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Mutation signatures inform the natural host of SARS-CoV-2

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National Science Review 2022年第2期9卷 9-12页

作者： Shanjun Deng Ke Xing Xionglei He State Key Laboratory of Biocontrol School of Life Sciences Sun Yat-Sen University school of Life sciences Guangzhou University

The origin of SARS-CoV-2,the causative virus of COVID-19,has been a mystery since the beginning of the outbreak and has been heavily debated lately.One of the main reasons for this is that RaTG13,the closest relative found to date [1](in the horseshoe bat Rhinolophus affinis),has only 96.1% nucleotide similarity to SARS-CoV-2 (with～1200 nucleotide differences).

关键词： CORONAVIRUS

Free energy perturbation(FEP)-guided scaffold hopping

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Acta Pharmaceutica Sinica B 2022年第3期12卷 1351-1362页

作者： Deyan Wu Xuehua Zheng Runduo Liu Zhe Li Zan Jiang Qian Zhou Yue Huang Xu-Nian Wu Chen Zhang Yi-You Huang Hai-Bin Luo school of Pharmaceutical sciences Hainan UniversityHaikou 570228China school of Pharmaceutical sciences Sun Yat-sen UniversityGuangzhou 510006China school of Pharmaceutical sciences Guangzhou Medical UniversityGuangzhou 511436China

Scaffold hopping refers to computer-aided screening for active compounds with different structures against the same receptor to enrich privileged scaffolds,which is a topic of high interest in organic and medicinal chemistry.However,most approaches cannot efficiently predict the potency level of candidates after scaffold hopping.Herein,we identified potent PDE5 inhibitors with a novel scaffold via a free energy perturbation(FEP)-guided scaffold-hopping strategy,and FEP shows great advantages to precisely predict the theoretical binding potenciesΔGFEPbetween ligands and their target,which were more consistent with the experimental binding potenciesΔGEXP(the mean absolute deviations|ΔGFEP-ΔGEXP|<2 kcal/mol)than thoseΔGMM-PBSAorΔGMM-GBSApredicted by the MM-PBSA or MM-GBSA method.Lead L12 had an IC_(50) of 8.7 nmol/L and exhibited a different binding pattern in its crystal structure with PDE5 from the famous starting drug tadalafil.Our work provides the first report via the FEPguided scaffold hopping strategy for potent inhibitor discovery with a novel scaffold,implying that it will have a variety of future applications in rational molecular design and drug discovery.

关键词： Free energy perturbation Scaffold hopping Privileged scaffolds Drug discovery Binding potencies Molecular design PDE5 inhibitors Pulmonary arterial hypertension

On symplectic automorphisms of elliptic surfaces acting on CH0

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Science China Mathematics 2023年第3期66卷 443-456页

作者： Jiabin Du Wenfei Liu school of Mathematical sciences Xiamen University

Let S be a complex smooth projective surface of Kodaira dimension one. We show that the group Auts(S) of symplectic automorphisms acts trivially on the Albanese kernel CH0(S)albof the 0-th Chow group CH0(S), unless possibly if the geometric genus and the irregularity satisfy pg(S) = q(S) ∈ {1, 2}. In the exceptional cases, the image of the homomorphism Auts(S) → Aut(CH0(S)alb) has the order at most 3. Our arguments actually take care of the group Autf(S) of fibration-preserving automorphisms of elliptic surfaces f : S → B. We prove that if σ ∈ Autf(S) induces the trivial action on Hi,0(S) for i > 0, then it induces the trivial action on CH0(S)alb. As a by-product we obtain that if S is an elliptic K3 surface, then Autf(S)∩Auts(S)acts trivially on CH0(S)alb.

关键词： symplectic automorphism elliptic surface Chow group 14J50 14J27 14C15 14J28

Forward Expansiveness and Entropies for Subsystems of Z+k-actions

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Acta Mathematica Sinica,English Series 2023年第4期39卷 633-662页

作者： Yao Jia GUO Xin Sheng WANG Yu Jun ZHU school of Mathematical sciences Xiamen University

In this paper,forward expansiveness and entropies of "subsystems"2) of Z+k-actions are investigated.Let α be a Z+k-action on a compact metric space.For each 1 ≤j≤k-1,denote Gj+={V+:=V ∩R+k:V is a j-dimensional subspace of Rk}.We consider the forward expansiveness and entropies for α along V+∈ Gj+.Adapting the technique of "coding",which was introduced by M.Boyle and D.Lind to investigate expansive subdynamics of Zk-actions,to the Z+kcases,we show that the set Ej+(α) of forward expansive j-dimensional V+is open in Gj+.The topological entropy and measure-theoretic entropy of j-dimensional subsystems of α are both continuous in Ej+(α),and moreover,a variational principle relating them is obtained.For a 1-dimensional ray L ∈G1+,we relate the 1-dimensional subsystem of α along L to an i.***.d.random transformation.Applying the techniques of random dynamical systems we investigate the entropy theory of 1-dimensional subsystems.In particular,we propose the notion of preimage entropy(including topological and measure-theoretical versions) via the preimage structure of α along L.We show that the preimage entropy coincides with the classical entropy along any L ∈E1+(α) for topological and measure-theoretical versions respectively.Meanwhile,a formula relating the measure-theoretical directional preimage entropy and the folding entropy of the generators is obtained.

关键词： ℤ k + -action forward expansiveness j -dimensional subsystems entropy preimage entropy folding entropy variational principle random transformation 37A35 37B40

On Minor Left Prime Factorization Problem for Multivariate Polynomial Matrices

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Journal of Systems Science & Complexity 2024年第3期37卷 1295-1307页

作者： LU Dong WANG Dingkang XIAO Fanghui school of Mathematics Southwest Jiaotong University KLMM Academy of Mathematics and Systems Science Chinese Academy of Sciences school of Mathematical sciences University of Chinese Academy of Sciences MOE-LCSM School of Mathematics and Statistics Hunan Normal University

A new necessary and sufficient condition for the existence of minor left prime factorizations of multivariate polynomial matrices without full row rank is presented. The key idea is to establish a relationship between a matrix and any of its full row rank submatrices. Based on the new result,the authors propose an algorithm for factorizing matrices and have implemented it on the computer algebra system Maple. Two examples are given to illustrate the effectiveness of the algorithm, and experimental data shows that the algorithm is efficient.

关键词： Free modules Gröbner bases minor left prime (MLP) multivariate polynomial matrices polynomial matrix factorizations

NeuroPrim:An attention-based model for solving NP-hard spanning tree problems

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Science China Mathematics 2024年第6期67卷 1359-1376页

作者： Yuchen Shi Congying Han Tiande Guo school of Mathematical sciences University of Chinese Academy of SciencesBeijing100049China

Spanning tree problems with specialized constraints can be difficult to solve in real-world scenarios,often requiring intricate algorithmic design and exponential time.Recently,there has been growing interest in end-to-end deep neural networks for solving routing problems.However,such methods typically produce sequences of vertices,which make it difficult to apply them to general combinatorial optimization problems where the solution set consists of edges,as in various spanning tree problems.In this paper,we propose NeuroPrim,a novel framework for solving various spanning tree problems by defining a Markov decision process for general combinatorial optimization problems on graphs.Our approach reduces the action and state space using Prim's algorithm and trains the resulting model using REINFORCE.We apply our framework to three difficult problems on the Euclidean space:the degree-constrained minimum spanning tree problem,the minimum routing cost spanning tree problem and the Steiner tree problem in graphs.Experimental results on literature instances demonstrate that our model outperforms strong heuristics and achieves small optimality gaps of up to 250 vertices.Additionally,we find that our model has strong generalization ability with no significant degradation observed on problem instances as large as 1,000.Our results suggest that our framework can be effective for solving a wide range of combinatorial optimization problems beyond spanning tree problems.

关键词： degree-constrained minimum spanning tree problem minimum routing cost spanning tree problem Steiner tree problem in graphs Prim's algorithm reinforcement learning

Visible-light-induced direct hydrodifluoromethylation of alkenes with difluoromethyltriphenylphosphonium iodide salt

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Chinese Chemical Letters 2023年第1期34卷 322-325页

作者： Xiaojian Ren Qiang Liu Zhixiang Wang Xiangyu Chen school of Chemical sciences University of the Chinese Academy of SciencesBeijing 100049China

Photoredox-catalyzed hydrodifluoromethylation of alkenes has become an effective method to introduce difluoromethyl group into organic molecules.As the reported methods involve either photocatalysts or superstoichiometric amounts of additives,we herein describe a simple alternative without using photocatalyst or additive for the hydrodifluoromethylation of alkenes,through photoactivation of difluoromethyltriphenylphosphonium iodide salt.Mechanistic studies shed light on how the transformation takes place.

关键词： Hydrodifluoromethylation Difluoromethyltriphenylphosphonium iodide salt Alkenes DFT studies Photoredox

Liposome cocktail activator modulates hepatocytes and remodels the microenvironment to mitigate acute liver failure

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Asian Journal of Pharmaceutical sciences 2022年第6期17卷 867-879页

作者： Na Yin Wenjun Zhang Runxiu Wei Qiang Yang Fengming He Ling Guo Min Feng school of Pharmaceutical sciences Sun Yat-Sen UniversityGuangzhou 510006China school of Pharmaceutical sciences Hainan UniversityHaikou 570228China school of Pharmaceutical sciences Xiamen UniversityXiamen 361102China

Acute liver failure(ALF)is a mortal and critical hepatic disease,in which oxidative stress,inflammation storm and hepatocyte death are crucial in the pathogenesis.Hence,in contrast to the control of a single link,a combination therapy targeting multiple pathogenic links of the disease will be a favorable means to control the progression of the disease.In this study,we constructed dimethyl itaconate-loaded liposomes modified with dodecyl gallate as a cocktail activator to investigate its functional role in acetaminophen(APAP)-induced ALF.Our results demonstrated that the cocktail activator acted on hepatocytes and triggered cocktail efficacy,thereby simultaneously attenuating APAP-induced hepatocyte damage and remodeling the damage microenvironment.The cocktail activator could effectively scavenge reactive oxygen species,inhibit excessive inflammatory responses and reduce cell death in impaired hepatocytes for detoxification.More importantly,the cocktail activator could remodel the damage microenvironment,thus further promoting hepatocyte expansion and specifically switching macrophages from the M1 to M2 phenotype for a favorable liver regeneration of ALF.Furthermore,in APAP-induced ALF mouse model,the cocktail activator improved liver function,alleviated histopathological damage and increased survival rate.In summary,these findings indicate that the cocktail activator may provide a promising therapeutic approach for ALF treatment as a nanomedicine.

关键词： Cocktail activator Dimethyl itaconate Dodecyl gallate Hepatocyte Microenvironment modulation

Impact of tourism on the vigilance behavior of the Cyprus rock agama(Laudakia cypriaca)

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Integrative Zoology 2024年第3期19卷 577-583页

作者： Artur GOLAWSKI Iris CHARALAMBIDOU Sylwia GOLAWSKA Faculty of sciences Siedlce University of Natural Sciences and HumanitiesSiedlcePolandand Department of Life sciences School of Life and Health SciencesUniversity of NicosiaNicosiaCyprus

Escape behavior is a common antipredator strategy among wild animals.Here,we investigated the effect of four factors on the vigilance behavior of the endemic Cyprus rock agama(Laudakia cypriaca).Flight initiation distance(FID,the minimum distance to which an observer can approach a lizard before it flees)was measured in relation to the type of location(tourist vs.nontourist area),the observer’s starting distance,air temperature,and substrate temperature.We collected data for 39 agamas in tourist areas and 34 of these lizards in nontourist areas.As a whole,the mean starting distance was 10.5 m and the FID was 3.6 m.The average substrate temperature was 34.0℃ and the average air temperature 29.6℃.Only the type of area affected the agamas’escape decisions with FID being 1.8 m shorter in tourist areas than in nontourist areas(2.7 m vs.4.5 m).This is probably due to the habituation of lizards to the presence of humans in the former areas.This study shows that tourism strongly affects the behavior of lizards,which may have consequences for the functioning of the population.Tourists can increase the safety of lizards by creating a human shield to deter predators.Once the tourist season is over,lizards may become more vulnerable to predators.

关键词： anthropogenic disturbance flight initiation distance lizards tourism vigilance behavior