality Research in Chinese MedicineMacao Institute for Applied Research in Medicine and HealthMacao University of Science and TechnologyMacao 999078China Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China. Faculty of Applied Sciences Macao Polytechnic UniversityMacao 999078China. CarbonSilicon AI Technology Co.Ltd HangzhouZhejiang 310018China Center of Chemistry and Chemical Biology Guangzhou Regenerative Medicine and Health Guangdong LaboratoryGuangzhou 510530China.

Deep learning(DL)-driven efficient synthesis planning may profoundly transform the paradigm for designing novel pharmaceuticals and ***,the progress of many DL-assisted synthesis planning(DASP)algorithms has suffered from the lack of reliable automated pathway evaluation *** a critical metric for evaluating chemical reactions,accurate prediction of reaction yields helps improve the practicality of DASP algorithms in the real-world ***,accurately predicting yields of interesting reactions still faces numerous challenges,mainly including the absence of high-quality generic reaction yield datasets and robust generic yield *** compensate for the limitations of high-throughput yield datasets,we curated a generic reaction yield dataset containing 12 reaction categories and rich reaction condition ***,by utilizing 2 pretraining tasks based on chemical reaction masked language modeling and contrastive learning,we proposed a powerful bidirectional encoder representations from transformers(BERT)-based reaction yield predictor named *** achieved comparable or even superior performance to the best previous models on 4 benchmark datasets and established state-of-the-art performance on the newly curated *** found that reaction-condition-based contrastive learning enhances the model’s sensitivity to reaction conditions,and Egret is capable of capturing subtle differences between reactions involving identical reactants and products but different reaction ***,we proposed a new scoring function that incorporated Egret into the evaluation of multistep synthesis *** results showed that yield-incorporated scoring facilitated the prioritization of literature-supported high-yield reaction pathways for target *** addition,through meta-learning strategy,we further improved the reliability of the model’s prediction for reaction types with limited data and lower data *** r

关键词： synthesis generic holds

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Programming nonlinear propagation for efficient optical learning machines

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Advanced Photonics 2024年第1期6卷 73-83页

作者： Ilker Oguz Jih-Liang hsieh Niyazi Ulas Dinc Ugur Tegin Mustafa Yildirim Carlo Gigli Christophe Moser Demetri Psaltis École Polytechnique Fédérale de Lausanne Institute of Electrical and Micro EngineeringEcublensSwitzerland Koc University Department of Electrical and Electronics EngineeringIstanbulTurkey

The ever-increasing demand for training and inferring with larger machine-learning models requires more efficient hardware solutions due to limitations such as power dissipation and *** is a promising contender for providing lower power computation,since light propagation through a nonabsorbing medium is a lossless ***,to carry out useful and efficient computations with light,generating and controlling nonlinearity optically is a necessity that is still *** fibers(MMFs)have been shown that they can provide nonlinear effects with microwatts of average power while maintaining parallelism and low *** propose an optical neural network architecture that performs nonlinear optical computation by controlling the propagation of ultrashort pulses in MMF by wavefront *** a surrogate model,optimal sets of parameters are found to program this optical computer for different tasks with minimal utilization of an electronic *** show a remarkable decrease of 97%in the number of model parameters,which leads to an overall 99%digital operation reduction compared to an equivalently performing digital neural *** further demonstrate that a fully optical implementation can also be performed with competitive accuracies.

关键词： neural networks nonlinear optics fiber optics surrogate optimization neuromorphic computing wavefront shaping

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Acupuncture and neuroregeneration in ischemic stroke

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Neural Regeneration Research 2018年第4期13卷 573-583页

作者： Qwang-Yuen Chang Yi-Wen Lin ching-Liang hsieh department of family medicine lin shin hospitaltaichungtaiwanchina research center for chinese medicine and acupuncture china medical universitytaichungtaiwanchina graduate institute of acupuncture science college of chinese medicinechina medical universitytaichungtaiwanchina graduate institute of integrated medicine college of chinese medicinechina medical universitytaichungtaiwanchina department of chinese medicine china medical university hospitaltaichungtaiwanchina

Acupuncture is potentially beneficial for post-stroke rehabilitation and is considered a promising preventive strategy for *** pretreatment or treatment after ischemic stroke by using appropriate electroacupuncture parameters generates neuroprotective and neuroregenerative effects that increase cerebral blood flow,regulate oxidative stress,attenuate glutamate excitotoxicity,maintain bloodbrain barrier integrity,inhibit apoptosis,increase growth factor production,and induce cerebral ischemic tolerance.

关键词： acupuncture neuroprotection neuroregeneration

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Numerical study of the effects of check dams on erosion and sedimentation in the Pachang River

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International Journal of Sediment Research 2013年第3期28卷 304-315页

作者： Hui-ming hsieh ching-ruey LUO Jinn-chuang YANG Rou-fei CHEN Department of Computer Science and Multimedia Design Taiwan Shoufu University Department of Civil Engineering National Chi-Nan University Dept.of Civil Engineering National Chiayio Tung University Department of Geology Chinese Culture University

Scouring and deposition processes resulting from variable rainfall and typhoon occurrence in tropical climatic conditions induce significant changes in the riverbeds of *** the Pachang River of western Taiwan,severe damage occurs during typhoons due to large and sudden variations in discharge,erosion,sediment transport and *** order to simulate this process,the NETSTARS numerical modeling tool was used in the present *** influence of existing and planned check dam structures on flow control was also analyzed to determine their capacity to resist river erosion or to not be buried beneath *** only does the modeling tool allow calculation of the erosion-deposition behavior at the scale of the whole river,but it also provides local determination of the optimum location and characteristics such as foundation depth and lateral encroachment of future check *** results of a 10-year,long-term modeling simulation in terms of riverbed stability and scouring potential thus provide insights about unsafe future behavior at 4 *** numerical model provides a better general understanding and useful information for the optimal prevention of both the scouring damage and the burial related to sediment deposition with large changes in discharge and sediment transport.

关键词： NETSTARS model River bed erosion Check dam Pachang River

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Vegetable/fruit, smoking, glutathione S-transferase polymorphisms and risk for colorectal cancer in Taiwan

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World Journal of Gastroenterology 2005年第10期11卷 1473-1480页

作者： Chih-ching Yeh Ling-Ling hsieh Reiping Tang Chung Rong Chang-Chieh Fung-Chang Sung Institute of Environmental Health Department of Public Health Colorectal Section

AIM: To investigate the colorectal cancer risk associated with polymorphic GSTM1, GSTT1 and GSTP1 and the effect of diet and ***: With consents, genotypes of the genes were determined using PCR methods for 727 cases and 736sex and age-matched healthy controls recruited at a medical center in the Northern Taiwan. Nurses who were blind to the study hypothesis conducted interviews with study participants for the information of socio-demographic variables, diet and ***: There was no significant association between GSTM1 genotypes and the disease. Men, not women, with GSTT1 null genotype were at significant risk of colorectal cancer, but limited to rectal tumor, and in men aged 60 years and less. The corresponding association with the GSTP1 with G allele compared to GSTP1 A/A genotype was at borderline significance. Compared to men with GSTT1 present and GSTP1 A/A combined, men with both GSTT1 null and GSTP1 with G allele genotypes were at significant risk (odds ratio (OR) = 1.91, 95% confidence interval (CI) = 1.21-3.02), also limited to the rectal tumor and younger men. The beneficial effects of vegetable/fruit intake on colorectal cancer were much higher for men with GSTT1 present (OR = 0.32, 95%CI = 0.20-0.50) or GSTP1 A/A genotypes (OR = 0.40, 95%CI = 0.25-0.64).These effects remained significant for women. But, the greatest protective effect from vegetable/fruit intake for women was observed in those with GSTT1 null or GSTP1 with G allele genotypes. In addition, non-smoking men benefitted significantly from combined effect of higher vegetable/fruit intake and GSTT1 present or GSTP1 A/A genotypes with OR = 0.17 and 0.21 ***: This study suggests that the GSTT1 gene can modulate the colorectal cancer risk and vegetable/fruit-related colorectal cancer risk, particularly in men of no smoking history.

关键词： Colorectal cancer Glutathione S-transferase Polymorphisms Vegetables Smoking

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ETF标的证券联动传染——基于网络结构的空间联动溢出效应研究

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金融评论 2024年第3期16卷 90-109,157页

作者：谢沛霖张露唐咏家张浩台湾省政治大学商学院财务管理系中国台湾厦门大学经济学院广东粤财投资控股有限公司

股票联动性是金融市场关注的重要问题之一。本文基于沪深2006年至2019年的权益ETF数据,通过ETF持仓明细数据建立股票网络,借助空间计量模型检验了ETF标的证券网络之间的联动溢出效应。研究发现ETF标的股三个主要交易特征,回报率、成交... 详细信息

股票联动性是金融市场关注的重要问题之一。本文基于沪深2006年至2019年的权益ETF数据,通过ETF持仓明细数据建立股票网络,借助空间计量模型检验了ETF标的证券网络之间的联动溢出效应。研究发现ETF标的股三个主要交易特征,回报率、成交量和流动性,都表现出空间网络联动溢出效应。随着时间的推移,ETF数量增加,更多股票被纳入ETF成分股范围,股票间的空间关系变得更为紧密,进一步增强了空间联动传染性,展示了ETF标的证券空间网络溢出效应的动态趋势。机制分析表明,ETF独特的套利活动是股票空间联动传染增加的重要微观机制。研究表明ETF持股网络结构对股票联动传染具有重要影响,机构投资者持股结构对金融稳定的综合影响具有重要意义。

关键词： ETF 空间联动传染网络结构机构投资者

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Study on the Amperometric Glucose Biosensor Based on Tin Oxide Electrode

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稀有金属材料与工程 2006年第S3期 291-294页

作者： Jung-chuan Chou Shen-Kan Hsiung Jui-Hsiang hsieh Graduate School of Electronic Engineering National Yunlin University of Science and TechnologyDouliouTaiwan 640China Institute of Electronic Engineering Chung Yuan Christian UniversityChung-LiTaiwan 320China Institute of Biomedical Engineering Chung Yuan Christian UniversityChung-LiTaiwan 320China

An amperometric glucose biosensor based on a tin oxide （SnO2） electrode has been *** SnO2electrode is prepared by depositing the SnO2thin film onto a carbon *** fabricate the SnO2amperometric glucose biosensor,the glucose oxidase and electron transfer mediator （ferrocenecarboxylic acid,FcA） are coimmobilized on the SnO2electrode using *** detection range is up to glucose concentration of 520mg/dl as the applied potential is set at 300mV. Moreover,the most merit for the SnO2electrode as the base electrode of the SnO2amperometric glucose biosensor is that it can be operated at 150mV constant applied *** interference reduction,detection range,sensitivity and linearity are improved as the SnO2thin film is deposited onto a carbon ***,due to the low cost substrate and simple fabrication characteristics,a disposable amperometric glucose biosensor based on the SnO2electrode has been realized in this study.

关键词： amperometric glucose oxidase tin oxide carbon mediator

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Study on the Amperometric Glucose Biosensor Based on Tin Oxide Electrode

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稀有金属材料与工程 2006年第A3期35卷 291-294页

作者： Cheng-Wei Liao Jung-chuan Chou Tai-Ping Sun Shen-Kan Hsiung Jui-Hsiang hsieh Institute of Biomedical Engineering Chung Yuan Christian University Chung-Li Taiwan 320 China Graduate School of Electronic Engineering National Yunlin University of Science and Technology Douliou Taiwan 640 China Department of Electrical Engineering National Chi Nan University Nantou Taiwan 545 China Institute of Electronic Engineering Chung Yuan Christian University Chung-Li Taiwan 320 China

An amperometric glucose biosensor based on a tin oxide (SnO_2) electrode has been *** SnO_2 electrode is prepared by depositing the SnO_2 thin film onto a carbon *** fabricate the SnO_2 amperometric glucose biosensor,the glucose oxidase and electron transfer mediator (ferrocenecarboxylic acid,FcA) are coimmobilized on the SnO_2 electrode using *** detection range is up to glucose concentration of 520mg/dl as the applied potential is set at 300mV. Moreover,the most merit for the SnO_2 electrode as the base electrode of the SnO_2 amperometric glucose biosensor is that it can be operated at 150mV constant applied *** interference reduction,detection range,sensitivity and linearity are improved as the SnO_2 thin film is deposited onto a carbon ***,due to the low cost substrate and simple fabrication characteristics,a disposable amperometric glucose biosensor based on the SnO_2 electrode has been realized in this study.

关键词： amperometric glucose oxidase tin oxide carbon mediator

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Molecular mechanism of therapeutic approaches for human gastric cancer stem cells

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World Journal of Stem Cells 2022年第1期14卷 76-91页

作者： Hsi-Lung hsieh Ming-Chin Yu Li-ching Cheng Ta-Sen Yeh Ming-Ming Tsai Department of Nursing Division of Basic Medical SciencesChang-Gung University of Science and TechnologyTaoyuan 333Taiwan Research Center for Chinese Herbal Medicine College of Human EcologyChang Gung University of Science and TechnologyTaoyuan 333Taiwan Department of Neurology Chang Gung Memorial HospitalTaoyuan 333Taiwan Department of General Surgery Chang Gung Memorial Hospital at LinkouTaoyuan 333Taiwan College of Medicine Chang Gung UniversityTaoyuan 333Taiwan Department of General Surgery New Taipei Municipal TuCheng HospitalNew Taipei 236Taiwan Department of General Surgery Chang Gung Memorial HospitalChiayi 613Taiwan

Gastric cancer(GC)is a primary cause of cancer-related mortality worldwide,and even after therapeutic gastrectomy,survival rates remain *** presence of gastric cancer stem cells(GCSCs)is thought to be the major reason for resistance to anticancer treatment(chemotherapy or radiotherapy),and for the development of tumor recurrence,epithelial–mesenchymal transition,and ***,GCSCs have the capacity for self-renewal,differentiation,and tumor *** also synthesize antiapoptotic factors,demonstrate higher performance of drug efflux pumps,and display cell plasticity ***,the tumor microenvironment(TME;tumor niche)that surrounds GCSCs contains secreted growth factors and supports angiogenesis and is thus responsible for the maintenance of the growing ***,the genesis of GCSCs is unclear and exploration of the source of GCSCs is *** this review,we provide up-todate information about GCSC-surface/intracellular markers and GCSC-mediated pathways and their role in tumor *** information will support improved diagnosis,novel therapeutic approaches,and better prognosis using GCSC-targeting agents as a potentially effective treatment choice following surgical resection or in combination with chemotherapy and *** date,most anti-GCSC blockers when used alone have been reported as unsatisfactory anticancer ***,when used in combination with adjuvant therapy,treatment can *** providing insights into the molecular mechanisms of GCSCs associated with tumors in GC,the aim is to optimize anti-GCSCs molecular approaches for GC therapy in combination with chemotherapy,radiotherapy,or other adjuvant treatment.

关键词： Gastric cancer stem cells Stem cell-surface markers Tumor niche Tumor microenvironment

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