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Emerging structures and dynamic mechanisms ofγ-secretase for Alzheimer’s disease

Neural Regeneration Research 2025年第1期20卷 174-180页

作者： Yinglong Miao Michael S.Wolfe computational Medicine program and Department of Pharmacology University of North Carolina–Chapel HillChapel HillNCUSA Department of Medicinal Chemistry University of KansasLawrenceKSUSA

γ-Secretase,called“the proteasome of the membrane,”is a membrane-embedded protease complex that cleaves 150+peptide substrates with central roles in biology and medicine,including amyloid precursor protein and the Notch family of cell-surface *** inγ-secretase and amyloid precursor protein lead to early-onset familial Alzheimer’s disease.γ-Secretase has thus served as a critical drug target for treating familial Alzheimer’s disease and the more common late-onset Alzheimer’s disease as ***,critical gaps remain in understanding the mechanisms of processive proteolysis of substrates,the effects of familial Alzheimer’s disease mutations,and allosteric modulation of substrate cleavage byγ-*** this review,we focus on recent studies of structural dynamic mechanisms ofγ-*** mechanisms,including the“Fit-Stay-Trim,”“Sliding-Unwinding,”and“Tilting-Unwinding,”have been proposed for substrate proteolysis of amyloid precursor protein byγ-secretase based on all-atom molecular dynamics *** an incorrect registry of the Notch1 substrate was identified in the cryo-electron microscopy structure of Notch1-boundγ-secretase,molecular dynamics simulations on a resolved model of Notch1-boundγ-secretase that was reconstructed using the amyloid precursor protein-boundγ-secretase as a template successfully capturedγ-secretase activation for proper cleavages of both wildtype and mutant Notch,being consistent with biochemical experimental *** approach could be potentially applied to decipher the processing mechanisms of various substrates byγ-*** addition,controversy over the effects of familial Alzheimer’s disease mutations,particularly the issue of whether they stabilize or destabilizeγ-secretase-substrate complexes,is ***,an outlook is provided for future studies ofγ-secretase,including pathways of substrate binding and product release,effects of modulators on familial Alzheimer’s disease mutations

关键词： Alzheimer’s disease amyloid precursor protein cryo-EM structures drug design intramembrane proteolysis molecular dynamics Notch

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Unraveling atomistic and electronic origins of multiaxial magnetic anisotropy

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Science China(Physics,Mechanics & Astronomy) 2025年第2期68卷 175-182页

作者： Boyu Liu Xueyang Li Junsheng Feng Changsong Xu Hongjun Xiang Key Laboratory of computational Physical Sciences(Ministry of Education) Institute of Computational Physical SciencesState Key Laboratory of Surface Physics and Department of PhysicsFudan UniversityShanghai200433China Shanghai Qi Zhi Institute Shanghai200030China School of Physics and Material Engineering Hefei Normal UniversityHefei230601China

Multiaxial magnetic anisotropy(MA)refers to the phenomenon that multiple axes of the magnetic crystal correspond to different energy *** with the common uniaxial magnetic anisotropy,multiaxial MA facilitates novel forms of applications in ***,by combining the first-principles-based spin Hamiltonian and tight-binding(TB)method,we reveal the microscopic origins,instead of the common phenomenological understanding,of biaxial MA and triaxial *** the example system of NiO,it is found that the multiple minima result from the fourth-order and the sixth-order single ion interactions,while the difference between[110]and[110]directions originates from a second-order bond-dependent anisotropic pair interaction(i.e.,the so-called Gamma interaction).Moreover,through the application of a newly developed general spin dependent TB approach,it is revealed that the triaxial MA arises from the special spin-orbital entangled Hund term,which is different from the orbital-independent Hund term in the usual Slater Koster TB *** work thus not only leads to a thorough understanding of the multiaxial MA in NiO,but also establishes a methodology that can be widely used to explore the microscopic origins of MA in different magnets.

关键词： multiaxial magnetic anisotropy origin of multiaxial magnetic mnisotropy effective spin Hamiltonian tight-binding model antiferromagnetism

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Graph based recurrent network for context specific synthetic lethality prediction

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Science China(Life Sciences) 2025年第2期68卷 527-540页

作者： Yuyang Jiang Jing Wang Yixin Zhang ZhiWei Cao Qinglong Zhang Jinsong Su Song He Xiaochen Bo Academy of Medical Engineering and Translational Medicine Tianjin UniversityTianjin 300072China Department of Bioinformatics Institute of Health Service and Transfusion MedicineBeijing 100850China School of Medicine Tsinghua UniversityBeijing 100084China School of informatics Xiamen UniversityXiamen 361005China

The concept of synthetic lethality(SL)has been successfully used for targeted *** further explore SL for cancer therapy,identifying more SL interactions with therapeutic potential are ***,graph neural network-based deep learning methods have been proposed for SL prediction,which reduce the SL search space of wet-lab based ***,these methods ignore that most SL interactions depend strongly on genetic context,which limits the application of the predicted *** this study,we proposed a graph recurrent network-based model for specific context-dependent SL prediction(SLGRN).In particular,we introduced a Graph Recurrent Network-based encoder to acquire a context-specific,low-dimensional feature representation for each node,facilitating the prediction of novel *** leveraged gate recurrent unit(GRU)and it incorporated a context-dependent-level state to effectively integrate information from all *** a result,SLGRN outperforms the state-of-the-arts models for SL *** subsequently validate novel SL interactions under different contexts based on combination therapy or patient survival *** in vitro experiments and retrospective clinical analysis,we emphasize the potential clinical significance of this context-specific SL prediction model.

关键词： synthetic lethality graph recurrent network context-specific graph combination therapy

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Small extrachromosomal circular DNA in amyotrophic lateral sclerosis matter

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Neural Regeneration Research 2025年第5期20卷 1411-1413页

作者： Marcos J.Arauzo-Bravo Daniela Gerovska Matthias Schwab Alexandra Kretz computational Biology and Systems Biomedicine Biodonostia Health Research InstituteSan SebastianSpain Basque Foundation for Science IKERBASQUEBilbaoSpainMax Planck Institute for Molecular BiomedicineComputational Biology and Bioinformatics GroupMünsterNorth Rhine-WestphaliaGermany Department of Cell Biology and Histology Faculty of Medicine and NursingUniversity of Basque Country(UPV/EHU)LeioaSpain Department of Neurology Jena University HospitalJenaThuringiaGermany

Comprehensive studies identify motor neuron spectrum disorders including amyotrophic lateral sclerosis(ALS)as globally rising fatal disorders with the highest prevalence in aging populations,influenced by ethnicity and ancestry(GBD 2016 Motor Neuron Disease Colla borators,2018).While~10% of diagnoses involve a family history(fALS),most cases are considered sporadic(sALS).However,population-based studies suggest that even cases without a common index mutation impart heritability(Ryan et al.,2019),indicating a crucial role of rare and as yet unknown genetic denominators.

关键词： amyotrophic sclerosis

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Flat-band based high-temperature ferromagnetic semiconducting state in the graphitic C4N3 monolayer

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Fundamental Research 2025年第1期5卷 138-144页

作者： Chaoyu He Yujie Liao Tao Ouyang Huimin Zhang Hongjun Xiang Jianxin Zhong Laboratory for Quantum Engineering and Micro-Nano Energy Technology and School of Physics and Optoelectronics Xiangtan UniversityXiangtan 411105China Key Laboratory of computational Physical Sciences(Ministry of Education) Institute of Computational Physical SciencesDepartment of PhysicsFudan UniversityShanghai 200433China

Half-filled isolated flat-band paves a new way to realize high-temperature ferromagnetic semiconductor for spintronics applications,but it is extremely rare in lattice models and lacking in realistic ***,the 2×2 super-cell of the honeycomb lattice with a single-hole defect is proposed as a new lattice model(HL-D-1/8)to realize nontrivial isolated *** further demonstrate that C_(4)N_(3)monolayer of the experimentally realized graphitic carbon nitride(***.,22,1004,2010;***.,9,3366,2018)is a perfect system holding such a lattice to host flat-bands.A new corrugated Pca21 configuration is proposed as the ground state for the free-standing C_(4)N_(3)monolayer,which is dynamically stable and energetically more favorable than the widely-used flat one without dynamical *** Pca21 configuration is found to be an intrinsic ferromagnetic half-semiconductor(T_(c)≈241 K)with one semiconducting spin-channel(1.75 eV)and one insulating spin-channel(3.64 eV),which is quite rare in two-dimensional *** ferromagnetic semiconducting property originates from the isolated pz-state flat-band as the corrugation shifts the flat-band upward to the Fermi ***,such a corrugated Pca21 C_(4)N_(3)monolayer is found to be both piezoelectric and ferroelectric,which makes it an unusual metal-free two-dimensional multiferroic.

关键词： Graphitic C_(4)N_(3) Isolated flat-band Ferromagnetic semiconductor Two-dimensional multiferroic First-principles calculation Tight-binding model

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H?rmander oscillatory integral operators: A revisit

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Science China Mathematics 2025年第04期 873-890页

作者： Chuanwei Gao Zhong Gao Changxing Miao School of Mathematical Sciences Capital Normal University Institute of Applied Physics and computational Mathematics

In this paper, we present new proofs for both the sharp Lpestimate and the decoupling theorem for the H?rmander oscillatory integral operator. The sharp Lpestimate was previously obtained by Stein（1986） and Bourgain and Guth（2011） via the TT*and multilinear methods, respectively. We provide a unified proof based on the bilinear method for both odd and even dimensions. The strategy is inspired by Barron's work（2022） on the restriction problem. The decoupling theorem for the H?rmander oscillatory integral operator can be obtained by the approach in Beltran et al.（2020）, where the key observation can be roughly formulated as follows: in a physical space of sufficiently small scale, the variable setting can be essentially viewed as *** contrast, we reprove the decoupling theorem for the H?rmander oscillatory integral operator through the Pramanik-Seeger approximation approach(Pramanik and Seeger（2007）). Both proofs rely on a scale-dependent induction argument, which can be used to deal with perturbation terms in the phase function.

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Soliton resolution for the energy-critical wave equation with an inverse-square potential in the radial case

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Science China Mathematics 2025年

作者： Xuanying Li Changxing Miao Lifeng Zhao School of Mathematical Sciences University of Science and Technology of China Institute of Applied Physics and computational Mathematics

In this paper, we present the soliton resolution for the energy-critical wave equation with an inverse square potential in the radial case and all dimensions N≥3. A crucial ingredient of our analysis involves the energy channel for the linearized wave equation with inverse square potentials, which incorporates the distorted Hankel transform.

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Time-series prediction of shellfish farm closure: A comparison of alternatives

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Information Processing in Agriculture 2014年第1期1卷 42-50页

作者： Ashfaqur Rahman Md Sumon Shahriar Claire D’Este Greg Smith John McCulloch Greg Timms Autonomous Systems program CSIRO Computational InformaticsHobartTAS 7000Australia

Shellfish farms are closed for harvest when microbial pollutants are *** pollutants are typically present in rainfall runoff from various land uses in *** currently use a number of observable parameters(river flow,rainfall,salinity)as proxies to determine when to close *** have proposed using the short term historical rainfall data as a time-series prediction problem where we aim to predict the closure of shellfish farms based only on ***-series event prediction consists of two steps:(i)feature extraction,and(ii)prediction.A number of data mining challenges exist for these scenarios:(i)which feature extraction method best captures the rainfall pattern over successive days that leads to opening or closure of the farms?,(ii)The farm closure events occur infrequently and this leads to a class imbalance problem;the question is what is the best way to deal with this problem?In this paper we have analysed and compared different combinations of balancing methods(under-sampling and over-sampling),feature extraction methods(cluster profile,curve fitting,Fourier Transform,Piecewise Aggregate Approximation,and Wavelet Transform)and learning algorithms(neural network,support vector machine,k-nearest neighbour,decision tree,and Bayesian Network)to predict closure events accurately considering the above data mining *** have identified the best combination of techniques to accurately predict shellfish farm closure from rainfall,given the above data mining challenges.

关键词： Aquaculture Shellfish farm closure Data mining Time series data

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Γ-convexity

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Acta Mathematica Scientia 2025年第1期45卷 3-15页

作者： Zhouqin JIA Wenzhi LIU Liping YUAN Tudor ZAMFIRESCU School of Mathematical Sciences Hebei Normal UniversityShijiazhuang050024China Hebei Key Laboratory of computational Mathematics and Applications Shijiazhuang050024China

Let F be a family of sets in R^(d)(always d≥2).A set M■R^(d)is called F-convex,if for any pair of distinct points a,y∈M,there is a set F∈F such that x,y∈F and F■*** obtain theΓ-convexity,when F consists of F-paths.AΓ-path is the union of both shorter sides of an isosceles right *** this paper we first characterize some I-convex sets,bounded or unbounded,including triangles,regular polygons,subsets of balls,right cylinders and cones,unbounded planar closed convex sets,***,we investigate the F-starshaped sets,and provide some conditions for a fan,a spherical sector and a right cylinder to be ***,we study theΓ-triple-convexity,which is a discrete generalization ofΓ-convexity,and provide characterizations for all the 4-point sets,some 5-point sets and Z^(d)to beΓ-triple-convex.

关键词： Γ-convexity Γ-starshaped sets Γ-triple-convexity

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On Weighted Compactness of Commutators of Bilinear Vector-valued Singular Integral Operators and Applications

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Acta Mathematica Sinica,English Series 2025年第1期41卷 169-190页

作者： Zhengyang Li Liu Lu Fanghui Liao Qingying Xue School of Mathematics&computational Science Hu’nan University of Science and TechnologyXiangtan 411201P.R.China School of Mathematics&computational Science Xiangtan UniversityXiangtan 411105P.R.China School of Mathematical Sciences Laboratory of Mathematics and Complex Systems Ministry of EducationBeijing Normal UniversityBeijing 100875P.R.China

Let T be a bilinear vector-valued singular integral operator satisfies some mild regularity conditions,which may not fall under the scope of the theory of standard Calder¬on–Zygmund *** anyb^(→)=(b_(1),b_(2))∈(CMO(R^(n)))^(2),let[T,b_(j)]e_(j)(j=1,2),[T,→b]_(α)be the commutators in the j-th entry and the iterated commutators of T,*** this paper,for all p_(0)>1,p0/2

关键词： Weighted compactness commutators multilinear square functions Fourier multiplier operator

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