Complementing Solutions to Optimization Problems Via Crowdsourcing on Video Game Plays
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Building Atlases of the Brain
© Copyright, Princeton University Press. No part of this book may be distributed, posted, or reproduced in any form by digital or mechanical means without prior written permission of the publisher. BUILDING AtLASES OF THE BRAIN Mike Hawrylycz With Chinh Dang, Christof Koch, and Hongkui Zeng A Very Brief History of Brain Atlases The earliest known significant works on human anatomy were collected by the Greek physician Claudius Galen around 200 BCE. This ancient corpus remained the dominant viewpoint through the Middle Ages until the classic work De humani corporis fabrica (On the Fabric of the Human Body) by Andreas Vesalius of Padua (1514–1564), the first mod- ern anatomist. Even today many of Vesalius’s drawings are astonishing to study and are largely accurate. For nearly two centuries scholars have recognized that the brain is compartmentalized into distinct regions, and this organization is preserved throughout mammals in general. However, comprehending the structural organization and function of the nervous system remains one of the primary challenges in neuro- science. To analyze and record their findings neuroanatomists develop atlases or maps of the brain similar to those cartographers produce. The state of our understanding today of an integrated plan of brain function remains incomplete. Rather than indicating a lack of effort, this observation highlights the profound complexity and interconnec- tivity of all but the simplest neural structures. Laying the foundation of cellular neuroscience, Santiago Ramón y Cajal (1852– 1934) drew and classified many types of neurons and speculated that the brain consists of an interconnected network of distinct neurons, as opposed to a more continuous web. -
Redesigning the Eterna100 for the Vienna 2 Folding Engine
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.26.457839; this version posted August 28, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Redesigning the Eterna100 for the Vienna 2 folding engine Rohan V. Koodli1,*, Boris Rudolfs2,*, Hannah K. Wayment-Steele3, Eterna Structure Designersγ, Rhiju Das4,5,^ 1Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA 94720 2Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92110 3Department of Chemistry, Stanford University, Stanford, CA 94305 4Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 5Department of Physics, Stanford University, Stanford, CA 94305 *Indicates equal contribution γ Group Author: Membership of Eterna participants and list of player names is provided in Acknowledgments ^Corresponding Author: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.08.26.457839; this version posted August 28, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract The rational design of RNA is becoming important for rapidly developing technologies in medicine and biochemistry. Recent work has led to the development of several RNA secondary structure design algorithms and corresponding benchmarks to evaluate their performance. However, the performance of these algorithms is linked to the nature of the underlying algorithms for predicting secondary structure from sequences. -
Poorna Roy Phd Dissertation
ANALYZING AND CLASSIFYING BIMOLECULAR INTERACTIONS: I. EFFECTS OF METAL BINDING ON AN IRON-SULFUR CLUSTER SCAFFOLD PROTEIN II. AUTOMATIC ANNOTATION OF RNA-PROTEIN INTERACTIONS FOR NDB Poorna Roy A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY August 2017 Committee: Neocles Leontis, Committee Co-Chair Andrew Torelli, Committee Co-Chair Vipaporn Phuntumart, Graduate Faculty Representative H. Peter Lu © 2017 Poorna Roy All Rights Reserved iii ABSTRACT Neocles B. Leontis and Andrew T. Torelli, Committee co-chairs This dissertation comprises two distinct parts; however the different research agendas are thematically linked by their complementary approaches to investigate the nature of important intermolecular interactions. The first part is the study of interactions between an iron-sulfur cluster scaffold protein, IscU, and different transition metal ions. Interactions between IscU and specific metal ions are investigated and compared with those of SufU, a homologous Fe-S cluster biosynthesis protein from Gram-positive bacteria whose metal-dependent conformational behavior remains unclear. These studies were extended with additional metal ions selected to determine whether coordination geometry at the active sites of IscU and its homolog influence metal ion selectivity. Comparing the conformational behavior and affinity for different transition metal ions revealed that metal-dependent conformational transitions exhibited by IscU may be a recurring strategy exhibited by U-type proteins involved in Fe-S cluster biosynthesis. The second part of the thesis focuses on automated detection and annotation of specific interactions between nucleotides and amino acid residues in RNA-protein complexes. -
Designing Learning with Citizen Science and Games
The Emerging Learning Design Journal Volume 4 Issue 1 Article 3 February 2018 Designing Learning with Citizen Science and Games Karen Schrier Marist College Follow this and additional works at: https://digitalcommons.montclair.edu/eldj Part of the Curriculum and Instruction Commons Recommended Citation Schrier, Karen (2018) "Designing Learning with Citizen Science and Games," The Emerging Learning Design Journal: Vol. 4 : Iss. 1 , Article 3. Available at: https://digitalcommons.montclair.edu/eldj/vol4/iss1/3 This Trends is brought to you for free and open access by Montclair State University Digital Commons. It has been accepted for inclusion in The Emerging Learning Design Journal by an authorized editor of Montclair State University Digital Commons. For more information, please contact [email protected]. Volume 4 (2017) pp. 19-26 http://eldj.montclair.edu eld.j ISSN 2474-8218 Emerging Learning Design Journal Trend Designing Learning with Citizen Science and Games Karen Schrier Marist College [email protected] April 29, 2017 ABSTRACT This emerging trends article introduces concepts such as citizen science (the inclusion of non-professionals in scientific knowledge production) and knowledge games (games that enable players to solve real-world problems through crowdsourcing and collective intelligence activities within a game). The article shares the strengths and limitations of using citizen science and knowledge games in the classroom, as well as initial tips and guidelines for bringing these types of experiences to -
Geometric and Statistical Methods for the Analysis and Prediction of Structural Interactions Between Biomolecules Julie Bernauer
Geometric and statistical methods for the analysis and prediction of structural interactions between biomolecules Julie Bernauer To cite this version: Julie Bernauer. Geometric and statistical methods for the analysis and prediction of structural interac- tions between biomolecules. Bioinformatics [q-bio.QM]. Université Paris-Sud XI, 2015. tel-01136261 HAL Id: tel-01136261 https://tel.archives-ouvertes.fr/tel-01136261 Submitted on 26 Mar 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Copyright Methodes´ geom´ etriques´ et statistiques pour l'analyse et la prediction´ des interactions structurales de biomolecules´ HABILITATION À DIRIGER DES RECHERCHES (Sp´ecialit´eInformatique) UNIVERSITÉ PARIS-SUD 11 pr´esent´eeet soutenue publiquement le 13 janvier 2015 Julie Bernauer Pr´esident: Philippe Dague Professeur, Universit´eParis Sud, LRI/LaDHAC Rapporteurs : Patrice Koehl Professor, University of California, Davis, Department of Computer Science Erik Lindahl Professor, KTH Royal Institute of Technology & Stockholm University, Department of Biochemistry -
Human Computation and Human Subject Tasks in Social Network Playful Applications
University of Bremen Doctoral Thesis Human Computation and Human Subject Tasks in Social Network Playful Applications Supervisors: Author: Dr. Rainer Malaka Aneta Takhtamysheva Dr. Andreas Breiter A thesis submitted in fulfilment of the requirements for the degree of Doctor of Engineering (Dr.-Ing.) in the Digital Media Mathematics and Informatics March 2016 Declaration of Authorship I, Aneta Takhtamysheva, declare that this thesis titled, ’Human Computation and Human Subject Tasks in Social Network Playful Applications’ and the work presented in it are my own. I confirm that: This work was done wholly or mainly while in candidature for a research degree at this University. Where any part of this thesis has previously been submitted for a degree or any other qualification at this University or any other institution, this has been clearly stated. Where I have consulted the published work of others, this is always clearly at- tributed. Where I have quoted from the work of others, the source is always given. With the exception of such quotations, this thesis is entirely my own work. I have acknowledged all main sources of help. Where the thesis is based on work done by myself jointly with others, I have made clear exactly what was done by others and what I have contributed myself. Signed: Date: ii UNIVERSITY OF BREMEN Abstract Mathematics and Informatics Doctor of Engineering (Dr.-Ing.) Human Computation and Human Subject Tasks in Social Network Playful Applications by Aneta Takhtamysheva Universal connectivity has made crowdsourcing - an online activity of a crowd toward the completion of a goal requested by someone in an open call - possible. -
UNDERSTANDING the BRAIN Tbook Collections
FROM THE NEW YORK TIMES ARCHIVES UNDERSTANDING THE BRAIN TBook Collections Copyright © 2015 The New York Times Company. All rights reserved. Cover Photograph by Zach Wise for The New York Times This ebook was created using Vook. All of the articles in this work originally appeared in The New York Times. eISBN: 9781508000877 The New York Times Company New York, NY www.nytimes.com www.nytimes.com/tbooks Obama Seeking to Boost Study of Human Brain By JOHN MARKOFF FEB. 17, 2013 The Obama administration is planning a decade-long scientific effort to examine the workings of the human brain and build a comprehensive map of its activity, seeking to do for the brain what the Human Genome Project did for genetics. The project, which the administration has been looking to unveil as early as March, will include federal agencies, private foundations and teams of neuroscientists and nanoscientists in a concerted effort to advance the knowledge of the brain’s billions of neurons and gain greater insights into perception, actions and, ultimately, consciousness. Scientists with the highest hopes for the project also see it as a way to develop the technology essential to understanding diseases like Alzheimer’sand Parkinson’s, as well as to find new therapies for a variety of mental illnesses. Moreover, the project holds the potential of paving the way for advances in artificial intelligence. The project, which could ultimately cost billions of dollars, is expected to be part of the president’s budget proposal next month. And, four scientists and representatives of research institutions said they had participated in planning for what is being called the Brain Activity Map project. -
RNA Structure Through Multidimensional Chemical Mapping
REVIEW RNA structure through multidimensional chemical mapping Siqi Tian1 and Rhiju Das1,2* 1 Department of Biochemistry, Stanford University, Stanford, CA 94305, USA 2 Department of Physics, Stanford University, Stanford, CA 94305, USA Quarterly Reviews of Biophysics (2016), 49, e7, page 1 of 30 doi:10.1017/S0033583516000020 Abstract. The discoveries of myriad non-coding RNA molecules, each transiting through multiple flexible states in cells or virions, present major challenges for structure determination. Advances in high-throughput chemical mapping give new routes for characterizing entire tran- scriptomes in vivo, but the resulting one-dimensional data generally remain too information-poor to allow accurate de novo structure deter- mination. Multidimensional chemical mapping (MCM) methods seek to address this challenge. Mutate-and-map (M2), RNA interaction groups by mutational profiling (RING-MaP and MaP-2D analysis) and multiplexed •OH cleavage analysis (MOHCA) measure how the chemical reactivities of every nucleotide in an RNA molecule change in response to modifications at every other nucleotide. A growing body of in vitro blind tests and compensatory mutation/rescue experiments indicate that MCM methods give consistently accurate secondary structures and global tertiary structures for ribozymes, ribosomal domains and ligand-bound riboswitch aptamers up to 200 nucleotides in length. Importantly, MCM analyses provide detailed information on structurally heterogeneous RNA states, such as ligand-free riboswitches that are functionally important but difficult to resolve with other approaches. The sequencing requirements of currently available MCM pro- tocols scale at least quadratically with RNA length, precluding general application to transcriptomes or viral genomes at present. We propose a modify-cross-link-map (MXM) expansion to overcome this and other current limitations to resolving the in vivo ‘RNA structurome’. -
Design and Evaluation of Interactive Proofreading Tools for Connectomics
Design and Evaluation of Interactive Proofreading Tools for Connectomics Daniel Haehn, Seymour Knowles-Barley, Mike Roberts, Johanna Beyer, Narayanan Kasthuri, Jeff W. Lichtman, and Hanspeter Pfister Fig. 1: Proofreading with Dojo. We present a web-based application for interactive proofreading of automatic segmentations of connectome data acquired via electron microscopy. Split, merge and adjust functionality enables multiple users to correct the labeling of neurons in a collaborative fashion. Color-coded structures can be explored in 2D and 3D. Abstract—Proofreading refers to the manual correction of automatic segmentations of image data. In connectomics, electron mi- croscopy data is acquired at nanometer-scale resolution and results in very large image volumes of brain tissue that require fully automatic segmentation algorithms to identify cell boundaries. However, these algorithms require hundreds of corrections per cubic micron of tissue. Even though this task is time consuming, it is fairly easy for humans to perform corrections through splitting, merging, and adjusting segments during proofreading. In this paper we present the design and implementation of Mojo, a fully-featured single- user desktop application for proofreading, and Dojo, a multi-user web-based application for collaborative proofreading. We evaluate the accuracy and speed of Mojo, Dojo, and Raveler, a proofreading tool from Janelia Farm, through a quantitative user study. We designed a between-subjects experiment and asked non-experts to proofread neurons in a publicly available connectomics dataset. Our results show a significant improvement of corrections using web-based Dojo, when given the same amount of time. In addition, all participants using Dojo reported better usability. We discuss our findings and provide an analysis of requirements for designing visual proofreading software. -
New Visions in Citizen Science
case study series vol 3 New Visions in Citizen Science by Anne Bowser and Lea Shanley New Visions in Citizen Science by Anne Bowser and Lea Shanley, Woodrow Wilson Center November 2013 Commons Lab | Case sTUDy series | vOL 3 NEW VISIONS IN CITIZEN SCIENCE Commons Lab Science and Technology Innovation Program Woodrow Wilson International Center for Scholars One Woodrow Wilson Plaza 1300 Pennsylvania Avenue, N.W. Washington, DC 20004-3027 www.CommonsLab.wilsoncenter.org Study Director: Lea Shanley Editor: Aaron Lovell Cover design: Kathy Butterfield and Diana Micheli © 2013, The Woodrow Wilson Center: This work is licensed under Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License: http://creativecommons. org/licenses/by-nc-nd/3.0/ This report may be reproduced in whole, or in part, for educational and non- commercial uses, pursuant to the Creative Commons Attribution-NonCommerical- NoDerivs 3.0 Unported License found at http://creativecommons.org/licenses/by-nc- nd/3.0/ and provided this copyright notice and the following attribution is given: Anne Bowser and Lea Shanley, New Visions in Citizen Science. Washington, DC: Wood- row Wilson International Center for Scholars, 2013. Users may not use technical measures to obstruct or control the reading or further copying of the copies that they make or distribute. Nongovernmental users may not accept compensation of any manner in exchange for copies. The Woodrow Wilson Center is open to certain derivative uses of this product beyond the limitations of the included Creative Commons License, particularly for educational materials targeted at expanding knowledge on the Commons Lab’s mandate. For more information, please contact [email protected]. -
Revisiting Citizen Science Through the Lens of Hybrid Intelligence
Revisiting Citizen Science Through the Lens of Hybrid Intelligence Janet Rafnera, Miroslav Gajdacza, Gitte Kragha, Arthur Hjortha, Anna Ganderb, Blanka Pala, Aleks Berditchevskaiac, François Greyd, Kobi Gale, Avi Segale, Mike Walmsleyf, Josh Aaron Millerg, Dominik Dellermanh, Muki Haklayi, Pietro Micheluccij, Jacob Shersona a Center for Hybrid Intelligence, Denmark b University of Gothenburg, Sweden c Centre for Collective Intelligence Design, United Kingdom d Citizen Cyberlab e Ben Gurion University, Israel f University of Oxford, England g Northwestern University, USA h Vencortex i University College London, England j Human Computation Institute, USA Abstract Articial Intelligence (AI) can augment and sometimes even replace human cognition. Inspired by eorts to value human agency alongside productivity, we discuss the benets of solving Citizen Science (CS) tasks with Hybrid Intelligence (HI), a synergetic mixture of human and articial intelligence. Currently there is no clear framework or methodology on how to create such an eective mixture. Due to the unique participant-centered set of values and the abundance of tasks drawing upon both human common sense and complex 21st century skills, we believe that the eld of CS oers an invaluable testbed for the development of HI and human-centered AI of the 21st century, while beneting CS as well. In order to investigate this potential, we rst relate CS to adjacent computational disciplines. Then, we demonstrate that CS projects can be grouped according to their potential for HI-enhancement by examining two key dimensions: the level of digitization and the amount of knowledge or experience required for participation. Finally, we propose a framework for types of human-AI interaction in CS based on established criteria of HI. -
Massive Data Management and Sharing Module for Connectome Reconstruction
brain sciences Article Massive Data Management and Sharing Module for Connectome Reconstruction Jingbin Yuan 1 , Jing Zhang 1, Lijun Shen 2,*, Dandan Zhang 2, Wenhuan Yu 2 and Hua Han 3,4,5,* 1 School of Automation, Harbin University of Science and Technology, Harbin 150080, China; [email protected] (J.Y.); [email protected] (J.Z.) 2 Research Center for Brain-inspired Intelligence, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; [email protected] (D.Z.); [email protected] (W.Y.) 3 The National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China 4 Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China 5 The School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China * Correspondence: [email protected] (L.S.); [email protected] (H.H); Tel.: +86-010-82544385 (L.S.); +86-010-82544710 (H.H) Received: 30 April 2020; Accepted: 20 May 2020; Published: 22 May 2020 Abstract: Recently, with the rapid development of electron microscopy (EM) technology and the increasing demand of neuron circuit reconstruction, the scale of reconstruction data grows significantly. This brings many challenges, one of which is how to effectively manage large-scale data so that researchers can mine valuable information. For this purpose, we developed a data management module equipped with two parts, a storage and retrieval module on the server-side and an image cache module on the client-side. On the server-side, Hadoop and HBase are introduced to resolve massive data storage and retrieval.