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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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Novel Polarimetric Analysis of Near Horizon Flaring Episodes in M87* in Millimeter Wavelength

arXiv

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arXiv 2025年

作者： Emami, Razieh Liska, Matthew Chatterjee, Koushik Bower, Geoffrey C. Benbow, Wystan Finkbeiner, Douglas Wielgus, Maciek Hernquist, Lars Smith, Randall Tremblay, Grant Ricarte, Angelo Steiner, James F. Broderick, Avery E. Saurabh Davelaar, Jordy Grindlay, Josh Vogelsberger, Mark Chan, Chi-Kwan Center for Astrophysics Harvard & Smithsonian 60 Garden Street CambridgeMA02138 United States Center for Relativistic Astrophysics Georgia Institute of Technology Howey Physics Bldg 837 State Street NW AtlantaGA30332 United States Department of Physics University of Maryland College ParkMD United States Academia Sinica Institute of Astronomy and Astrophysics 645 N. A’ohoku Place HiloHI96720 United States Instituto de Astrofísica de Andalucía-CSIC Glorieta de la Astronomía s/n GranadaE-18008 Spain Black Hole Initiative Harvard University 20 Garden Street CambridgeMA02138 United States Perimeter Institute for Theoretical Physics 31 Caroline Street North WaterlooONN2L 2Y5 Canada Department of Physics and Astronomy University of Waterloo 200 University Avenue West WaterlooONN2L 3G1 Canada Max-Planck-Institut für Radioastronomie Auf dem Hügel 69 BonnD-53121 Germany Department of Astrophysical Sciences Peyton Hall Princeton University PrincetonNJ08544 United States NASA Hubble Fellowship Program Department of Physics Kavli Institute for Astrophysics and Space Research Massachusetts Institute of Technology CambridgeMA02139 United States Department of Astronomy and Steward Observatory University of Arizona 933 North Cherry Avenue TucsonAZ85721 United States Data Science Institute University of Arizona 1230 N. Cherry Ave. TucsonAZ85721 United States Program in Applied Mathematics University of Arizona 617 N. Santa Rita TucsonAZ85721 United States

Recent multi-wavelength observations of M87* (Algaba et al. 2024) revealed a high-energy γ-ray flare without a corresponding millimeter counterpart. We present a theoretical polarimetric study to evaluate the presence and nature of a potential millimeter flare in M87*, using a suite of general relativistic magnetohydrodynamical simulations with varying black hole (BH) spins and magnetic field configurations. We find that the emergence of a millimeter flare is strongly influenced by both spin and magnetic structure, with limited sensitivity to the electron distribution (thermal vs. non-thermal). We model the intensity light curve with a damped random walk (DRW) and compare the characteristic timescale (τ) with recent SMA observations, finding that the simulated τ exceeds observed values by over an order of magnitude. In a flaring case with BH spin a=+0.5, we identify a distinct millimeter flare followed by an order-of-magnitude flux drop. All Stokes parameters show variability near the flare, including a sign reversal in the electric vector position angle. While most βm modes remain stable, the EB-correlation phase is highly sensitive to both the flare peak and decay. We examine polarimetric signatures in photon sub-rings, focusing on modes ns=0 and ns=1. The ns=0 signal closely matches the full image, while ns=1 reveals distinct behaviors, highlighting the potential of space VLBI to isolate sub-ring features. Finally, we analyze the magnetic and velocity field evolution during the flare, finding that magnetic reconnection weakens during the flux decay, and the clockwise velocity flow transitions into an outflow-dominated regime. These results suggest that transient radio variability near flares encodes key information about BH spin and magnetic field structure, offering a novel probe into the physics of active galactic nuclei. © 2025, CC BY.

关键词： Magnetohydrodynamics

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Interface-driven unusual anomalous Hall effect in MnxGa/Pt bilayers: No correlation with chiral spin structures

arXiv

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arXiv 2019年

作者： Meng, Kangkang Zhu, Lijun Jin, Zhenhu Liu, Enke Zhao, Xupeng Malik, Iftikhar Ahmed Fu, Zhenguo Wu, Yong Miao, Jun Xu, Xiaoguang Zhang, Jinxing Zhao, Jianhua Jiang, Yong Beijing Advanced Innovation Center for Materials Genome Engineering School of Materials Science and Engineering University of Science and Technology Beijing Beijing China Cornell University IthacaNY14853 United States Department of Applied Physics Graduate School of Engineering Tohoku University 6-6-05 Aoba-yama Sendai980-8579 Japan Institute of Physics Chinese Academy of Sciences Beijing China State Key Laboratory of Superlattices and Microstructures Institute of Semiconductors Chinese Academy of Sciences Beijing China Department of Physics Beijing Normal University Beijing China Institute of Applied Physics and Computational Mathematics Beijing China

The effects of spin-orbit coupling and symmetry breaking at the interface between a ferromagnet and heavy metal are particularly important for spin-based information storage and computation. Recent discoveries suggest they can create chiral spin structures (e.g. skyrmions), which have often been identified through the appearance of the bump/dip features of Hall signals, the so-called topological Hall effect (THE). In this work, however, we have present an unusual anomalous Hall effect (UAHE) in MnxGa/Pt bilayers and demonstrated that the features extremely similar to THE can be generated without involving any chiral spin structures. The low temperature magnetic force microscopy has been used to explore the magnetic field-dependent behavior of spin structures, and the UAHE as a function of magnetic field does not peak near the maximal density of magnetic bubbles. The results unambiguously evidence that the UAHE in MnxGa/Pt bilayers shows no correlation with chiral spin structures but is driven by the modified interfacial properties. The bump/dip features of Hall signals cannot be taken as an unambiguous signature for the emergence of chiral spin structures, and a wealth of underlying and interesting physics need explored. Copyright © 2019, The Authors. All rights reserved.

关键词： Temperature

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A third-order moving mesh cell-centered scheme for one-dimensional elastic-plastic flows

arXiv

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arXiv 2017年

作者： Cheng, Jun-Bo Huang, Weizhang Jiang, Song Tian, Baolin Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing China Department of Mathematics University of Kansas LawrenceKS66045 United States Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Beijing China

A third-order moving mesh cell-centered scheme without the remapping of physical variables is developed for the numerical solution of one-dimensional elastic-plastic flows with the Mie-Grüneisen equation of state, the Wilkins constitutive model, and the von Mises yielding criterion. The scheme combines the Lagrangian method with the MMPDE moving mesh method and adaptively moves the mesh to better resolve shock and other types of waves while preventing the mesh from crossing and tangling. It can be viewed as a direct arbitrarily Lagrangian-Eulerian method but can also be degenerated to a purely Lagrangian scheme. It treats the relative velocity of the fluid with respect to the mesh as constant in time between time steps, which allows high-order approximation of free boundaries. A time dependent scaling is used in the monitor function to avoid possible sudden movement of the mesh points due to the creation or diminishing of shock and rarefaction waves or the steepening of those waves. A two-rarefaction Riemann solver with elastic waves is employed to compute the Godunov values of the density, pressure, velocity, and deviatoric stress at cell interfaces. Numerical results are presented for three examples. The third-order convergence of the scheme and its ability to concentrate mesh points around shock and elastic rarefaction waves are demonstrated. The obtained numerical results are in good agreement with those in literature. The new scheme is also shown to be more accurate in resolving shock and rarefaction waves than an existing third-order cell-centered Lagrangian scheme.65N08, 76M12 Copyright © 2017, The Authors. All rights reserved.

关键词： Elastoplasticity

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UNBIASED INFERENCE for DISCRETELY OBSERVED HIDDEN MARKOV MODEL DIFFUSIONS

arXiv

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arXiv 2018年

作者： Chada, Neil K. Franks, Jordan Jasra, Ajay Law, Kody J.H. Vihola, Matti Applied Mathematics and Computational Science King Abdullah University of Science and Technology Thuwal23955 Saudi Arabia School of Mathematics Statistics and Physics Herschel Building NE1 7RU Newcastle University United Kingdom Department of Mathematics and Statistics University of Jyväskylä P.O.Box 35 FIFI-40014 Finland School of Mathematics University of Manchester ManchesterM13 9PL United Kingdom

We develop a Bayesian inference method for diffusions observed discretely and with noise, which is free of discretisation bias. Unlike existing unbiased inference methods, our method does not rely on exact simulation techniques. Instead, our method uses standard time-discretised approximations of diffusions, such as the Euler-Maruyama scheme. Our approach is based on particle marginal Metropolis-Hastings, a particle filter, randomised multilevel Monte Carlo, and importance sampling type correction of approximate Markov chain Monte Carlo. The resulting estimator leads to inference without a bias from the time-discretisation as the number of Markov chain iterations increases. We give convergence results and recommend allocations for algorithm inputs. Our method admits a straightforward parallelisation, and can be computationally efficient. The user-friendly approach is illustrated on three examples, where the underlying diffusion is an Ornstein-Uhlenbeck process, a geometric Brownian motion, and a 2d non-reversible Langevin *** Codes 65C05 (primary), 60H35, 65C35, 65C40 (secondary) Copyright © 2018, The Authors. All rights reserved.

关键词： Diffusion

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Inventory of fungi from termite nests at Gunung Leuser National Park, northern Sumatra

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IOP Conference Series: Earth and Environmental Science 2021年第1期667卷

作者： S Hanum L Fitri O Lisa S Samingan A Alfizar D Sutekad N Novita S Muarrif S Syaukani Master Program in Biological Science Faculty of Mathematic and Natural Sciences Universitas Syiah Kuala Darussalam 23111 Banda Aceh Indonesia Biology Department Faculty of Mathematic and Natural Sciences Universitas Syiah Kuala Darussalam 23111 Banda Aceh Indonesia Faculty of Teacher Training and Education Universitas Syiah Kuala Darussalam 23111 Banda Aceh Indonesia Plant Protection Department Faculty of Agriculture Universitas Syiah Kuala Darussalam 23111 Banda Aceh Indonesia Graduate School of Mathematics and Applied Science Universitas Syiah Kuala Darussalam 23111 Banda Aceh Indonesia

Fungi and termite coexisted each other and have diverse symbiotic relationship in tropical forest. This research aims to determine the fungus found on termite nests in Suaq Balimbing Research Station so it can be used that as initial information in developing environmentally friendly termite control. The method used for collecting samples of fungus is a Standarized Sampling Protocol and for identification used slide culture method. The results showed that 5 of 12 termites nest are invaded by fungi. Based on macroscopic and microscopic observation, fungus species that obtained from termite nests are 2 species, namely: Penicillium sp.1, Trichoderma sp. 1

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Structural variability from noisy tomographic projections

arXiv

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arXiv 2017年

作者： Andén, Joakim Singer, Amit Center for Computational Biology Flatiron Institute New YorkNY United States Department of Mathematics and Program in Applied and Computational Mathematics Princeton University NJ United States

In cryo-electron microscopy, the 3D electric potentials of an ensemble of molecules are projected along arbitrary viewing directions to yield noisy 2D images. The volume maps representing these potentials typically exhibit a great deal of structural variability, which is described by their 3D covariance matrix. Typically, this covariance matrix is approximately low-rank and can be used to cluster the volumes or estimate the intrinsic geometry of the conformation space. We formulate the estimation of this covariance matrix as a linear inverse problem, yielding a consistent least-squares estimator. For n images of size N-by-N pixels, we propose an algorithm for calculating this covariance estimator with computational complexity O(nN4 + √κN6 log N), where the condition number κ is empirically in the range 10-200. Its efficiency relies on the observation that the normal equations are equivalent to a deconvolution problem in 6D. This is then solved by the conjugate gradient method with an appropriate circulant preconditioner. The result is the first computationally efficient algorithm for consistent estimation of the 3D covariance from noisy projections. It also compares favorably in runtime with respect to previously proposed non-consistent estimators. Motivated by the recent success of eigenvalue shrinkage procedures for high-dimensional covariance matrix estimation, we incorporate a shrinkage procedure that improves accuracy at lower signal-to-noise ratios. We evaluate our methods on simulated datasets and achieve classification results comparable to state-of-the-art methods in shorter running time. We also present results on clustering volumes in an experimental dataset, illustrating the power of the proposed algorithm for practical determination of structural variability.92C55, 68U10, 44A12, 65R32, 62G05, 62H30, 62J10, 62J07 Copyright © 2017, The Authors. All rights reserved.

关键词： Conjugate gradient method

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Observation of indirect ionization of W7+ in EBIT plasma

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Journal of Physics: Conference Series 2020年第13期1412卷

作者： Q Lu J He H Tian M Li Y Yang K Yao C Chen J Xiao J G Li B Tu Y Zou Institute of Modern Physics Department of Nuclear Science and Technology Fudan University Shanghai 200433 China Key Laboratory of Nuclear Physics and Ion-beam Application (MOE) Fudan University Shanghai 200433 China Institute of Applied Physics and Computational Mathematics Beijing 100088 China Max-Planck-Institute für Kernphysik Saupfercheckweg 1 69117 Heidelberg Germany

In this work, visible and EUV spectra of W7+ have been measured using the high-temperature super-conducting electron-beam ion trap at the Shanghai EBIT laboratory under extremely low-energy conditions. The relevant atomic structure has been calculated by using the flexible atomic code package and the GRASP2K code. A hypothesis for the charge-state evolution of W7+ is proposed based on our results. The occurrence of W7+ ions results from indirect ionization caused by stepwise excitation between some metastable states of lower-charge-state W ions, at the nominal electron beam energy of 59 eV.

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Setting the physical scale of dimensional reduction in causal dynamical triangulations

arXiv

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arXiv 2018年

作者： Cooperman, Joshua H. Dorghabekov, Manuchehr Department of Physics and Astronomy Bucknell University LewisburgPA United States Physics Program Bard College Annandale-on-Hudson NY United States Applied Mathematics and Informatics Program American University of Central Asia Bishkek Kyrgyzstan

Within the causal dynamical triangulations approach to the quantization of gravity, striking evidence has emerged for the dynamical reduction of spacetime dimension on sufficiently small scales. Specifically, the spectral dimension decreases from the topological value of 4 towards a value near 2 as the scale being probed decreases. The physical scales over which this dimensional reduction occurs have not previously been ascertained. We present and implement a method to determine these scales in units of either the Planck length or the quantum spacetime geometry’s effective de Sitter length. We find that dynamical reduction of the spectral dimension occurs over physical scales of the order of 10 Planck lengths, which, for the numerical simulation considered below, corresponds to the order of 10−1 de Sitter lengths. Copyright © 2018, The Authors. All rights reserved.

关键词： Triangulation

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3D ab initio modeling in cryo-em by autocorrelation analysis

arXiv

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arXiv 2017年

作者： Levin, Eitan Bendory, Tamir Boumal, Nicolas Kileel, Joe Singer, Amit Princeton University Program in Applied and Computational Mathematics PrincetonNJ United States

Single-Particle Reconstruction (SPR) in Cryo-Electron Microscopy (cryo-EM) is the task of estimating the 3D structure of a molecule from a set of noisy 2D projections, taken from unknown viewing directions. Many algorithms for SPR start from an initial reference molecule, and alternate between refining the estimated viewing angles given the molecule, and refining the molecule given the viewing angles. This scheme is called iterative refinement. Reliance on an initial, user-chosen reference introduces model bias, and poor initialization can lead to slow convergence. Furthermore, since no ground truth is available for an unsolved molecule, it is difficult to validate the obtained results. This creates the need for high quality ab initio models that can be quickly obtained from experimental data with minimal priors, and which can also be used for validation. We propose a procedure to obtain such an ab initio model directly from raw data using Kam's autocorrelation method. Kam's method has been known since 1980, but it leads to an underdetermined system, with missing orthogonal matrices. Until now, this system has been solved only for special cases, such as highly symmetric molecules or molecules for which a homologous structure was already available. In this paper, we show that knowledge of just two clean projections is sufficient to guarantee a unique solution to the system. This system is solved by an optimization-based heuristic. For the first time, we are then able to obtain a low-resolution ab initio model of an asymmetric molecule directly from raw data, without 2D class averaging and without tilting. Numerical results are presented on both synthetic and experimental data. Copyright © 2017, The Authors. All rights reserved.

关键词： Molecules

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