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FinnGen provides genetic insights from a well-phenotyped isolated population (vol 613, pg 508, 2023)

NATURE 2023年第7952期615卷 E19-E19页

作者： Kurki, Mitja I. Karjalainen, Juha Palta, Priit Sipila, Timo P. Kristiansson, Kati Donner, Kati M. Reeve, Mary P. Laivuori, Hannele Aavikko, Mervi Kaunisto, Mari A. Loukola, Anu Lahtela, Elisa Mattsson, Hannele Laiho, Paivi Parolo, Pietro Della Briotta Lehisto, Arto A. Kanai, Masahiro Mars, Nina Ramo, Joel Kiiskinen, Tuomo Heyne, Henrike O. Veerapen, Kumar Rueger, Sina Lemmela, Susanna Zhou, Wei Ruotsalainen, Sanni Parn, Kalle Hiekkalinna, Tero Koskelainen, Sami Paajanen, Teemu Llorens, Vincent Gracia-Tabuenca, Javier Siirtola, Harri Reis, Kadri Elnahas, Abdelrahman G. Sun, Benjamin Foley, Christopher N. Aalto-Setala, Katriina Alasoo, Kaur Arvas, Mikko Auro, Kirsi Biswas, Shameek Bizaki-Vallaskangas, Argyro Carpen, Olli Chen, Chia-Yen Dada, Oluwaseun A. Ding, Zhihao Ehm, Margaret G. Eklund, Kari Farkkila, Martti Finucane, Hilary Ganna, Andrea Ghazal, Awaisa Graham, Robert R. Green, Eric M. Hakanen, Antti Hautalahti, Marco Hedman, Asa K. Hiltunen, Mikko Hinttala, Reetta Hovatta, Iiris Hu, Xinli Huertas-Vazquez, Adriana Huilaja, Laura Hunkapiller, Julie Jacob, Howard Jensen, Jan-Nygaard Joensuu, Heikki John, Sally Julkunen, Valtteri Jung, Marc Junttila, Juhani Kaarniranta, Kai Kahonen, Mika Kajanne, Risto Kallio, Lila Kalviainen, Reetta Kaprio, Jaakko Kerimov, Nurlan Kettunen, Johannes Kilpelainen, Elina Kilpi, Terhi Klinger, Katherine Kosma, Veli-Matti Kuopio, Teijo Kurra, Venla Laisk, Triin Laukkanen, Jari Lawless, Nathan Liu, Aoxing Longerich, Simonne Magi, Reedik Makela, Johanna Makitie, Antti Malarstig, Anders Mannermaa, Arto Maranville, Joseph Matakidou, Athena Meretoja, Tuomo Mozaffari, Sahar V. Niemi, Mari E. K. Niemi, Marianna Niiranen, Teemu O'Donnell, Christopher J. Obeidat, Ma'En Okafo, George Ollila, Hanna M. Palomaki, Antti Palotie, Tuula Partanen, Jukka Paul, Dirk S. Pelkonen, Margit Pendergrass, Rion K. Petrovski, Slave Pitkaranta, Anne Platt, Adam Pulford, David Punkka, Eero Pussinen, Pirkko Raghavan, Neha Rahimov, Fedik Rajpal, Deepak Renaud, Nicole A. Riley-Gillis, Bridget Rodosthenous, Rodostheni Institute for Molecular Medicine Finland (FIMM) Helsinki Institute of Life Science (HiLIFE) University of Helsinki Helsinki Finland Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA Stanley Center for Psychiatric Research Broad Institute of Harvard and MIT Cambridge MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Estonian Genome Centre Institute of Genomics University of Tartu Tartu Estonia Medical and Clinical Genetics University of Helsinki and Helsinki University Hospital Helsinki Finland Department of Obstetrics and Gynecology Tampere University Hospital Tampere Finland Faculty of Medicine and Health Technology Center for Child Adolescent and Maternal Health University of Tampere Tampere Finland Department of Biomedical Informatics Harvard Medical School Boston MA USA Digital Health Center Hasso Plattner Institute for Digital Engineering University of Potsdam Potsdam Potsdam Germany Hasso Plattner Institute for Digital Health at Mount Sinai Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York NY USA Finnish Institute for Health and Welfare (THL) Helsinki Finland Department of Public Health University of Helsinki Helsinki Finland Anesthesia Critical Care and Pain Medicine Massachusetts General Hospital Boston MA USA Abdominal Center Endocrinology Helsinki University Hospital Helsinki Finland Folkhalsan Research Center Helsinki Finland Research Program of Clinical and Molecular Metabolism University of Helsinki Helsinki Finland Biocenter Oulu University of Oulu Oulu Finland Computational Medicine Center for Life Course Health Research Faculty of Medicine University of Oulu Oulu Finland Turku University Hospital and University of Turku Turku Finland University of Turku Turku Finland Helsinki Biobank University of Helsinki and Hospital District of Helsinki and Uusimaa Helsinki Finland TAUCHI Research Center

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iSAT: a visual learning analytics tool for instructors

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Research and Practice in Technology Enhanced Learning 2016年第1期11卷 1-22页

作者： Majumdar, Rwitajit Iyer, Sridhar Inter-disciplinary Program in Educational Technology Indian Institute of Technology Bombay Powai Mumbai 400076 India Department of Computer Science and Engineering Indian Institute of Technology Bombay Powai Mumbai 400076 India

Interactive Stratified Attribute Tracking (iSAT) is a visual analytics tool for cohort analysis. In this paper, we show how instructors can use iSAT to visualize transitions of groups of students during teaching-learning activities. Interactive visual analytics gives the instructor the affordance of understanding the dynamics of the class of students and their activities from the data collected in their own teaching-learning context. We take an example of a peer instruction (PI) activity and describe how iSAT can be used to analyze its clicker responses. During PI, typically instructors only use histograms to visualize the distribution of clicker responses in the pre- and post-discussion phases. We show that the use of iSAT to analyze clicker data in real time to trace transitions of participants’ responses during various voting phases can support them in planning for their post-PI activities. Seven patterns of transitions that emerge are aligned, returns, starburst, slide, attractor, switching, and void. We interpret them in the context of the example. Such transition patterns are neither available in multiple histograms of individual voting phase nor generated in real time to be visualized as a flow diagram. We had conducted two workshops to introduce iSAT to the instructors and demonstrated the workflow of using iSAT with their dataset. Here, we report usefulness and usability data collected from those workshops. In conclusion, we highlight the power of iSAT for instructors to do cohort analysis in their teaching-learning practice. © 2016, The Author(s).

关键词： Active learning Cohort analysis iSAT Learning analytics Peer instruction Teacher training Visual analytics

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Composite skyrmion bags in two-dimensional materials

arXiv

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arXiv 2018年

作者： Foster, David Kind, Charles Ackerman, Paul J. Tai, Jung-Shen B. Dennis, Mark R. Smalyukh, Ivan I. H. H. Wills Physics Laboratory University of Bristol BristolBS8 1TL United Kingdom School of Mathematics University of Bristol BristolBS8 1TW United Kingdom Department of Physics and Soft Materials Research Center University of Colorado BoulderCO80309 United States School of Physics and Astronomy University of Birmingham BirminghamB12 2TT United Kingdom 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 and University of Colorado BoulderCO80309 United States

Skyrmions are particle-like topological excitations, studied in various condensed matter systems and models of high-energy physics (HEP). They occur as stable spin textures in certain planar magnetic materials [1-4] and as configurations in chiral nematic liquid crystals [5], having been originally proposed as model of atomic nuclei [10]. Since magnetic Skyrmions can be accelerated with a current [6-8], they have the potential to encode bits in low-power magnetic storage devices [9]. Drawing on techniques from HEP, we demonstrate that magnetic and liquid crystal Skyrmions interact like orientation dependent, localised particles, explaining previously observed Skyrmion behaviour. This interaction motivates the construction of Skyrmion bags: Textures of high topological degree which we realise experimentally in liquid crystals, and in magnetic materials by computer simulations. These Skyrmion bags configurations are nested multiple Skyrmions, which act like single Skyrmions in pairwise interaction, and under the inuence of a current in magnetic materials. These results emphasize equivalent Skyrmion behaviour in different physical systems, and suggest new, high-density magnetic memory storage devices based on Skyrmion bags. Copyright © 2018, The Authors. All rights reserved.

关键词： Magnetic storage

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Intra-operative ultrasound-based augmented reality guidance for laparoscopic surgery

Intra-operative ultrasound-based augmented reality guidance ...

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作者： Singla, Rohit Edgcumbe, Philip Pratt, Philip Nguan, Christopher Rohling, Robert Department of Electrical and Computer Engineering University of British Columbia VancouverV6T1Z4 Canada MD/PhD Program University of British Columbia VancouverV6T1Z4 Canada Department of Surgery and Cancer Imperial College London SW72BX United Kingdom Department of Urological Sciences University of British Columbia VancouverV6T1Z4 Canada Department of Mechanical Engineering University of British Columbia VancouverV6T1Z4 Canada

In laparoscopic surgery, the surgeon must operate with a limited field of view and reduced depth perception. This makes spatial understanding of critical structures difficult, such as an endophytic tumour in a partial nephrectomy. Such tumours yield a high complication rate of 47%, and excising them increases the risk of cutting into the kidney's collecting system. To overcome these challenges, an augmented reality guidance system is proposed. Using intra-operative ultrasound, a single navigation aid, and surgical instrument tracking, four augmentations of guidance information are provided during tumour excision. Qualitative and quantitative system benefits are measured in simulated robot-assisted partial nephrectomies. Robot-to-camera calibration achieved a total registration error of 1.0 ± 0.4 mm while the total system error is 2.5 ± 0.5 mm. The system significantly reduced healthy tissue excised from an average (±standard deviation) of 30.6 ± 5.5 to 17.5 ± 2.4 cm3 (p

关键词： Tumors

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HCVMultiscaleDyn: A simulator for the multiscale model of hepatitis C virus dynamics

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AIP Conference Proceedings 2018年第1期1978卷

作者： Alexander Churkin Vladimir Reinharz Harel Dahari Danny Barash 1Department of Software Engineering Shamoon College of Engineering Beer-Sheva Israel 2Department of Computer Science Ben-Gurion Universty Beer-Sheva Israel 3The Program for Experimental and Theoretical Modeling Division of Hepatology Department of Medicine Loyola University Medical Center Maywood Illinois USA

Multiscale mathematical models that incorporate both intracellular and extracellular hepatitis C virus (HCV) dynamics have been developed in recent years to study HCV-host dynamics and antivirals mode of action and efficacy. They were built upon the standard HCV dynamic model that keeps track of uninfected hepatocytes, HCV-infected hepatocytes, and free virus in blood (for each there is a differential equation), along with a fourth equation that considers the intracellular viral RNA (vRNA) dynamics in an infected cell. A multiscale model with vRNA dynamics consideration is substantially more difficult to solve and the governing differential equations are stiff. In one of the derived differential equations there is also an integral involving the vRNA that is more accurately computed by considering previous iterations, impeding the use of canned solvers. To solve this problem we have chosen to implement a stable and efficient numerical method that belongs to the family of adaptive stepsize methods and is implicit, the Rosenbrock method. We provide a user friendly simulator called HCVMultiscaleDyn with a Graphical User Interface that applies this method and is useful to simulate viral dynamics during antiviral treatment.

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Topic modeling the Hàn diăn ancient classics

arXiv

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arXiv 2017年

作者： Allen, Colin Luo, Hongliang Murdock, Jaimie Pu, Jianghuai Wang, Xiaohong Zhai, Yanjie Zhao, Kun Department of Philosophy School of Humanities and Social Sciences Xi'an Jiaotong University Shaanxi China Cognitive Science Program Indiana University BloomingtonIN United States Institute of Computer Software and Theory School of Electronic and Information Engineering Xi'an Jiaotong University Shaanxi China

Ancient Chinese texts present an area of enormous challenge and opportunity for humanities scholars interested in exploiting computational methods to assist in the development of new insights and interpretations of culturally significant materials. In this paper we describe a collaborative effort between Indiana University and Xi'an Jiaotong University to support exploration and interpretation of a digital corpus of over 18,000 ancient Chinese documents, which we refer to as the "Handian" ancient classics corpus (汉典古籍 or Hàn diăn gŭ jí, i.e, the "Han canon" or "Chinese classics"). It contains classics of ancient Chinese philosophy, documents of historical and biographical significance, and literary works. We begin by describing the Digital Humanities context of this joint project, and the advances in humanities computing that made this project feasible. We describe the corpus and introduce our application of probabilistic topic modeling to this corpus, with attention to the particular challenges posed by modeling ancient Chinese documents. We give a specific example of how the software we have developed can be used to aid discovery and interpretation of themes in the corpus. We outline more advanced forms of computer-aided interpretation that are also made possible by the programming interface provided by our system, and the general implications of these methods for understanding the nature of meaning in these texts. Copyright © 2017, The Authors. All rights reserved.

关键词： Distributed computer systems

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Visualization of 3-Dimensional Vectors in a Dynamic Embryonic System—WormGUIDES

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Journal of computer and Communications 2017年第12期5卷 70-79页

作者： Eric Wang Anthony Santella Zi Wang Dali Wang Zhirong Bao Department of Electric Engineering and Computer Science University of Tennessee Knoxville TN USA Coding Club Farragut High School Knoxville TN USA Developmental Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Environmental Science Division Oak Ridge National Laboratory Oak Ridge TN USA

WormGUIDES is an open-source dynamic embryonic system designed to facilitate global understanding of cellular decisions in the developing nervous system of the nematode C. elegans. WormGUIDES was designed to allow investigation and exploration of the observational results of the C. elegans life cycle from laboratory experiments. In the process of a mechanistic C. elegans model development, some functionalities of WormGUIDES needed to be enhanced to support model validation and verification. In this study, a new way to visualize 3-dimentional vectors within WormGUIDES was investigated and presented. Then, the practical values of this method were demonstrated by visualizing two biologically significant directions (i.e., division orientation and cell polarity) of individual embryonic cells in C. elegans. Lastly, a mathematic approach was designed to illustrate the differences between these two sets of vectors and provide easy indications of the location of these individual cells that have large data discrepancies within the C. elegans embryonic system.

关键词： Embryonic Data Visualization WormGUIDES Workflow Software Architecture Division Orientation Cell Polarity C. elegans

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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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Internal nanostructure diagnosis with hyperbolic phonon polaritons in hexagonal boron nitride

arXiv

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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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Guest editorial: The 2016 capstone design conference

Guest editorial: The 2016 capstone design conference

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作者： Brackin, Patsy Howe, Susannah Rogers, Peter Stanfill, R. Keith Beyerlein, Steven Kanai, Junichi Vallino, Jim Palo, Scott Department of Mechanical Engineering Rose-Hulman Institute of Technology 5500 Wabash Avenue CM 165 Terre HauteIN47803 United States Picker Engineering Program Smith College 151 Ford Hall NorthamptonMA01063 United States Department of Engineering Education Ohio State University 3070 Smith Laboratory 174 W. 18th Avenue ColumbusOH43210 United States Engineering Innovation Institute University of Florida P.O. Box 116000 GainesvilleFL32611-6000 United States Department of Mechanical Engineering University of Idaho 875 Perimeter Drive MoscowID83844-0902 United States Department of Electrical Computer and Systems Engineering Rensselaer Polytechnic Institute TroyNY United States Department of Software Engineering Rochester Institute of Technology 134 Lomb Memorial Drive RochesterNY14623-5608 United States Department of Aerospace Engineering Sciences University of Colorado 429 UCB BoulderCO80309 United States

The goal of the 2016 Capstone Design Conference held in Columbus, OH was to build upon the success of previous conferences (2007 and 2010 in Boulder, CO, 2012 in Champaign, IL, and 2014 in Columbus, OH) and expand the community of educators, students, and industry members engaged in discussing, analyzing, and improving capstone design education. Sessions at the 2016 Capstone Design Conference were designed for vibrant sharing of ideas and experiences across the capstone community via interactive panel sessions, poster session socials, hands-on workshops, and other formal and informal networking activities. This editorial discusses conference planning, structure, and feedback. Technical papers that follow in this issue document scholarship surrounding noteworthy capstone course innovations. Most of these began as four page peer-reviewed papers included in the conference proceedings. © 2017 TEMPUS Publications.

关键词： Teaching

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