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| 1 | High-speed image reconstruction for optically sectioned,super-resolution structured illumination microscopy显示文摘Super-resolution structured illumination microscopy(SR-SIM)is an outstanding method for visualizing the subcellular dynamics in living cells.To date,by using elaborately designed systems and algorithms,SR-SIM can achieve rapid,optically sectioned,SR observation with hundreds to thousands of time points.However,real-time observation is still out of reach for most SIM setups as conventional algorithms for image reconstruction involve a heavy computing burden.To address this limitation,an accelerated reconstruction algorithm was developed by implementing a simplified workflow for SR-SIM,termed joint space and frequency reconstruction.This algorithm results in an 80-fold improvement in reconstruction speed relative to the widely used Wiener-SIM.Critically,the increased processing speed does not come at the expense of spatial resolution or sectioning capability,as demonstrated by live imaging of microtubule dynamics and mitochondrial tubulation. | Zhaojun Wang Tianyu Zhao Huiwen Hao Yanan Cai Kun Feng Xue Yun Yansheng Liang Shaowei Wang Yujie Sun Piero RBianco Kwangsung Oh Ming Lei | 2022 | Advanced Photonics2022，4，2： | 9 |
| 2 | RIP1-dependent linear and nonlinear recruitments of caspase-8 and RIP3 respectively to necrosome specify distinct cell death outcomes显示文摘There remains a significant gap in our quantitative understanding of crosstalk between apoptosis and necroptosis pathways.By employing the SWATH-MS technique,we quantified absolute amounts of up to thousands of proteins in dynamic assembling/de-assembling of TNF signaling complexes.Combining SWATH-MS-based network modeling and experimental validation,we found that when RIP1 level is below~1000 molecules/cell(mpc),the cell solely undergoes TRADD-dependent apoptosis.When RIP1 is above~1000 mpc,pro-caspase-8 and RIP3 are recruited to necrosome respectively with linear and nonlinear dependence on RIP1 amount,which well explains the co-occurrence of apoptosis and necroptosis and the paradoxical obser-vations that RIP1 is required for necroptosis but its increase down-regulates necroptosis.Higher amount of RIP1(>~46,000 mpc)suppresses apoptosis,leading to necroptosis alone.The relation between RIP1 level and occurrence of necroptosis or total cell death is biphasic.Our study provides a resource for encoding the com-plexity of TNF signaling and a quantitative picture how distinct dynamic interplay among proteins function as basis sets in signaling complexes,enabling RIP1 to play diverse roles in governing cell fate decisions. | Xiang Li Chuan-Qi Zhong Rui Wu Xiaozheng Xu Zhang-Hua Yang Shaowei Cai Xiurong Wu Xin Chen Zhiyong Yin Qingzu He Dianjie Li Fei Xu Yihua Yan Hong Qi Changchuan Xie Jianwei Shuai Jiahuai Han | 2021 | Protein & Cell2021，12，11： | 5 |
| 3 | Empirical investigation of stochastic local search for maximum satisfiability显示文摘The maximum satisfiability (MAX-SAT)problem is an important NP-hard problem in theory,and has a broad range of applications in practice.Stochastic local search (SLS)is becoming an increasingly popular method for solving MAX-SAT.Recently,a powerful SLS algorithm called CCLS shows efficiency on solving random and crafted MAX-SAT instances.However,the performance of CCLS on solving industrial MAX-SAT instances lags far behind.In this paper,we focus on experimentally analyzing the performance of SLS algorithms for solving industrial MAXSAT instances.First,we conduct experiments to analyze why CCLS performs poor on industrial instances.Then we propose a new strategy called additive BMS (Best from Multiple Selections)to ease the serious issue.By integrating CCLS and additive BMS,we develop a new SLS algorithm for MAXSAT called CCABMS,and related experiments indicate the efficiency of CCABMS.Also,we experimentally analyze the effectiveness of initialization methods on SLS algorithms for MAX-SAT,and combine an effective initialization method with CCABMS,resulting in an enhanced algorithm.Experimental results show that our enhanced algorithm performs better than its state-of-the-art SLS competitors on a large number of industrial MAX-SAT instances. | Yi CHU Chuan LUO Shaowei CAI Haihang YOU | 2019 | Frontiers of Computer Science2019，13，1： | 3 |
| 4 | Efficient zonal diagnosis with maximum satisfiability显示文摘Model-based diagnosis(MBD) has been widely acknowledged as an effective diagnosis paradigm.However, for large scale circuits, it is difficult to find all cardinality-minimal diagnoses within a reasonable time. This paper proposes a novel method that takes a significant step in this direction. The idea is to divide a circuit into zones and compute the cardinality-minimal diagnoses by finding subset-minimal diagnoses with cardinality-minimal via a maximum satisfiability(MaxSAT) solver on an abstracted circuit that is composed of these zones instead of all components. We also propose a new propagate-extend method for extending the seed-TLDs to obtain all cardinality-minimal diagnoses efficiently. We implement our method with a state-of-the-art core-guided MaxSAT solver, and present evidence that it significantly improves the diagnosis efficiency on ISCAS-85 circuits. Our method outperforms SATbD, which was recently shown to outperform most complete MBD approaches using satisfiability(SAT). | Meng LIU Dantong OUYANG Shaowei CAI Liming ZHANG | 2018 | Science China(Information Sciences)2018，61，11： | 3 |
| 5 | A clique-superposition model for social networks显示文摘How does a social network evolve? Sociologists have studied this question for many years.According to some famous sociologists,social links are driven by social intersections.Actors who affiliate with the shared intersections tend to become interpersonally linked and form a cluster.In the social network,an actor cluster could be a clique or a group of several smaller-sized cliques.Thus we can conclude that a social network is composed of superposed cliques of different sizes.However,sociologists did not verify the theory in large scale data due to lack of computing ability.Motivated by this challenge,incorporated with the theory,we utilize data mining technologies to study the evolution patterns of large scale social networks in real world.Then,we propose a novel Clique-superposition generative model,which generates undirected weighted networks.By extensive experiments,we demonstrate that our model can generate networks with static and time evolving patterns observed not only in earlier literature but also in our work. | YAN Fei CAI ShaoWei ZHANG Ming LIU GuoJun DENG ZhiHong | 2013 | Science China(Information Sciences)2013，56，5： | 1 |
| 6 | Blockade of deubiquitinase YOD1 degrades oncogenic PML/RARα and eradicates acute promyelocytic leukemia cells显示文摘In most acute promyelocytic leukemia(APL)cells,promyelocytic leukemia(PML)fuses to retinoic acid receptor α (RARα)due to chromosomal translocation,thus generating PML/RARαoncoprotein,which is a relatively stable oncoprotein for degradation in APL.Elucidating the mechanism regulating the stability of PML/RARαmay help to degrade PML/RARαand eradicate APL cells.Here,we describe a deubiquitinase(DUB)-involved regulatory mechanism for the maintenance of PML/RARαstability and develop a novel pharmacological approach to degrading PML/RARαby inhibiting DUB.We utilized a DUB siRNA library to identify the ovarian tumor protease(OTU)family member deubiquitinase YOD1 as a critical DUB of PML/RARα.Suppression of YOD1 promoted the degradation of PML/RARα,thus inhibiting APL cells and prolonging the survival time of APL cell-bearing mice.Subsequent phenotypic screening of small molecules allowed us to identify ubiquitin isopeptidase inhibitor I(G5)as the first YOD1 pharmacological inhibitor.As expected,G5 notably degraded PML/RARαprotein and eradicated APL,particularly drug-resistant APL cells.Importantly,G5 also showed a strong killing effect on primary patient-derived APL blasts.Overall,our study not only reveals the DUB-involved regulatory mechanism on PML/RARαstability and validates YOD1 as a potential therapeutic target for APL,but also identifies G5 as a YOD1 inhibitor and a promising candidate for APL,particularly drug-resistant APL treatment. | Xuejing Shao Yingqian Chen Wei Wang Wenxin Du Xingya Zhang Minyi Cai Shaowei Bing Ji Cao Xiaojun Xu Bo Yang Qiaojun He Meidan Ying | 2022 | Acta Pharmaceutica Sinica B2022，12，4： | 1 |
| 7 | Controllable Synthesis of Well-aligned ZnO Nanorod Arrays on Varying Substrates via Rapid Electrodeposition显示文摘A facile and rapid electrodeposition route was developed to controllably synthesize well-aligned Zn O nanorod arrays on diverse substrates, such as seed-layer pre-formed, pristine indium tin oxide(ITO) and Si, using Zn(NO3)2$6H2O and hexamethylenetetramine(HMT) as the precursors. X-ray diffraction(XRD) and transmission electron microscopy(TEM) results indicated that seed-layer pre-modified of Zn O nanorod arrays(ZNRs) possessed single crystalline, a wurtzite crystal structure with preferential growth orientation along[0001] direction. The ZNRs on pre-modified Zn O seed-layer(ZSL) had diameters of 30e50 nm, and aligned vertically to the substrates. ZNRs on ZSL/ITO substrate exhibited a high transmittance(above 80%) in visible wavelength range and the red-shift of band gap energy. An electrochemical reaction model was proposed to explain the growth process of Zn O nanorods. Importantly, the rapid synthesis of ZNRs provided the feasibility of preparation of SERS(surface enhanced Raman scattering) nanocomposite within shorter time by a subsequent electrochemical etching. | Haibao Zhang Shaowei Jin Guotao Duan Jingjing Wang Weiping Cai | 2014 | Journal of Materials Science & Technology2014，30，11： | 0 |
| 8 | Rapid,artifact-reduced,image reconstruction for super-resolution structured illumination microscopy显示文摘Super-resolution structured ilumination microscopy(SR-SIM)is finding increasing application in biomedical research due to its superior ability to visualize subcellular dynamics in living cells.However,during image reconstruction artifacts can be introduced and when coupled with time-consuming postprocessing procedures,limits this technique from becoming a routine imaging tool for biologists.To address these issues,an accelerated,artifact-reduced reconstruction algorithm termed joint space frequency reconstruction-based artifact reduction algorithm(JSFR-AR-SIM)was developed by integrating a high-speed reconstruc tion framework with a high-fidelity optimization approach designed to suppress the sidelobe artifact.Consequently,JSFR-AR-SIM produces high-quality,super-resolution images with minimal artifacts,and the reconstruction speed is increased.We anticipate this algorithm to facilitate SR-SIM becoming a routine tool in biomedical laboratories. | Zhaojun Wang Tianyu Zhao Yanan Cai Jingxiang Zhang Huiwen Hao Yansheng Liang Shaowei Wang Yujie Sun Tongsheng Chen Piero R.Bianco Kwangsung Oh Ming Lei | 2023 | The Innovation2023，4，3： | 0 |
| 9 | Constrained maximum weighted bipartite matching:a novel approach to radio broadcast scheduling显示文摘Given a set of radio broadcast programs, the radio broadcast scheduling problem is to allocate a set of devices to transmit the programs to achieve the optimal sound quality. In this article, we propose a complete algorithm to solve the problem, which is based on a branch-and-bound(BnB) algorithm. We formulate the problem with a new model, called constrained maximum weighted bipartite matching(CMBM),i.e., the maximum matching problem on a weighted bipartite graph with constraints. For the reduced matching problem, we propose a novel BnB algorithm by introducing three new strategies, including the highest quality first, the least conflict first and the more edge first. We also establish an upper bound estimating function for pruning the search space of the algorithm. The experimental results show that our new algorithm can quickly find the optimal solution for the radio broadcast scheduling problem at small scales, and has higher scalability for the problems at large scales than the existing complete algorithm. | Shaojiang WANG Tianyong WU Yuan YAO Dongbo BU Shaowei CAI | 2019 | Science China(Information Sciences)2019，62，7： | 0 |
| 10 | Current situation and development trend of design methods for subgrade structure of high speed railways显示文摘Purpose–This method will become a new development trend in subgrade structure design for high speed railways.Design/methodology/approach–This paper summarizes the structural types and design methods of subgrade bed for high speed railways in China,Japan,France,Germany,the United States and other countries based on the study and analysis of existing literature and combined with the research results and practices of high speed railway subgrade engineering at home and abroad.Findings–It is found that in foreign countries,the layered reinforced structure is generally adopted for the subgrade bed of high speed railways,and the unified double-layer or multi-layer structure is adopted for the surface layer of subgrade bed,while the simple structure is adopted in China;in foreign countries,different inspection parameters are adopted to evaluate the compaction state of fillers according to their respective understanding and practice,while in China,compaction coefficient,subsoil coefficient and dynamic deformation modulus are adopted for such evaluation;in foreign countries,the subgrade top deformation control method,the subgrade bottom deformation control method,the subsurface fill strength control method are mainly adopted in subgrade bed structure design of high speed railways,while in China,dynamic deformation control of subgrade surface and dynamic strain control of subgrade bed bottom layer is adopted in the design.However,the cumulative deformation of subgrade caused by train cyclic vibration load is not considered in the existing design methods.Originality/value–This paper introduces a new subgrade structure design method based on whole-process dynamics analysis that meets subgrade functional requirements and is established on the basis of the existing research at home and abroad on prediction methods for cumulative deformation of subgrade soil. | Yangsheng Ye Degou Cai Qianli Zhang Shaowei Wei Hongye Yan Lin Geng | 2023 | Railway Sciences2023，2，3： | 0 |
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