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Are Tits Really Unsuitable Hosts for the Common Cuckoo?
Ornis Fennica 91:0000. 2014 Are tits really unsuitable hosts for the Common Cuckoo? Tomá Grim*, Peter Sama, Petr Procházka & Jarkko Rutila T. Grim & P. Sama, Department of Zoology and Laboratory of Ornithology, Palacký University, 17. listopadu 50, CZ-77146 Olomouc, Czech Republic. * Corresponding au- thors e-mail: [email protected] P. Procházka, Institute of Vertebrate Biology, Academy of Sciences of the Czech Repub- lic, v. v. i., Kvìtná 8, CZ-60365 Brno, Czech Republic J. Rutila, Kannelkatu 5 as 26, 53100 Lappeenranta, Finland Received 19 January 2014, accepted 18 March 2014 Avian brood parasites exploit hosts that have accessible nests and a soft insect diet. Com- mon Cuckoo (Cuculus canorus) hosts were traditionally classified as suitable if both pa- rameters were fulfilled or unsuitable if one, or both, were not. In line with this view, hole- nesting tits (Paridae) have become a text-book example of unsuitable Cuckoo hosts. Our extensive literature search for Cuckoo eggs hatched and chicks raised by hosts revealed 16 Cuckoo nestlings in Great Tit (Parus major) nests, 2 nestlings and 2 fledglings in Blue Tits (Cyanistes caeruleus), and 1 nestling in a Crested Tit (Lophophanes cristatus)nest. Our own data from natural observations and cross-fostering experiments concur with lit- erature data that Great Tits are able to rear Cuckoo chicks to fledging. The natural obser- vations involve the first known cases where a bird species became parasitized as a by- product of nest usurpation (take-over). Surprisingly, Cuckoo chicks raised by Great Tits grew better than Cuckoo chicks raised by common hosts, even alongside host own chicks. -
Journal of Molecular Graphics and Modelling 73 (2017) 179–190
Journal of Molecular Graphics and Modelling 73 (2017) 179–190 Contents lists available at ScienceDirect Journal of Molecular Graphics and Modelling journa l homepage: www.elsevier.com/locate/JMGM Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates a b c d,1 Weihong Zhang , Steven C. Howell , David W. Wright , Andrew Heindel , e a, b, Xiangyun Qiu , Jianhan Chen ∗, Joseph E. Curtis ∗∗ a Kansas State University, Manhattan, KS, USA b NIST Center for Neutron Research, 100 Bureau Drive, Gaithersburg, MD, USA c Centre for Computational Science, Department of Chemistry, University College London, 10 Gordon St., London, UK d James Madison University, Department of Chemistry & Biochemistry, Harrisonburg, VA, USA e Department of Physics, The George Washington University, Washington, DC, USA a r t i c l e i n f o a b s t r a c t Article history: We describe a general method to use Monte Carlo simulation followed by torsion-angle molecular dynam- Received 13 October 2016 ics simulations to create ensembles of structures to model a wide variety of soft-matter biological systems. Received in revised form 19 January 2017 Our particular emphasis is focused on modeling low-resolution small-angle scattering and reflectivity Accepted 17 February 2017 structural data. We provide examples of this method applied to HIV-1 Gag protein and derived fragment Available online 23 February 2017 proteins, TraI protein, linear B-DNA, a nucleosome core particle, and a glycosylated monoclonal antibody. This procedure will enable a large community of researchers to model low-resolution experimental data MSC: with greater accuracy by using robust physics based simulation and sampling methods which are a 00-01 99-00 significant improvement over traditional methods used to interpret such data. -
Biological Sciences 1
Biological Sciences 1 BIOL UN3208 Introduction to Evolutionary Biology or EEEB UN2001 BIOLOGICAL SCIENCES Environmental Biology I: Elements to Organisms. Departmental Office: 600 Fairchild, 212-854-4581; Interested students should consult listings in other departments for [email protected]; [email protected] courses related to biology. For courses in environmental studies, see listings for Earth and environmental sciences or for ecology, evolution, Director of Undergraduate Studies, Undergraduate Programs and and environmental biology. For courses in human evolution, see listings Laboratories: for anthropology or for ecology, evolution, and environmental biology. Prof. Deborah Mowshowitz, 744D Mudd; 212-854-4497; For courses in the history of evolution, see listings for history and for [email protected] philosophy of science. For a list of courses in computational biology and genomics, visit http://systemsbiology.columbia.edu/courses. Biology Major and Concentration Advisers: For a list of current biology, biochemistry, biophysics, and neuroscience and behavior advisers, please visit http://biology.columbia.edu/ Advanced Placement programs/advisors Transfer Credit A-F: Prof. Alice Heicklen, 744B Mudd; [email protected] Transfer credits granted toward the degree are not automatically counted G-O: Prof. Mary Ann Price, 744A Mudd; [email protected] toward the major. The department determines which transfer credits P-Z: Prof. Tulle Hazelrigg, 753A Mudd, [email protected] can be counted toward the major. For most majors, at least four biology Backup Advisor: Prof. Deborah Mowshowitz, 744D Mudd; 212-854-4497; or biochemistry courses and at least 18 credits of the total (biology, [email protected] biochemistry, math, physics, and chemistry) must be taken at Columbia. -
CCP4 Molecular Graphics Documentation Contents Documentation On-Line Documentation Tutorials Ccp4mg Home Contents Quick Reference Print Version Contact References
CCP4 Molecular Graphics file:///E:/ccp4mg-win/help/index.html CCP4 Molecular Graphics Documentation Contents Documentation On-line Documentation Tutorials CCP4mg Home Contents Quick Reference Print version Contact References Documentation Contents General Graphics Window - mouse bindings and short cuts The Tools menu The View menu Projects - data organisation Installation of support programs Molecular models Reading coordinate files and atom typing The Coordinate Model Interface Atom selection Structure Analysis Surfaces and Electrostatic Potentials Symmetry Related Models Animations Other types of data Electron density maps Vectors Electron density in GAUSSIAN cube format Text and imported images Applications Superpose automatic protein superposition and interactive superposition of any structures Presentation Graphics Picture Wizard set up complex pictures quickly Movies Presentations Geometry Run Coot Other utilities Web tools History and Scripting Editing and Saving Files PDF Creator - PDF4Free v2.0 http://www.pdf4free.com 1 of 3 01/11/2007 18:42 CCP4 Molecular Graphics file:///E:/ccp4mg-win/help/index.html Lighting Saving the program status Picture Definition Files (also Object attributes and Introduction to Python) Making presentations Quick Reference See Display Table for general overview of the display table. For information on specific type of data click the appropriate data type in the File list below. File Tools View Applications Coordinate Files General tools General tools Movies Downloading Coordinate .. .. Superpose Files Read electron density Picture Save/restore view Lighting map/MTZ Wizard Read QM maps Save/restore status Transparency Geometry Add vectors/labels Picture definition files View from Rotate,translate,align Add image History and Scripting view Add legend Presentation/Notebook RocknRoll Add crystal List monomer definition Model definition file Preferences Open presentation Tutorials Output screen image Windows Bring a 'lost' window to the front. -
Coot: Model-Building Tools for Molecular Graphics Crystallography ISSN 0907-4449
research papers Acta Crystallographica Section D Biological Coot: model-building tools for molecular graphics Crystallography ISSN 0907-4449 Paul Emsley* and Kevin Cowtan CCP4mg is a project that aims to provide a general-purpose Received 26 February 2004 tool for structural biologists, providing tools for X-ray Accepted 4 August 2004 structure solution, structure comparison and analysis, and York Structural Biology Laboratory, University of York, Heslington, York YO10 5YW, England publication-quality graphics. The map-®tting tools are avail- able as a stand-alone package, distributed as `Coot'. Correspondence e-mail: [email protected] 1. Introduction Molecular graphics still plays an important role in the deter- mination of protein structures using X-ray crystallographic data, despite on-going efforts to automate model building. Functions such as side-chain placement, loop, ligand and fragment ®tting, structure comparison, analysis and validation are routinely performed using molecular graphics. Lower Ê resolution (dmin worse than 2.5 A) data in particular need interactive ®tting. The introduction of FRODO (Jones, 1978) and then O (Jones et al., 1991) to the ®eld of protein crystallography was in each case revolutionary, each in their time breaking new ground in demonstrating what was possible with the current hardware. These tools allowed protein crystallographers to enjoy what is widely held to be the most thrilling part of their work: giving birth (as it were) to a new protein structure. The CCP4 program suite (Collaborative Computational Project, Number 4, 1994) is an integrated collection of software for macromolecular crystallography, with a scope ranging from data processing to structure re®nement and validation. -
Architecture De Dataflow Pour Des Systèmes Modulaires Et Génériques De Simulation De Plante Christophe Pradal
Architecture de dataflow pour des systèmes modulaires et génériques de simulation de plante Christophe Pradal To cite this version: Christophe Pradal. Architecture de dataflow pour des systèmes modulaires et génériques desim- ulation de plante. Modélisation et simulation. Université Montpellier, 2019. Français. NNT : 2019MONTS034. tel-02879776 HAL Id: tel-02879776 https://tel.archives-ouvertes.fr/tel-02879776 Submitted on 24 Jun 2020 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. THESE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITE DE MONTPELLIER PAR LA VALIDATION DES ACQUIS DE L’EXPERIENCE Année universitaire 2018-2019 En Informatique École doctorale I2S – Information, Structures, Systèmes Unité de recherche UMR AGAP – Université de Montpellier SYNTHÈSE DES TRAVAUX DE RECHERCHE Architecture de Dataflow pour des systèmes modulaires et génériques de simulation de plante Présentée par Christophe PRADAL Le 17 juillet 2019 Référent : Christophe GODIN RAPPORT DE GESTION Devant le jury composé de Christophe GODIN, Directeur de recherche, Inria, Lyon -
SCIENCE CITATION INDEX EXPANDED - JOURNAL LIST Total Journals: 8631
SCIENCE CITATION INDEX EXPANDED - JOURNAL LIST Total journals: 8631 1. 4OR-A QUARTERLY JOURNAL OF OPERATIONS RESEARCH 2. AAPG BULLETIN 3. AAPS JOURNAL 4. AAPS PHARMSCITECH 5. AATCC REVIEW 6. ABDOMINAL IMAGING 7. ABHANDLUNGEN AUS DEM MATHEMATISCHEN SEMINAR DER UNIVERSITAT HAMBURG 8. ABSTRACT AND APPLIED ANALYSIS 9. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 10. ACADEMIC EMERGENCY MEDICINE 11. ACADEMIC MEDICINE 12. ACADEMIC PEDIATRICS 13. ACADEMIC RADIOLOGY 14. ACCOUNTABILITY IN RESEARCH-POLICIES AND QUALITY ASSURANCE 15. ACCOUNTS OF CHEMICAL RESEARCH 16. ACCREDITATION AND QUALITY ASSURANCE 17. ACI MATERIALS JOURNAL 18. ACI STRUCTURAL JOURNAL 19. ACM COMPUTING SURVEYS 20. ACM JOURNAL ON EMERGING TECHNOLOGIES IN COMPUTING SYSTEMS 21. ACM SIGCOMM COMPUTER COMMUNICATION REVIEW 22. ACM SIGPLAN NOTICES 23. ACM TRANSACTIONS ON ALGORITHMS 24. ACM TRANSACTIONS ON APPLIED PERCEPTION 25. ACM TRANSACTIONS ON ARCHITECTURE AND CODE OPTIMIZATION 26. ACM TRANSACTIONS ON AUTONOMOUS AND ADAPTIVE SYSTEMS 27. ACM TRANSACTIONS ON COMPUTATIONAL LOGIC 28. ACM TRANSACTIONS ON COMPUTER SYSTEMS 29. ACM TRANSACTIONS ON COMPUTER-HUMAN INTERACTION 30. ACM TRANSACTIONS ON DATABASE SYSTEMS 31. ACM TRANSACTIONS ON DESIGN AUTOMATION OF ELECTRONIC SYSTEMS 32. ACM TRANSACTIONS ON EMBEDDED COMPUTING SYSTEMS 33. ACM TRANSACTIONS ON GRAPHICS 34. ACM TRANSACTIONS ON INFORMATION AND SYSTEM SECURITY 35. ACM TRANSACTIONS ON INFORMATION SYSTEMS 36. ACM TRANSACTIONS ON INTELLIGENT SYSTEMS AND TECHNOLOGY 37. ACM TRANSACTIONS ON INTERNET TECHNOLOGY 38. ACM TRANSACTIONS ON KNOWLEDGE DISCOVERY FROM DATA 39. ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE 40. ACM TRANSACTIONS ON MODELING AND COMPUTER SIMULATION 41. ACM TRANSACTIONS ON MULTIMEDIA COMPUTING COMMUNICATIONS AND APPLICATIONS 42. ACM TRANSACTIONS ON PROGRAMMING LANGUAGES AND SYSTEMS 43. ACM TRANSACTIONS ON RECONFIGURABLE TECHNOLOGY AND SYSTEMS 44. -
Understanding Performance of Protein Structural Classifiers
Understanding Performance of Protein Structural Classifiers Alper Sarikaya∗ Danielle Albers† Michael Gleicher‡ University of Wisconsin – Madison University of Wisconsin – Madison University of Wisconsin – Madison ABSTRACT of proteins. The individual molecular detail view shows a surface- Many bioinformatics applications utilize machine learning tech- abstracted three-dimensional view of the protein, providing a scaf- niques to create models for predicting which parts of proteins will fold to display data mapped to the surface in a manner similar to bind to targets. Understanding the results of these protein surface canonical molecular graphics applications such as PyMol [3]. How- binding classifiers is challenging, as the individual answers are em- ever, we group spatially-congruent results on the molecular surface bedded spatially on the surface of the molecules, yet the perfor- to help collapse the data into a small set of regions that supports mance needs to be understood over an entire corpus of molecules. interactive and guided exploration. Our analytical approach is real- In this project, we introduce a multi-scale approach for assessing ized by a prototype that we have applied to various structural bind- the performance of these structural classifiers, providing coordi- ing classifiers. nated views for both corpus level overviews as well as spatially- 2 TASK ANALYSIS embedded results on the three-dimensional structures of proteins. Our problem domain focuses on proteins: large macro-molecules Keywords: J.3.1 [Computer Applications]: Life and Medical Sci- that are composed of 20 naturally-occurring amino acids (residues) ences — Biology and Genetics; chained together in sequence. The residues, in turn, fold over one another to form the conformation that governs the protein’s biolog- 1 INTRODUCTION ical and chemical function. -
Python Molecular Viewer
Python Molecular Viewer Written by Ruth Huey and Michel Sanner The Scripps Research Institute Molecular Graphics Laboratory 10550 N. Torrey Pines Rd. La Jolla, California 92037-1000 USA 11 October 2005 1 Contents Contents .......................................................................... 2 Introduction ..................................................................... 4 Before We Start….............................................................................4 FAQ – Frequently Asked Questions ..................................... 5 Exercise One: Getting Started: PMV Basics .......................... 7 Procedure: .......................................................................................8 Summary: what have we learned?....................................................12 Bonus Section: MSMS surfaces .......................................................13 Bonus Section: Binding Commands to Keys ......................................14 Hemolysin: Secondary Structure colored by Chain. .............. 16 Procedure: .....................................................................................16 Summary: what have we learned?....................................................20 Bonus Section: Color by Secondary Structure...................................21 Bonus Section: Measure hemolysin beta barrel.................................21 HIV Protease: Active Site Residues and Inhibitor ................. 23 Procedure: .....................................................................................24 Summary: -
Visualization of Polymer Processing at the Continuum Level Jeremy Hicks Clemson University, [email protected]
Clemson University TigerPrints All Theses Theses 12-2006 Visualization of Polymer Processing at the Continuum Level Jeremy Hicks Clemson University, [email protected] Follow this and additional works at: https://tigerprints.clemson.edu/all_theses Part of the Computer Sciences Commons Recommended Citation Hicks, Jeremy, "Visualization of Polymer Processing at the Continuum Level" (2006). All Theses. 15. https://tigerprints.clemson.edu/all_theses/15 This Thesis is brought to you for free and open access by the Theses at TigerPrints. It has been accepted for inclusion in All Theses by an authorized administrator of TigerPrints. For more information, please contact [email protected]. VISUALIZATION OF POLYMER PROCESSING AT THE CONTINUUM LEVEL A Thesis Presented to the Graduate School of Clemson University In Partial Fulfillment of the Requirements for the Degree Master of Fine Arts Digital Production Arts by Jeremy L. Hicks December 2006 Accepted by: Dr. Timothy Davis, Committee Chair Dr. John Kundert-Gibbs Dr. Christopher Cox ABSTRACT Computer animation, coupled with scientific experimentation and modeling, allows scientists to produce detailed visualizations that potentially enable more comprehensive perception of physical phenomena and ultimately, new discoveries. With the use of Maya, an animation and modeling program that incorporates the natural laws of physics to control the behavior of virtual objects in computer animation, data from the modeling of physical processes such as polymer fibers and films can be explored in the visual realm. Currently, few attempts have been made at the continuum level to represent polymer properties via computer animation using advanced graphics. As a result, scientists may be unable to recognize patterns and trends in a specific polymer quickly and efficiently, and thus, lose time and money commonly required for further experiments. -
DSCVR: Designing a Commodity Hybrid Virtual Reality System
Noname manuscript No. (will be inserted by the editor) DSCVR: designing a commodity hybrid virtual reality system Kevin Ponto · Joe Kohlmann · Ross Tredinnick Received: date / Accepted: date Abstract This paper presents the design considerations, specifications and lessons learned while building DSCVR, a commodity hybrid reality environ- ment (HRE). Consumer technology has enabled a reduced cost for both 3D tracking and display, enabling a new means for the creation of immersive dis- play environments. However, this technology also presents many challenges which need to be designed for and around. We compare the DSCVR system to other existing VR environments to analyze the tradeoffs being made. Keywords Hybrid Reality · Virtual Reality · Display Wall · Immersive Systems · Commodity Hardware · 3D · High Resolution · Passive Stereo 1 Introduction Recent advancements in consumer grade 3D display and gesture input tech- nology have enabled new pathways for the creation of immersive Virtual Re- ality systems. Previous methods for constructing immersive display systems Kevin Ponto Wisconsin Institute for Discovery Room 3176, 330 N. Orchard Street Madison, WI 53715 Tel.: +(608) 316-4330 E-mail: [email protected] Joe Kohlmann Wisconsin Institute for Discovery 330 N. Orchard Street Madison, WI 53715 E-mail: [email protected]> Ross Tredinnick Wisconsin Institute for Discovery Room 1144B, 330 N. Orchard Street Madison, WI 53715 E-mail: [email protected] 2 Kevin Ponto et al. (a) (b) (c) Fig. 1 Design schematics for the DSCVR System. (a) shows a subset of the designs consid- ered, including horizontally-oriented displays, larger displays, a wider or tighter curvature, and positioning techniques to hide bezels. -
A Script to Highlight Hydrophobicity and Charge on Protein Surfaces
METHODS published: 13 October 2015 doi: 10.3389/fmolb.2015.00056 A script to highlight hydrophobicity and charge on protein surfaces Dominique Hagemans, Ianthe A. E. M. van Belzen, Tania Morán Luengo and Stefan G. D. Rüdiger * Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands The composition of protein surfaces determines both affinity and specificity of protein-protein interactions. Matching of hydrophobic contacts and charged groups on both sites of the interface are crucial to ensure specificity. Here, we propose a highlighting scheme, YRB, which highlights both hydrophobicity and charge in protein structures. YRB highlighting visualizes hydrophobicity by highlighting all carbon atoms that are not bound to nitrogen and oxygen atoms. The charged oxygens of glutamate and aspartate are highlighted red and the charged nitrogens of arginine and lysine are highlighted blue. For a set of representative examples, we demonstrate that YRB highlighting intuitively Edited by: Ophry Pines, visualizes segments on protein surfaces that contribute to specificity in protein-protein Hebrew University of Jerusalem, Israel interfaces, including Hsp90/co-chaperone complexes, the SNARE complex and a Reviewed by: transmembrane domain. We provide YRB highlighting in form of a script that runs using Paolo De Los Rios, the software PyMOL. Ecole Polytechnique Fédérale de Lausanne, Switzerland Keywords: protein-protein interaction, surface hydrophobicity, charge pairs, PyMOL, amino acid properties Eilika Weber-Ban, ETH Zurich, Switzerland *Correspondence: Introduction Stefan G. D. Rüdiger, Cellular Protein Chemistry, Bijvoet Protein-protein interactions underlie all processes in the cell. Specificity of protein-protein Center for Biomolecular Research, interactions is determined by matching of complementary functional groups with those of Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands the opposite surface (Chothia and Janin, 1975; Eaton et al., 1995).