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2012 IEEE Symposium on Electrical and Electronics Engineering, EEESYM 2012

作者： wang, xuwen Lin, Ye wang, Xiaojie Tan, Yongmei Center for Intelligence Science and Technology Beijing University of Posts and Telecommunications Beijing China

ISBN: (纸本)9781467323659

Bilingual parallel corpora provide rich source of translate information for tasks such as cross-language information retrieval and data-driven machine translation systems. However, they are often scarce resources: limited in size, language coverage and language register. Researchers have to struggle to transfer and adapt the available technologies because only some small scale corpora are suitable. In this paper we introduce a large parallel corpus of Chinese and English constructed by crawling and processing bilingual web documents from Internet. It currently contains about 300,000 parallel sentence pairs. The tools and methodology used in this collection project are also described. In a cross-language retrieval task we experimented with this self-constructed corpus to improve the quality of query translation, so as to achieve better retrieval performance. © 2012 IEEE.

关键词： Search engines

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Drug Discovery Targeting Anaplastic Lymphoma Kinase (ALK)

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JOURNAL OF MEDICINAL CHEMISTRY 2019年第24期62卷 10927-10954页

作者： Kong, Xiaotian Pan, Peichen Sun, Huiyong Xia, Hongguang wang, xuwen Li, Youyong Hou, Tingjun Zhejiang Univ Hangzhou Inst Innovat Med Coll Pharmaceut Sci Hangzhou 310058 Zhejiang Peoples R China Zhejiang Univ Dept Biochem Hangzhou 310058 Zhejiang Peoples R China Zhejiang Univ Affiliated Hosp 1 Res Ctr Clin Pharm Hangzhou 310058 Zhejiang Peoples R China Soochow Univ Inst Funct Nano & Soft Mat FUNSOM Suzhou 215123 Jiangsu Peoples R China

As a receptor tyrosine kinase of insulin receptor (IR) subfamily, anaplastic lymphoma kinase (ALK) has been validated to play important roles in various cancers, especially anaplastic large cell lymphoma (ALCL), nonsmall cell lung cancer (NSCLC), and neuroblastomas. Currently, five small-molecule inhibitors of ALK, including Crizotinib, Ceritinib, Alectinib, Brigatinib, and Lorlatinib, have been approved by the U.S. Food and Drug Administration (FDA) against ALK-positive NSCLCs. Novel type-I-1/2 and type-II ALK inhibitors with improved kinase selectivity and enhanced capability to combat drug resistance have also been reported. Moreover, the "proteolysis targeting chimera" (PROTAC) technique has been successfully applied in developing ALK degraders, which opened a new avenue for targeted ALK therapies. This review provides an overview of the physiological and biological functions of ALK, the discovery and development of drugs targeting ALK by focusing on their chemotypes, activity, selectivity, and resistance as well as potential therapeutic strategies to overcome drug resistance.

关键词： Cancer Drug resistance Peptides and proteins Genetics Inhibitors

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Changes in water quality along the process of coal chemical reverse osmosis wastewater advanced treatment: Spectral analysis and molecular level exploration

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SEPARATION AND PURIFICATION TECHNOLOGY 2025年 360卷

作者： Yuan, Run Qin, Yihe wang, Hao He, xuwen Dongguan Univ Technol Sch Environm & Civil Engn Dongguan 523808 Peoples R China CNPC Res Inst Safety & Environm Technol Beijing 102206 Peoples R China China Univ Min & Technol Sch Chem & Environm Engn Beijing 100083 Peoples R China

Investigating changes in the organic pollutant composition of coal chemical wastewater during the advanced treatment process is crucial for enhancing the efficiency of wastewater treatment systems. In this study, the molecular composition and changes in dissolved organic matter (DOM) were analyzed in a typical coal gasification reverse osmosis concentrate during various advanced treatment processes, including flocculation, ultrafiltration, adsorption, and catalytic ozonation, were investigated using conventional water quality analysis, ultraviolet spectroscopy, fluorescence spectroscopy, molecular weight fractionation analysis, organic component fractionation methods, and Fourier-transform ion cyclotron resonance mass spectrometry. After the advanced treatment process, the concentrations of organic pollutants in the effluent decreased significantly, and the final treated effluent COD was reduced to 90 mg/L. Analysis of the molecular weight fractions showed that after treatment, the proportion of low-molecular-weight organic pollutants (<3k Da) in the coal chemical reverse osmosis concentrate exceeded 50 %. The mass-to-charge ratio of organics in wastewater ranged between 100 and 800, most DOM molecules were unsaturated reduced-state recalcitrant organic molecules, and the DOM molecules in wastewater were mainly distributed among lignin-like, condensed aromatic, and protein-like organics. Compared to the other advanced treatment processes, catalytic ozonation efficiently removed refractory ligninlike organics from wastewater. We revealed the characteristics of organic pollutants in coal chemical reverse osmosis concentrates during the advanced treatment process using various characterization methods, which can assist in further exploring the degradation mechanisms of organics in actual wastewater to enhance the efficiency of wastewater treatment units.

关键词： Water quality analysis Coal chemical wastewater Advanced treatment technology Dissolved organic pollutants

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DNA methyltransferases: emerging targets for the discovery of inhibitors as potent anticancer drugs

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DRUG DISCOVERY TODAY 2019年第12期24卷 2323-2331页

作者： Yu, Jie Xie, Tianli wang, Zhe wang, xuwen Zeng, Su Kang, Yu Hou, Tingjun Zhejiang Univ Coll Pharmaceut Sci Hangzhou 310058 Zhejiang Peoples R China

DNA methyltransferases (DNMTs) are a conserved family of cytosine methylases with crucial roles in epigenetic regulation. They have been considered as promising therapeutic targets for the epigenetic treatment of cancer. Therefore, DNMT inhibitors (DNMTis) have attracted considerable interest in recent years for the modulation of the aberrant DNA methylation pattern in a reversible way. In this review, we provide a structure-based overview of the therapeutic importance of DNMTs against different cancer types, and then summarize recently investigated DNMTis as well as their inhibitory mechanisms, focusing on recent advances in the development of DNMTis with specificity and/or selectivity using computational approaches.

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Metabolomics coupled with SystemsDock reveal the protective effect and the potential active components of Naozhenning granule against traumatic brain injury

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JOURNAL OF ETHNOPHARMACOLOGY 2020年 246卷 112247-000页

作者： Cao, Jianhua Duan, Yahui Liu, Yanzhi Liu, Haixia Wei, Chunhong wang, Jiang Qin, Xuemei wang, xuwen Li, Zhenyu Shanxi Univ Modern Res Ctr Tradit Chinese Med Taiyuan 030006 Shanxi Peoples R China Shanxi Univ Coll Chem & Chem Engn Taiyuan 030006 Shanxi Peoples R China Shanxi Zhendong Ante Biol Pharmaceut Co Ltd Jinzhong 030600 Peoples R China

Ethnopharmacological relevance: Naozhenning granule (NZN), a widely traditional Chinese medicine (TCM) prescription with a long history of clinical, which is mainly used in the treatment of concussion, cerebral post-traumatic syndrome, consists of Di Huang (Radix of Rehmannia glutinosa (Gaertn.) DC.), Dang Gui (Radix of Angelica sinensis (Olio.) Diels), Chen Pi (Pericarpium of Citrus reticulata Blanco), Dan shen (Radix of Salvia Miltiorrhiza Bunge.), Di Long (Pheretima aspergillum (E. Perrier)), Mu Dan Pi (Cortex of Paeonia suffruticosa Andrews), Suan Zao Ren (Semen of Ziziphus jujuba Mill.), Chuan Xiong (Rhizoma of Ligusticum striatum DC.), Zhu Ru (Phyllostachys nigra (Lodd. Ex Lindl.) Munro), Bai Zi Ren (Semen of Platycladus orientalis (L.) Franco) and Fu Ling (sclerotium of Poria cocos (Schw.)Wolf). Aim of the study: This study aimed to unravel the mechanism and material basis of NZN against traumatic brain injury. Materials and methods: In this study, a H-1 nuclear magnetic resonance (NMR) based metabolomic approach combined with systemsDock was employed to study the protective effect of NZN against traumatic brain injury using a cerebral concussion rat model. The morris water maze test and biochemical indexes were used to evaluate the efficacy of NZN. Results: The results of morris water maze test suggested NZN can improve the spatial learning and memory of model rats, and the superoxide dismutas (SOD) and malonyldialdehyde (MDA) level indicated that the effect of NZN was related with the regulation of oxidative stress. Multivariate analysis revealed that the effect of NZN was related with regulation of 18 brain metabolites, and the corresponding metabolic pathways were further revealed by MetPA analysis. 13 serum absorbed components were found to hit the targets both related with the metabolic regulation and cerebral trauma through systemsDock-aided molecular docking experiments, and these compounds might be served as the active compounds in NZN against cerebr

关键词： Naozhenning granule Cerebral concussion Metabolomics Molecular docking

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FilterLAP: Filtering False-positive Mutation Calls via a Label Propagation Framework

FilterLAP: Filtering False-positive Mutation Calls via a Lab...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： wang, xuwen Zhu, Xiaoyan Xiao, Xiao wang, Shenjie Zhang, Xuanping Lai, Xin wang, Jiayin Xi An Jiao Tong Univ Sch Comp Sci & Technol Xian Peoples R China Xi An Jiao Tong Univ Shaanxi Engn Res Ctr Med & Hlth Big Data Xian Peoples R China Xi An Jiao Tong Univ Sch Publ Policy & Adm Xian Peoples R China

ISBN: (纸本)9781728118673

Benefiting from the recent advantages of genomic sequencing, detecting genomic mutations becomes a routine work in precise diagnoses and treatments for cancers. In clinical practices, many factors, such as tumor purity, clonal structure, etc., interfere the performance of calling mutations. The computational pipelines prefer to sensitively report the candidate calls, while a filter is applied for removing the false-positive calls. The existing filters rely on the whole genome/exome sequencing data, which can provide sufficient samples for training the filters. However, the gene-panel sequencing is more popular in clinical practices, but there is no practical filter for limited training samples. In light of this, we develop a semi-learning filter for gene-panel sequencing data, FilterLAP, which implemented via a label propagation framework. Given few labeled samples with a set of unlabeled ones, its basic idea is to predict the label information of unlabeled nodes from the label information of labeled nodes, and establishes a complete graph model by using the relationship between samples, by combining transductive inference with label propagation algorithm. For each node in the network, tags are propagated to adjacent nodes according to similarity and the probability distribution of similar nodes tends to be similar and can be divided into a class. We perform multiple sets of experiments on gene-panel sequencing data captured from Illumina platform. FilterLAP outperforms on both SNV and INDEL filtering, where the AUCs reach 0.90-0.97, and the average accuracies on overall mutation calls are over 90%. Comparing to GATK hard filters, FilterLAP present a 5% improvement on accuracy. These results demonstrate that the proposed method can better reduce the false positive mutation calls on gene-panel sequencing data. In addition, it is stable and efficient, which can be used as a practical tool for mutation call filtering for gene-panel sequencing data.

关键词： Cancer genomics NGS data analysis Gene-panel sequencing Mutation Filter transductive inference Label propagation

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IMageSEM at ImagecleFmed caption 2019 task: A two-stage medical concept detection strategy 20

IMageSEM at ImagecleFmed caption 2019 task: A two-stage medi...

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20th Working Notes of CLEF Conference and Labs of the Evaluation Forum, CLEF 2019

作者： Guo, Zhen wang, xuwen Zhang, Yu Li, Jiao Institute of Medical Information Medical Library Chinese Academy of Medical Sciences Peking Union Medical College Beijing100020 China

This paper presents the participation of the Image Semantics group (ImageSem) of the Institute of Medical Information at the ImageCLEFmed Caption task, which was launched by ImageCLEF 2019. The Concept Detection sub-task aims at identifying 5,528 semantic concepts from 70,786 training images and 10,000 test images. In this study, we proposed the two-stage concept detection strategy, including the medical image pre-classification based on body parts and the transfer learning-based multi-label classification model. We totally submitted 10 runs in the final evaluation. The evaluation results showed that we achieved an F1 Score of 0.2235, which ranked 8th overall. There is still a great room for improving the performance of concept detection from large-scale medical images. © 2019 CEUR-WS. All rights reserved.

关键词： Classification (of information)

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InDel variations and gene expression analysis related to Fusarium wilt resistance in Gossypium barbadense

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CROP SCIENCE 2024年第6期64卷 3112-3125页

作者： Liu, Baojun Han, Wanli Bai, Jianyu Yu, Yu wang, xuwen Qu, Yanying Gu, Aixing Xinjiang Agr Univ Minist Educ Coll Agr Engn Res Ctr Cotton Urumqi 830052 Peoples R China Xinjiang Acad Agr & Reclamat Sci Shihezi Peoples R China Xinjiang Acad Forestry Sci Inst Econ Forestry Urumqi Peoples R China

Fusarium wilt resistance of Gossypium barbadense is very important to maintain its yield and quality, and to disease resistance breeding. Although many individual genes, which are quantitative trait loci associated with wilt resistance have been identified, knowledge of genes controlling wilt resistance in G. barbadense is still limited. In order to screen the InDel fragment related to Fusarium wilt resistance in G. barbadense, a genome-wide association study was conducted using 110 recombinant inbred lines of Xinhai 14 (susceptible cotton) and 06-146 (resistant cotton). In this study, 207,040 high-quality InDel loci were identified, of which 595 and 632 InDels were significantly associated (p < 1 x 10(-3)) with wilt resistance in G. barbadense in the additive and dominant effect module analyses, respectively. Combined transcriptome expression analysis within the FOV7 stably inherited qFOV7-D03-1 interval identified three >= 2 bp InDels for two differentially expressed genes. qPCR analysis was used to further validate that the expression of GB_D03G0204 and GB_D03G0238 was significantly different in the parental, resistant, and high susceptibility varieties. The GB_D03G0238 gene InDel was significant in both additive and dominant effect models, and the GB_D03G0204 gene InDel was significantly associated with wilt resistance in G. barbadense in the dominant effect model. The InDel fragments related to wilt resistance in G. barbadense discovered in this study can help gain insights into the genetic basis of wilt resistance and improve cotton breeding with excellent wilt resistance and high fiber quality traits.

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Attribute Reduction Method Using Adaptive Genetic Algorithm and Particle Swarm Optimization 2021

Attribute Reduction Method Using Adaptive Genetic Algorithm ...

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7th International Conference on Computing and Artificial Intelligence, ICCAI 2021

作者： Wu, Shangzhi Zhang, Fan wang, xuwen Xia, Ning Northwest Normal University College of Computer Science and Engineering Lanzhou China

ISBN: (纸本)9781450389501

Attribute reduction is one of the core contents in rough set knowledge discovery, how to find the minimal attribute reduction, proposes an attribute reduction method using adaptive Genetic Algorithm(GA) and Particle Swarm Optimization(PSO). On the basis of the condition attributes for decision attribute support degree, the method reset the fitness function, can dynamically adjust the parameters of the function, thus to ensure the obtained results for minimal reduction, combined with the genetic algorithm of adaptive crossover and mutation operation, to ensure that the particles in the feasible solution can be fully retain and use, the method to strengthen the local search ability at the same time, but also keep the global search ability. Experiments results show that the method has obvious advantages in solving the minimum attribute reduction. © 2021 ACM.

关键词： Genetic algorithms

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farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods

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BIOINFORMATICS 2019年第10期35卷 1777-1779页

作者： wang, Zhe wang, xuwen Li, Youyong Lei, Tailong wang, Ercheng Li, Dan Kang, Yu Zhu, Feng Hou, Tingjun Zhejiang Univ Coll Pharmaceut Sci Hangzhou 310058 Zhejiang Peoples R China Soochow Univ Inst Funct Nano & Soft Mat FUNSOM Suzhou 215123 Jiangsu Peoples R China Zhejiang Univ State Key Lab CAD&CG Hangzhou 310058 Zhejiang Peoples R China

Protein-protein interactions (PPIs) have been regarded as an attractive emerging class of therapeutic targets for the development of new treatments. Computational approaches, especially molecular docking, have been extensively employed to predict the binding structures of PPI-inhibitors or discover novel small molecule PPI inhibitors. However, due to the relatively undruggable' features of PPI interfaces, accurate predictions of the binding structures for ligands towards PPI targets are quite challenging for most docking algorithms. Here, we constructed a non-redundant pose ranking benchmark dataset for small-molecule PPI inhibitors, which contains 900 binding poses for 184 protein-ligand complexes. Then, we evaluated the performance of MM/PB(GB)SA approaches to identify the correct binding poses for PPI inhibitors, including two Prime MM/GBSA procedures from the Schrodinger suite and seven different MM/PB(GB)SA procedures from the Amber package. Our results showed that MM/PBSA outperformed the Glide SP scoring function (success rate of 58.6%) and MM/GBSA in most cases, especially the PB3 procedure which could achieve an overall success rate of approximate to 74%. Moreover, the GB6 procedure (success rate of 68.9%) performed much better than the other MM/GBSA procedures, highlighting the excellent potential of the GBNSR6 implicit solvation model for pose ranking. Finally, we developed the webserver of Fast Amber Rescoring for PPI Inhibitors (farPPI), which offers a freely available service to rescore the docking poses for PPI inhibitors by using the MM/PB(GB)SA methods. Availability and implementation farPPI web server is freely available at http://***/farppi/. Supplementary information Supplementary data are available at Bioinformatics online.

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