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Author Correction: A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features

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Nature medicine 2025年 2025 Mar 28页

作者： Johanna Klughammer Daniel L Abravanel Åsa Segerstolpe Timothy R Blosser Yury Goltsev Yi Cui Daniel R Goodwin Anubhav Sinha Orr Ashenberg Michal Slyper Sébastien Vigneau Judit Jané-Valbuena Shahar Alon Chiara Caraccio Judy Chen Ofir Cohen Nicole Cullen Laura K DelloStritto Danielle Dionne Janet Files Allison Frangieh Karla Helvie Melissa E Hughes Stephanie Inga Abhay Kanodia Ana Lako Colin MacKichan Simon Mages Noa Moriel Evan Murray Sara Napolitano Kyleen Nguyen Mor Nitzan Rebecca Ortiz Miraj Patel Kathleen L Pfaff Caroline B M Porter Asaf Rotem Sarah Strauss Robert Strasser Aaron R Thorner Madison Turner Isaac Wakiro Julia Waldman Jingyi Wu Jorge Gómez Tejeda Zañudo Diane Zhang Nancy U Lin Sara M Tolaney Eric P Winer Edward S Boyden Fei Chen Garry P Nolan Scott J Rodig Xiaowei Zhuang Orit Rozenblatt-Rosen Bruce E Johnson Aviv Regev Nikhil Wagle Klarman Cell Observatory Broad Institute of Harvard and MIT Cambridge MA USA. klughammer@genzentrum.lmu.de. Gene Center and Department of Biochemistry Ludwig Maximilians Universität München Munich Germany. klughammer@genzentrum.lmu.de. Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA. daniel_abravanel@dfci.harvard.edu. Harvard Medical School Boston MA USA. daniel_abravanel@dfci.harvard.edu. Klarman Cell Observatory Broad Institute of Harvard and MIT Cambridge MA USA. Department of Chemistry and Chemical Biology Harvard University Cambridge MA USA. Baxter Laboratory in Stem Cell Biology Department of Microbiology and Immunology Stanford University School of Medicine Stanford CA USA. Department of Media Arts and Sciences McGovern Institute Massachusetts Institute of Technology Cambridge MA USA. Center for Cancer Genomics Dana-Farber Cancer Institute Boston MA USA. Faculty of Engineering Gonda Brain Research Center and Institute of Nanotechnology Bar-Ilan University Ramat Gan Israel. Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA. Broad Institute of Harvard and MIT Cambridge MA USA. Department of Microbiology Immunology and Genetics Faculty of Health Sciences Ben-Guiron University Beersheba Israel. Center for Immuno-Oncology Dana-Farber Cancer Institute Boston MA USA. Gene Center and Department of Biochemistry Ludwig Maximilians Universität München Munich Germany. School of Computer Science and Engineering The Hebrew University of Jerusalem Jerusalem Israel. Racah Institute of Physics The Hebrew University of Jerusalem Jerusalem Israel. Faculty of Medicine The Hebrew University of Jerusalem Jerusalem Israel. AstraZeneca R&D Boston MA USA. Department of Microbiology Immunology and Cancer Biology University of Virginia Charlottesville VA USA. Department of Media Arts and Sciences Massachusetts Institute of Technology Cambridge MA USA. Department of Biological Engineering Massachusetts I

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Comparison of Polarized Radiative Transfer Codes Used by the EHT Collaboration

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The Astrophysical Journal 2023年第1期950卷 35-35页

作者： Ben S. Prather Jason Dexter Monika Moscibrodzka Hung-Yi Pu Thomas Bronzwaer Jordy Davelaar Ziri Younsi Charles F. Gammie Roman Gold George N. Wong Kazunori Akiyama Antxon Alberdi Walter Alef Juan Carlos Algaba Richard Anantua Keiichi Asada Rebecca Azulay Uwe Bach Anne-Kathrin Baczko David Ball Mislav Baloković John Barrett Michi Bauböck Bradford A. Benson Dan Bintley Lindy Blackburn Raymond Blundell Katherine L. Bouman Geoffrey C. Bower Hope Boyce Michael Bremer Christiaan D. Brinkerink Roger Brissenden Silke Britzen Avery E. Broderick Dominique Broguiere Sandra Bustamante Do-Young Byun John E. Carlstrom Chiara Ceccobello Andrew Chael Chi-kwan Chan Dominic O. Chang Koushik Chatterjee Shami Chatterjee Ming-Tang Chen Yongjun Chen Xiaopeng Cheng Ilje Cho Pierre Christian Nicholas S. Conroy John E. Conway James M. Cordes Thomas M. Crawford Geoffrey B. Crew Alejandro Cruz-Osorio Yuzhu Cui Mariafelicia De Laurentis Roger Deane Jessica Dempsey Gregory Desvignes Vedant Dhruv Sheperd S. Doeleman Sean Dougal Sergio A. Dzib Ralph P. Eatough Razieh Emami Heino Falcke Joseph Farah Vincent L. Fish Ed Fomalont H. Alyson Ford Raquel Fraga-Encinas William T. Freeman Per Friberg Christian M. Fromm Antonio Fuentes Peter Galison Roberto García Olivier Gentaz Boris Georgiev Ciriaco Goddi Arturo I. Gómez-Ruiz José L. Gómez Minfeng Gu Mark Gurwell Kazuhiro Hada Daryl Haggard Kari Haworth Michael H. Hecht Ronald Hesper Dirk Heumann Luis C. Ho Paul Ho Mareki Honma Chih-Wei L. Huang Lei Huang David H. Hughes Shiro Ikeda C. M. Violette Impellizzeri Makoto Inoue Sara Issaoun David J. James Buell T. Jannuzi Michael Janssen Britton Jeter Wu Jiang Alejandra Jiménez-Rosales Michael D. Johnson Svetlana Jorstad Abhishek V. Joshi Taehyun Jung Mansour Karami Ramesh Karuppusamy Tomohisa Kawashima Garrett K. Keating Mark Kettenis Dong-Jin Kim Jae-Young Kim Jongsoo Kim Junhan Kim Motoki Kino Jun Yi Koay Prashant Kocherlakota Yutaro Kofuji Shoko Koyama Carsten Kramer Michael Kramer Thomas P. Krichbaum Cheng-Yu Kuo Noemi La Bella Tod R. Lauer Daeyoung L CCS-2 Los Alamos National Laboratory P.O. Box 1663 Los Alamos NM 87545 USA bprather@lanl.gov JILA and Department of Astrophysical and Planetary Sciences University of Colorado Boulder CO 80309 USA Department of Astrophysics/IMAPP Radboud University P.O. Box 9010 6500 GL Nijmegen The Netherlands Department of Physics National Taiwan Normal University No. 88 Sec.4 Tingzhou Road Taipei 116 Taiwan R.O.C. Center of Astronomy and Gravitation National Taiwan Normal University No. 88 Sec. 4 Tingzhou Road Taipei 116 Taiwan R.O.C. Institute of Astronomy and Astrophysics Academia Sinica 11F of Astronomy-Mathematics Building AS/NTU No. 1 Sec. 4 Roosevelt Road Taipei 10617 Taiwan R.O.C. Department of Astronomy and Columbia Astrophysics Laboratory Columbia University 550 W. 120th Street New York NY 10027 USA Center for Computational Astrophysics Flatiron Institute 162 Fifth Avenue New York NY 10010 USA Department of Astrophysics Institute for Mathematics Astrophysics and Particle Physics (IMAPP) Radboud University P.O. Box 9010 6500 GL Nijmegen The Netherlands Mullard Space Science Laboratory University College London Holmbury St. Mary Dorking Surrey RH5 6NT UK Institut für Theoretische Physik Goethe-Universität Frankfurt Max-von-Laue-Straße 1 D-60438 Frankfurt am Main Germany Department of Physics University of Illinois 1110 West Green Street Urbana IL 61801 USA Department of Astronomy University of Illinois at Urbana-Champaign 1002 West Green Street Urbana IL 61801 USA NCSA University of Illinois 1205 W. Clark Street Urbana IL 61801 USA CP3-Origins University of Southern Denmark Campusvej 55 DK-5230 Odense M Denmark School of Natural Sciences Institute for Advanced Study 1 Einstein Drive Princeton NJ 08540 USA Princeton Gravity Initiative Princeton University Princeton NJ 08544 USA Massachusetts Institute of Technology Haystack Observatory 99 Millstone Road Westford MA 01886 USA National Astronomical Observatory of Japan 2-21-1 Osaw

Interpretation of resolved polarized images of black holes by the Event Horizon Telescope (EHT) requires predictions of the polarized emission observable by an Earth-based instrument for a particular model of the black hole accretion system. Such predictions are generated by general relativistic radiative transfer (GRRT) codes, which integrate the equations of polarized radiative transfer in curved spacetime. A selection of ray-tracing GRRT codes used within the EHT Collaboration is evaluated for accuracy and consistency in producing a selection of test images, demonstrating that the various methods and implementations of radiative transfer calculations are highly consistent. When imaging an analytic accretion model, we find that all codes produce images similar within a pixel-wise normalized mean squared error (NMSE) of 0.012 in the worst case. When imaging a snapshot from a cell-based magnetohydrodynamic simulation, we find all test images to be similar within NMSEs of 0.02, 0.04, 0.04, and 0.12 in Stokes I, Q, U, and V, respectively. We additionally find the values of several image metrics relevant to published EHT results to be in agreement to much better precision than measurement uncertainties.

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Management of intellectual capital in a system of management accounting information 6

Management of intellectual capital in a system of management...

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6th International Conference on computers Communications and Control, ICCCC 2016

作者： Piontkewicz, Regiane Freitas, Maria Do Carmo D. Kemczinski, Avanilde Martin, Claudia Duran San Department of Industrial Engineering Federal University of Paraná Curitiba Brazil Department of Science and Information Management Faculty of Information Management Federal University of Paraná Curitiba Brazil Graduate Program in Applied Computing Computer Science Department Santa Catarina State University Joinville Brazil Department of Industrial Engineering Faculty of Engineering University of Santiago de Chile Santiago Chile

ISBN: (纸本)9781509017355

The recognition of Intellectual Capital as a source of competitive advantage and differentiation element for organizations requires an application of new management strategies that include this feature. Considering the importance of the Accounting Information System (AIS) in organizations, the research has the main objective to investigate the contributions of accounting as Management Information System in management of Intellectual Capital in an organization. Therefore, it was adopted a single case study as research strategy, applied in a Brazilian industry of consumption goods, on the market for over 85 years. The results obtained in the documentary analysis, questionnaires, interviews and literature show that the Accounting Management Information System (AMIS) contributes to the management of Intellectual Capital. In the investigated organization, AMIS is widely used and shows similarities with the specifications found in the literature, possessing the ability of adaptation to receive indicators or variables that enable the management of Intellectual Capital. It was found that the incorporation of the variables of Intellectual Capital in AMIS could be accomplished by adopting the method proposed by López-Ruiz and Nevado-Pena, that uses both traditional financial indicators and indicators of Intellectual Capital, not conflicting with the traditional AMIS, but complementing it. Inserting variables of Intellectual Capital in AMIS also allows uniformity of understanding on the subject by all company managers. © 2016 IEEE.

关键词： Competition

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On Social Network Firewall Selection

On Social Network Firewall Selection

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International Conference on Computing, Networking and Communications

作者： Anisha Mazumder Arunabha Sen Computer Science and Engineering Program School of Computing Informatics and Decision System Engineering Arizona State University

ISBN: (纸本)9781467385800

It is common knowledge that the decision of an individual regarding adoption of a product or technology is, more often than not, heavily influenced by their friends and acquaintances. In real world, there are different competing products and innovations that try to garner as many loyal followers as possible. Over the past few years, there has been a significant interest in the research community to study social network problems with a flavor of competition. Such problems often focus on identification of a set of people in a given social network by the competing players in order to achieve some goal. In this paper, we introduce the weighted Segregating Vertex Set (wSVS) problem, in which we are given a weighted undirected graph with a subset of nodes identified as the seedset of the first player and the goal for the second player is to identify a subset of nodes (firewall) of minimum cumulative weight, such that the total weight of the nodes reachable by the first player is strictly less than the total weight of the nodes not reachable by the first player. Thus, the second player tries to contain the reach of the first player within the social network community. This problem is also relevant for containment of disease in epidemiology, containment of forest fire and several other domains. We prove that this problem is NP-complete and provide an optimal solution through the use of Mixed Integer Linear programming. We also provide a heuristic solution for the wSVS problem and show its efficacy through detailed experimentation. Our heuristic solution delivers near optimal solution in lesser time compared to that needed to find the optimal solution.

关键词： Social network services Sociology Statistics Companies Particle separators Diseases Social computing

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Imaging of director fields in liquid crystals using stimulated Raman scattering microscopy

arXiv

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arXiv 2017年

作者： Lee, Taewoo Mundoor, Haridas Gann, Derek G. Callahan, Timothy J. Smalyukh, Ivan I. Department of Physics Liquid Crystal Materials Research Center University of Colorado BoulderCO80309 United States Department of Electrical Computer and Energy Engineering and Materials Science Engineering Program University of Colorado BoulderCO80309 United States Renewable and Sustainable Energy Institute National Renewable Energy Laboratory University of Colorado BoulderCO80309 United States

We demonstrate an approach for background-free three-dimensional imaging of director fields in liquid crystals using stimulated Raman scattering microscopy. This imaging technique is implemented using a single femtosecond pulsed laser and a photonic crystal fiber, providing Stokes and pump frequencies needed to access Raman shifts of different chemical bonds of molecules and allowing for chemically selective and broadband imaging of both pristine liquid crystals and composite materials. Using examples of model three-dimensional structures of director fields, we show that the described technique is a powerful tool for mapping of long-range molecular orientation patterns in soft matter via polarized chemical-selective imaging. Copyright © 2017, The Authors. All rights reserved.

关键词： Liquid crystals

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Optical patterning of magnetic domains and defects in ferromagnetic liquid crystal colloids

arXiv

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arXiv 2017年

作者： Hess, Andrew J. Liu, Qingkun Smalyukh, Ivan I. Department of Physics University of Colorado BoulderCO80309 United States Materials Science and Engineering Program Department of Electrical Computer and Energy Engineering Liquid Crystal Materials Research Center University of Colorado BoulderCO80309 United States Renewable and Sustainable Energy Institute National Renewable Energy Laboratory University of Colorado BoulderCO80309 United States

A promising approach in designing composite materials with unusual physical behavior combines solid nanostructures and orientationally ordered soft matter at the mesoscale. Such composites not only inherit properties of their constituents but also can exhibit emergent behavior, such as ferromagnetic ordering of colloidal metal nanoparticles forming mesoscopic magnetization domains when dispersed in a nematic liquid crystal. Here we demonstrate the optical patterning of domain structures and topological defects in such ferromagnetic liquid crystal colloids, which allows for altering their response to magnetic fields. Our findings reveal the nature of the defects in this soft matter system which is different as compared to non-polar nematics and ferromagnets alike. Copyright © 2017, The Authors. All rights reserved.

关键词： Ferromagnetic materials

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Electric switching of fluorescence decay in gold-silica-dye nematic nanocolloids mediated by surface plasmons

arXiv

引用

arXiv 2017年

作者： Jiang, Li Mundoor, Haridas Liu, Qingkun Smalyukh, Ivan I. Department of Physics and Soft Materials Research Center University of Colorado BoulderCO80309 United States Department of Electrical Computer and Energy Engineering Materials Science and Engineering Program University of Colorado BoulderCO80309 United States Renewable and Sustainable Energy Institute National Renewable Energy Laboratory University of Colorado BoulderCO80309 United States

Tunable composite materials with interesting physical behavior can be designed through integrating unique optical properties of solid nanostructures with the facile responses of soft matter to weak external stimuli, but this approach remains challenged by their poorly controlled co-assembly at the mesoscale. Using scalable wet chemical synthesis procedures, we fabricated anisotropic gold-silica-dye colloidal nanostructures and then organized them into the device-scale (demonstrated for square inch cells) electrically tunable composites by simultaneously invoking molecular and colloidal self-assembly. We show that the ensuing ordered colloidal dispersions of shape-anisotropic nanostructures exhibit tunable fluorescence decay rates and intensity. We characterize how these properties depend on low-voltage fields and polarization of both the excitation and emission light, demonstrating a great potential for the practical realization of an interesting breed of nanostructured composite materials. Copyright © 2017, The Authors. All rights reserved.

关键词： Self assembly

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Iterative segmented least square method for functional microRNA-mRNA module discovery in breast cancer

Iterative segmented least square method for functional micro...

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IEEE International Conference on Bioinformatics and Biomedicine

作者： Sungmin Rhee Sangsoo Lim Sun Kim Computer Science and Engineering Seoul National University Republic of Korea Interdisciplinary Program in Bioinformatics Seoul National University Republic of Korea Computer Science and Engineering Interdisciplinary Program in Bioinformatics Seoul National University Republic of Korea

ISBN: (纸本)9781509016129

MicroRNAs (miRNAs) have significant biological roles at the molecular level by regulating genes post-transcriptionally. To understand the functional effects of miRNAs in different biological contexts, it is essential to elucidate miRNA -mRNA regulatory modules (MRMs). The computational complexity for inferencing MRMs is very high due to the many-to-many relationships between miRNAs and mRNAs and inferencing MRMs is still a challenging unresolved problem. In this paper, we propose a novel iterative segmented least square method for functional MRM discovery. Our method operates in two steps: 1) grouping and ordering the miRNAs and mRNAs to build per-sample matrices representing miRNA-mRNA regulations, and 2) determining maximum sized modules from structured miRNA-mRNA matrices. In experiments with human breast cancer data sets from TCGA, we show that our method outperforms existing methods in terms of both GO similarity and cluster evaluation. In addition, we show that modules determined by our method can be used for breast cancer survival prediction and subtype classification.

关键词： Optimization microRNA Regulatory network inference

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Liquid crystal self-assembly of upconversion nanorods enriched by depletion forces for mesostructured material preparation

arXiv

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arXiv 2017年

作者： Xie, Yong Li, Yuanyuan Wei, Guoqing Liu, Qingkun Mundoor, Haridas Chen, Ziyu Smalyukh, Ivan I. Department of Physics Material Science and Engineering Program Department of Electrical Computer& Energy Engineering Liquid Crystal Materials Research Center University of Colorado BoulderCO80309 United States Department of Physics Beihang University Beijing100191 China National Renewable Energy Laboratory and University of Colorado Renewable and Sustainable Energy Institute BoulderCO80309 United States

Monodisperse rod-like colloidal particles are known for spontaneously forming both nematic and smectic liquid crystal phases, but their self-assembly was typically exploited from the fundamental soft condensed matter physics perspective. Here we demonstrate that depletion interactions, driven by non-adsorbing polymers like dextran and surfactants, can be used to enrich self-organization of photon-upconversion nanorods into orientationally ordered nematic and smectic-like membrane colloidal superstructures. We study thermodynamic phase diagrams and demonstrate polarization-dependent photon upconversion exhibited by the ensuing composites, which arises from the superposition of unique properties of the solid nanostructures and the long-range ordering enabled by liquid crystalline self-organization. Finally, we discuss how our method of utilizing self-assembly due to the steric and electrostatic interactions, along with attractive depletion forces, can enable technological uses of lyotropic colloidal liquid crystals and mesostructured composite materials enabled by them, even when they are formed by anisotropic nanoparticles with relatively small aspect ratios. Copyright © 2017, The Authors. All rights reserved.

关键词： Nanorods

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Stop paying attention: the need for explicit stopping in inhibitory control 38

Stop paying attention: the need for explicit stopping in inh...

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38th Annual Meeting of the cognitive science Society: Recognizing and Representing Events, CogSci 2016

作者： Ma, Ning Yu, Angela J. Department of Electrical and Computer Engineering University of California 9500 Gilman Drive La Jolla San DiegoCA92037 United States Department of Cognitive Science University of California 9500 Gilman Drive La Jolla San DiegoCA92037 United States

ISBN: (纸本)9780991196739

Inhibitory control, the ability to stop inappropriate actions, is an important cognitive function often investigated via the stop-signal task, in which an infrequent stop signal instructs the subject to stop a default go response. Previously, we proposed a rational decision-making model for stopping, suggesting the observer makes a repeated Go versus Wait choice at each instant, so that a Stop response is realized by repeatedly choosing to Wait. We propose an alternative model here that incorporates a third choice, Stop. Critically, unlike the Wait action, choosing the Stop action not only blocks a Go response at the current moment but also for the remainder of the trial - the disadvantage of losing this flexibility is balanced by the benefit of not having to pay attention anymore. We show that this new model both reproduces known behavioral effects and has internal dynamics resembling presumed Go neural activations in the brain. © 2016 Proceedings of the 38th Annual Meeting of the cognitive science Society, CogSci 2016. All rights reserved.

关键词： Decision making

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