Michel Foucault Ronald C Kessler Graham Colditz Sigmund Freud
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Applied Category Theory for Genomics – an Initiative
Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4]. -
ERC Advanced Grant 2008 Project Acronym Title Principal Investigator Host Institution Host Country 226037 NSYS Nonlinear System
ERC Advanced Grant 2008 Project Acronym Title Principal Investigator Host Institution Host Country Nonlinear System Identification and Analysis in the Time, Prof. Stephen Alec 226037 NSYS THE UNIVERSITY OF SHEFFIELD UK Frequency, and Spatio-Temporal Domains Billings HOWTOCONT Search for mechanisms to control massless electrons in 226043 ROLGRAPHE Prof. Carlo Beenakker UNIVERSITEIT LEIDEN. NL graphene NE THE HEBREW UNIVERSITY OF 226135 EXPANDERS Expander Graphs in Pure and Applied Mathematics Prof. Alexander Lubotzky IL JERUSALEM. 226136 VISCHEM Visualizing Molecular Change Prof. Villy Sundström LUNDS UNIVERSITET SE Consistent computation of the chemistry-cloud THE CYPRUS RESEARCH AND 226144 C8 Prof. Johannes Lelieveld CY continuum and climate change in Cyprus EDUCATIONAL FOUNDATION Modern Approaches to Temperature Reconstructions in 226172 MATRICS Dr. Hubertus Fischer UNIVERSITAET BERN CH polar Ice Cores FUndamental studies and innovative appROaches of Prof. Roland Martin 226180 FURORE UNIVERSITAET HAMBURG DE REsearch on magnetism Wiesendanger EBERHARD KARLS 226187 SOCATHES Solid State/Cold Atom Hybrid Quantum Devices Prof. Reinhold Kleiner DE UNIVERSITAET TUEBINGEN KUNGLIGA TEKNISKA 226203 APPROXNP Approximation of NP-hard optimization problems Prof. Johan Håstad SE HOEGSKOLAN Patchy colloidal particles: a powerful arsenal for the PATCHYCOLL fabrication of tomorrow new super-molecules . A UNIVERSITA DEGLI STUDI DI 226207 Prof. Francesco Sciortino IT OIDS theoretical and numerical study of their assembly ROMA LA SAPIENZA processes. ERC Advanced Grant 2008 Analytic Techniques for Geometric and Functional UNIVERSITA DEGLI STUDI DI 226234 ANTEGEFI Prof. Nicola Fusco IT Inequalities NAPOLI FEDERICO II. Multiscale Models for Catalytic-Reaction-Coupled 226238 MMFCS Prof. Bengt Sundén LUNDS UNIVERSITET SE Transport Phenomena in Fuel Cells WEIZMANN INSTITUTE OF 226246 NANOSQUID Scanning Nano-SQUID on a Tip Prof. -
Nature Medicine Essay
COMMENTARY LASKER BASIC MEDICAL RESEARCH AWARD Of maize and men, or peas and people: case histories to justify plants and other model systems David Baulcombe One of the byproducts of molecular biology cork is altogether filled with air, and that air is has been support for the ‘model system’ con- perfectly enclosed in little boxes or cells distinct cept. All living organisms are based on the same from one another.”)2 (Fig. 1). Two hundred fifty genetic code, they have similar subcellular years later, Beijerinck discovered a contagium structures and they use homologous metabolic vivum fluidum in extracts of diseased tobacco pathways. So, mechanisms can be investigated plants that he later referred to as a virus3. using organisms other than those in which In contemporary science, a green alga— the knowledge will be exploited for practical Chlamydomonas reinhardtii—is a useful model benefit. Model systems are particularly use- in the analysis of kidney disease4. However, ful in the early discovery phase of a scientific in this article, I refer to the contribution of endeavor, and recent progress in biomedical plant biology to a family of mechanisms that I science has fully vindicated their use. Jacques refer to as RNA silencing. This topic has been Monod, for example, famously justified his reviewed comprehensively elsewhere5,6, so here work on a bacterial model system by stating I focus on personal experience and my view of that “what is true for Escherichia coli is also future potential from this work. true for elephants.” My fellow laureates, Victor Ambros and Gary Ruvkun, can defend the use The early history of RNA silencing in of the worm Caenorhabditis elegans as a good plants model system and so I will focus on plants. -
Masthead (PDF)
Proceedings of the National Academy ofPNAS Sciences of the United States of America www.pnas.org PRESIDENT OF Robert G. Roeder Geophysics John J. Mekalanos THE ACADEMY Michael Rosbash Michael L. Bender Peter Palese Ralph J. Cicerone David D. Sabatini Thomas E. Shenk Gertrud M. Schupbach Human Environmental Thomas J. Silhavy SENIOR EDITOR Robert Tjian Sciences Peter K. Vogt Solomon H. Snyder Susan Hanson Cellular and Molecular Physics ASSOCIATE EDITORS Neuroscience Immunology Anthony Leggett William C. Clark Pietro V. De Camilli Peter Cresswell Paul C. Martin Alan Fersht Richard L. Huganir Douglas T. Fearon Jack Halpern L. L. Iversen Richard A. Flavell Physiology and Jeremy Nathans Charles F. Stevens Dan R. Littman Pharmacology Thomas C. Su¨dhof Tak Wah Mak Susan G. Amara Joseph S. Takahashi William E. Paul David Julius EDITORIAL BOARD Hans Thoenen Michael Sela Ramon Latorre Ralph M. Steinman Masashi Yanagisawa Animal, Nutritional, and Chemistry Applied Microbial Sciences Stephen J. Benkovic Mathematics Plant Biology David L. Denlinger Bruce J. Berne Richard V. Kadison Maarten J. Chrispeels R. Michael Roberts Harry B. Gray Robion C. Kirby Enrico Coen Robert Haselkorn Linda J. Saif Mark A. Ratner George H. Lorimer Ryuzo Yanagimachi Barry M. Trost Medical Genetics, Hematology, and Nicholas J. Turro Anthropology Oncology Plant, Soil, and Charles T. Esmon Microbial Sciences Jeremy A. Sabloff Computer and Joseph L. Goldstein Roger N. Beachy Information Sciences Mark T. Groudine Steven E. Lindow Applied Mathematical Sciences Shafrira Goldwasser David O. Siegmund Tony Hunter M. S. Swaminathan Philip W. Majerus Susan R. Wessler Economic Sciences Newton E. Morton Applied Physical Sciences Ronald W. -
Medical Advisory Board September 1, 2006–August 31, 2007
hoWard hughes medical iNstitute 2007 annual report What’s Next h o W ard hughes medical i 4000 oNes Bridge road chevy chase, marylaNd 20815-6789 www.hhmi.org N stitute 2007 a nn ual report What’s Next Letter from the president 2 The primary purpose and objective of the conversation: wiLLiam r. Lummis 6 Howard Hughes Medical Institute shall be the promotion of human knowledge within the CREDITS thiNkiNg field of the basic sciences (principally the field of like medical research and education) and the a scieNtist 8 effective application thereof for the benefit of mankind. Page 1 Page 25 Page 43 Page 50 seeiNg Illustration by Riccardo Vecchio Südhof: Paul Fetters; Fuchs: Janelia Farm lab: © Photography Neurotoxin (Brunger & Chapman): Page 3 Matthew Septimus; SCNT images: by Brad Feinknopf; First level of Rongsheng Jin and Axel Brunger; iN Bruce Weller Blake Porch and Chris Vargas/HHMI lab building: © Photography by Shadlen: Paul Fetters; Mouse Page 6 Page 26 Brad Feinknopf (Tsai): Li-Huei Tsai; Zoghbi: Agapito NeW Illustration by Riccardo Vecchio Arabidopsis: Laboratory of Joanne Page 44 Sanchez/Baylor College 14 Page 8 Chory; Chory: Courtesy of Salk Janelia Farm guest housing: © Jeff Page 51 Ways Illustration by Riccardo Vecchio Institute Goldberg/Esto; Dudman: Matthew Szostak: Mark Wilson; Evans: Fred Page 10 Page 27 Septimus; Lee: Oliver Wien; Greaves/PR Newswire, © HHMI; Mello: Erika Larsen; Hannon: Zack Rosenthal: Paul Fetters; Students: Leonardo: Paul Fetters; Riddiford: Steitz: Harold Shapiro; Lefkowitz: capacity Seckler/AP, © HHMI; Lowe: Zack Paul Fetters; Map: Reprinted by Paul Fetters; Truman: Paul Fetters Stewart Waller/PR Newswire, Seckler/AP, © HHMI permission from Macmillan Page 46 © HHMI for Page 12 Publishers, Ltd.: Nature vol. -
Testing Working Memory: an Experimental and Analytical Approach
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Supervised Undergraduate Student Research Chancellor’s Honors Program Projects and Creative Work Spring 5-2005 Testing Working Memory: An Experimental and Analytical Approach Nicholas Duane Bennett University of Tennessee - Knoxville Follow this and additional works at: https://trace.tennessee.edu/utk_chanhonoproj Recommended Citation Bennett, Nicholas Duane, "Testing Working Memory: An Experimental and Analytical Approach" (2005). Chancellor’s Honors Program Projects. https://trace.tennessee.edu/utk_chanhonoproj/820 This is brought to you for free and open access by the Supervised Undergraduate Student Research and Creative Work at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Chancellor’s Honors Program Projects by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Running head: TESTING WORKING MEMORY Testing Working Memory: An Experimental and Analytical Approach 2005 Senior Honors Project Nicholas D. Bennett Mentor: Dr. Srinivasan Mahadevan The University of Tennessee Knoxville Abstract The following paper is basically a brief review of my studies in the concentration of cognition under the guidance of Dr. Mahadevan. In addition to demonstrating laboratory procedures, Dr. Mahadevan recommended many of the subsequent references to literature pertaining to various memory constructs. Having acquired a broad taste (but admitted novice skill) for many interpretations, clarifications by and conversations with Dr. Mahadevan have enabled me to document some conclusions here. My hope is to convey some understanding of the history, methods, theories and models I have found to be instrumental to the present-day empirical study of memory. -
The Chemistry of Professor Craig Jon Hawker Born on January 11, 1964 in Queensland, Australia
The Chemistry of Professor Craig Jon Hawker Born on January 11, 1964 in Queensland, Australia Education University of Queensland, Australia. B.Sc. 1981-1984 Cambridge University, UK. Ph.D. 1985-1988 Professor Sir A.R. Battersby (Biosynthesis of Vitamin B12 – Model Studies) Cornell University, Postdoc 1988-1990 Professor J.M.J. Fréchet (dendrimer synthesis) Academic Appointments Queen Elizabeth II Research Fellow – University of Queensland. 1990-1993 Research Staff Member – IBM Almaden Research Center. 1993-2004 Professor of Materials, Chemistry, and Biochemistry – UCSB, 2004-2016 Clarke Professor – UCSB, 2013-Present Director, Dow Materials Institute – UCSB, 2013-Present Craig Jon Hawker Ph.D. Director, California Nanosystems Institute – UCSB, 2013-Present Research Interests: synthetic polymer chemistry, Mentored around 200 Graduate Students and Postdocs nanomaterials, dendrimer, Recipient of dozens of awards radical polymerization, Approximately 450 publications and 50 patents. biomaterials. Founder of Olaplex LLC and Tricida, Inc. The Chemistry of Professor Craig Jon Hawker - Outline I. Dendrimer Chemistry II. Nitroxide & Alkoxyamine Mediated “Living” Radical Polymerization III. “Living” Radical Polymerization by Light IV. Click Chemistry in Polymerizations and Bioapplications V. Industrial Success and Olaplex J. Polym. Sci. Part A: Polym. Chem. 2002, 40, 2719. Dendrimer Synthesis: Divergent Approach Reactive groups increases exponentially after each generation. Incomplete reaction at chain terminal lead to imperfections or failure sequences in the next generation. Large excess of reagents required in latter stages. Tomalia, D. A, et al. Polym. J. 1985, 17, 117. Mixture of inseparable multi-generation dendrimers. Tomalia, D. A, et al. Macromolecules 1986, 19, 2466. Dendrimer Synthesis: Convergent Approach Hawker, C. J.; Frechet, J. M. J. J. -
10. Scientific Programme 10.1
10. SCIENTIFIC PROGRAMME 10.1. OVERVIEW (a) Invited Discourses Plenary Hall B 18:00-19:30 ID1 “The Zoo of Galaxies” Karen Masters, University of Portsmouth, UK Monday, 20 August ID2 “Supernovae, the Accelerating Cosmos, and Dark Energy” Brian Schmidt, ANU, Australia Wednesday, 22 August ID3 “The Herschel View of Star Formation” Philippe André, CEA Saclay, France Wednesday, 29 August ID4 “Past, Present and Future of Chinese Astronomy” Cheng Fang, Nanjing University, China Nanjing Thursday, 30 August (b) Plenary Symposium Review Talks Plenary Hall B (B) 8:30-10:00 Or Rooms 309A+B (3) IAUS 288 Astrophysics from Antarctica John Storey (3) Mon. 20 IAUS 289 The Cosmic Distance Scale: Past, Present and Future Wendy Freedman (3) Mon. 27 IAUS 290 Probing General Relativity using Accreting Black Holes Andy Fabian (B) Wed. 22 IAUS 291 Pulsars are Cool – seriously Scott Ransom (3) Thu. 23 Magnetars: neutron stars with magnetic storms Nanda Rea (3) Thu. 23 Probing Gravitation with Pulsars Michael Kremer (3) Thu. 23 IAUS 292 From Gas to Stars over Cosmic Time Mordacai-Mark Mac Low (B) Tue. 21 IAUS 293 The Kepler Mission: NASA’s ExoEarth Census Natalie Batalha (3) Tue. 28 IAUS 294 The Origin and Evolution of Cosmic Magnetism Bryan Gaensler (B) Wed. 29 IAUS 295 Black Holes in Galaxies John Kormendy (B) Thu. 30 (c) Symposia - Week 1 IAUS 288 Astrophysics from Antartica IAUS 290 Accretion on all scales IAUS 291 Neutron Stars and Pulsars IAUS 292 Molecular gas, Dust, and Star Formation in Galaxies (d) Symposia –Week 2 IAUS 289 Advancing the Physics of Cosmic -
GSA Welcomes 2012 Board Members
7INTERs3PRING 4HE'3!2EPORTER winter s spring 2012 New Executive GSA Welcomes 2012 Board Members Director Now on Board The Genetics Society of America New Members of the GSA Board of welcomes four new members elected Directors Adam P. Fagen, by the general membership to the Ph.D., stepped in as 2012 GSA Board of Directors. The VICE PRESIDENT: GSA’s new Executive new members are: Michael Lynch Michael Lynch, Director beginning (Indiana University), who serves as Distinguished December 1, 2011. vice president in 2012 and as GSA Professor of Dr. Fagen previously president in 2013 and Marnie E. Biology, Class of was at the American Halpern (Carnegie Institution for 1954 Professor, Society of Plant Science); Mohamed Noor (Duke Department of Biologists (ASPB), University); and John Schimenti Biology, Indiana where he was the director of public (Cornell University), who will serve as University, continued on page nineteen directors. Bloomington. Dr. Lynch is a population and evolutionary biologist and a In addition to these elected officers, long-time member of GSA. Dr. Lynch 2012 Brenda J. Andrews (University of sees GSA as the home for geneticists Toronto), Editor-in-Chief of GSA’s who study a broad base of topics GSA Award journal, G3: Genes|Genomes|Genetics, and organisms, and as a forum Recipients which was first published online in where general discussion occurs, June 2011, becomes a member of the whether based on the principles Announced Board of Directors. The bylaws have of genetics, the most pressing historically included the GENETICS GSA is pleased to announce the issues within the discipline itself, or editor-in-chief on the Board and as a responses to societal concerns and/ 2012 recipients of its five awards result of a 2011 bylaw revision, the G3 for distinguished service in the or conflicts within applied genetics. -
Chemistry NEWSLETTER
University of Michigan DEPARTMENT OF Chemistry NEWSLETTER Letter from the Chair Greetings from Ann Arbor and the chemical biology. In addition to these that Jim has done. He will be replaced by Department of Chemistry. After one full two outstanding senior hires, we welcome Professor Masato Koreeda. Professor year as Department Chair, I have come to Dr. Larry Beck from Cal Tech as the Dow Mark Meyerhoff will continue as Associ- realize the full scope of this administra- CorningAssistant Professor of analytical ate Chair for Graduate Student Affairs for tive challenge. It’s been a very busy and chemistry in September. Larry brings a another year after which he will take a exciting year as we forge ahead to meet broad spectrum of research expertise in well deserved sabbatical leave. the goals and implement the plans set out solid state NMR, zeolites and We have had another excellent year for in our new 5-year plan. nanostructures. Faculty recruiting will recruiting graduate students. In the fall, One of the most ambitious parts of our continue at a vigorous pace in the coming 45 new Ph.D. students will join the De- plan is the recruitment of new faculty at year with no less than four searches in the partment. This summer has also been a the senior and junior levels. During the area of theoretical physical chemistry, very productive one for undergraduate past year, Professor William Roush organic and chemical biology and inor- research participation with a total of 20 settled in the Department as the first ganic/materials chemistry. -
A Planet Made of Diamond (W/ Video) 25 August 2011
A planet made of diamond (w/ video) 25 August 2011 beam of radio waves. As the star spins and the radio beam sweeps repeatedly over Earth, radio telescopes detect a regular pattern of radio pulses. For the newly discovered pulsar, known as PSR J1719-1438, the astronomers noticed that the arrival times of the pulses were systematically modulated. They concluded that this was due to the gravitational pull of a small companion planet, orbiting the pulsar in a binary system. The pulsar and its planet are part of the Milky Way's plane of stars and lie 4,000 light-years away in the constellation of Serpens (the Snake). The system is about an eighth of the way towards the Galactic Centre from the Earth. The modulations in the radio pulses tell An artist's visualisation of the pulsar and its orbiting astronomers a number of things about the planet. planet. Image credit - Swinburne Astronomy Productions First, it orbits the pulsar in just two hours and ten minutes, and the distance between the two objects is 600,000 km-a little less than the radius of our A once-massive star that's been transformed into a Sun. small planet made of diamond: that is what University of Manchester astronomers think they've Second, the companion must be small, less than found in the Milky Way. 60,000 km (that's about five times the Earth's diameter). The planet is so close to the pulsar that, The discovery has been made by an international if it were any bigger, it would be ripped apart by the research team, led by Professor Matthew Bailes of pulsar's gravity. -
Rehabilitation Information Pack a Range of Products from Pearson Assessment for Professionals Working in the Area of Rehabilitation
Rehabilitation Information Pack A range of products from Pearson Assessment for professionals working in the area of rehabilitation The Functional UK Administration and Scoring Manual TFL S Living Scale UK Edition Examiner’s Manual C. Munro Cullum Myron F. Weiner Kathleen C. Saine www.pearsonclinical.co.uk Welcome... Introducing our 2013 Rehabilitation Information Pack Dear Colleague, Pearson (Assessment) is one of the UK’s leading publishers of standardised assessments. Our tests are used by a number of professionals in both health and education settings and we strive to develop and distribute tools that are timely and in line with good practice guidelines. For example, we are mindful of targets set by the Department of Health, for the early recognition of debilitating neurological and cognitive disorders including dementia and the aim for ‘two-thirds of people with dementia [to be] identified and given appropriate support by 2015’. In this pack you will find a range of products that can aid you inidentifying cognitive impairments and assist you in the evaluation of your clients; helping you to plan intervention strategies and enhance your evidence- based practice. Among these assessments is the new Brief Cognitive Status Exam (BCSE) which is designed to assess a client’s cognitive ability quickly and reliably, and the RBANS™ - Update which can be used as a stand-alone “core” battery for the detection and characterization of dementia in the elderly. Together with early diagnosis, assessment of activities of daily living can be vital in assisting service users maintain independence or return to everyday life. The UK-normed Rivermead Behavioural Memory Test- Third Edition, Rookwood Driving Battery and The Functional Living Scales – UK Version all have excellent ecological validity which places assessment in real life context; making the results more meaningful to you as a professional, and your clients.