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Publisher Correction: Ageing limits stemness and tumorigenesis by reprogramming iron homeostasis

Nature 2025年 2025 May 22页

作者： Xueqian Zhuang Qing Wang Simon Joost Alexander Ferrena David T Humphreys Zhuxuan Li Melissa Blum Klavdija Krause Selena Ding Yuna Landais Yingqian Zhan Yang Zhao Ronan Chaligne Joo-Hyeon Lee Sebastian E Carrasco Umeshkumar K Bhanot Richard P Koche Matthew J Bott Pekka Katajisto Yadira M Soto-Feliciano Thomas Pisanic Tiffany Thomas Deyou Zheng Emily S Wong Tuomas Tammela Cancer Biology and Genetics Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York NY USA. Victor Chang Cardiac Research Institute Sydney New South Wales Australia. Institute for Clinical and Translational Research Albert Einstein College of Medicine New York NY USA. Weill Cornell Graduate School of Medical Science Weill Cornell Medicine New York NY USA. Center for Epigenetics Research Memorial Sloan Kettering Cancer Center New York NY USA. Department of Biomedical Engineering Johns Hopkins University Baltimore MD USA. Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York NY USA. Wellcome-MRC Cambridge Stem Cell Institute Jeffrey Cheah Biomedical Centre University of Cambridge Cambridge UK. Department of Physiology Development and Neuroscience University of Cambridge Cambridge UK. Laboratory of Comparative Pathology Weill Cornell Medicine Memorial Sloan Kettering Cancer Center and Rockefeller University New York NY USA. Pathology Core Facility Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA. Institute of Biotechnology HiLIFE University of Helsinki Helsinki Finland. Department of Cell and Molecular Biology Karolinska Institute Stockholm Sweden. Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland. David H. Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge MA USA. Department of Biology Massachusetts Institute of Technology Cambridge MA USA. Institute for NanoBioTechnology Department of Oncology-Cancer Genetics and Epigenetics Johns Hopkins University Baltimore MD USA. Department of Pathology and Cell Biology Columbia University College of Physicians and Surgeons New York NY USA. Departments of Genetics Neurology and Neuroscience Albert Einstein College of Medicine New York NY USA. School of Biotechnology and Biomolecular Sciences UNSW Sy

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From laptops to supercomputers: a single highly scalable code base for spiking neuronal network simulations

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BMC Neuroscience 2013年第1期14卷 1-2页

作者： Susanne Kunkel Abigail Morrison Markus Diesmann Maximilian Schmidt Jochen M Eppler Moritz Helias Hans E Plesser Jun Igarashi Tomoki Fukai Gen Masumoto Shin Ishii Simulation Laboratory Neuroscience - Bernstein Facility Simulation and Database Technology Institute for Advanced Simulation Jülich Aachen Research Alliance Jülich Research Centre Germany Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) Jülich Research Centre and JARA Germany Bernstein Center Freiburg Albert-Ludwig University of Freiburg Germany Institute of Cognitive Neuroscience Faculty of Psychology Ruhr-University Bochum Germany Medical Faculty RWTH University Aachen Germany Laboratory for Neural Circuit Theory RIKEN Brain Science Institute Wako Japan Department of Mathematical Sciences and Technology Norwegian University of Life Sciences Aas Norway High-Performance Computing Team RIKEN Computational Science Research Program Kobe Japan Integrated Systems Biology Laboratory Department of Systems Science Graduate School of Informatics Kyoto University Japan

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Space distribution of the rescattering electron wavepacket in the laser-atom interactions

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Journal of Physics: Conference Series 2009年第1期185卷

作者： X M Tong K Sasaki K Hino N Toshima Doctoral Program in Materials Science Graduate School of Pure and Applied Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305–8573 Japan Center for Computational Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305–8577 Japan Doctoral Program in Frontier Science Graduate School of Pure and Applied Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305–8573 Japan

We investigated the space distribution of the rescattering electron wavepacket created in the laser-atom interaction by a full quantum simulation and a semiclassical calculation. Both the quantum simulation and the semiclassical calculation showed that the rescattering electron beam current intensity can reach the order of 109 A/cm2, much intense than the conventional electron beam. Different from the convention electron beam, the rescattering electron beam is of a non-uniform distribution both in energy and space. The simulated information is important for analyzing the molecular structure in the rescattering imaging experiments.

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A new time-dependent scattering theory and its application to the capture of antiprotons by atoms

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Journal of Physics: Conference Series 2009年第1期185卷

作者： X M Tong K Hino N Toshima Doctoral Program in Materials Science Graduate School of Pure and Applied Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305–8573 Japan Center for Computational Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305–8577 Japan Doctoral Program in Frontier Science Graduate School of Pure and Applied Sciences University of Tsukuba 1-1-1 Tennodai Tsukuba Ibaraki 305–8573 Japan

We presented a theoretical method to study the capture of the antiprotrons by atoms solving a Chew-Goldberger-type integral equation directly. The scattering boundary conditions are automatically satisfied by adiabatically switching on the interaction between the antiprotons and targets. Hence the outgoing wave function is obtained without the tedious procedure of adjusting the total wave function in the asymptotic region. All the dynamical information can be derived from the scattering wave function obtained on pseudo-spectral grids numerically. Using this method, we obtained the state-specified capture cross sections when antiprotons collide with helium atoms. Differing from the capture processes of antiprotons by hydrogen atoms, the anomalous bumpy structures are revealed in the angular momentum dependent capture cross sections by helium atoms. Further analysis shows that the bumps arise from the partial channel closing due to the removal of the energy degeneracy in the antiprotonic helium atoms.

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Universal mechanical response of metallic glasses during strain-rate-dependent uniaxial compression

arXiv

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arXiv 2022年

作者： Jin, Weiwei Datye, Amit Schwarz, Udo D. Shattuck, Mark D. O'Hern, Corey S. Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Chemical and Environmental Engineering Yale University New HavenCT06520 United States Benjamin Levich Institute Physics Department The City College of New York New YorkNY10031 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States

Experimental data on the compressive strength σmax versus strain rate Ε eng for metallic glasses undergoing uniaxial compression shows significantly different behavior for different alloys. For some metallic glasses, σmax decreases with increasing Ε eng, for others, σmax increases with increasing Ε eng, and for others σmax versus Ε eng is nonmonotonic. Using numerical simulations of metallic glasses undergoing uniaxial compression at nonzero strain rate and temperature, we show that they obey a universal relation for the compressive strength versus temperature, which determines their mechanical response. At low Ε eng, increasing strain rate leads to increases in temperature and decreases in σmax∗, whereas at high Ε eng, increasing strain rate leads to decreases in temperature and increases in σmax∗. This non-monotonic behavior of σmax∗ versus temperature causes the nonmonotonic behavior of σmax∗ versus Ε eng. Variations in the internal dissipation change the characteristic strain rate at which the nonmonotonic behavior occurs. These results are general for a wide range of metallic glasses with different atomic interactions, damping coefficients, and chemical compositions. © 2022, CC BY.

关键词： Strain rate

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Efficient Formulation of Polarizable Gaussian Multipole Electrostatics for Biomolecular Simulations

arXiv

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arXiv 2020年

作者： Wei, Haixin Qi, Ruxi Wang, Junmei Cieplak, Piotr Duan, Yong Luo, Ray Departments of Molecular Biology and Biochemistry Chemical and Biomolecular Engineering Materials Science and Engineering and Biomedical Engineering Graduate Program in Chemical and Materials Physics University of California Irvine IrvineCA92697 United States Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center School of Pharmacy University of Pittsburgh PittsburghPA15261 United States SBP Medical Discovery Institute 10901 North Torrey Pines Road San diegoCA92037 United States UC Davis Genome Center Department of Biomedical Engineering University of California Davis One Shields Avenue DavisCA95616 United States

Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing polarizable force fields for handling more complicated biomolecular processes. Here we focus on a recently proposed polarizable Gaussian Multipole (pGM) model for biomolecular simulations. A key benefit of pGM is its screening of all short-range electrostatic interactions in a physically consistent manner, which is critical for stable charge-fitting and is needed to reproduce molecular anisotropy. Another advantage of pGM is that each atom’s multipoles are represented by a single Gaussian function or its derivatives, allowing for more efficient electrostatics than other Gaussian-based models. In this study we present an efficient formulation for the pGM model defined with respect to a local frame formed with a set of covalent basis vectors. The covalent basis vectors are chosen to be along each atom’s covalent bonding directions. The new local frame allows molecular flexibility during molecular simulations and facilitates an efficient formulation of analytical electrostatic forces without explicit torque computation. Subsequent numerical tests show that analytical atomic forces agree excellently with numerical finite-difference forces for the tested system. Finally, the new pGM electrostatics algorithm is interfaced with the PME implementation in Amber for molecular simulations under the periodic boundary conditions. To validate the overall pGM/PME electrostatics, we conducted an NVE simulation for a small water box of 512 water molecules. Our results show that, to achieve energy conservation in the polarizable model, it is important to ensure enough accuracy on both PME and induction iteration. It is hoped that the reformulated pGM model will facilitate the development of future force fields based on the pGM electrostatics for applicatio

关键词： Electrostatics

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Chemical complexity of phosphorous bearing species in various regions of the interstellar medium

arXiv

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arXiv 2021年

作者： Sil, Milan Srivastav, Satyam Bhat, Bratati Mondal, Suman Kumar Gorai, Prasanta Ghosh, Rana Shimonishi, Takashi Chakrabarti, Sandip K. Sivaraman, Bhalamurugan Pathak, Amit Nakatani, Naoki Furuya, Kenji Das, Ankan Indian Centre for Space Physics 43 Chalantika Garia Station Road Kolkata700084 India Department of Physics Institute of Science Banaras Hindu University Varanasi221005 India Department of Space Earth & Environment Chalmers University of Technology GothenburgSE-412 96 Sweden Center for Transdisciplinary Research Niigata University Nishi-ku Niigata950-2181 Japan Environmental Science Program Department of Science Faculty of Science Niigata University Nishi-ku Niigata950-2181 Japan Physical Research Laboratory Navrangpura Ahmedabad380009 India Institute for Catalysis Hokkaido University N21W10 Kita-ku Sapporo Hokkaido001-0021 Japan Department of Chemistry Graduate School of Science and Engineering Tokyo Metropolitan University 1-1 Minami-Osawa Hachioji Tokyo192-0397 Japan Center for Computational Sciences University of Tsukuba Tsukuba305-8577 Japan National Astronomical Observatory of Japan Tokyo181-8588 Japan

Phosphorus related species are not known to be as omnipresent in space as hydrogen, carbon, nitrogen, oxygen, and sulfur-bearing species. Astronomers spotted very few P-bearing molecules in the interstellar medium and circumstellar envelopes. Limited discovery of the P-bearing species imposes severe constraints in modeling the P-chemistry. In this paper, we carry out extensive chemical models to follow the fate of P-bearing species in diffuse clouds, photon-dominated or photodissociation regions (PDRs), and hot cores/corinos. We notice a curious correlation between the abundances of PO and PN and atomic nitrogen. Since N atoms are comparatively abundant in diffuse clouds and PDRs than in the hot core/corino region, PO/PN reflects 1 in the late warm-up evolutionary phase of the hot core/corino regions. During the end of the post-warm-up phase, we obtain PO/PN > 1 for hot core and 3along with various impurities. We notice that SO2overlaps with the PH3bending-scissoring modes around ∼ (1000 - 1100) cm-1. We also find that the presence of CO2can strongly influence the intensity of the stretching modes around ∼ 2400 cm-1of PH3 © 2021, CC0.

关键词： Radiative transfer

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Considering discrepancy when calibrating a mechanistic electrophysiology model

arXiv

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arXiv 2020年

作者： Lei, Chon Lok Ghosh, Sanmitra Whittaker, Dominic G. Aboelkassem, Yasser Beattie, Kylie A. Cantwell, Chris D. Delhaas, Tammo Houston, Charles Novaes, Gustavo Montes Panfilov, Alexander V. Pathmanathan, Pras Riabiz, Marina Weber dos Santos, Rodrigo Worden, Keith Mirams, Gary R. Wilkinson, Richard D. Computational Biology & Health Informatics Dept. of Computer Science University of Oxford United Kingdom MRC Biostatistics Unit University of Cambridge United Kingdom Centre for Mathematical Medicine & Biology School of Mathematical Sciences University of Nottingham United Kingdom Department of Bioengineering University of California San Diego United States Systems Modeling and Translational Biology GlaxoSmithKline R&D Stevenage United Kingdom ElectroCardioMaths Programme Centre for Cardiac Engineering Imperial College London United Kingdom CARIM School for Cardiovascular Diseases Maastricht University Netherlands Graduate Program in Computational Modeling Universidade Federal de Juiz de Fora Brazil Department of Physics and Astronomy Ghent University Belgium Laboratory of Computational Biology and Medicine Ural Federal University Ekaterinburg Russia U.S. Food and Drug Administration Center for Devices and Radiological Health Office of Science and Engineering Laboratories United States Department of Biomedical Engineering King’s College London Alan Turing Institute United Kingdom Dynamics Research Group Department of Mechanical Engineering University of Sheffield United Kingdom School of Mathematics and Statistics University of Sheffield United Kingdom

Uncertainty quantification (UQ) is a vital step in using mathematical models and simulations to take decisions. The field of cardiac simulation has begun to explore and adopt UQ methods to characterise uncertainty in model inputs and how that propagates through to outputs or predictions. In this perspective piece we draw attention to an important and under-addressed source of uncertainty in our predictions — that of uncertainty in the model structure or the equations themselves. The difference between imperfect models and reality is termed model discrepancy, and we are often uncertain as to the size and consequences of this discrepancy. Here we provide two examples of the consequences of discrepancy when calibrating models at the ion channel and action potential scales. Furthermore, we attempt to account for this discrepancy when calibrating and validating an ion channel model using different methods, based on modelling the discrepancy using Gaussian processes (GPs) and autoregressive-moving-average (ARMA) models, then highlight the advantages and shortcomings of each approach. Finally, suggestions and lines of enquiry for future work are provided. Copyright © 2020, The Authors. All rights reserved.

关键词： Uncertainty analysis

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TGF-β and RAS jointly unmask primed enhancers to drive metastasis

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Cell 2024年第22期187卷 6182-6199.e29页

作者： Lee, Jun Ho Sánchez-Rivera, Francisco J. He, Lan Basnet, Harihar Chen, Fei Xavier Spina, Elena Li, Liangji Torner, Carles Chan, Jason E. Yarlagadda, Dig Vijay Kumar Park, Jin Suk Sussman, Carleigh Rudin, Charles M. Lowe, Scott W. Tammela, Tuomas Macias, Maria J. Koche, Richard P. Massagué, Joan Cancer Biology and Genetics Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York 10065 NY United States Institute for Research in Biomedicine The Barcelona Institute of Science and Technology Barcelona 08028 Spain Department of Medicine Memorial Sloan Kettering Cancer Center New York 10065 NY United States Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New York 10065 NY United States Tri-Institutional Graduate Program in Computational Biology and Medicine Weill Cornell Medical College New York 10065 NY United States Howard Hughes Medical Institute Memorial Sloan Kettering Cancer Center New York 10065 NY United States Institució Catalana de Recerca i Estudis Avançats (ICREA) Barcelona 08010 Spain Center for Epigenetics Research Memorial Sloan Kettering Cancer Center New York 10065 NY United States Department of Biology Massachusetts Institute of Technology Cambridge 02142 MA United States

Epithelial-to-mesenchymal transitions (EMTs) and extracellular matrix (ECM) remodeling are distinct yet important processes during carcinoma invasion and metastasis. Transforming growth factor β (TGF-β) and RAS, signaling through SMAD and RAS-responsive element-binding protein 1 (RREB1), jointly trigger expression of EMT and fibrogenic factors as two discrete arms of a common transcriptional response in carcinoma cells. Here, we demonstrate that both arms come together to form a program for lung adenocarcinoma metastasis and identify chromatin determinants tying the expression of the constituent genes to TGF-β and RAS inputs. RREB1 localizes to H4K16acK20ac marks in histone H2A.Z-loaded nucleosomes at enhancers in the fibrogenic genes interleukin-11 (IL11), platelet-derived growth factor-B (PDGFB), and hyaluronan synthase 2 (HAS2), as well as the EMT transcription factor SNAI1, priming these enhancers for activation by a SMAD4-INO80 nucleosome remodeling complex in response to TGF-β. These regulatory properties segregate the fibrogenic EMT program from RAS-independent TGF-β gene responses and illuminate the operation and vulnerabilities of a bifunctional program that promotes metastatic outgrowth. © 2024 Elsevier Inc.

关键词： chromatin EMT enhancer fibrosis lung adenocarcinoma metastasis RAS SMAD TGF-β

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Enriching and Characterizing T-Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products

arXiv

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arXiv 2022年

作者： Jivanjee, Tasneem Ibrahim, Samira Nyquist, Sarah K. James Gatter, G. Bromley, Joshua D. Jaiswal, Swati Berger, Bonnie Behar, Samuel M. Christopher Love, J. Shalek, Alex K. Institute for Medical Engineering & Science Department of Chemistry Massachusetts Institute of Technology CambridgeMA United States Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology CambridgeMA United States Ragon Institute of MGH MIT and Harvard CambridgeMA United States Broad Institute of MIT and Harvard CambridgeMA United States Massachusetts Institute of Technology CambridgeMA United States Program in Computational and Systems Biology Massachusetts Institute of Technology CambridgeMA United States Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology CambridgeMA United States Microbiology Graduate Program Massachusetts Institute of Technology CambridgeMA02139 United States Department of Microbiology and Physiological Systems University of Massachusetts Medical School WorcesterMA United States Department of Mathematics Massachusetts Institute of Technology CambridgeMA United States Department of Chemical Engineering Massachusetts Institute of Technology CambridgeMA United States

Antigen-specific T cells play an essential role in immunoregulation and many diseases such as cancer. Characterizing the T cell receptor (TCR) sequences that encode T cell specificity is critical for elucidating the antigenic determinants of immunological diseases and designing therapeutic remedies. However, methods of obtaining single-cell TCR sequencing data are labor and cost intensive, typically requiring both cell sorting and full length single-cell RNA-sequencing (scRNA-seq). New high-throughput 3' cell-barcoding scRNA-seq methods can simplify and scale this process;however, they do not routinely capture TCR sequences during library preparation and sequencing. While 5' cell-barcoding scRNA-seq methods can be used to examine TCR repertoire at single-cell resolution, doing so requires specialized reagents which cannot be applied to samples previously processed using 3' cell-barcoding methods. Here, we outline a method for sequencing TCRα and TCRβ transcripts from samples already processed using 3' cell-barcoding scRNA-seq platforms, ensuring TCR recovery at a single-cell resolution. In short, a fraction of the 3' barcoded whole transcriptome amplification (WTA) product typically used to generate a massively parallel 3' scRNA-seq library is enriched for TCR transcripts using biotinylated probes, and further amplified using the same universal primer sequence from WTA. Primer extension using TCR V-region primers and targeted PCR amplification using a second universal primer results in a 3' barcoded single-cell CDR3-enriched library that can be sequenced with custom sequencing primers. Coupled with 3' scRNA-seq of the same WTA, this method enables simultaneous analysis of single-cell transcriptomes and TCR sequences which can help interpret inherent heterogeneity among antigen-specific T cells and salient disease biology. The method presented here can also be adapted readily to enrich and sequence other transcripts of interest from both 3' and 5' barcoded scRNA-seq

关键词： RNA

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