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Pindel-TD:A Tandem Duplication Detector Based on A Pattern Growth Approach

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Genomics, Proteomics & bioinformatics 2024年第1期22卷 99-104页

作者： Xiaofei Yang Gaoyang Zheng Peng Jia Songbo Wang Kai Ye School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China Center for Mathematical Medical the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China Genome Institute the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China moe key lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China School of Automation Science and Engineering Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China School of Life Science and Technology Xi’an Jiaotong UniversityXi’an 710049China Faculty of Science Leiden UniversityLeiden 2311 EZNetherland

Tandem duplication(TD)is a major type of structural variations(SVs)that plays an important role in novel gene formation and human ***,TDs are often missed or incorrectly classified as insertions by most modern SV detection methods due to the lack of specialized operation on TD-related mutational ***,we developed a TD detection module for the Pindel tool,referred to as Pindel-TD,based on a TD-specific pattern growth ***-TD is capable of detecting TDs with a wide size range at single nucleotide *** simulated and real read data from HG002,we demonstrated that Pindel-TD outperforms other leading methods in terms of precision,recall,F1-score,and ***,by applying Pindel-TD to data generated from the K562 cancer cell line,we identified a TD located at the seventh exon of SAGE1,providing an explanation for its high ***-TD is available for non-commercial use at https://***/xjtu-omics/pindel.

关键词： Tandem duplication Pattern growth Short-read sequencing Structural variation SAGE1

Improving cis-regulatory elements modeling by consensus scaffolded mixture models

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Science China(Information Sciences) 2013年第1期56卷 219-229页

作者： JIANG HongShan ZHAO Ying CHEN WenGuang ZHANG XueGong Department of Computer Science and Technology Tsinghua University moe key laboratory of bioinformatics and the bioinformatics Division Department of AutomationTsinghua University

A position weight matrix(PWM) is widely accepted as a probabilistic representation for modeling protein-DNA binding *** studies showed that for factors which bind to divergent binding sites,mixtures of multiple PWMs improve *** propose a consensus scaffolded mixutre PWM(CSM) model to improve cis-regulatory elements modeling by allowing overlapping components represented by a set of PWMs,each of which corresponds to a binding pattern and is scaffolded by a degenerate *** addition,we propose a learning algorithm that involves an initial structure learning stage based on the frequent pattern mining and a refining stage based on the expectation maximization(EM) *** assess the merits of CSM using three independent *** a case-study of transcription factor Leu3,the derived CSM models agree with conventional mixtures but show better fitness according to Fermi-Dirac *** of the human-mouse conservation of predicted binding sites of 83 JASPAR transcription factors(TFs) shows that the CSM is as good as or better than the simple mixture,the context-specific independent(CSI) mixture,and the single PWM model,for 83%,84%,and 75% of the cases,***-fold cross validation on 46 TRANSFAC datasets shows that CSM model has better generality than other mixture models.

关键词： position weight matrix cis-regulatory elements mixture models frequent pattern mining EM algorithm

A fuzzy crisis in a Duffing-van der Pol system

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Chinese Physics B 2010年第3期19卷 182-187页

作者：洪灵 moe key lab for Strength and Vibration Xi'an Jiaotong University

A crisis in a Duffing-van del Pol system with fuzzy uncertainties is studied by means of the fuzzy generalised cell mapping （FGCM） method. A crisis happens when two fuzzy attractors collide simultaneously with a fuzzy saddle on the basin boundary as the intensity of fuzzy noise reaches a critical point. The two fuzzy attractors merge discontinuously to form one large fuzzy attractor after a crisis. A fuzzy attractor is characterized by its global topology and membership function. A fuzzy saddle with a complicated pattern of several disjoint segments is observed in phase space. It leads to a discontinuous merging crisis of fuzzy attractors. We illustrate this crisis event by considering a fixed point under additive and multiplicative fuzzy noise. Such a crisis is fuzzy noise-induced effects which cannot be seen in deterministic systems.

关键词： fuzzy dynamical systems fuzzy noise fuzzy bifurcation cell mapping methods

Toward a unified information framework for cell atlas assembly

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National Science Review 2022年第3期9卷 7-10页

作者： Sijie Chen Yanting Luo Haoxiang Gao Fanhong Li Jiaqi Li Yixin Chen Renke You Hairong Lv Kui Hua Rui Jiang Xuegong Zhang bioinformatics Division of BNRIST and Department of Automation MOE Key Lab of BioinformaticsTsinghua University Fuzhou Institute of Data Technology School of Medicine Tsinghua University School of Life Sciences Center for Synthetic and Systems Biology Tsinghua University

Cells are the basic structural and functional unit of the human body. Virtually all cells of a human body possess the same genome, but they exhibit colorful heterogeneities in phenotypes and *** heterogeneities includ...

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Role of the globus pallidus in motor and non-motor symptoms of Parkinson's disease

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Neural Regeneration Research 2025年第6期20卷 1628-1643页

作者： Yimiao Jiang Zengxin Qi Huixian Zhu Kangli Shen Ruiqi Liu Chenxin Fang Weiwei Lou Yifan Jiang Wangrui Yuan Xin Cao Liang Chen Qianxing Zhuang Department of Physiology School of MedicineNantong UniversityNantongJiangsu ProvinceChina Department of Neurosurgery Huashan HospitalShanghai Medical CollegeFudan UniversityShanghaiChina National Center for Neurological Disorders ShanghaiChina Shanghai key laboratory of Brain Function Restoration and Neural Regeneration ShanghaiChina State key laboratory of Medical Neurobiology and moe Frontiers Center for Brain Science Institute of Brain ScienceFudan UniversityShanghaiChina

The globus pallidus plays a pivotal role in the basal ganglia circuit. Parkinson's disease is characterized by degeneration of dopamine-producing cells in the substantia nigra, which leads to dopamine deficiency in the brain that subsequently manifests as various motor and non-motor symptoms. This review aims to summarize the involvement of the globus pallidus in both motor and non-motor manifestations of Parkinson's disease. The firing activities of parvalbumin neurons in the medial globus pallidus, including both the firing rate and pattern, exhibit strong correlations with the bradykinesia and rigidity associated with Parkinson's disease. Increased beta oscillations, which are highly correlated with bradykinesia and rigidity, are regulated by the lateral globus pallidus. Furthermore,bradykinesia and rigidity are strongly linked to the loss of dopaminergic projections within the cortical-basal ganglia-thalamocortical loop. Resting tremors are attributed to the transmission of pathological signals from the basal ganglia through the motor cortex to the cerebellum-ventral intermediate nucleus circuit. The cortico–striato–pallidal loop is responsible for mediating pallidi-associated sleep disorders. Medication and deep brain stimulation are the primary therapeutic strategies addressing the globus pallidus in Parkinson's disease. Medication is the primary treatment for motor symptoms in the early stages of Parkinson's disease, while deep brain stimulation has been clinically proven to be effective in alleviating symptoms in patients with advanced Parkinson's disease,particularly for the movement disorders caused by levodopa. Deep brain stimulation targeting the globus pallidus internus can improve motor function in patients with tremordominant and non-tremor-dominant Parkinson's disease, while deep brain stimulation targeting the globus pallidus externus can alter the temporal pattern of neural activity throughout the basal ganglia–thalamus network. Therefore, the comp

关键词： anxiety basal ganglia bradykinesia deep brain stimulation depression globus pallidus externus globus pallidus internus lateral globus pallidus medial globus pallidus neural circuit Parkinson's disease

Anti-atherosclerotic effects and molecular targets of ginkgolide B from Ginkgo biloba

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Acta Pharmaceutica Sinica B 2024年第1期14卷 1-19页

作者： Weile Ye Jiaojiao Wang Peter JLittle Jiami Zou Zhihua Zheng Jing Lu Yanjun Yin Hao Liu Dongmei Zhang Peiqing Liu Suowen Xu Wencai Ye Zhiping Liu International Cooperative laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education(moe)of China Jinan UniversityGuangzhou 510632China Guangdong Province key laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine and New Drugs Research College of PharmacyJinan UniversityGuangzhou 510632China State key laboratory of Bioactive Molecules and Druggability Assessment Jinan UniversityGuangzhou 510632China Pharmacy Australia Centre of Excellence School of PharmacyUniversity of QueenslandWoolloongabba QLD 4102Australia Sunshine Coast Health Institute and School of Health and Behavioural Sciences University of the Sunshine CoastBirtinya QLD 4575Australia National-Local Joint Engineering lab of Druggability and New Drugs Evaluation Guangdong Provincial Key Laboratory of New Drug Design and EvaluationSun Yat-sen UniversityGuangzhou 510006China School of Pharmacy Bengbu Medical CollegeBengbu 233030China Institute of Endocrine and Metabolic Diseases the First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230026China

Bioactive compounds derived from herbal medicinal plants modulate various therapeutic targets and signaling pathways associated with cardiovascular diseases(CVDs),the world’s primary cause of *** biloba,a well-known traditional Chinese medicine with notable cardiovascular actions,has been used as a cardio-and cerebrovascular therapeutic drug and nutraceutical in Asian countries for *** studies have shown that ginkgolide B,a bioactive component in Ginkgo biloba,can ameliorate atherosclerosis in cultured vascular cells and disease *** clinical relevance,several clinical trials are ongoing or being completed to examine the efficacy and safety of ginkgolide B-related drug preparations in the prevention of cerebrovascular diseases,such as ischemia ***,we present a comprehensive review of the pharmacological activities,pharmacokinetic characteristics,and mechanisms of action of ginkgolide B in atherosclerosis prevention and *** highlight new molecular targets of ginkgolide B,including nicotinamide adenine dinucleotide phosphate oxidases(NADPH oxidase),lectin-like oxidized LDL receptor-1(LOX-1),sirtuin 1(SIRT1),platelet-activating factor(PAF),proprotein convertase subtilisin/kexin type 9(PCSK9)and ***,we provide an overview and discussion of the therapeutic potential of ginkgolide B and highlight the future perspective of developing ginkgolide B as an effective therapeutic agent for treating atherosclerosis.

关键词： Cardiovascular disease Atherosclerosis Ginkgo biloba Ginkgolide B Endothelial dysfunction LOX-1 PCSK9 PAF-R antagonist

Crystal Structure of the MH2 domain of Drosophila Mad

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Science China(Life Sciences) 2009年第6期52卷 539-544页

作者： WANG Chong,CHEN Lei,WANG Le & WU JiaWei moe key laboratory of bioinformatics,Department of Biological Sciences and Biotechnology,Tsinghua University,Beijing 100084,China moe key laboratory of bioinformatics Department of Biological Sciences and Biotechnology Tsinghua University Beijing China

The decapentaplegic(Dpp),a member of the TGF-β superfamily,plays a pivotal role in the control of proliferation,global patterning and induction of specific cell fates during Drosophila *** against Dpp(Mad) is the founding member of the conserved Smad protein family which spe-cifically transduces the intracellular TGF-β signaling *** we report the 2.80 structure of the MH2 domain of Mad(Mad-MH2) that was readily superposed to the mammal Smad-MH2 *** unphosphorylated Mad-MH2 forms a symmetric homotrimer in crystals,consistent with the result of the size-exclusion chromatography that Mad-MH2 exhibited a propensity for concentration-dependent oligomerization prior to *** analysis revealed that the formation of homotrimeric Mad-MH2 is mainly mediated by contacts involving the extreme C-terminal SSVS motif,and is strengthened by phosphorylation of the last two Ser residues which was confirmed by the gel filtration analysis of the pseudophosphorylated Mad-MH2(DVD).Intriguingly,the homotrimer within an asymmetric unit only possesses two ordered C-terminal tails,reminiscent of the arrangement of the R-Smad/Smad4 complexes,indicating that the subunit with a flexible SSXS motif would be readily replaced by Co-Smad to form a functional heterotrimer.

关键词： TGF-β signaling Smad protein family MH2 domain crystal structure homotrimerization

Reciprocal translation between SAR and optical remote sensing images with cascaded-residual adversarial networks

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Science China(Information Sciences) 2021年第2期64卷 154-168页

作者： Shilei FU Feng XU Ya-Qiu JIN key lab for Information Science of Electromagnetic Waves (moe) Fudan University

Despite the advantages of all-weather and all-day high-resolution imaging, synthetic aperture radar(SAR) images are much less viewed and used by general people because human vision is not adapted to microwave scattering phenomenon. However, expert interpreters can be trained by comparing side-byside SAR and optical images to learn the mapping rules from SAR to optical. This paper attempts to develop machine intelligence that is trainable with large-volume co-registered SAR and optical images to translate SAR images to optical version for assisted SAR image interpretation. Reciprocal SAR-optical image translation is a challenging task because it is a raw data translation between two physically very different sensing modalities. Inspired by recent progresses in image translation studies in computer vision,this paper tackles the problem of SAR-optical reciprocal translation with an adversarial network scheme where cascaded residual connections and hybrid L1-GAN loss are employed. It is trained and tested on both spaceborne Gaofen-3(GF-3) and airborne Uninhabited Airborne Vehicle Synthetic Aperture Radar(UAVSAR) images. Results are presented for datasets of different resolutions and polarizations and compared with other state-of-the-art methods. The Frechet inception distance(FID) is used to quantitatively evaluate the translation performance. The possibility of unsupervised learning with unpaired/unregistered SAR and optical images is also explored. Results show that the proposed translation network works well under many scenarios and it could potentially be used for assisted SAR interpretation.

关键词： synthetic aperture radar generative adversarial network (GAN) image translation cascaded residual connection Frechet inception distance

FUSAR-Ship:building a high-resolution SAR-AIS matchup dataset of Gaofen-3 for ship detection and recognition

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Science China(Information Sciences) 2020年第4期63卷 40-58页

作者： Xiyue HOU Wei AO Qian SONG Jian LAI Haipeng WANG Feng XU key lab for Information Science of Electromagnetic Waves (moe) Fudan University

Gaofen-3(GF-3) is China’s first civil C-band fully polarimetric spaceborne synthetic aperture radar(SAR) primarily missioned for ocean remote sensing and marine monitoring. This paper proposes an automatic sea segmentation, ship detection, and SAR-AIS matchup procedure and an extensible marine target taxonomy of 15 primary ship categories, 98 sub-categories, and many non-ship targets. The FUSARShip high-resolution GF-3SAR dataset is constructed by running the procedure on a total of 126 GF-3 scenes covering a large variety of sea, land, coast, river and island scenarios. It includes more than 5000 ship chips with AIS messages as well as samples of strong scatterer, bridge, coastal land, islands, sea and land clutter. FUSAR-Ship is intended as an open benchmark dataset for ship and marine target detection and recognition. A preliminary 8-type ship classification experiment based on convolutional neural networks demonstrated that an average of 79% test accuracy can be achieved.

关键词： FUSAR-Ship Gaofen-3 SAR-AIS matchup automatic target recognition multi-scale CFAR deep learning