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arXiv 2018年

作者： Dai, Siyuan Tymchenko, Mykhailo Xu, Zai-Quan Tran, Toan T. Yang, Yafang Ma, Qiong Watanabe, Kenji Taniguchi, Takashi Jarillo-Herrero, Pablo Aharonovich, Igor Basov, Dimitri N. Tao, Tiger H. Alù, Andrea Department of Electrical & Computer Engineering University of Texas AustinTX78712 United States Institute of Biomedical Materials and Devices Faculty of Science University of Technology Sydney UltimoNSW2007 Australia Department of Physics Massachusetts Institute of Technology CambridgeMA02215 United States National Institute for Materials Science Namiki 1-1 Tsukuba Ibaraki305-0044 Japan Department of Physics Columbia University New YorkNY10027 United States Department of Mechanical Engineering University of Texas AustinTX78712 United States Photonics Initiative Advanced Science Research Center City University of New York New York10031 United States Physics Program Graduate Center City University of New York New York10016 United States Department of Electrical Engineering City College of the City University of New York New York10031 United States

Imaging materials and inner structures with resolution below the diffraction limit has become of fundamental importance in recent years for a wide variety of applications. In this work, we report sub-diffractive internal structure diagnosis of hexagonal boron nitride by exciting and imaging hyperbolic phonon polaritons. Based on their unique propagation properties, we are able to accurately locate defects in the crystal interior with nanometer resolution. The precise location, size and geometry of the concealed defects is reconstructed by analyzing the polariton wavelength, reflection coefficient and their dispersion. We have also studied the evolution of polariton reflection, transmission and scattering as a function of defect size and photon frequency. The nondestructive high-precision polaritonic structure diagnosis technique introduced here can be also applied to other hyperbolic or waveguide systems, and may be deployed in the next-generation bio-medical imaging, sensing and fine structure analysis. Copyright © 2018, The Authors. All rights reserved.

关键词： Van der Waals forces

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Interactions between species introduce spurious associations in microbiome studies

arXiv

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arXiv 2017年

作者： Menon, Rajita Ramanan, Vivek Korolev, Kirill S. Department of Physics Boston University BostonMA United States BRITE Bioinformatics REU Program Boston University BostonMA United States Graduate Program in Bioinformatics Boston University BostonMA United States Department of Biology and Computer Science Swarthmore College SwarthmorePA United States

Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance differences, however, reflect not only direct associations with the phenotype, but also indirect effects due to microbial interactions. We found that microbial interactions could easily generate a large number of spurious associations that provide no mechanistic insight. Using techniques from statistical physics, we developed a method to remove indirect associations and applied it to the largest dataset on pediatric inflammatory bowel disease. Our method corrected the inflation of p-values in standard association tests and showed that only a small subset of associations is directly linked to the disease. Direct associations had a much higher accuracy in separating cases from controls and pointed to immunomodulation, butyrate production, and the brain-gut axis as important factors in the inflammatory bowel disease. Copyright © 2017, The Authors. All rights reserved.

关键词： Association reactions

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Gene expression imputation across multiple brain regions provides insights into schizophrenia risk (vol 51, pg 659, 2019)

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NATURE GENETICS 2019年第6期51卷 1068-1068页

作者： Huckins, Laura M. Dobbyn, Amanda Ruderfer, Douglas M. Hoffman, Gabriel Wang, Weiqing Pardinas, Antonio F. Rajagopal, Veera M. Als, Thomas D. Nguyen, Hoang T. Girdhar, Kiran Boocock, James Roussos, Panos Fromer, Menachem Kramer, Robin Domenici, Enrico Gamazon, Eric R. Purcell, Shaun Demontis, Ditte Borglum, Anders D. Walters, James T. R. O'Donovan, Michael C. Sullivan, Patrick Owen, Michael J. Devlin, Bernie Sieberts, Solveig K. Cox, Nancy J. Im, Hae Kyung Sklar, Pamela Stahl, Eli A. Pamela Sklar Division of Psychiatric Genomics Icahn School of Medicine at Mount Sinai New York NY USA Department of Genetics and Genomics Icahn School of Medicine at Mount Sinai New York NY USA Department of Psychiatry Icahn School of Medicine at Mount Sinai New York NY USA Icahn Institute for Genomics and Multiscale Biology Icahn School of Medicine at Mount Sinai New York NY USA Vanderbilt University Medical Center Nashville TN USA MRC Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff UK Department of Biomedicine Aarhus University Aarhus Denmark The Lundbeck Foundation Initiative for Integrative Psychiatric Research iPSYCH Denmark Center for Integrative Sequencing Aarhus University Aarhus Denmark Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA Human Brain Collection Core National Institute of Mental Health Bethesda MD USA Laboratory of Neurogenomic Biomarkers Centre for Integrative Biology (CIBIO) University of Trento Trento Italy Clare Hall University of Cambridge Cambridge UK University of North Carolina at Chapel Hill Chapel Hill NC USA Karolinska Institutet Stockholm Sweden Department of Psychiatry University of Pittsburgh Pittsburgh PA USA Systems Biology Sage Bionetworks Seattle WA USA Section of Genetic Medicine Department of Medicine University of Chicago Chicago IL USA Integrated Technology Research Laboratories Pharmaceutical Research Division Takeda Pharmaceutical Company Limited Fujisawa Japan Neuropsychiatry Section Department of Psychiatry Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Neuropsychiatric Signaling Program Department of Psychiatry Perelman School of Medicine University of Pennsylvania Philadelphia PA USA Psychiatry JJ Peters Virginia Medical Center Bronx NY USA Department of Neuroscience Icahn School of Medicine at Mount Sinai New York New York NY USA Friedman Brain Institute

Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression.

关键词： Gene expression Genome-wide association studies Schizophrenia Transcriptomics

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Intrinsic Raman signatures of pristine hybrid perovskite CH3NH3PbI3 and its multiple stages of structure transformation 44

Intrinsic Raman signatures of pristine hybrid perovskite CH3...

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44th IEEE Photovoltaic Specialist Conference, PVSC 2017

作者： Chen, Qiong Liu, Henan Kim, Hui-Seon Liu, Yucheng Yang, Mengjin Yue, Naili Ren, Gang Zhu, Kai Liu, Shengzhong Frank Park, Nam-Gyu Zhang, Yong Department of Electrical and Computer Engineering Korea Republic of Optical Science and Engineering Graduate Program University of North Carolina at Charlotte CharlotteNC28223 United States School of Chemical Engineering and Department of Energy Science Sungkyunkwan University Suwon440-746 Korea Republic of Key Laboratory of Applied Surface and Colloid Chemistry National Ministry of EducationInstitute for Advanced Energy Materials School of Materials Science and Engineering Shaanxi Normal University Xi'an710062 China Chemical and Materials Science Center National Renewable Energy Laboratory GoldenCO80401 United States Molecular Foundry Lawrence Berkeley National Laboratory BerkeleyCA94720 United States

ISBN: (纸本)9781509056057

By performing spatially resolved Raman and photoluminescence spectroscopy with different illumination conditions, we have achieved a unified understanding towards the spectroscopy signatures of the organic-inorganic hybrid perovskite, transforming from the pristine state (CH3NH3PbI3 or MAPbI3) to fully degraded state (i.e., PbI2), for samples with varying crystalline domain size from mesoscopic scale to macroscopic size, synthesized by three different techniques. © 2017 IEEE.

关键词： Perovskite

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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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Acoustic supercoupling in a zero-compressibility waveguide

arXiv

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arXiv 2018年

作者： Esfahlani, H. Byrne, M.S. McDermott, M. Alù, A. Photonics Initiative Advanced Science Research Center City University of New York New York CityNY10031 United States Department of Electrical and Computer Engineering University of Texas at Austin AustinTX78712 United States LausanneCH-1015 Switzerland Naval Surface Warfare Center Carderock Division West BethesdaMD20817 United States Physics Program Graduate Center City University of New York New York CityNY10026 United States Department of Electrical Engineering City College of New York New York CityNY10031 United States

Funneling acoustic waves through largely mismatched channels is of fundamental importance to tailor and transmit sound for a variety of applications. In electromagnetics, zero-permittivity metamaterials have been used to enhance the coupling of energy in and out of ultranarrow channels, based on a phenomenon known as supercoupling. These metamaterial channels can support total transmission and complete phase uniformity, independent of the channel length, despite being geometrically mismatched to their input and output ports. In the field of acoustics, this phenomenon is challenging to achieve, since it requires zero-density metamaterials, typically realized with waveguides periodically loaded with membranes or resonators. Compared to electromagnetics, the additional challenge is due to the fact that conventional acoustic waveguides do not support a cut-off for the dominant mode of propagation, and therefore zero-index can be achieved only based on a collective resonance of the loading elements. Here we propose and experimentally realize acoustic supercoupling in a dual regime, using a compressibility-near-zero acoustic channel. Rather than engineering the channel with subwavelength inclusions, we operate at the cut-off of a higher-order acoustic mode, demonstrating the realization and efficient excitation of a zero-compressibility waveguide with effective soft boundaries. We experimentally verify strong transmission through a largely mismatched channel and uniform phase distribution, independent of the channel length. Our results open interesting pathways towards the realization of extreme acoustic parameters, and their implementation in relevant applications, such as ultrasound imaging, sonar technology, and sound transmission. Copyright © 2018, The Authors. All rights reserved.

关键词： Compressibility

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Doubly Penalized LASSO for Reconstruction of Biological Networks

Doubly Penalized LASSO for Reconstruction of Biological Netw...

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作者： Asadi, Behrang Maurya, Mano Ram Tartakovsky, Daniel M. Subramaniam, Shankar Departments of Bioengineering and Mechanical and Aerospace Engineering University of California San Diego Danaher Labs la Jolla Santa ClaraCA United States San Diego Supercomputer Center Department of Bioengineering University of California San Diego San DiegoCA United States Department of Mechanical Aerospace Engineering University of California San Diego San DiegoCA United States Department of Bioengineering Departments of Computer Science and Engineering Cellular and Molecular Medicine and the Graduate Program in Bioinformatics University of California San Diego San DiegoCA United States

Reconstruction of biological and biochemical networks is a crucial step in extracting knowledge and causal information from large biological data sets. This task is particularly challenging when dealing with time-series data from dynamic networks. We have developed a new method, called doubly penalized least absolute shrinkage and selection operator (DPLASSO), for the reconstruction of dynamic biological networks. Our method consists of two components: statistical significance testing of model coefficients and penalized/constrained optimization. A partial least squares (PLS) with statistical significance testing acts as a supervisory-level filter to extract the most informative components of the network from a data set. Then, LASSO with extra weights on the smaller parameters identified in the first layer is employed to retain the main predictors and to set the smallest coefficients to zero. We present two case studies to compare the relative performance of DPLASSO and LASSO in terms of several metrics, such as sensitivity, specificity, and accuracy. The first case study employs a synthetic data set;it demonstrates that DPLASSO substantially improves network reconstruction in terms of accuracy and specificity. The second case study relies on simulated data sets for cell division cycle of fission yeast and shows that DPLASSO overall outperforms LASSO and PLS in terms of sensitivity, specificity, and accuracy. Combining PLS with statistical significance testing and LASSO provides good performance with respect to several metrics. DPLASSO is well suited for reconstruction of networks with low and moderate density. For high-density networks, high specificity is desired, making PLS a more suitable approach. © 1963-2012 IEEE.

关键词： Least squares approximations

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Investigation of the visual attention role in clinical bioethics decision-making using machine learning algorithms

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Procedia computer science 2017年 108卷 1165-1174页

作者： Daniel L. Fernandes Rodrigo Siqueira-Batista Andréia P. Gomes Camila R. Souza Israel T. da Costa Felippe da S.L. Cardoso João V. de Assis Gustavo H.L. Caetano Fabio R. Cerqueira Graduate Program in Computer Science Universidade Federal de Viçosa Minas Gerais Brazil Department of Medicine and Nursing Universidade Federal de Viçosa Minas Gerais Brazil Department of Physical Education Universidade Federal de Viçosa Minas Gerais Brazil Department of Production Engineering Universidade Federal Fluminense Rio de Janeiro Brazil

This study proposes the use of a computational approach based on machine learning (ML) algorithms to build predictive models using eye tracking data. Our intention is to provide results that may support the study of medical investigation in the decision-making process in clinical bioethics, particularly in this work, in cases of euthanasia. The data used in the approach were collected from 75 students of the nursing undergraduate course using an eye tracker. The available data were processed through feature selection methods, and were later used to create models capable of predicting the euthanasia decision through ML algorithms. Statistical experiments showed that the predictive model resultant from the multilayer perceptron (MLP) algorithm led to the best performance compared with the other tested algorithms, presenting an accuracy of 90.7% and a mean area under the ROC curve of 0.90. Interesting knowledge (patterns and rules) for the studied bioethical decision-making was extracted using simulations with MLP models and inspecting the obtained decision-tree rules. The good performance shown by the obtained MLP predictive model demonstrates that the proposed investigation approach may be used to test scientific hypotheses related to visual attention and decision-making.

关键词： Visual attention Decision-making in bioethics Mobile eye tracking Machine learning in medicine

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How Do I Look? Publicity Mining From Distributed Keyword Representation of Socially Infused News Articles 4

How Do I Look? Publicity Mining From Distributed Keyword Rep...

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4th ACM Workshop on Natural Language Processing for Social Media, SocialNLP 2016, associated with the Conference on Empirical Methods in Natural Language Processing, EMNLP 2016

作者： Hsieh, Yu-Lun Chang, Yung-Chun Chu, Chun-Han Hsu, Wen-Lian SNHCC Taiwan International Graduate Program Institute of Information Science Academia Sinica Department of Computer Science National Chengchi University Taipei Taiwan Institute of Information Science Academia Sinica Taipei Taiwan

ISBN: (纸本)9781945626326

Previous work on opinion mining and sentiment analysis mainly concerns product, movie, or literature reviews;few applied this technique to analyze the publicity of person. We present a novel document modeling method that utilizes embeddings of emotion keywords to perform reader's emotion classification, and calculates a publicity score that serves as a quantifiable measure for the publicity of a person of interest. Experiments are conducted on two Chinese corpora that in total consists of over forty thousand users' emotional response after reading news articles. Results demonstrate that the proposed method can outperform state-of-the-art reader-emotion classification methods, and provide a substantial ground for publicity score estimation for candidates of political elections. We believe it is a promising direction for mining the publicity of a person from online social and news media that can be useful for propaganda and other purposes. © 2016 Association for Computational Linguistics

关键词： Sentiment analysis

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Magnetoresistance in the superconducting state at the (111) LaAlO3/SrTiO3 interface

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Physical Review B 2017年第13期96卷 134502-134502页

作者： S. Davis Z. Huang K. Han Ariando T. Venkatesan V. Chandrasekhar Graduate Program in Applied Physics Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA NUSNNI-Nanocore National University of Singapore 117411 Singapore Department of Physics National University of Singapore 117551 Singapore NUS Graduate School for Integrative Sciences & Engineering National University of Singapore 117456 Singapore Department of Electrical and Computer Engineering National University of Singapore 117576 Singapore Department of Material Science and Engineering National University of Singapore 117575 Singapore Department of Physics and Astronomy Graduate Program in Applied Physics Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA

Condensed-matter systems that simultaneously exhibit superconductivity and ferromagnetism are rare due the antagonistic relationship between conventional spin-singlet superconductivity and ferromagnetic order. In materials in which superconductivity and magnetic order are known to coexist (such as some heavy-fermion materials), the superconductivity is thought to be of an unconventional nature. Recently, the conducting gas that lives at the interface between the perovskite band insulators LaAlO3 (LAO) and SrTiO3 (STO) has also been shown to host both superconductivity and magnetism. Most previous research has focused on LAO/STO samples in which the interface is on the (001) crystal plane. Relatively little work has focused on the (111) crystal orientation, which has hexagonal symmetry at the interface, and has been predicted to have potentially interesting topological properties, including unconventional superconducting pairing states. Here we report measurements of the magnetoresistance of (111) LAO/STO heterostructures at temperatures at which they are also superconducting. As with the (001) structures, the magnetoresistance is hysteretic, indicating the coexistence of magnetism and superconductivity, but in addition, we find that this magnetoresistance is anisotropic. Such an anisotropic response is completely unexpected in the superconducting state and suggests that (111) LAO/STO heterostructures may support unconventional superconductivity.

关键词： Coherence length Ferromagnetism Magnetotransport Phase diagrams Superconducting phase transition Superconductivity Hall bar Resistivity measurements

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