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BIBC: A Chinese Named Entity Recognition Model for Diabetes Research

Lei Yang, Yufan Fu, Yu Dai
2021 Applied Sciences  
In the medical field, extracting medical entities from text by Named Entity Recognition (NER) has become one of the research hotspots. This thesis takes the chapter-level diabetes literature as the research object and uses a deep learning method to extract medical entities in the literature. Based on the deep and bidirectional transformer network structure, the pre-training language model BERT model can solve the problem of polysemous word representation, and supplement the features by
more » ... le unlabeled data, combined with BiLSTM-CRF model extracts of the long-distance features of sentences. On this basis, in view of the problem that the model cannot focus on the local information of the sentence, resulting in insufficient feature extraction, and considering the characteristics of Chinese data mainly in words, this thesis proposes a Named Entity Recognition method based on BIBC. This method combines Iterated Dilated CNN to enable the model to take into account global and local features at the same time, and uses the BERT-WWM model based on whole word masking to further extract semantic information from Chinese data. In the experiment of diabetic entity recognition in Ruijin Hospital, the accuracy rate, recall rate, and F1 score are improved to 79.58%, 80.21%, and 79.89%, which are better than the evaluation indexes of existing studies. It indicates that the method can extract the semantic information of diabetic text more accurately and obtain good entity recognition results, which can meet the requirements of practical applications.
doi:10.3390/app11209653 fatcat:grlagc4vevcupgp3nlseutihym

PBRnet: Pyramidal Bounding Box Refinement to Improve Object Localization Accuracy [article]

Li Xiao, Yufan Luo, Chunlong Luo, Lianhe Zhao, Quanshui Fu, Guoqing Yang, Anpeng Huang, Yi Zhao
2020 arXiv   pre-print
Many recently developed object detectors focused on coarse-to-fine framework which contains several stages that classify and regress proposals from coarse-grain to fine-grain, and obtains more accurate detection gradually. Multi-resolution models such as Feature Pyramid Network(FPN) integrate information of different levels of resolution and effectively improve the performance. Previous researches also have revealed that localization can be further improved by: 1) using fine-grained information
more » ... which is more translational variant; 2) refining local areas which is more focused on local boundary information. Based on these principles, we designed a novel boundary refinement architecture to improve localization accuracy by combining coarse-to-fine framework with feature pyramid structure, named as Pyramidal Bounding Box Refinement network(PBRnet), which parameterizes gradually focused boundary areas of objects and leverages lower-level feature maps to extract finer local information when refining the predicted bounding boxes. Extensive experiments are performed on the MS-COCO dataset. The PBRnet brings a significant performance gains by roughly 3 point of mAP when added to FPN or Libra R-CNN. Moreover, by treating Cascade R-CNN as a coarse-to-fine detector and replacing its localization branch by the regressor of PBRnet, it leads an extra performance improvement by 1.5 mAP, yielding a total performance boosting by as high as 5 point of mAP.
arXiv:2003.04541v1 fatcat:tauotkjwdrc7xbsucrlyxr245i

One-Step Synthesis of Ag@TiO2 Nanoparticles for Enhanced Photocatalytic Performance

Yufan Zhang, Fan Fu, Yuzhou Li, Desuo Zhang, Yuyue Chen
2018 Nanomaterials  
Polyamide network polymers (PNP) modified TiO2 nanoparticles (NPs) were decorated with Ag NPs in hydrothermal gel method, forming one-step synthesized photocatalysts, Ag@TiO2 NPs. The effect of PNP and the amount of Ag NPs added were investigated in this work. PNP acted as a nanocage to prevent TiO2 aggregation and capture Ag accurately, which could effectively control product sizes and improve dispersibility in solvents. Simultaneously, TiO2 NPs modified with Ag NPs exhibited remarkable
more » ... talytic effects. One-step synthesis simplified the experimental process and avoided the agglomeration of silver ions during the secondary reaction, achieving the purpose of uniform distribution at a specific location of TiO2 NPs. The prepared Ag@TiO2 NPs-0.5 could remove 79.49% of Methyl Orange (MO) after 3 h of ultraviolet light irradiation, which was 2.7 times higher than the reaction rate of pure TiO2 NPs. It also exhibited good photoactivity under Visible light conditions. Moreover, the mineralization rate of MO over the Ag@TiO2 NPs-0.5 could be up to 72.32% under UV light and 47.08% under Visible light irradiation, which revealed that the prepared catalysts could effectively degrade most of the MO to CO2 and H2O. The samples also demonstrated the excellent stability and easy recyclability with over 90% of the original catalytic level for MO degradation. The photocatalysts studied also exerted broad application prospects such as photovoltaic hydrogen production, electronic sensors and biomedicine.
doi:10.3390/nano8121032 pmid:30545034 pmcid:PMC6316728 fatcat:vpoxzvyhf5ab5h755qtgyufcyi

A Multiple-Choice Machine Reading Comprehension Model with Multi-Granularity Semantic Reasoning

Yu Dai, Yufan Fu, Lei Yang
2021 Applied Sciences  
To address the problem of poor semantic reasoning of models in multiple-choice Chinese machine reading comprehension (MRC), this paper proposes an MRC model incorporating multi-granularity semantic reasoning. In this work, we firstly encode articles, questions and candidates to extract global reasoning information; secondly, we use multiple convolution kernels of different sizes to convolve and maximize pooling of the BERT-encoded articles, questions and candidates to extract local semantic
more » ... oning information of different granularities; we then fuse the global information with the local multi-granularity information and use it to make an answer selection. The proposed model can combine the learned multi-granularity semantic information for reasoning, solving the problem of poor semantic reasoning ability of the model, and thus can improve the reasoning ability of machine reading comprehension. The experiments show that the proposed model achieves better performance on the C3 dataset than the benchmark model in semantic reasoning, which verifies the effectiveness of the proposed model in semantic reasoning.
doi:10.3390/app11177945 fatcat:srjlgtiabvge7oq3e36hxaordq

Precise phase control of large-scale inorganic perovskites via vapor-phase anion-exchange strategy [article]

Guobiao Cen, Yufan Xia, Chuanxi Zhao, Yong Fu, Yipeng An, Ye Yuan, Tingting Shi, Wenjie Mai
2020 arXiv   pre-print
Supporting Information Precise phase control of large-scale inorganic perovskites via vapor-phase anionexchange strategy Guobiao Cen #1 , Yufan Xia #1 , Chuanxi Zhao 1 *, Yong Fu 1 , Yipeng An 2 , Ye Yuan  ... 
arXiv:2009.14350v1 fatcat:nvib2327e5bwbh5ggwvxh6tu4m

Mendelian randomization analysis revealed potential causal factors for systemic lupus erythematosus

Xingbo Mo, Yufan Guo, Qiyu Qian, Mengzhen Fu, Shufeng Lei, Yonghong Zhang, Huan Zhang
2019 Immunology  
Genome-wide association studies (GWAS) have identified many loci for systemic lupus erythematosus (SLE). However, identification of functionally relevant genes remains a challenge. The aim of this study was to highlight potential causal genes for SLE in the GWAS loci. By applying Mendelian randomization (MR) methods, such as summary data-based MR (SMR), generalized SMR and MR pleiotropy residual sum and outlier, we identified DNA methylations in 15 loci and mRNA expression of 21 genes that were
more » ... causally associated with SLE. The identified genes enriched in 14 specific KEGG pathways (e.g. SLE, viral carcinogenesis) and two GO terms (interferon-γ-mediated signaling pathway and innate immune response). Among the identified genes, UBE2L3 and BLK variants were significantly associated with UBE2L3 and BLK methylations and gene expressions, respectively. UBE2L3 was up-regulated in SLE patients in several types of immune cells. Methylations (e.g. cg06850285) and mRNA expression of UBE2L3 were causally associated with SLE. Methylation site cg09528494 and mRNA expression of BLK were causally associated with SLE. BLK single nucleotide polymorphisms that were significantly associated with SLE were strongly associated with plasma cathepsin B level. Deep analysis identified that plasma cathepsin B level was causally associated with SLE. In summary, this study identified hundreds of DNA methylations and genes as potential risk factors for SLE. Genetic variants in UBE2L3 gene might affect SLE by influencing gene expression. Genetic variants in BLK gene might affect SLE by influencing BLK gene expression and plasma cathepsin B protein level.
doi:10.1111/imm.13144 pmid:31670388 pmcid:PMC7011638 fatcat:aaecm3vej5chdb5xal4g5zfaou

Estimating Multiple Socioeconomic Attributes via Home Location—A Case Study in China

Shichang Ding, Xin Gao, Yufan Dong, Yiwei Tong, Xiaoming Fu
2021 Journal of Social Computing  
Xiaoming Fu received the PhD degree in computer science from Tsinghua University, Beijing, China in 2000.  ...  Yufan Dong received the BS degree from University of Göttingen, Germany in 2020. He is a master student at Department of Computer Engineering, Technical University of Berlin.  ... 
doi:10.23919/jsc.2021.0003 fatcat:2adp54wxivcfjcy7shqoiaai7e

Numerical Simulation and Experimental Study on Flow Field in a Swirl Nozzle

Yicheng Sun, Yufan Fu, Baohui Chen, Jiaxing Lu, Wanquan Deng, Ling Zhou
2021 Shock and Vibration  
Data Availability e data used to support the findings of this study are available from the #2 author (Yufan Fu) upon request.  ... 
doi:10.1155/2021/6626715 fatcat:3sdrau4jirezvk3npu5ag5k7rq

PrEP: AIDS-Free Hope in Namibia?

Eben-Eser Ndaamenwa Namhindo, Fanghua Mei, Rui Cao, Shenghai Lai, Yufan Dai, Hong Lai, Meng Zhu, Huimin Fu, Huang Huang, Jun Wang
2017 International Journal of Biology  
Human immunodeficiency virus (HIV) is a lentivirus that causes infections and over time leads to acquired immunodeficiency syndrome (AIDS). HIV causes a loss of immune function in human and subsequent development of opportunistic infections. Namibia, one important country in West Africa, has been suffering HIV/AIDS incidence over years. Among people between 15 to 49 years old, the national HIV prevalence rate is more than 10%, which causes huge health and economic loss. Recently, Pre-exposure
more » ... ophylaxis (PrEP) has been approved in Namibia for better prevention of HIV/AIDS. In this paper, we will review the current epidemic condition of HIV and the role played by PrEP in Namibia.
doi:10.5539/ijb.v10n1p13 fatcat:opatkwpkn5a7hmdq3jc7qzrsqm

Stiffness-mediated mesenchymal stem cell fate decision in 3D-bioprinted hydrogels

Yufan Liu, Zhao Li, Jianjun Li, Siming Yang, Yijie Zhang, Bin Yao, Wei Song, Xiaobing Fu, Sha Huang
2020 Burns & Trauma  
Background Hydrogels with tuneable mechanical properties are an attractive material platform for 3D bioprinting. Thus far, numerous studies have confirmed that the biophysical cues of hydrogels, such as stiffness, are known to have a profound impact on mesenchymal stem cell (MSC) differentiation; however, their differentiation potential within 3D-bioprinted hydrogels is not completely understood. Here, we propose a protocol for the exploration of how the stiffness of alginate–gelatin (Alg-Gel)
more » ... omposite hydrogels (the widely used bioink) affects the differentiation of MSCs in the presence or absence of differentiation inducing factors. Methods Two types of Alg-Gel composite hydrogels (Young's modulus: 50 kPa vs. 225 kPa) were bioprinted independently of porosity. Then, stiffness-induced biases towards adipogenic and osteogenic differentiation of the embedded MSCs were analysed by co-staining with alkaline phosphatase (ALP) and oil red O. The expression of specific markers at the gene level was detected after a 3-day culture. Results Confocal microscopy indicated that all tested hydrogels supported MSC growth and viability during the culture period. Higher expression of adipogenic and osteogenic markers (ALP and lipoprotein lipase (LPL)) in stiffer 3D-bioprinted matrices demonstrated a more significant response of MSCs to stiffer hydrogels with respect to differentiation, which was more robust in differentiation-inducing medium. However, the LPL expression in stiffer 3D-bioprinted constructs was reduced at day 3 regardless of the presence of differentiation-inducing factors. Although MSCs embedded in softer hydrogels to some extent proceeded toward adipogenic and osteogenic lineages within a few days, their differentiation seemed to be slower and more limited. Interestingly, the hydrogel itself (without differentiation-inducing factors) exhibited a slight effect on whether MSCs differentiated towards an adipogenic or an osteogenic fate. Considering that the mechano-regulated protein Yes-associated protein (YAP) is involved in MSC fate decisions, we further found that inhibition of YAP significantly downregulated the expression of ALP and LPL in MSCs in stiffer constructs regardless of the induced growth factors present. Conclusions These results demonstrate that the differentiation of MSCs in 3D-bioprinted matrices is dependent on hydrogel stiffness, which emphasizes the importance of biophysical cues as a determinant of cellular behaviour.
doi:10.1093/burnst/tkaa029 pmid:32733974 pmcid:PMC7382973 fatcat:o5dwzjyicjc3xjxmro2gckh2ga

A new isopentenyl diphosphate isomerase gene from sweet potato: cloning, characterization and color complementation

Zhihua Liao, Min Chen, Yijian Yang, Chunxian Yang, Yufan Fu, Qitang Zhang, Qiang Wang
2008 Biologia (Bratislava)  
AbstractIsopentenyl diphosphate isomerase (IDI, EC 5.3.3.2) catalyzes the revisable conversion of 5-carbon isopentenyl diphosphate and its isomer dimethylallyl diphosphate, which are the essential precursors for isoprenoids, including carotenoids. Here we report on the cloning and characterization of a novel cDNA encoding IDI from sweet potato. The full-length cDNA is 1155 bp with an ORF of 892 bp encoding a polypeptide of 296 amino acids, which was designated as IbIDI (GenBank Acc. No:
more » ... ). The computational molecular weight is 33.8 kDa and the theoretical isoelectric point is 5.76. The deduced amino acid sequence of IbIDI is similar to the known plant IDIs. The tissue expression analysis revealed that IbIDI expressed at higher level in sweet-potato's mature leaves and tender leaves than that in tubers, meanwhile, no expression signal could be detected in veins. Recombinant IbIDI was heterologously expressed in engineered Escherichia coli which led to the reconstruction of the carotenoid pathway. In the engineered E. coli, IbIDI could take the role of Arabidopsis IDI gene to produce the orange β-carotene. In summary, cloning and characterization of the novel IDI gene from sweet potato will facilitate our understanding of the molecular genetical mechanism of carotenoid biosynthesis and promote the metabolic engineering studies of carotenoid in sweet potato.
doi:10.2478/s11756-008-0038-7 fatcat:lwsskmyyb5f67ctqbufa7gql4i

Stereoconvergent Negishi Arylations of Racemic Secondary Alkyl Electrophiles: Differentiating between a CF3 and an Alkyl Group

Yufan Liang, Gregory C. Fu
2015 Journal of the American Chemical Society  
Liang and Fu Page 4  ...  Thus, excellent enantioselectivity is observed with an array of fluorinated substituents, including perfluoroalkyl, CF 2 Cl, CF 2 COPh, and CF 2 CO 2 Et (eq 4-7). 26 (4) Liang and Fu Page 3 (5) (6) In  ... 
doi:10.1021/jacs.5b04725 pmid:26203662 pmcid:PMC4610818 fatcat:nx3fceydv5cgboqwqdr5hr6gwm

Tuning Alginate-Gelatin Bioink Properties by Varying Solvent and Their Impact on Stem Cell Behavior

Zhao Li, Sha Huang, Yufan Liu, Bin Yao, Tian Hu, Haigang Shi, Jiangfan Xie, Xiaobing Fu
2018 Scientific Reports  
Bioink optimization is considered as one of main challenges in cell-laden 3D bioprinting. Alginate-Gelatin (Alg-Gel) hydrogel have been extensively used as bioink. However, its properties could be influenced by various parameters, and little is known about the evidence featuring the impact of solvent. Here we investigated four Alg-Gel bioink by varying solvent ionic strength (named B-1, B-2, B-3 and B-4). Mechanical properties and printability of bioink samples and their impacts on behaviors of
more » ... encapsulated epidermal stem cells (ESCs) were tested. Bioink with increased ionic strength of solvent showed decreased stiffness and viscosity, and increased swelling and degradation by printability and mechanical property tests. Due to the increased swelling and degradation was associated with shapemaintenance of post-printing constructs, B-3 and B-4 were hardly observable after 14 days. Cellular behaviors were assessed through viability, proliferation, aggregation and differentiation tests. B-2 with optimal properties resulted in higher viability and proliferation of ESCs , and further facilitated cellular aggregation and lineage differentiation. We demonstrated that the solvent can be tuned by ionic strength to control the properties of Alg-Gel bioink and post-printing constructs, which represented a promising avenue for promotion of therapeutic stem cell behaviors in 3D bioprinting. Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 SCIENTIFIC REPORTS | (2018) 8:8020 |
doi:10.1038/s41598-018-26407-3 pmid:29789674 pmcid:PMC5964146 fatcat:r2bufclcffaghfl3ksvd2f6yba

Redirecting differentiation of mammary progenitor cells by 3D bioprinted sweat gland microenvironment

Rui Wang, Yihui Wang, Bin Yao, Tian Hu, Zhao Li, Yufan Liu, Xiaoli Cui, Liuhanghang Cheng, Wei Song, Sha Huang, Xiaobing Fu
2019 Burns & Trauma  
Mammary progenitor cells (MPCs) maintain their reproductive potency through life, and their specific microenvironments exert a deterministic control over these cells. MPCs provides one kind of ideal tools for studying engineered microenvironmental influence because of its accessibility and continually undergoes postnatal developmental changes. The aim of our study is to explore the critical role of the engineered sweat gland (SG) microenvironment in reprogramming MPCs into functional SG cells.
more » ... e have utilized a three-dimensional (3D) SG microenvironment composed of gelatin-alginate hydrogels and components from mouse SG extracellular matrix (SG-ECM) proteins to reroute the differentiation of MPCs to study the functions of this microenvironment. MPCs were encapsulated into the artificial SG microenvironment and were printed into a 3D cell-laden construct. The expression of specific markers at the protein and gene levels was detected after cultured 14 days. Compared with the control group, immunofluorescence and gene expression assay demonstrated that MPCs encapsulated in the bioprinted 3D-SG microenvironment could significantly express the functional marker of mouse SG, sodium/potassium channel protein ATP1a1, and tend to express the specific marker of luminal epithelial cells, keratin-8. When the Shh pathway is inhibited, the expression of SG-associated proteins in MPCs under the same induction environment is significantly reduced. Our evidence proved the ability of differentiated mouse MPCs to regenerate SG cells by engineered SG microenvironment in vitro and Shh pathway was found to be correlated with the changes in the differentiation. These results provide insights into regeneration of damaged SG by MPCs and the role of the engineered microenvironment in reprogramming cell fate.
doi:10.1186/s41038-019-0167-y pmid:31559316 pmcid:PMC6755689 fatcat:pjimvpeyvnebzkzt4k53fdk3ey

Catalytic Asymmetric Synthesis of Tertiary Alkyl Fluorides: Negishi Cross-Couplings of Racemic α,α-Dihaloketones

Yufan Liang, Gregory C. Fu
2014 Journal of the American Chemical Society  
The development of new approaches to the construction of fluorine-containing target molecules is important for a variety of scientific disciplines, including medicinal chemistry. In this Article, we describe a method for the catalytic enantioselective synthesis of tertiary alkyl fluorides through Negishi reactions of racemic α-haloα-fluoroketones, which represents the first catalytic asymmetric crosscoupling that employs geminal dihalides as electrophiles. Thus, selective reaction of a C−Br (or
more » ... C−Cl) bond in the presence of a C−F bond can be achieved with the aid of a nickel/bis(oxazoline) catalyst. The products of the stereoconvergent cross-couplings, enantioenriched tertiary α-fluoroketones, can be converted into an array of interesting organofluorine compounds.
doi:10.1021/ja501815p pmid:24678878 pmcid:PMC4004247 fatcat:4wfbbyrjnzahfk3kripkr7ofge
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