WorldWideScience

Sample records for existing protein information

  1. INFORMATION SECURITY RISK ASSESSMENT USING EXISTING LEGAL AND METHODOLOGICAL BASE

    Directory of Open Access Journals (Sweden)

    A. I. Trubei

    2015-01-01

    Full Text Available The article provides a survey of the existing regulatory framework for information security riskmanagement. Practical methods for information security risk and vulnerability assessment are proposed.

  2. Incorporating existing network information into gene network inference.

    Directory of Open Access Journals (Sweden)

    Scott Christley

    2009-08-01

    Full Text Available One methodology that has met success to infer gene networks from gene expression data is based upon ordinary differential equations (ODE. However new types of data continue to be produced, so it is worthwhile to investigate how to integrate these new data types into the inference procedure. One such data is physical interactions between transcription factors and the genes they regulate as measured by ChIP-chip or ChIP-seq experiments. These interactions can be incorporated into the gene network inference procedure as a priori network information. In this article, we extend the ODE methodology into a general optimization framework that incorporates existing network information in combination with regularization parameters that encourage network sparsity. We provide theoretical results proving convergence of the estimator for our method and show the corresponding probabilistic interpretation also converges. We demonstrate our method on simulated network data and show that existing network information improves performance, overcomes the lack of observations, and performs well even when some of the existing network information is incorrect. We further apply our method to the core regulatory network of embryonic stem cells utilizing predicted interactions from two studies as existing network information. We show that including the prior network information constructs a more closely representative regulatory network versus when no information is provided.

  3. Information contained in protein shapes

    Science.gov (United States)

    Sundaram, K.; Viswanadhan, V. N.; Macelroy, R. D.

    1983-01-01

    The sequence of local conformations at C-alpha atoms of a protein has been considered as an informational message string. The total self-information contents and self-information per letter have been evaluated for 83 globular proteins whose structures are known from X-ray crystallography. The derived information contents provide a method of quantitating structural specificity of proteins. This method of analysis enables repeating, intricate structural features to be recognized. Among the globular proteins whose structures have been solved, high potential iron protein stands out with the largest three-letter dependence.

  4. Existence of an Equilibrium for Lower Semicontinuous Information Acquisition Functions

    Directory of Open Access Journals (Sweden)

    Agnès Bialecki

    2014-01-01

    Full Text Available We consider a two-period model in which a continuum of agents trade in a context of costly information acquisition and systematic heterogeneous expectations biases. Because of systematic biases agents are supposed not to learn from others' decisions. In a previous work under somehow strong technical assumptions a market equilibrium was proved to exist and the supply and demand functions were proved to be strictly monotonic with respect to the price. Here we extend these results under very weak technical assumptions. We also prove that the equilibrium price maximizes the trading volume and further additional properties (such as the antimonotonicity of the trading volume with respect to the marginal information price.

  5. 77 FR 18256 - Agency Information Collection Activities: Revision of an Existing Information Collection, Comment...

    Science.gov (United States)

    2012-03-27

    ... information collection. (2) Title of the Form/Collection: Employment Eligibility Verification. (3) Agency form... SECURITY U.S. Citizenship and Immigration Services Agency Information Collection Activities: Revision of an Existing Information Collection, Comment Request ACTION: 60-Day notice of information collection under...

  6. 77 FR 24507 - Agency Information Collection Activities: Form N-25, Extension of an Existing Information...

    Science.gov (United States)

    2012-04-24

    ... SECURITY U.S. Citizenship and Immigration Services Agency Information Collection Activities: Form N-25, Extension of an Existing Information Collection Request; Comment Request ACTION: 30-Day Notice of Information Collection Under Review: Form N- 25, Request for Verification of Naturalization. The Department of...

  7. 77 FR 9258 - Agency Information Collection Activities: Extension of an Existing Information Collection Request...

    Science.gov (United States)

    2012-02-16

    ... SECURITY U.S. Citizenship and Immigration Services Agency Information Collection Activities: Extension of an Existing Information Collection Request; Comment Request ACTION: 60-Day Notice of Information Collection Under Review: Form N- 25, Request for Verification of Naturalization. The Department of Homeland...

  8. 75 FR 14179 - Agency Information Collection Activities: Form I-9 CNMI; Revision to an Existing Information...

    Science.gov (United States)

    2010-03-24

    ... SECURITY U.S. Citizenship and Immigration Services Agency Information Collection Activities: Form I-9 CNMI; Revision to an Existing Information Collection; Comment Request ACTION: 30-Day Notice of Information Collection under Review: Form I-9 CNMI, CNMI Employment Eligibility Verification; OMB Control No. 1615- 0112...

  9. The Existence of Equilibrium Asset Price Under Diverse Information

    Directory of Open Access Journals (Sweden)

    R. Agus Sartono

    2005-09-01

    Our model shows that the more diverse the information, the higher the lambda coefficient which means the market becomes less liquid. The models consistent with Miller (1977 who found that the bigger the gap of private information is, the less liquid the market will be. If both informed traders have the same information they will demand the same amount of risky asset and it turns out to be similar as in the Kyle (1985 model.

  10. Molecular dynamics study of naturally existing cavity couplings in proteins.

    Science.gov (United States)

    Barbany, Montserrat; Meyer, Tim; Hospital, Adam; Faustino, Ignacio; D'Abramo, Marco; Morata, Jordi; Orozco, Modesto; de la Cruz, Xavier

    2015-01-01

    Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. We have divided this problem into two parts. In the first part, we have explored the presence of cavity couplings in the natural dynamics of 75 proteins, using 20 ns molecular dynamics simulations. For each of these proteins, we have obtained two trajectories around their native state. After applying a stringent filtering procedure, we found significant cavity correlations in 60% of the proteins. We analyze and discuss the structure origins of these correlations, including neighbourhood, cavity distance, etc. In the second part of our study, we have used longer simulations (≥100 ns) from the MoDEL project, to obtain a broader view of cavity couplings, particularly about their dependence on time. Using moving window computations we explored the fluctuations of cavity couplings along time, finding that these couplings could fluctuate substantially during the trajectory, reaching in several cases correlations above 0.25/0.5. In summary, we describe the structural origin and the variations with time of cavity couplings. We complete our work with a brief discussion of the biological implications of these results.

  11. Information Equality for Individuals with Disabilities: Does It Exist?

    Science.gov (United States)

    Lewis, Jill

    2013-01-01

    Drawing on the author's experience as an information professional for individuals with disabilities, this article discusses the challenges faced by both library users and staff in obtaining and providing information to this community. It poses four questions: Where do individuals with disabilities fit into diversity studies? Do individuals with…

  12. Thriving in the Information Age: Why Marine Corps Commanders Must Maximize Their Existing Information Related Capabilities

    Science.gov (United States)

    2016-04-20

    skills within a business that make it more valuable or competitive, https://dictionary.cambridge.org/us/dictionary/ english / skill . Examples of knowledge...MAXIMIZE THEIR EXISTING INFORMATION-RELATED CAPABILITIES AUTHOR: MAJ JAMEL L. NEVILE, USMC AY 15-16 Mentor and Oral Defense... Oral Defense Committee Member: ______________________________________ Approved: ______________________________________ Date

  13. Benchmark Design and Installation: A synthesis of Existing Information.

    Science.gov (United States)

    1987-07-01

    guidelines that present such data. This report synthesizes these data and provides Districts with information on benchmark designs and installa- tions...adjustment of the North American Vertical Datum. ACSM Bulletin, December, p. 21-22. Jarman, J.T. (1955) Movement of triangulation marks set in permafrost

  14. Does Informal Employment Exist in the United States and Other Developed Countries?

    Science.gov (United States)

    Siqueira, Carlos E

    2016-08-01

    This editorial argues that informal employment does exist in developed countries and needs to be studied as such to complement the existing literature mostly published on informal work in developing countries. © The Author(s) 2016.

  15. Existing pavement input information for the mechanistic-empirical pavement design guide.

    Science.gov (United States)

    2009-02-01

    The objective of this study is to systematically evaluate the Iowa Department of Transportations (DOTs) existing Pavement Management Information System (PMIS) with respect to the input information required for Mechanistic-Empirical Pavement Des...

  16. Informational Way to Protein Alphabet: Entropic Classification of Amino Acids

    CERN Document Server

    Gorban, A N; Popova, T

    2007-01-01

    What are proteins made from, as the working parts of the living cells protein machines? To answer this question, we need a technology to disassemble proteins onto elementary func-tional details and to prepare lumped description of such details. This lumped description might have a multiple material realization (in amino acids). Our hypothesis is that informational approach to this problem is possible. We propose a way of hierarchical classification that makes the primary structure of protein maximally non-random. The first steps of the suggested research program are realized: the method and the analysis of optimal informational protein binary alphabet. The general method is used to answer several specific questions, for example: (i) Is there a syntactic difference between Globular and Membrane proteins? (ii) Are proteins random sequences of amino acids (a long discussion)? For these questions, the answers are as follows: (i) There exists significant syntactic difference between Globular and Membrane proteins,...

  17. Sal-Site: Integrating new and existing ambystomatid salamander research and informational resources

    Directory of Open Access Journals (Sweden)

    Weisrock David W

    2005-12-01

    Full Text Available Abstract Salamanders of the genus Ambystoma are a unique model organism system because they enable natural history and biomedical research in the laboratory or field. We developed Sal-Site to integrate new and existing ambystomatid salamander research resources in support of this model system. Sal-Site hosts six important resources: 1 Salamander Genome Project: an information-based web-site describing progress in genome resource development, 2 Ambystoma EST Database: a database of manually edited and analyzed contigs assembled from ESTs that were collected from A. tigrinum tigrinum and A. mexicanum, 3 Ambystoma Gene Collection: a database containing full-length protein-coding sequences, 4 Ambystoma Map and Marker Collection: an image and database resource that shows the location of mapped markers on linkage groups, provides information about markers, and provides integrating links to Ambystoma EST Database and Ambystoma Gene Collection databases, 5 Ambystoma Genetic Stock Center: a website and collection of databases that describe an NSF funded salamander rearing facility that generates and distributes biological materials to researchers and educators throughout the world, and 6 Ambystoma Research Coordination Network: a web-site detailing current research projects and activities involving an international group of researchers. Sal-Site is accessible at http://www.ambystoma.org.

  18. Combination of existing and alternative technologies to promote oilseeds and pulses proteins in food applications

    Directory of Open Access Journals (Sweden)

    Chéreau Denis

    2016-07-01

    Full Text Available The continuous world population growth induces a total protein demand increase based mainly on plant sources. To meet these global nutritional challenges, existing and innovative dry and wet fractionation processes will have to be combined to better valorise plant protein fraction from pulses and oilseeds. The worldwide success of soy protein isolates originate from the intrinsic qualities of soybean proteins but also from a continuous R&D effort since mid-twenty century. Therefore, the soy protein development model can be applied to protein isolates from diverse pulses and oilseeds meals as rapeseed which has already been recognised as novel food protein in Europe. To boost the delivery of plant proteins, agrofood-industries and academics must pool their respective expertise. Innovative and issue solving R&D projects have to be launched to better valorise pulses and oilseed proteins by (i creating oil extraction processes which preserve native proteins structure; (ii developing novel protein extraction processes from lab up to industrial pilot scale; (iii producing plant protein isolates having comparable foaming, emulsifying or gelling functionality than animal; and (iv generating hydrolysed proteins with high digestibility adapted to human nutrition. It is also essential to initiate research programs to innovate in wet and dry fractionations of plants or to design in vitro models to evaluate proteins digestibility and allergenicity. The increased awareness regarding plant protein valorisation resulted in the creation by agro-industries and academics of the open platform IMPROVE which propose a combination of competencies and equipment to boost market uptake of Plant Based Proteins.

  19. 77 FR 66862 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-11-07

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... Immigration and Customs Enforcement (ICE), will submit the following information collection request for review... Immigration and Customs Enforcement, Department of Homeland Security, and sent via electronic mail to...

  20. 76 FR 4930 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2011-01-27

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... Immigration and Customs Enforcement (ICE), will be submitting the following information collection request for... Immigration and Customs Enforcement, Department of Homeland Security, and sent via electronic mail to oira...

  1. 78 FR 14592 - Proposed Extension of Existing Information Collection; Emergency Mine Evacuation

    Science.gov (United States)

    2013-03-06

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF LABOR Mine Safety and Health Administration Proposed Extension of Existing Information Collection; Emergency Mine Evacuation AGENCY: Mine Safety and Health Administration, Labor. ACTION: Request for public comments. SUMMARY...

  2. 76 FR 3178 - Proposed Extension of Existing Information Collection; Rock Burst Control Plan, Metal and...

    Science.gov (United States)

    2011-01-19

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF LABOR Mine Safety and Health Administration Proposed Extension of Existing Information Collection; Rock Burst Control Plan, Metal and Nonmetal Mines AGENCY: Mine Safety and Health Administration, Labor. ACTION...

  3. 77 FR 65901 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-10-31

    ... Security (DHS), Student and Exchange Visitor Program (SEVP) office within 30 days of admission. (5) An... Information Collection for Review; File No. I- 515A, Notice to Student or Exchange Visitor; OMB Control No... currently approved information collection. (2) Title of the Form/Collection: Notice to Student or Exchange...

  4. 77 FR 50147 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-08-20

    ... appropriate automated, electronic, mechanical, or other technological collection techniques or other forms of information technology, e.g., permitting electronic submission of responses. Overview of This Information..., cashier's check, certified check or ] money order, he or she is issued a Receipt of Immigration Officer--U...

  5. 78 FR 28894 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2013-05-16

    ... initially complete and prepare an IMAGE application so that ICE can properly evaluate the company for... the following four points: (1) Evaluate whether the proposed collection of information is necessary for the proper performance of the functions of the agency, including whether the information will have...

  6. 78 FR 11216 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2013-02-15

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities... Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will submit the following information... Managment, U.S. Immigration and Customs Enforcement, 801 I Street NW., Stop 5800, Washington, DC 20536; (202...

  7. 75 FR 24720 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2010-05-05

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... Immigration and Customs Enforcement (USICE), has submitted the following information collection request for... Management Branch, U.S. Immigration and Customs Enforcement, 500 12th Street, SW., Room 3138, Washington, DC...

  8. 77 FR 38651 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-06-28

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities... Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will submit the following information..., Management and Program Analyst, U.S. Immigration and Customs Enforcement, 500 12th Street SW., Stop 5705...

  9. 77 FR 42322 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-07-18

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities... Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will submit the following information..., Chief, Records Management, U.S. Immigration and Customs Enforcement, 500 12th Street SW., Stop 5705...

  10. 77 FR 50147 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-08-20

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities... Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will submit the following information..., Chief, Records Management, U.S. Immigration and Customs Enforcement, 500 12th Street SW., Stop 5705...

  11. 75 FR 68372 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2010-11-05

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... Immigration and Customs Enforcement (USICE), will be submitting the following information collection request... Management Branch, U.S. Immigration and Customs Enforcement, 500 12th Street, SW., STOP 5705 Washington, DC...

  12. 76 FR 11513 - Agency Information Collection Activities; Existing Collection; Comments Requested

    Science.gov (United States)

    2011-03-02

    ... Requested ACTION: 60-Day Notice of Information Collection Under Review: Approval of a existing collection; The National Instant Criminal Background Check System (NICS) Point of Contact (POC) State Final...), Criminal Justice Information Services (CJIS) Division's NICS Section will be submitting the following...

  13. 76 FR 8373 - Agency Information Collection Activities: Revision of an Existing Information Collection; Comment...

    Science.gov (United States)

    2011-02-14

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities..., * * * * * The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will be... should be addressed to OMB Desk Officer, for United States Immigration and Customs Enforcement...

  14. 75 FR 53322 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2010-08-31

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities... Department of Homeland Security, U.S. Immigration and Customs Enforcement (USICE), will submit the following... United States Immigration and Customs Enforcement, Department of Homeland Security, and sent via...

  15. The Proteins API: accessing key integrated protein and genome information.

    Science.gov (United States)

    Nightingale, Andrew; Antunes, Ricardo; Alpi, Emanuele; Bursteinas, Borisas; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd; Martin, Maria

    2017-07-03

    The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to 'talk' to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. The Proteins API: accessing key integrated protein and genome information

    Science.gov (United States)

    Antunes, Ricardo; Alpi, Emanuele; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd

    2017-01-01

    Abstract The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to ‘talk’ to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). PMID:28383659

  17. Recording information on protein complexes in an information management system.

    Science.gov (United States)

    Savitsky, Marc; Diprose, Jonathan M; Morris, Chris; Griffiths, Susanne L; Daniel, Edward; Lin, Bill; Daenke, Susan; Bishop, Benjamin; Siebold, Christian; Wilson, Keith S; Blake, Richard; Stuart, David I; Esnouf, Robert M

    2011-08-01

    The Protein Information Management System (PiMS) is a laboratory information management system (LIMS) designed for use with the production of proteins in a research environment. The software is distributed under the CCP4 licence, and so is available free of charge to academic laboratories. Like most LIMS, the underlying PiMS data model originally had no support for protein-protein complexes. To support the SPINE2-Complexes project the developers have extended PiMS to meet these requirements. The modifications to PiMS, described here, include data model changes, additional protocols, some user interface changes and functionality to detect when an experiment may have formed a complex. Example data are shown for the production of a crystal of a protein complex. Integration with SPINE2-Complexes Target Tracker application is also described. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. 75 FR 51095 - Agency Information Collection Activities: Form N-336; Extension of an Existing Information...

    Science.gov (United States)

    2010-08-18

    ... SECURITY U.S. Citizenship and Immigration Services Agency Information Collection Activities: Form N-336... Collection under Review; Form N- 336, Request for Hearing on a Decision in Naturalization Proceedings Under Section 336; OMB Control No. 1615-0050. The Department of Homeland Security, U.S. Citizenship and...

  19. 75 FR 78264 - Agency Information Collection Activities: Form N-336, Revision to an Existing Information...

    Science.gov (United States)

    2010-12-15

    ... SECURITY U.S. Citizenship and Immigration Services Agency Information Collection Activities: Form N-336... collection under review: Form N- 336, Request for Hearing on a Decision in Naturalization Proceedings Under Section 336; OMB Control No. 1615-0050. On August 18, 2010, USCIS published a 60-day notice in the Federal...

  20. 77 FR 50145 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-08-20

    ...: Primary: Individuals or Households. When an academic student (F-1), vocational student (M-1), exchange...) Evaluate whether the proposed collection of information is necessary for the proper performance of the... under section 101(a)(15) of the Immigration and Nationality Act (Act), he or she is required to have...

  1. 76 FR 4931 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2011-01-27

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities...-0019. The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will be... Officer, for United States Immigration and Customs Enforcement, Department of Homeland Security, and sent...

  2. 75 FR 2881 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2010-01-19

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities...-0026. The Department of Homeland Security, U.S. Immigration and Customs Enforcement (USICE), has... collection: Form G-79A, U.S. Immigration and Customs Enforcement. (4) Affected public who will be asked or...

  3. 75 FR 24721 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2010-05-05

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... The Department of Homeland Security, U.S. Immigration and Customs Enforcement (USICE), will be... collection: U.S. Immigration and Customs Enforcement. (4) Affected public who will be asked or required to...

  4. 78 FR 32429 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2013-05-30

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... The Department of Homeland Security, U.S. Immigration and Customs Enforcement (USICE), will submit the... Desk Officer for U.S. Immigration and Customs Enforcement, Department of Homeland Security, and sent...

  5. 77 FR 15115 - Agency Information Collection Activities: Extension, without Change, of an Existing Information...

    Science.gov (United States)

    2012-03-14

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... 1653- 0019. The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), is.... Comments should be addressed to OMB Desk Officer, for United States Immigration and Customs Enforcement...

  6. 76 FR 20996 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2011-04-14

    ... SECURITY U.S. Immigration and Customs Enforcement Agency Information Collection Activities: Extension of an... Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will be submitting the... Officer/OAA/Records Branch, U.S. Immigration and Customs Enforcement, 500 12th Street, SW., STOP 5705...

  7. 77 FR 50146 - Agency Information Collection Activities: Extension, With Change, of an Existing Information...

    Science.gov (United States)

    2012-08-20

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities... Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will submit the following... Mattison, Chief, Records Management, U.S. Immigration and Customs Enforcement, 500 12th Street SW., Stop...

  8. 76 FR 20998 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2011-04-14

    ... SECURITY U. S. Immigration and Customs Enforcement Agency Information Collection Activities: Extension of... Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will be submitting the following.../Records Branch, U.S. Immigration and Customs Enforcement, 500 12th Street, SW., STOP 5705 Washington, DC...

  9. 75 FR 69095 - Agency Information Collection Activities: Revision of an Existing Information Collection; Comment...

    Science.gov (United States)

    2010-11-10

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will be... collection: Forms I-17 and I-20; U.S. Immigration and Customs Enforcement. (4) Affected public who will be...

  10. 76 FR 27081 - Agency Information Collection Activities: Extension of an existing information Collection...

    Science.gov (United States)

    2011-05-10

    ... SECURITY U. S. Immigration and Customs Enforcement Agency Information Collection Activities: Extension of.... The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will be... Budget. Comments should be addressed to OMB Desk Officer, for U.S. Immigration and Customs Enforcement...

  11. 77 FR 65901 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-10-31

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will submit the... addressed to OMB Desk Officer, for United States Immigration and Customs Enforcement, Department of Homeland...

  12. 77 FR 38651 - Agency Information Collection Activities: Extension, With Change, of an Existing Information...

    Science.gov (United States)

    2012-06-28

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities... Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will submit the following... Mattison, Chief, Records Management, U.S. Immigration and Customs Enforcement, 500 12th Street SW., Stop...

  13. 78 FR 45550 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2013-07-29

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... 1653-0048. The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will... addressed to the OMB Desk Officer for U.S. Immigration and Customs Enforcement, Department of Homeland...

  14. 76 FR 17936 - Agency Information Collection Activities: Revision of an Existing Information Collection; Comment...

    Science.gov (United States)

    2011-03-31

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities... Control No. 1653-0040. The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE... Office of the Chief Financial Officer/OAA/Records Branch, U.S. Immigration and Customs Enforcement, 500...

  15. 77 FR 50148 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-08-20

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities... Control No. 1653-0026. The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE.... Comments should be addressed to OMB Desk Officer, for United States Immigration and Customs Enforcement...

  16. 75 FR 68371 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2010-11-05

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities...-0019. The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will be... Chief Financial Officer/OAM/Records Branch, U.S. Immigration and Customs Enforcement, 500 12th Street...

  17. 76 FR 79204 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2011-12-21

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... ] The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will submit the... Security (DHS), John Ramsay, Program Manager, U.S. Immigration and Customs Enforcement, 500 12th Street SW...

  18. 77 FR 33478 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-06-06

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... 1653- 0019). The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), is... should be addressed to OMB Desk Officer, for United States Immigration and Customs Enforcement...

  19. 78 FR 23577 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2013-04-19

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities... Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will submit the following... Officer, for United States Immigration and Customs Enforcement, Department of Homeland Security, and sent...

  20. 76 FR 11255 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2011-03-01

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities...-0026. The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will be... Financial Officer/OAA/Records Branch, U.S. Immigration and Customs Enforcement, 500 12th Street, SW., STOP...

  1. 78 FR 18620 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2013-03-27

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... The Department of Homeland Security, U.S. Immigration and Customs Enforcement (USICE), will submit the...), Scott Elmore, Forms Manager, U.S. Immigration and Customs Enforcement, 801 I Street NW., Mailstop 5800...

  2. 77 FR 65900 - Agency Information Collection Activities: Extension, With Change, of an Existing Information...

    Science.gov (United States)

    2012-10-31

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... 1653- 0043. The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will... should be addressed to OMB Desk Officer, for United States Immigration and Customs Enforcement...

  3. 77 FR 49823 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-08-17

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities.... Immigration and Customs Enforcement, 500 12th Street SW., Stop 5705, Washington, DC 20536; (202) 732-4356... Management, U.S. Immigration and Customs Enforcement, 500 12th Street SW., Stop 5705, Washington, DC 20536...

  4. 77 FR 47656 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-08-09

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities... Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will submit the following... Mattison, Chief, Records Management, U.S. Immigration and Customs Enforcement, 500 12th Street SW., Stop...

  5. 75 FR 16158 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2010-03-31

    ... SECURITY United States Immigration and Customs Enforcement Agency Information Collection Activities...-0026. The Department of Homeland Security, U.S. Immigration and Customs Enforcement (USICE), has... should be addressed to OMB Desk Officer, for U. S. Immigration and Customs Enforcement, Department of...

  6. Existence of an information unit as a postulate of quantum theory.

    Science.gov (United States)

    Masanes, Lluís; Müller, Markus P; Augusiak, Remigiusz; Pérez-García, David

    2013-10-08

    Does information play a significant role in the foundations of physics? Information is the abstraction that allows us to refer to the states of systems when we choose to ignore the systems themselves. This is only possible in very particular frameworks, like in classical or quantum theory, or more generally, whenever there exists an information unit such that the state of any system can be reversibly encoded in a sufficient number of such units. In this work, we show how the abstract formalism of quantum theory can be deduced solely from the existence of an information unit with suitable properties, together with two further natural assumptions: the continuity and reversibility of dynamics, and the possibility of characterizing the state of a composite system by local measurements. This constitutes a set of postulates for quantum theory with a simple and direct physical meaning, like the ones of special relativity or thermodynamics, and it articulates a strong connection between physics and information.

  7. Recording information on protein complexes in an information management system

    Science.gov (United States)

    Savitsky, Marc; Diprose, Jonathan M.; Morris, Chris; Griffiths, Susanne L.; Daniel, Edward; Lin, Bill; Daenke, Susan; Bishop, Benjamin; Siebold, Christian; Wilson, Keith S.; Blake, Richard; Stuart, David I.; Esnouf, Robert M.

    2011-01-01

    The Protein Information Management System (PiMS) is a laboratory information management system (LIMS) designed for use with the production of proteins in a research environment. The software is distributed under the CCP4 licence, and so is available free of charge to academic laboratories. Like most LIMS, the underlying PiMS data model originally had no support for protein–protein complexes. To support the SPINE2-Complexes project the developers have extended PiMS to meet these requirements. The modifications to PiMS, described here, include data model changes, additional protocols, some user interface changes and functionality to detect when an experiment may have formed a complex. Example data are shown for the production of a crystal of a protein complex. Integration with SPINE2-Complexes Target Tracker application is also described. PMID:21605682

  8. The digital pen and paper technology: implementation and use in an existing clinical information system.

    Science.gov (United States)

    Despont-Gros, Christelle; Bœuf, Christophe; Geissbuhler, Antoine; Lovis, Christian

    2005-01-01

    Evaluation of the technical feasibility of tight integration of the digital pen and paper technology in an existing computerized patient record.Technology: The digital pen is a normal pen able to record all actions of the user and to analyze a micro pattern printed on the paper. The digital paper is a normal paper printed with an almost invisible micro pattern of small dots encoding information such as position and identifiers. We report our experience in the implementation and the use of this technology in an existing large clinical information system for acquiring clinical information. It is possible to print uniquely identified forms using the digital paper technology. These forms can be pre-filled with clinical readable information about the patient. When care providers complete these forms using the digital pen, it is possible to acquire the data in a structured computerized patient record. The technology is easy to integrate in a component-based architecture based on Web Services. The digital pen and paper is a cost-effective technology that can be integrated in an existing clinical information system and allows fast and easy bedside clinical information acquisition without the need for an expensive infrastructure based on traditional portable devices or wireless devices.

  9. 75 FR 79030 - Proposed Extension of Existing Information Collection; Training Plans and Records of Training

    Science.gov (United States)

    2010-12-17

    ... teach; the location where training will be given for each course; a description of the teaching methods... Safety and Health Administration Proposed Extension of Existing Information Collection; Training Plans and Records of Training AGENCY: Mine Safety and Health Administration, Labor. ACTION: Notice of...

  10. 77 FR 16865 - Proposed Extension of Existing Information Collection; Occupational Noise Exposure

    Science.gov (United States)

    2012-03-22

    ... Noise Exposure AGENCY: Mine Safety and Health Administration, Labor. ACTION: Request for public comments... extension of an existing information collection, OMB Control Number 1219-0120, Occupational Noise Exposure... originally titled ``Noise exposure assessment; audiometric testing, evaluation, and records and training in...

  11. 77 FR 4574 - Agency Information Collection Activities: USCIS Case Status Online; Extension of an Existing...

    Science.gov (United States)

    2012-01-30

    ... Status Online; Extension of an Existing Information Collection; Comment Request ACTION: 60-Day Notice of... the USCIS Case Status Online. Written comments and suggestions regarding items contained in this... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HOMELAND...

  12. 77 FR 64360 - Proposed Extension of Existing Information Collection; Mine Rescue Teams for Underground Metal...

    Science.gov (United States)

    2012-10-19

    ... Safety and Health Administration Proposed Extension of Existing Information Collection; Mine Rescue Teams...) to publish regulations which provide that mine rescue teams be available for rescue and recovery work... arrangements for such teams are to be borne by the operator of each such mine. II. Desired Focus of Comments...

  13. 77 FR 17098 - Proposed Extension of Existing Information Collection; Independent Contractor Registration and...

    Science.gov (United States)

    2012-03-23

    ... concerning the proposed extension of an existing information collection, OMB Control Number 1219-00040... Control Number 1219- 0040'' and sent to both the Office of Management and Budget (OMB) and MSHA. Comments..., including activities such as clearing land, excavating ore, processing minerals, maintaining, or repairing...

  14. Analyzing existing conventional soil information sources to be incorporated in thematic Spatial Data Infrastructures

    Science.gov (United States)

    Pascual-Aguilar, J. A.; Rubio, J. L.; Domínguez, J.; Andreu, V.

    2012-04-01

    New information technologies give the possibility of widespread dissemination of spatial information to different geographical scales from continental to local by means of Spatial Data Infrastructures. Also administrative awareness on the need for open access information services has allowed the citizens access to this spatial information through development of legal documents, such as the INSPIRE Directive of the European Union, adapted by national laws as in the case of Spain. The translation of the general criteria of generic Spatial Data Infrastructures (SDI) to thematic ones is a crucial point for the progress of these instruments as large tool for the dissemination of information. In such case, it must be added to the intrinsic criteria of digital information, such as the harmonization information and the disclosure of metadata, the own environmental information characteristics and the techniques employed in obtaining it. In the case of inventories and mapping of soils, existing information obtained by traditional means, prior to the digital technologies, is considered to be a source of valid information, as well as unique, for the development of thematic SDI. In this work, an evaluation of existing and accessible information that constitutes the basis for building a thematic SDI of soils in Spain is undertaken. This information framework has common features to other European Union states. From a set of more than 1,500 publications corresponding to the national territory of Spain, the study was carried out in those documents (94) found for five autonomous regions of northern Iberian Peninsula (Asturias, Cantabria, Basque Country, Navarra and La Rioja). The analysis was performed taking into account the criteria of soil mapping and inventories. The results obtained show a wide variation in almost all the criteria: geographic representation (projections, scales) and geo-referencing the location of the profiles, map location of profiles integrated with edaphic

  15. Information theory in systems biology. Part II: protein-protein interaction and signaling networks.

    Science.gov (United States)

    Mousavian, Zaynab; Díaz, José; Masoudi-Nejad, Ali

    2016-03-01

    By the development of information theory in 1948 by Claude Shannon to address the problems in the field of data storage and data communication over (noisy) communication channel, it has been successfully applied in many other research areas such as bioinformatics and systems biology. In this manuscript, we attempt to review some of the existing literatures in systems biology, which are using the information theory measures in their calculations. As we have reviewed most of the existing information-theoretic methods in gene regulatory and metabolic networks in the first part of the review, so in the second part of our study, the application of information theory in other types of biological networks including protein-protein interaction and signaling networks will be surveyed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Using Existing Response Repertoires to Make Sense of Information System Implementation

    DEFF Research Database (Denmark)

    Jensen, Tina Blegind; Kjærgaard, Annemette Leonhardt

    2010-01-01

    The implementation of information systems (IS) in organizations often triggers new situations in which users experience a disruption of existing work patterns and routines. Sensemaking becomes central in making users’ meanings explicit, serving as a foundation for further actions and interactions...... with the new technology. The purpose of this paper is to study how users make sense of new technologies by building on existing response repertoires. Empirically, we present findings from a study of an Electronic Patient Record (EPR) system implementation in two Danish hospital wards. Our findings illustrate...... to existing literature by providing a detailed account of how users’ early sensemaking of a technology influences their subsequent actions and reactions towards it. Our findings support managers in understanding users’ perceptions of a new technology, helping them in planning and executing the implementation...

  17. Military Leadership in the Context of Challenges and Threats Existing in Information Environment

    Directory of Open Access Journals (Sweden)

    Tomasz Kacała

    2015-06-01

    Full Text Available The aim of the paper is to present the role of a military leader in engaging the challenges and threats existing in the I nformation Environment (IE. Military leadership is crucial for the functioning of a particular form of hierarchical institution, namely the armed forces, in their external surrounding called O perational Environment (OE. A specific type of O E is I nformation Environment (IE characterized by the three dimensions: physical, informational and cognitive. Moreover, its characteristics include the occurrence of a number of challenges and threats. The most important challenges include: overabundance of information, unstructured information, problematic value of information and low information-related competences of its users. I n turn, the most important of the threats identified in the I E are disinformation and propaganda. The role of an effective leader is to prevent, and if it is impossible, to alleviate the consequences of the challenges and threats that may disrupt or even prevent the achievement of the objectives set by an organisation.

  18. Patient Information about Gout: An International Review of Existing Educational Resources.

    Science.gov (United States)

    Johnston, Megan E; Treharne, Gareth J; Chapman, Peter T; Stamp, Lisa K

    2015-06-01

    Inadequate patient information about gout may contribute to poor disease outcomes. We reviewed existing educational resources for gout to identify strengths and weaknesses and compare resources cross-nationally. Content, readability, and dietary recommendations were reviewed using a sample of 30 resources (print and Web-based) from 6 countries. More than half of the resources were written at a highly complex level. Some content areas were lacking coverage, including comorbidity risks, uric acid target levels, and continuing allopurinol during acute attacks. Our findings suggest significant room for improvement in gout patient educational resources, particularly regarding self-management.

  19. A Review of Avian Monitoring and Mitigation Information at Existing Utility-Scale Solar Facilities

    Energy Technology Data Exchange (ETDEWEB)

    Walston, Leroy J. [Argonne National Lab. (ANL), Argonne, IL (United States); Rollins, Katherine E. [Argonne National Lab. (ANL), Argonne, IL (United States); Smith, Karen P. [Argonne National Lab. (ANL), Argonne, IL (United States); LaGory, Kirk E. [Argonne National Lab. (ANL), Argonne, IL (United States); Sinclair, Karin [National Renewable Energy Lab. (NREL), Golden, CO (United States); Turchi, Craig [National Renewable Energy Lab. (NREL), Golden, CO (United States); Wendelin, Tim [National Renewable Energy Lab. (NREL), Golden, CO (United States); Souder, Heidi [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2015-01-01

    There are two basic types of solar energy technology: photovoltaic and concentrating solar power. As the number of utility-scale solar energy facilities using these technologies is expected to increase in the United States, so are the potential impacts on wildlife and their habitats. Recent attention is on the risk of fatality to birds. Understanding the current rates of avian mortality and existing monitoring requirements is an important first step in developing science-based mitigation and minimization protocols. The resulting information also allows a comparison of the avian mortality rates of utility-scale solar energy facilities with those from other technologies and sources, as well as the identification of data gaps and research needs. This report will present and discuss the current state of knowledge regarding avian issues at utility-scale solar energy facilities.

  20. Kullback-Leibler information in resolving natural resource conflicts when definitive data exist

    Science.gov (United States)

    Anderson, D.R.; Burnham, K.P.; White, Gary C.

    2001-01-01

    Conflicts often arise in the management of natural resources. Often they result from differing perceptions, varying interpretations of the law, and self-interests among stakeholder groups (for example, the values and perceptions about spotted owls and forest management differ markedly among environmental groups, government regulatory agencies, and timber industries). We extend the conceptual approach to conflict resolution of Anderson et al. (1999) by using information-theoretic methods to provide quantitative evidence for differing stakeholder positions. Importantly, we assume that relevant empirical data exist that are central to the potential resolution of the conflict. We present a hypothetical example involving an experiment to assess potential effects of a chemical on monthly survival probabilities of the hen clam (Spisula solidissima). The conflict centers on 3 stakeholder positions: 1) no effect, 2) an acute effect, and 3) an acute and chronic effect of the chemical treatment. Such data were given to 18 analytical teams to make independent analyses and provide the relative evidence for each of 3 stakeholder positions in the conflict. The empirical evidence strongly supports only one of the 3 positions in the conflict: the application of the chemical causes acute and chronic effects on monthly survival, following treatment. Formal inference from all the stakeholder positions is provided for the 2 key parameters underlying the hen clam controversy. The estimates of these parameters were essentially unbiased (the relative bias for the control and treatment group's survival probability was -0.857% and 1.400%, respectively) and precise (coefficients of variation were 0.576% and 2.761%, respectively). The advantages of making formal inference from all the models, rather than drawing conclusions from only the estimated best model, is illustrated. Finally, we contrast information-theoretic and Bayesian approaches in terms of how positions in the controversy enter

  1. Protein, peptide, amino acid composition, and potential functional properties of existing and novel dietary protein sources for monogastrics

    NARCIS (Netherlands)

    Kar, S.K.; Jansman, A.J.M.; Boeren, S.; Kruijt, L.; Smits, M.A.

    2016-01-01

    Replacement of current protein resources for novel or alternative sources may be one of the solutions to abolish the expected scarcity of dietary protein for animal feeds. However, little is known about the nutritional, protein composition, and potential functional value of such novel or

  2. Informing the Human Plasma Protein Binding of ...

    Science.gov (United States)

    The free fraction of a xenobiotic in plasma (Fub) is an important determinant of chemical adsorption, distribution, metabolism, elimination, and toxicity, yet experimental plasma protein binding data is scarce for environmentally relevant chemicals. The presented work explores the merit of utilizing available pharmaceutical data to predict Fub for environmentally relevant chemicals via machine learning techniques. Quantitative structure-activity relationship (QSAR) models were constructed with k nearest neighbors (kNN), support vector machines (SVM), and random forest (RF) machine learning algorithms from a training set of 1045 pharmaceuticals. The models were then evaluated with independent test sets of pharmaceuticals (200 compounds) and environmentally relevant ToxCast chemicals (406 total, in two groups of 238 and 168 compounds). The selection of a minimal feature set of 10-15 2D molecular descriptors allowed for both informative feature interpretation and practical applicability domain assessment via a bounded box of descriptor ranges and principal component analysis. The diverse pharmaceutical and environmental chemical sets exhibit similarities in terms of chemical space (99-82% overlap), as well as comparable bias and variance in constructed learning curves. All the models exhibit significant predictability with mean absolute errors (MAE) in the range of 0.10-0.18 Fub. The models performed best for highly bound chemicals (MAE 0.07-0.12), neutrals (MAE 0

  3. Molecular eyes: proteins that transform light into biological information

    NARCIS (Netherlands)

    Kennis, J.T.M.; Mathes, T.

    2013-01-01

    Most biological photoreceptors are protein/cofactor complexes that induce a physiological reaction upon absorption of a photon. Therefore, these proteins represent signal converters that translate light into biological information. Researchers use this property to stimulate and study various

  4. 30 CFR 778.9 - Certifying and updating existing permit application information.

    Science.gov (United States)

    2010-07-01

    ... information already in AVS is accurate and complete may certify to us by swearing or affirming, under oath and... corrections and swear or affirm, under oath and in writing, that the information you submit is accurate and... swear or affirm, under oath and in writing, that all information you provide in an application is...

  5. 75 FR 79034 - Proposed Extension of Existing Information Collection; Escape and Evacuation Plans (Pertains to...

    Science.gov (United States)

    2010-12-17

    ... information is required with each escape and evacuation plan submission: (1) Mine maps or diagrams showing...) A statement of the availability of emergency communication and transportation facilities, emergency...

  6. 76 FR 31989 - Agency Information Collection Activities: Existing Collection; Comment Requested; Extension and...

    Science.gov (United States)

    2011-06-02

    ...; Extension and Revision of Existing Collection; Annual Parole Survey, Annual Probation Survey, and Annual... Corrections or state probation and parole authority. Others: The Federal Bureau of Prisons, city and county... probation; (k) Whether the probation authority supervised adult probationers who were also on parole...

  7. Residential dynamics: the co-existence of formal and informal systems in Khartoum, Sudan

    CSIR Research Space (South Africa)

    Osman, A

    2010-05-01

    Full Text Available blanket solutions. Many agents act on an environment at any given time and decision makers need to engage with that complexity. Enterprises emerging from informal settlements or through informal processes may be better suited to low-income groups, thus...

  8. Clinical trials information in drug development and regulation : existing systems and standards

    NARCIS (Netherlands)

    Valkenhoef, Gert van; Tervonen, Tommi; Brock, Bert de; Hillege, Hans

    2012-01-01

    Clinical trials provide pivotal evidence on drug efficacy and safety. The evidence, information from clinical trials, is currently used by regulatory decision makers in marketing authorization decisions, but only in an implicit manner. For clinical trials information to be used in a transparent and

  9. 75 FR 80072 - Proposed Extension of Existing Information Collection; Radiation Sampling and Exposure Records

    Science.gov (United States)

    2010-12-21

    ... 21st floor. FOR FURTHER INFORMATION CONTACT: Mario Distasio, Chief of the Economic Analysis Division... readings of 0.1 WL to 0.3 WL and every 3 months in non-uranium underground mines where the readings are 0.1..., mechanical, or other technological collection techniques or other forms of information technology, e.g...

  10. 75 FR 79033 - Proposed Extension of Existing Information Collection; Radiation Sampling and Exposure Records...

    Science.gov (United States)

    2010-12-17

    ... 21st floor. FOR FURTHER INFORMATION CONTACT: Mario Distasio, Chief of the Economic Analysis Division... readings of 0.1 WL to 0.3 WL and every 3 months in non-uranium underground mines where the readings are 0.1..., mechanical, or other technological collection techniques or other forms of information technology, e.g...

  11. RNA editing sites exist in protein-coding genes in the chloroplast genome of Cycas taitungensis.

    Science.gov (United States)

    Chen, Haiyan; Deng, Likun; Jiang, Yuan; Lu, Ping; Yu, Jianing

    2011-12-01

    RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C-to-U changes, especially in seed plants. Using prediction and experimental determination, we investigated RNA editing in 40 protein-coding genes from the chloroplast genome of Cycas taitungensis. A total of 85 editing sites were identified in 25 transcripts. Comparison analysis of the published editotypes of these 25 transcripts in eight species showed that RNA editing events gradually disappear during plant evolution. The editing in the first and third codon position disappeared quicker than that in the second codon position. ndh genes have the highest editing frequency while serine and proline codons were more frequently edited than the codons of other amino acids. These results imply that retained RNA editing sites have imbalanced distribution in genes and most of them may function by changing protein structure or interaction. Mitochondrion protein-coding genes have three times the editing sites compared with chloroplast genes of Cycas, most likely due to slower evolution speed. © 2011 Institute of Botany, Chinese Academy of Sciences.

  12. 75 FR 18833 - Agency Information Collection Activities: Existing Collection; Emergency Extension

    Science.gov (United States)

    2010-04-13

    ... confidential. EEO-4 data are used by the EEOC to investigate charges of discrimination against State and local governments and to provide information on the employment status of minorities and women. The data are shared...

  13. 75 FR 18832 - Agency Information Collection Activities: Existing Collection; Emergency Extension

    Science.gov (United States)

    2010-04-13

    ... confidential. EEO-1 data is used by EEOC to investigate charges of employment discrimination against employers in private industry and to provide information about the employment status of minorities and women...

  14. 75 FR 63179 - Agency Information Collection Activities: Existing Collection; Emergency Extension

    Science.gov (United States)

    2010-10-14

    ... confidential. EEO-1 data is used by EEOC to investigate charges of employment discrimination against employers in private industry and to provide information about the employment status of minorities and women...

  15. 75 FR 40829 - Agency Information Collection Activities: Existing Collection; Emergency Extension

    Science.gov (United States)

    2010-07-14

    ... discrimination against State and local governments and to provide information on the employment status of minorities and women. The data are shared with several other Federal agencies. Pursuant to section 709(d) of...

  16. 75 FR 40830 - Agency Information Collection Activities: Existing Collection; Emergency Extension

    Science.gov (United States)

    2010-07-14

    ... discrimination against employers in private industry and to provide information about the employment status of minorities and women. The data is shared with the Office of Federal Contract Compliance Programs (OFCCP), U.S...

  17. 76 FR 3629 - Agency Information Collection Activities: Existing Collection; Emergency Extension

    Science.gov (United States)

    2011-01-20

    ... confidential. EEO-1 data is used by EEOC to investigate charges of employment discrimination against employers in private industry and to provide information about the employment status of minorities and women...

  18. 75 FR 63180 - Agency Information Collection Activities: Existing Collection; Emergency Extension

    Science.gov (United States)

    2010-10-14

    ... charges of discrimination against State and local governments and to provide information on the employment status of minorities and women. The data are shared with several other federal agencies. Pursuant to...

  19. 77 FR 25206 - Proposed Extension of Existing Information Collection; Underground Retorts

    Science.gov (United States)

    2012-04-27

    ... geological area in which the mine is located). At present, this applies only to underground oil shale mines... enhance the quality, utility, and clarity of the information to be collected; and Address the use of...

  20. 78 FR 55122 - Submission for Review: Revision of an Existing Information Collection, USAJOBS®

    Science.gov (United States)

    2013-09-09

    ... Reduction Act of 1995, (Pub. L. 104-13, 44 U.S.C. chapter 35) as amended by the Clinger-Cohen Act (Pub. L... technological collection techniques or other forms of information technology, e.g., permitting electronic...

  1. 76 FR 36581 - Submission for Review: Revision of an Existing Information Collection, USAJOBS

    Science.gov (United States)

    2011-06-22

    ... Reduction Act of 1995, (Pub. L. 104-13, 44 U.S.C. chapter 35) as amended by the Clinger-Cohen Act (Pub. L... technological collection techniques or other forms of information technology, e.g., permitting electronic...

  2. 75 FR 69141 - Submission for Review: Revision of an Existing Information Collection, USAJOBS

    Science.gov (United States)

    2010-11-10

    ... Reduction Act of 1995, (Pub. L. 104-13, 44 U.S.C. chapter 35) as amended by the Clinger-Cohen Act (Pub. L... technological collection techniques or other forms of information technology, e.g., permitting electronic...

  3. Overview Of Coupling Of Data, Models And Information Through The Web Using Existing Standards

    NARCIS (Netherlands)

    de Boer, G.J.; Baart, F.; Jagers, B; Becker, B.P.J.; Piasecki, M.

    2014-01-01

    Assessment of environmental status and integral safety requires combination of information from many sources, coming from either databases or increasingly via live model (scenario) simulations. Many of these models require input from one another, sometimes unidirectional, but more and more

  4. Assessment of Existing Information for Atlantic Coastal Fish Habitat Partnership (ACFHP)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The ACFHP database consist of three primary data tables, joined within SQL Server, a relational DBMS: 1. The Bibliographic table provides information on over 500...

  5. Social Loafing in the Refugee Crisis: Information about Existing Initiatives Decreases Willingness to Help

    Directory of Open Access Journals (Sweden)

    Simon Schindler

    2017-05-01

    Full Text Available In light of the European refugee situation, we investigate how information about others’ support influences individuals’ willingness to help. When individuals see information about other people supporting refugees, they may either be influenced by a descriptive norm, and act accordingly. Alternatively, they may perceive that others are already doing the job, and thus engage in social loafing. In an experiment (N = 132, we tested these competing predictions. Specifically, participants were exposed to a map of Germany that either indicated many or few helping initiatives across the country. In a control group, no map was shown. Subsequently, participants were asked about their willingness to help. While there was no effect between the two map conditions, results revealed that participants reported lower willingness to help in both map conditions, compared with the control group. Thus, providing information about helping projects results in social loafing, jeopardizing widespread communication strategies to increase solidarity.

  6. 75 FR 79029 - Proposed Extension of Existing Information Collection; Request for MSHA Individual Identification...

    Science.gov (United States)

    2010-12-17

    ... or safety standards for the protection of life and prevention of injuries in coal or other mines... FOR FURTHER INFORMATION CONTACT section of this notice, or viewed on the Internet by selecting ``Rules.... Agency: Mine Safety and Health Administration. OMB Number: 1219-0143. Frequency: On Occasion. Affected...

  7. 77 FR 58172 - Proposed Renewal of Existing Information Collection; Records of Preshift and Onshift Inspections...

    Science.gov (United States)

    2012-09-19

    ... gases can be expected to infiltrate the work environment at any time. The working environment is... environment for the slope and shaft sinking employees. The record is maintained at the mine site for the... technological collection techniques or other forms of information technology (e.g., permitting electronic...

  8. 76 FR 9374 - Proposed Extension of Existing Information Collection; Examinations and Testing of Electrical...

    Science.gov (United States)

    2011-02-17

    ... who use them in making decisions during accident investigations to establish root causes and to... methods: (1) Electronic mail: [email protected] . (2) Facsimile: 202-693-9441. (3) Regular Mail... collection and the collection of this information does not employ statistical methods. ] Type of Review...

  9. 77 FR 49828 - Agency Information Collection Activities; Existing Collection; Comments Requested: Extension of a...

    Science.gov (United States)

    2012-08-17

    ... movements of adult offenders through state correctional systems, as well as to examine long term trends in... information is required contact: Jerri Murray, Department Clearance Officer, United States Department of... NE., Washington, DC 20530. Jerri Murray, Department Clearance Officer, PRA, U.S. Department of...

  10. 75 FR 12566 - Agency Information Collection Activities: Existing Collection; Comments Requested

    Science.gov (United States)

    2010-03-16

    ... integral part of the justice system, operating at the front end (that is, following arrest or referral) as well as the back end (discharging inmates and holding those sentenced to jail). Their broad functions..., mechanical, or other technological collection techniques or other forms of information technology, e.g...

  11. 78 FR 16534 - Agency Information Collection Activities; Existing Collection; Comments Requested;Extension of a...

    Science.gov (United States)

    2013-03-15

    ... justice system, operating at the front end (that is, following arrest or referral) as well as the back end..., mechanical, or other technological collection techniques or other forms of information technology, e.g... appearances and bringing them back to detention, discharging inmates at the behest of the court or other...

  12. 78 FR 959 - Agency Information Collection Activities: Existing Collection; Comments Requested: Extension of a...

    Science.gov (United States)

    2013-01-07

    ... justice system, operating at the front end (that is, following arrest or referral) as well as the back end..., mechanical, or other technological collection techniques or other forms of information technology, e.g... appearances and bringing them back to detention, discharging inmates at the behest of the court or other...

  13. 77 FR 74876 - Agency Information Collection Activities; Existing Collection, Comments Requested; Federal...

    Science.gov (United States)

    2012-12-18

    ... techniques or other forms of information technology, e.g., permitting electronic submission of responses... reading the directions for the Federal Bureau of Investigation National Instant Criminal Background Check... two minutes to read which would be 3,000 x 2 minutes/60 = 100 hours. The entire process of reading the...

  14. 77 FR 63340 - Agency Information Collection Activities; Existing Collection, Comments Requested: Federal...

    Science.gov (United States)

    2012-10-16

    ... collection techniques or other forms of information technology, e.g., permitting electronic submission of... to read which would be 3,000 x 2 minutes/60 = 100 hours. The entire process of reading the letter and... and reading the accompanying letter would be 3,000 x 15/60 = 750 hours. (5) An estimate of the total...

  15. 77 FR 62534 - Agency Information Collection Activities; Existing Collection, Comments Requested: Federal...

    Science.gov (United States)

    2012-10-15

    ... collection techniques or other forms of information technology, e.g., permitting electronic submission of... to read which would be 3,000 x 2 minutes/60 = 100 hours. The entire process of reading the letter and... and reading the accompanying letter would be 3,000 x 15/60 = 750 hours. (5) An estimate of the total...

  16. 75 FR 1410 - Agency Information Collection Activities: Existing Collection; Comments Requested

    Science.gov (United States)

    2010-01-11

    ...; Medical, mental health, and substance abuse treatment services issues in jails; Suicide prevention, domestic violence counseling, sex offender treatment, educational programs, and inmate work assignments... from the largest county and city jails. Information on mental and medical health and substance abuse...

  17. 78 FR 56940 - Agency Information Collection Activities; Existing Collection-Reinstatement, Comments Requested...

    Science.gov (United States)

    2013-09-16

    ...-- Reinstatement, Comments Requested: Friction Ridge Cards: Arrest and Institution; Applicant; Personal...) Enhance the quality, utility, and clarity of the information to be collected; and (4) Minimize the burden... form/collection: Friction Ridge Cards: Arrest and Institution; Applicant; Personal Identification; FBI...

  18. Embedding security messages in existing processes: a pragmatic and effective approach to information security culture change

    CERN Document Server

    Lopienski, Sebastian

    Companies and organizations world-wide depend more and more on IT infrastructure and operations. Computer systems store vital information and sensitive data; computing services are essential for main business processes. This high dependency comes with a number of security risks, which have to be managed correctly on technological, organizational and human levels. Addressing the human aspects of information security often boils down just to procedures, training and awareness raising. On the other hand, employees and collaborators do not adopt security attitude and habits simply when told to do so – a real change in behaviour requires an established security culture. But how to introduce a security culture? This thesis outlines the need of developing or improving security culture, and discusses how this can be done. The proposed approach is to gradually build security knowledge and awareness, and influence behaviours. The way to achieve this is to make security communication pervasive by embedding security me...

  19. Existence and perception of textural information predictive of atypical nevi: preliminary insights

    Science.gov (United States)

    Wighton, Paul; Lee, Tim K.; McLean, David; Lui, Harvey; Atkins, M. Stella

    2008-03-01

    Texture is known to predict atypicality in pigmented skin lesions. This paper describes an experiment that was conducted to determine 1) if this textural information is present in the center of skin lesions, and 2) how color affects the perception of this information. Images of pigmented skin lesions from three categories were shown to subjects in such a way that only textural information could be perceived; other factors known to predict atypicality were removed or held constant. These images were shown in both color and grayscale. Each subject assigned a score of atypicality to each image. The experiment was conducted on 5 subjects of varying backgrounds, including one expert. Each subject's accuracy under each modality was measured by calculating the volume under a 3-way ROC surface. The modalities were compared using the Dorfman-Berbaum-Metz (DBM) method of ROC analysis, giving a p-value of 0.8611. Therefore the null hypothesis that there is no difference between the predictive power of the modalities cannot be rejected. Also, a two one-sided test of equivalence (TOST) was performed giving a p-value pair of pigmented skin lesions.

  20. Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information

    Directory of Open Access Journals (Sweden)

    Sikder Abdur

    2010-05-01

    Full Text Available Abstract Background Most of the existing in silico phosphorylation site prediction systems use machine learning approach that requires preparing a good set of classification data in order to build the classification knowledge. Furthermore, phosphorylation is catalyzed by kinase enzymes and hence the kinase information of the phosphorylated sites has been used as major classification data in most of the existing systems. Since the number of kinase annotations in protein sequences is far less than that of the proteins being sequenced to date, the prediction systems that use the information found from the small clique of kinase annotated proteins can not be considered as completely perfect for predicting outside the clique. Hence the systems are certainly not generalized. In this paper, a novel generalized prediction system, PPRED (Phosphorylation PREDictor is proposed that ignores the kinase information and only uses the evolutionary information of proteins for classifying phosphorylation sites. Results Experimental results based on cross validations and an independent benchmark reveal the significance of using the evolutionary information alone to classify phosphorylation sites from protein sequences. The prediction performance of the proposed system is better than those of the existing prediction systems that also do not incorporate kinase information. The system is also comparable to systems that incorporate kinase information in predicting such sites. Conclusions The approach presented in this paper provides an efficient way to identify phosphorylation sites in a given protein primary sequence that would be a valuable information for the molecular biologists working on protein phosphorylation sites and for bioinformaticians developing generalized prediction systems for the post translational modifications like phosphorylation or glycosylation. PPRED is publicly available at the URL http://www.cse.univdhaka.edu/~ashis/ppred/index.php.

  1. Existence of a Consistent Quantum Gravity Model from Minimum Microscopic Information

    Science.gov (United States)

    Mandrin, P. A.

    2014-12-01

    It is shown that a quantum gravity formulation exists on the basis of quantum number conservation, the laws of thermodynamics, unspecific interactions, and locally maximizing the ratio of resulting degrees of freedom per imposed degree of freedom of the theory. The First Law of thermodynamics is evaluated by imposing boundary conditions to the theory. These boundary conditions determine the details of the complex world structure. No explicite microscopic quantum structure is required, and thus no ambiguity arises on how to construct the model. Although no dynamical computations of quantum systems are possible on this basis, all well established physics may be recovered, and all measurable quantities may be computed. The recovery of physical laws is shown by extremizing the entropy, which means varying the action on the bulk and boundary of small volumes of curved space-time. It is sketched how Quantum Field Theory (QFT) and General Relativity (GR) are recovered with no further assumptions except for imposing the dimension of a second derivative of the metric on the gravitational field equations. The new concepts are 1. the abstract organization of statistical quantum states, allowing for the possibility of absent quantum microstructure, 2. the optimization of the locally resulting degrees of freedom per imposed degree of freedom of the theory, allowing for the reconstruction of the spacetime dimensions, 3. the reconstruction of physical and geometric quantities by means of stringent mathematical or physical justifications, 4. the fully general recovery of GR by quasi-local variation methods applied on small portions of spacetime.

  2. Acquisition of 3D urban models by analysis of aerial images, digital surface models, and existing 2D building information

    Science.gov (United States)

    Haala, Norbert; Anders, Karl-Heinrich

    1997-08-01

    For a task like 3D building reconstruction, there are three main data sources carrying information which is reburied for a highly automated data acquisition. These data sources are aerial images, digital surface models (DSM), which can either be derived by stereo matching from aerial images or be directly measured by scanning laser systems, and -- at least for highly developed countries -- existing (2D) GIS information on the ground plan or usage of buildings. The way these different data sources should be utilized by a process of 3D building reconstruction depends on the distinctive characteristics of the different, partly complementary type of information they contain. Image data contains much information, but just this complexity causes enormous problems for the automatic interpretation of this data type. The GIS as a secondary data source provides information on the 2D shape, i.e. the ground plan of a building, which is very reliable, although information on the third dimension is missing and therefore has to be provided by other data sources. As the information of a DSM is restricted to surface geometry, the interpretation of this kind of data is easier compared to the interpretation of image data. Nevertheless, due to insufficient spatial resolution or quality of the DSM, optimal results can only be achieved by the combination of all data sources. Within this paper two approaches aiming on the combination of aerial images, digital surface models and existing ground plans for the reconstruction of three- dimensional building reconstructions are demonstrated.

  3. How to use not-always-reliable binding site information in protein-protein docking prediction.

    Science.gov (United States)

    Li, Lin; Huang, Yanzhao; Xiao, Yi

    2013-01-01

    In many protein-protein docking algorithms, binding site information is used to help predicting the protein complex structures. Using correct and accurate binding site information can increase protein-protein docking success rate significantly. On the other hand, using wrong binding sites information should lead to a failed prediction, or, at least decrease the success rate. Recently, various successful theoretical methods have been proposed to predict the binding sites of proteins. However, the predicted binding site information is not always reliable, sometimes wrong binding site information could be given. Hence there is a high risk to use the predicted binding site information in current docking algorithms. In this paper, a softly restricting method (SRM) is developed to solve this problem. By utilizing predicted binding site information in a proper way, the SRM algorithm is sensitive to the correct binding site information but insensitive to wrong information, which decreases the risk of using predicted binding site information. This SRM is tested on benchmark 3.0 using purely predicted binding site information. The result shows that when the predicted information is correct, SRM increases the success rate significantly; however, even if the predicted information is completely wrong, SRM only decreases success rate slightly, which indicates that the SRM is suitable for utilizing predicted binding site information.

  4. Existence of life-time stable proteins in mature rats-Dating of proteins' age by repeated short-term exposure to labeled amino acids throughout age

    DEFF Research Database (Denmark)

    Bechshøft, Cecilie Leidesdorff; Schjerling, Peter; Bornø, Andreas

    2017-01-01

    . The aim of this study is to investigate whether we can verify the presence of protein pools within the same tissue with very distinct turnover rates over the life-span of rats with special focus on connective tissue. Male and female Lewis rats (n = 35) were injected with five different isotopically...... of tracer enrichments throughout the rat's life, indicating that myofibrillar and cytoskeleton proteins have a high turnover. In contrast, the connective tissue protein in the eye lens and patellar tendon of the mature rat showed detainment of tracer enrichment injected during fetal development and first...... living days, indicating very slow turnover. The data support the hypothesis that some proteins synthesized during the early development and growth still exist much later in life of animals and hence has a very slow turnover rate....

  5. A 9-state hidden Markov model using protein secondary structure information for protein fold recognition.

    Science.gov (United States)

    Lee, Sun Young; Lee, Jong Yun; Jung, Kwang Su; Ryu, Keun Ho

    2009-06-01

    In protein fold recognition, the main disadvantage of hidden Markov models (HMMs) is the employment of large-scale model architectures which require large data sets and high computational resources for training. Also, HMMs must consider sequential information about secondary structures of proteins, to improve prediction performance and reduce model parameters. Therefore, we propose a novel method for protein fold recognition based on a hidden Markov model, called a 9-state HMM. The method can (i) reduce the number of states using secondary structure information about proteins for each fold and (ii) recognize protein folds more accurately than other HMMs.

  6. POSSIBILITY OF IMPROVING EXISTING STANDARDS AND METHODOLOGIES FOR AUDITING INFORMATION SYSTEMS TO PROVIDE E-GOVERNMENT SERVICES

    Directory of Open Access Journals (Sweden)

    Евгений Геннадьевич Панкратов

    2014-03-01

    Full Text Available This article analyzes the existing methods of e-government systems audit, their shortcomings are examined.  The approaches to improve existing techniques and adapt them to the specific characteristics of e-government systems are suggested. The paper describes the methodology, providing possibilities of integrated assessment of information systems. This methodology uses systems maturity models and can be used in the construction of e-government rankings, as well as in the audit of their implementation process. Maturity models are based on COBIT, COSO methodologies and models of e-government, developed by the relevant committee of the UN. The methodology was tested during the audit of information systems involved in the payment of temporary disability benefits. The audit was carried out during analysis of the outcome of the pilot project for the abolition of the principle of crediting payments for disability benefits.DOI: http://dx.doi.org/10.12731/2218-7405-2014-2-5

  7. Waste Municipal Service and Informal Recycling Sector in Fast-Growing Asian Cities: Co-Existence, Opposition or Integration?

    Directory of Open Access Journals (Sweden)

    Rémi de Bercegol

    2017-12-01

    Full Text Available Despite being generally poorly recognized by public authorities, informal recycling remains nevertheless a major component in the waste sector, which questions the legitimacy of the official waste arrangements. A look at the current transformation in Hanoi (Vietnam, Delhi (India and Surabaya (Indonesia allows us to understand the socio-technical aspects of infrastructural choices in the management of waste generated in fast-growing Asian cities. The three cases present similar traditional recycling practices yet contrasted (non- regulation within their waste policies. From the co-existence of a municipal waste management service with a traditional informal recycling sector, to an opposition between both, there is also a possibility of making use of the existing local practices to achieve a more sustainable system.

  8. Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure.

    Science.gov (United States)

    Lenaerts, Tom; Ferkinghoff-Borg, Jesper; Stricher, Francois; Serrano, Luis; Schymkowitz, Joost W H; Rousseau, Frederic

    2008-10-08

    Efficient communication between distant sites within a protein is essential for cooperative biological response. Although often associated with large allosteric movements, more subtle changes in protein dynamics can also induce long-range correlations. However, an appropriate formalism that directly relates protein structural dynamics to information exchange between functional sites is still lacking. Here we introduce a method to analyze protein dynamics within the framework of information theory and show that signal transduction within proteins can be considered as a particular instance of communication over a noisy channel. In particular, we analyze the conformational correlations between protein residues and apply the concept of mutual information to quantify information exchange. Mapping out changes of mutual information on the protein structure then allows visualizing how distal communication is achieved. We illustrate the approach by analyzing information transfer by the SH2 domain of Fyn tyrosine kinase, obtained from Monte Carlo dynamics simulations. Our analysis reveals that the Fyn SH2 domain forms a noisy communication channel that couples residues located in the phosphopeptide and specificity binding sites and a number of residues at the other side of the domain near the linkers that connect the SH2 domain to the SH3 and kinase domains. We find that for this particular domain, communication is affected by a series of contiguous residues that connect distal sites by crossing the core of the SH2 domain. As a result, our method provides a means to directly map the exchange of biological information on the structure of protein domains, making it clear how binding triggers conformational changes in the protein structure. As such it provides a structural road, next to the existing attempts at sequence level, to predict long-range interactions within protein structures.

  9. Hidden information revealed by optimal community structure from a protein-complex bipartite network improves protein function prediction.

    Science.gov (United States)

    Lee, Juyong; Lee, Jooyoung

    2013-01-01

    The task of extracting the maximal amount of information from a biological network has drawn much attention from researchers, for example, predicting the function of a protein from a protein-protein interaction (PPI) network. It is well known that biological networks consist of modules/communities, a set of nodes that are more densely inter-connected among themselves than with the rest of the network. However, practical applications of utilizing the community information have been rather limited. For protein function prediction on a network, it has been shown that none of the existing community-based protein function prediction methods outperform a simple neighbor-based method. Recently, we have shown that proper utilization of a highly optimal modularity community structure for protein function prediction can outperform neighbor-assisted methods. In this study, we propose two function prediction approaches on bipartite networks that consider the community structure information as well as the neighbor information from the network: 1) a simple screening method and 2) a random forest based method. We demonstrate that our community-assisted methods outperform neighbor-assisted methods and the random forest method yields the best performance. In addition, we show that using the optimal community structure information is essential for more accurate function prediction for the protein-complex bipartite network of Saccharomyces cerevisiae. Community detection can be carried out either using a modified modularity for dealing with the original bipartite network or first projecting the network into a single-mode network (i.e., PPI network) and then applying community detection to the reduced network. We find that the projection leads to the loss of information in a significant way. Since our prediction methods rely only on the network topology, they can be applied to various fields where an efficient network-based analysis is required.

  10. Learning in the informal spaces and re-signification of the existence of undergraduate students of nursing.

    Science.gov (United States)

    de Jesus, Isabel Silva; Sena, Edite Lago da Silva; Andrade, Luana Machado

    2014-10-01

    To describe the perception of lecturers and undergraduate nursing students regarding the dialogic experience in the informal spaces and its relationship with training in health. Experiential descriptions were collected in the context of a public university in the non-metropolitan region of the state of Bahia, Brazil, using open interviews. These descriptions were analyzed according to the principles of the phenomenology of Maurice Merleau-Ponty. It was revealed that the informal spaces contribute significantly to the construction of knowledge and professional training strengthening teaching and promoting the re-signification of the subjects' experience. It is evidenced that the dialogic experience has relevancy for rethinking the teaching-learning process in the university, such that the informal spaces should be included and valued as producers of meanings for the personal and academic life of lecturers and students, with the ability to re-signify existence.

  11. Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins.

    Science.gov (United States)

    Das, Sreetama; Bhadra, Pratiti; Ramakumar, Suryanarayanarao; Pal, Debnath

    2017-08-04

    cis-Peptide bonds, whose occurrence in proteins is rare but evolutionarily conserved, are implicated to play an important role in protein function. This has led to their previous use in a homology-independent, fragment-match-based protein function annotation method. However, proteins are not static molecules; dynamics is integral to their activity. This is nicely epitomized by the geometric isomerization of cis-peptide to trans form for molecular activity. Hence we have incorporated both static (cis-peptide) and dynamics information to improve the prediction of protein molecular function. Our results show that cis-peptide information alone cannot detect functional matches in cases where cis-trans isomerization exists but 3D coordinates have been obtained for only the trans isomer or when the cis-peptide bond is incorrectly assigned as trans. On the contrary, use of dynamics information alone includes false-positive matches for cases where fragments with similar secondary structure show similar dynamics, but the proteins do not share a common function. Combining the two methods reduces errors while detecting the true matches, thereby enhancing the utility of our method in function annotation. A combined approach, therefore, opens up new avenues of improving existing automated function annotation methodologies.

  12. From Point Clouds to Building Information Models: 3D Semi-Automatic Reconstruction of Indoors of Existing Buildings

    Directory of Open Access Journals (Sweden)

    Hélène Macher

    2017-10-01

    Full Text Available The creation of as-built Building Information Models requires the acquisition of the as-is state of existing buildings. Laser scanners are widely used to achieve this goal since they permit to collect information about object geometry in form of point clouds and provide a large amount of accurate data in a very fast way and with a high level of details. Unfortunately, the scan-to-BIM (Building Information Model process remains currently largely a manual process which is time consuming and error-prone. In this paper, a semi-automatic approach is presented for the 3D reconstruction of indoors of existing buildings from point clouds. Several segmentations are performed so that point clouds corresponding to grounds, ceilings and walls are extracted. Based on these point clouds, walls and slabs of buildings are reconstructed and described in the IFC format in order to be integrated into BIM software. The assessment of the approach is proposed thanks to two datasets. The evaluation items are the degree of automation, the transferability of the approach and the geometric quality of results of the 3D reconstruction. Additionally, quality indexes are introduced to inspect the results in order to be able to detect potential errors of reconstruction.

  13. Building toy models of proteins using coevolutionary information

    Science.gov (United States)

    Cheng, Ryan; Raghunathan, Mohit; Onuchic, Jose

    2015-03-01

    Recent developments in global statistical methodologies have advanced the analysis of large collections of protein sequences for coevolutionary information. Coevolution between amino acids in a protein arises from compensatory mutations that are needed to maintain the stability or function of a protein over the course of evolution. This gives rise to quantifiable correlations between amino acid positions within the multiple sequence alignment of a protein family. Here, we use Direct Coupling Analysis (DCA) to infer a Potts model Hamiltonian governing the correlated mutations in a protein family to obtain the sequence-dependent interaction energies of a toy protein model. We demonstrate that this methodology predicts residue-residue interaction energies that are consistent with experimental mutational changes in protein stabilities as well as other computational methodologies. Furthermore, we demonstrate with several examples that DCA could be used to construct a structure-based model that quantitatively agrees with experimental data on folding mechanisms. This work serves as a potential framework for generating models of proteins that are enriched by evolutionary data that can potentially be used to engineer key functional motions and interactions in protein systems. This research has been supported by the NSF INSPIRE award MCB-1241332 and by the CTBP sponsored by the NSF (Grant PHY-1427654).

  14. association between daily protein intake and outcome events only exist in patients with inflammation on peritoneal dialysis

    Directory of Open Access Journals (Sweden)

    Jie Dong

    2012-06-01

    Full Text Available Whether the association between decreased protein intake and raised risk for all–cause, cardiovascular death and peritonitis is confounded by inflammation status is unknown. This study aimed to explore the predicting role of daily protein intake (DPI in above outcome events in patients with and without inflammation respectively. Our study enrolled 305 incident patients who could be followed regularly. Demographic data was collected at baseline. Biochemical, dietary and nutritional data, dialysis adequacy were measured at the baseline and thereafter at regular intervals. A total of 127 patients died during the 44.5-month follow-up. Total 129 first-episode peritonitis were observed. Patients with high tertile of baseline DPI had significantly higher serum albumin, prealbumin, hemoglobin, lean body mass and hand grip strength compared to low tertile group (P<0.05∼0.001. They also had significantly lower risk for all–cause, cardiovascular death and first-episode peritonitis than low tertile group adjusted for commonly recognized confounders. When the whole cohort was divided into two groups according to the C-reactive levels higher or lower than 3 mg/L, the predicting role of baseline DPI only existed in patients with inflammation status.Conclusions: The decreased DPI predicted the increase risk for all-cause and cardiovascular death, and the first-episode peritonitis only in PD patients with chronic inflammation. The target of DPI may differ for patients with and without chronic inflammation

  15. Recombinant lysyl oxidase propeptide protein inhibits growth and promotes apoptosis of pre-existing murine breast cancer xenografts.

    Directory of Open Access Journals (Sweden)

    Manish V Bais

    Full Text Available Lysyl oxidase propeptide (LOX-PP ectopic overexpression inhibits the growth of cancer xenografts. Here the ability and mode of action of purified recombinant LOX-PP (rLOX-PP protein to inhibit the growth of pre-existing xenografts was determined. Experimental approaches employed were direct intratumoral injection (i.t. of rLOX-PP protein into murine breast cancer NF639 xenografts, and application of a slow release formulation of rLOX-PP implanted adjacent to tumors in NCR nu/nu mice (n = 10. Tumors were monitored for growth, and after sacrifice were subjected to immunohistochemical and Western blot analyses for several markers of proliferation, apoptosis, and for rLOX-PP itself. Direct i.t. injection of rLOX-PP significantly reduced tumor volume on days 20, 22 and 25 and tumor weight at harvest on day 25 by 30% compared to control. Implantation of beads preloaded with 35 micrograms rLOX-PP (n = 10 in vivo reduced tumor volume and weight at sacrifice when compared to empty beads (p<0.05. A 30% reduction of tumor volume on days 22 and 25 (p<0.05 and final tumor weight on day 25 (p<0.05 were observed with a reduced tumor growth rate of 60% after implantation. rLOX-PP significantly reduced the expression of proliferation markers and Erk1/2 MAP kinase activation, while prominent increases in apoptosis markers were observed. rLOX-PP was detected by immunohistochemistry in harvested rLOX-PP tumors, but not in controls. Data provide pre-clinical findings that support proof of principle for the therapeutic anti-cancer potential of rLOX-PP protein formulations.

  16. Equalizing the information amounts of protein and mRNA by information theory.

    Science.gov (United States)

    Adiguzel, Y

    2017-09-01

    Based on the Shannon's information communication theory, information amount of the entire length of a polymeric macromolecule can be calculated in bits through adding the entropies of each building block. Proteins, DNA and RNA are such macromolecules. When only the building blocks' variation is considered as the source of entropy, there is seemingly lower information in case of the protein if this approach is applied directly on a protein of specific size and the coding sequence size of the mRNA corresponding to the particular length of the protein. This decrease in the information amount seems contradictory but this apparent conflict is resolved by considering the conformational variations in proteins as a new variable in the calculation and balancing the approximated entropy of the coding part of the mRNA and the protein. Probabilities can change therefore we also assigned hypothetical probabilities to the conformational states, which represent the uneven distribution as the time spent in one conformation, providing the probability of the presence in either or one of the possible conformations. Results that are obtained by using hypothetical probabilities are in line with the experimental values of variations in the conformational-state of protein populations. This equalization approach has further biological relevance that it compensates for the degeneracy in the codon usage during protein translation and it leads to the conclusion that the alphabet size for the protein is rather optimal for the proper protein functioning within the thermodynamic milieu of the cell. The findings were also discussed in relation to the codon bias and have implications in relation to the codon evolution concept. Eventually, this work brings the fields of protein structural studies and molecular protein translation processes together with a novel approach. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. A study on the relevance and influence of the existing regulation and risk informed/performance based regulation

    Energy Technology Data Exchange (ETDEWEB)

    Cheong, B. J.; Kang, J. M.; Kim, H. S.; Koh, S. H.; Kang, D. H.; Park, C. H. [Cheju Univ., Jeju (Korea, Republic of)

    2003-02-15

    The goal of this study is to estimate the relevance and Influence of the Existing Regulation and the RI-PBR to the institutionalization of the regulatory system. This study reviews the current regulatory system and the status of the RI-PBR implementation of the US NRC and Korea based upon SECY Papers, Risk Informed Regulation Implementation Plan (RIRIP) of the US NRC and other domestic studies. In order to investigate the perceptions, knowledge level, ground for the regulatory change, a survey was performed to Korean nuclear utilities, researchers and regulators on the perception on the RIR. The questionnaire was composed of 50 questions regarding personal details on work experience, level of education and specific field of work ; level of knowledge on the risk informed performance based regulation (RI-PBR); the perception of the current regulation, the effectiveness, level of procedure, flexibility, dependency on the regulator and personal view, and the perception of the RI-PBR such as flexibility of regulation, introduction time and the effect of RI-PBR, safety improvement, public perception, parts of the existing regulatory system that should be changed, etc. 515 answered from all sectors of the nuclear field; utilities, engineering companies, research institutes, and regulatory bodies.

  18. Highly Accurate Prediction of Protein-Protein Interactions via Incorporating Evolutionary Information and Physicochemical Characteristics

    Directory of Open Access Journals (Sweden)

    Zheng-Wei Li

    2016-08-01

    Full Text Available Protein-protein interactions (PPIs occur at almost all levels of cell functions and play crucial roles in various cellular processes. Thus, identification of PPIs is critical for deciphering the molecular mechanisms and further providing insight into biological processes. Although a variety of high-throughput experimental techniques have been developed to identify PPIs, existing PPI pairs by experimental approaches only cover a small fraction of the whole PPI networks, and further, those approaches hold inherent disadvantages, such as being time-consuming, expensive, and having high false positive rate. Therefore, it is urgent and imperative to develop automatic in silico approaches to predict PPIs efficiently and accurately. In this article, we propose a novel mixture of physicochemical and evolutionary-based feature extraction method for predicting PPIs using our newly developed discriminative vector machine (DVM classifier. The improvements of the proposed method mainly consist in introducing an effective feature extraction method that can capture discriminative features from the evolutionary-based information and physicochemical characteristics, and then a powerful and robust DVM classifier is employed. To the best of our knowledge, it is the first time that DVM model is applied to the field of bioinformatics. When applying the proposed method to the Yeast and Helicobacter pylori (H. pylori datasets, we obtain excellent prediction accuracies of 94.35% and 90.61%, respectively. The computational results indicate that our method is effective and robust for predicting PPIs, and can be taken as a useful supplementary tool to the traditional experimental methods for future proteomics research.

  19. RBO Aleph: leveraging novel information sources for protein structure prediction.

    Science.gov (United States)

    Mabrouk, Mahmoud; Putz, Ines; Werner, Tim; Schneider, Michael; Neeb, Moritz; Bartels, Philipp; Brock, Oliver

    2015-07-01

    RBO Aleph is a novel protein structure prediction web server for template-based modeling, protein contact prediction and ab initio structure prediction. The server has a strong emphasis on modeling difficult protein targets for which templates cannot be detected. RBO Aleph's unique features are (i) the use of combined evolutionary and physicochemical information to perform residue-residue contact prediction and (ii) leveraging this contact information effectively in conformational space search. RBO Aleph emerged as one of the leading approaches to ab initio protein structure prediction and contact prediction during the most recent Critical Assessment of Protein Structure Prediction experiment (CASP11, 2014). In addition to RBO Aleph's main focus on ab initio modeling, the server also provides state-of-the-art template-based modeling services. Based on template availability, RBO Aleph switches automatically between template-based modeling and ab initio prediction based on the target protein sequence, facilitating use especially for non-expert users. The RBO Aleph web server offers a range of tools for visualization and data analysis, such as the visualization of predicted models, predicted contacts and the estimated prediction error along the model's backbone. The server is accessible at http://compbio.robotics.tu-berlin.de/rbo_aleph/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-05-25

    The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

  1. Using the clustered circular layout as an informative method for visualizing protein-protein interaction networks.

    Science.gov (United States)

    Fung, David C Y; Wilkins, Marc R; Hart, David; Hong, Seok-Hee

    2010-07-01

    The force-directed layout is commonly used in computer-generated visualizations of protein-protein interaction networks. While it is good for providing a visual outline of the protein complexes and their interactions, it has two limitations when used as a visual analysis method. The first is poor reproducibility. Repeated running of the algorithm does not necessarily generate the same layout, therefore, demanding cognitive readaptation on the investigator's part. The second limitation is that it does not explicitly display complementary biological information, e.g. Gene Ontology, other than the protein names or gene symbols. Here, we present an alternative layout called the clustered circular layout. Using the human DNA replication protein-protein interaction network as a case study, we compared the two network layouts for their merits and limitations in supporting visual analysis.

  2. CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences

    Directory of Open Access Journals (Sweden)

    Charalambos Chrysostomou

    2015-01-01

    Full Text Available Complex informational spectrum analysis for protein sequences (CISAPS and its web-based server are developed and presented. As recent studies show, only the use of the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including absolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case study in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes can present similarities or differences according to the features extracted from CISAPS web server. These associations are probable to be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as zero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino acid indices where each one represents a different property to perform the analysis. This web-based server enables researchers with little knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work.

  3. PROGRAM SYSTEM AND INFORMATION METADATA BANK OF TERTIARY PROTEIN STRUCTURES

    Directory of Open Access Journals (Sweden)

    T. A. Nikitin

    2013-01-01

    Full Text Available The article deals with the architecture of metadata storage model for check results of three-dimensional protein structures. Concept database model was built. The service and procedure of database update as well as data transformation algorithms for protein structures and their quality were presented. Most important information about entries and their submission forms to store, access, and delivery to users were highlighted. Software suite was developed for the implementation of functional tasks using Java programming language in the NetBeans v.7.0 environment and JQL to query and interact with the database JavaDB. The service was tested and results have shown system effectiveness while protein structures filtration.

  4. Integrating landslide and liquefaction hazard and loss estimates with existing USGS real-time earthquake information products

    Science.gov (United States)

    Allstadt, Kate E.; Thompson, Eric M.; Hearne, Mike; Nowicki Jessee, M. Anna; Zhu, J.; Wald, David J.; Tanyas, Hakan

    2017-01-01

    The U.S. Geological Survey (USGS) has made significant progress toward the rapid estimation of shaking and shakingrelated losses through their Did You Feel It? (DYFI), ShakeMap, ShakeCast, and PAGER products. However, quantitative estimates of the extent and severity of secondary hazards (e.g., landsliding, liquefaction) are not currently included in scenarios and real-time post-earthquake products despite their significant contributions to hazard and losses for many events worldwide. We are currently running parallel global statistical models for landslides and liquefaction developed with our collaborators in testing mode, but much work remains in order to operationalize these systems. We are expanding our efforts in this area by not only improving the existing statistical models, but also by (1) exploring more sophisticated, physics-based models where feasible; (2) incorporating uncertainties; and (3) identifying and undertaking research and product development to provide useful landslide and liquefaction estimates and their uncertainties. Although our existing models use standard predictor variables that are accessible globally or regionally, including peak ground motions, topographic slope, and distance to water bodies, we continue to explore readily available proxies for rock and soil strength as well as other susceptibility terms. This work is based on the foundation of an expanding, openly available, case-history database we are compiling along with historical ShakeMaps for each event. The expected outcome of our efforts is a robust set of real-time secondary hazards products that meet the needs of a wide variety of earthquake information users. We describe the available datasets and models, developments currently underway, and anticipated products. 

  5. Use of reconnaissance level information for environmental assessment. [Information available from existing sources that satisfies information needs of siting and operational aspects of NPP

    Energy Technology Data Exchange (ETDEWEB)

    Foster, R.F.; Rickard, W.H.; Strand, J.A.; Warner, M.L.

    1979-11-01

    Reconnaissance level information (RLI) sufficient for comparing the environmental and socio-economic features of candidate sites for nuclear power stations and for guiding plant design, baseline surveys, and operational practices is usually available from published reports, public records, and knowledgeable individuals. Environmental concerns of special importance for site evaluation include: aquatic ecology, terrestrial ecology, land and water use, socio-economics, and institutional constraints. A scheme is suggested for using RLI to assign classifications to candidate sites based on the potential level of concern associated with the different environmental features.

  6. Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices

    Directory of Open Access Journals (Sweden)

    Liao Li

    2007-01-01

    Full Text Available Abstract Background Protein-protein interactions are critical for cellular functions. Recently developed computational approaches for predicting protein-protein interactions utilize co-evolutionary information of the interacting partners, e.g., correlations between distance matrices, where each matrix stores the pairwise distances between a protein and its orthologs from a group of reference genomes. Results We proposed a novel, simple method to account for some of the intra-matrix correlations in improving the prediction accuracy. Specifically, the phylogenetic species tree of the reference genomes is used as a guide tree for hierarchical clustering of the orthologous proteins. The distances between these clusters, derived from the original pairwise distance matrix using the Neighbor Joining algorithm, form intermediate distance matrices, which are then transformed and concatenated into a super phylogenetic vector. A support vector machine is trained and tested on pairs of proteins, represented as super phylogenetic vectors, whose interactions are known. The performance, measured as ROC score in cross validation experiments, shows significant improvement of our method (ROC score 0.8446 over that of using Pearson correlations (0.6587. Conclusion We have shown that the phylogenetic tree can be used as a guide to extract intra-matrix correlations in the distance matrices of orthologous proteins, where these correlations are represented as intermediate distance matrices of the ancestral orthologous proteins. Both the unsupervised and supervised learning paradigms benefit from the explicit inclusion of these intermediate distance matrices, and particularly so in the latter case, which offers a better balance between sensitivity and specificity in the prediction of protein-protein interactions.

  7. Cognitive and emotional information processing: protein synthesis and gene expression.

    Science.gov (United States)

    Sajikumar, Sreedharan; Navakkode, Sheeja; Korz, Volker; Frey, Julietta U

    2007-10-15

    Recent findings suggest that functional plasticity phenomena such as long-term potentiation (LTP) and long-term depression (LTD) - cellular processes underlying memory - are restricted to functional dendritic compartments. It was also shown, however, that a relatively strong activation of a synaptic input can abolish compartment restrictions. Our data support these findings and we present one cellular pathway responsible for uncompartmentalization of the normally localized plasticity processes by the action of rolipram, an inhibitor of type 4 phosphodiesterases. In contrast with compartment-restricted information processing, uncompartmentalization requires transcription. In the search for system relevance of compartmentalization versus uncompartmentalization we describe firstly data which show that more cognitive information processing in rats' behaviour may follow rules of compartmentalization, whereas stressful, more life-threatening, inputs abolish compartment-restricted information processing involving transcription. Our findings allow us to suggest that consolidation of processes which take place during the cognitive event most probably depend on local protein synthesis, whereas stress immediately induces gene expression in addition, resulting in a compartment-unspecific up-regulation of plasticity-related proteins (PRPs), providing the entire neuron with a higher level of 'reactiveness'. These data would provide a specific functional cellular mechanism to respond differentially and effectively to behaviourally weighted inputs.

  8. 12 CFR 792.56 - Notice of existence of records, access decisions and disclosure of requested information; time...

    Science.gov (United States)

    2010-01-01

    ... decisions and disclosure of requested information; time limits. 792.56 Section 792.56 Banks and Banking... ADMINISTRATION REQUESTS FOR INFORMATION UNDER THE FREEDOM OF INFORMATION ACT AND PRIVACY ACT, AND BY SUBPOENA..., access decisions and disclosure of requested information; time limits. (a) The system manager identified...

  9. Integrating semantic information into multiple kernels for protein-protein interaction extraction from biomedical literatures.

    Directory of Open Access Journals (Sweden)

    Lishuang Li

    Full Text Available Protein-Protein Interaction (PPI extraction is an important task in the biomedical information extraction. Presently, many machine learning methods for PPI extraction have achieved promising results. However, the performance is still not satisfactory. One reason is that the semantic resources were basically ignored. In this paper, we propose a multiple-kernel learning-based approach to extract PPIs, combining the feature-based kernel, tree kernel and semantic kernel. Particularly, we extend the shortest path-enclosed tree kernel (SPT by a dynamic extended strategy to retrieve the richer syntactic information. Our semantic kernel calculates the protein-protein pair similarity and the context similarity based on two semantic resources: WordNet and Medical Subject Heading (MeSH. We evaluate our method with Support Vector Machine (SVM and achieve an F-score of 69.40% and an AUC of 92.00%, which show that our method outperforms most of the state-of-the-art systems by integrating semantic information.

  10. From existing data to novel hypotheses : design and application of structure-based Molecular Class Specific Information Systems

    NARCIS (Netherlands)

    Kuipers, R.K.P.

    2012-01-01

    As the active component of many biological systems, proteins are of great interest to life scientists. Proteins are used in a large number of different applications such as the production of precursors and compounds, for bioremediation, as drug targets, to diagnose patients suffering from genetic

  11. Combining Physicochemical and Evolutionary Information for Protein Contact Prediction

    Science.gov (United States)

    Schneider, Michael; Brock, Oliver

    2014-01-01

    We introduce a novel contact prediction method that achieves high prediction accuracy by combining evolutionary and physicochemical information about native contacts. We obtain evolutionary information from multiple-sequence alignments and physicochemical information from predicted ab initio protein structures. These structures represent low-energy states in an energy landscape and thus capture the physicochemical information encoded in the energy function. Such low-energy structures are likely to contain native contacts, even if their overall fold is not native. To differentiate native from non-native contacts in those structures, we develop a graph-based representation of the structural context of contacts. We then use this representation to train an support vector machine classifier to identify most likely native contacts in otherwise non-native structures. The resulting contact predictions are highly accurate. As a result of combining two sources of information—evolutionary and physicochemical—we maintain prediction accuracy even when only few sequence homologs are present. We show that the predicted contacts help to improve ab initio structure prediction. A web service is available at http://compbio.robotics.tu-berlin.de/epc-map/. PMID:25338092

  12. Degradation kinetics of fisetin and quercetin in solutions affected by medium pH, temperature and co-existed proteins

    Directory of Open Access Journals (Sweden)

    Wang Jing

    2016-01-01

    Full Text Available Impacts of medium pH, temperature and coexisted proteins on the degradation of two flavonoids fisetin and quercetin were assessed by spectroscopic method in the present study. Based on the measured degradation rate constants (k, fisetin was more stable than quercetin in all cases. Increasing medium pH from 6.0 to 7.5 at 37°C enhanced respective k values of fisetin and quercetin from 8.30x10−3 and 2.81x10−2 to 0.202 and 0.375 h-1 (P<0.05. In comparison with their degradation at 37°C, fisetin and quercetin showed larger k values at higher temperature (0.124 and 0.245 h−1 at 50°C, or 0.490 and 1.42 h−1 at 65°C. Four protein products in medium could stabilize the two flavonoids (P<0.05, as these proteins at 0.10 g L-1 decreased respective k values of fisetin and quercetin to 2.28x10−2-2.98x10−2 and 4.37´10−2-5.97x10−2 h−1. Hydrophobic interaction between the proteins and the two flavonoids was evidenced responsible for the stabilization, as sodium dodecyl sulfate could destroy the stabilization significantly (P<0.05. Casein and soybean protein provided greater stabilization than whey protein isolate. It is thus concluded that higher temperature and alkaline pH can enhance flavonoid loss, whereas coexisted proteins as flavonoid stabilizers can inhibit flavonoid degradation.

  13. Computational methods using weighed-extreme learning machine to predict protein self-interactions with protein evolutionary information.

    Science.gov (United States)

    An, Ji-Yong; Zhang, Lei; Zhou, Yong; Zhao, Yu-Jun; Wang, Da-Fu

    2017-08-18

    Self-interactions Proteins (SIPs) is important for their biological activity owing to the inherent interaction amongst their secondary structures or domains. However, due to the limitations of experimental Self-interactions detection, one major challenge in the study of prediction SIPs is how to exploit computational approaches for SIPs detection based on evolutionary information contained protein sequence. In the work, we presented a novel computational approach named WELM-LAG, which combined the Weighed-Extreme Learning Machine (WELM) classifier with Local Average Group (LAG) to predict SIPs based on protein sequence. The major improvement of our method lies in presenting an effective feature extraction method used to represent candidate Self-interactions proteins by exploring the evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix (PSSM); and then employing a reliable and robust WELM classifier to carry out classification. In addition, the Principal Component Analysis (PCA) approach is used to reduce the impact of noise. The WELM-LAG method gave very high average accuracies of 92.94 and 96.74% on yeast and human datasets, respectively. Meanwhile, we compared it with the state-of-the-art support vector machine (SVM) classifier and other existing methods on human and yeast datasets, respectively. Comparative results indicated that our approach is very promising and may provide a cost-effective alternative for predicting SIPs. In addition, we developed a freely available web server called WELM-LAG-SIPs to predict SIPs. The web server is available at http://219.219.62.123:8888/WELMLAG/ .

  14. Bayesian statistical modelling of human protein interaction network incorporating protein disorder information

    Directory of Open Access Journals (Sweden)

    Eils Roland

    2010-01-01

    Full Text Available Abstract Background We present a statistical method of analysis of biological networks based on the exponential random graph model, namely p2-model, as opposed to previous descriptive approaches. The model is capable to capture generic and structural properties of a network as emergent from local interdependencies and uses a limited number of parameters. Here, we consider one global parameter capturing the density of edges in the network, and local parameters representing each node's contribution to the formation of edges in the network. The modelling suggests a novel definition of important nodes in the network, namely social, as revealed based on the local sociality parameters of the model. Moreover, the sociality parameters help to reveal organizational principles of the network. An inherent advantage of our approach is the possibility of hypotheses testing: a priori knowledge about biological properties of the nodes can be incorporated into the statistical model to investigate its influence on the structure of the network. Results We applied the statistical modelling to the human protein interaction network obtained with Y2H experiments. Bayesian approach for the estimation of the parameters was employed. We deduced social proteins, essential for the formation of the network, while incorporating into the model information on protein disorder. Intrinsically disordered are proteins which lack a well-defined three-dimensional structure under physiological conditions. We predicted the fold group (ordered or disordered of proteins in the network from their primary sequences. The network analysis indicated that protein disorder has a positive effect on the connectivity of proteins in the network, but do not fully explains the interactivity. Conclusions The approach opens a perspective to study effects of biological properties of individual entities on the structure of biological networks.

  15. A guild of 45 CRISPR-associated (Cas protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.

    Directory of Open Access Journals (Sweden)

    Daniel H Haft

    2005-11-01

    Full Text Available Clustered regularly interspaced short palindromic repeats (CRISPRs are a family of DNA direct repeats found in many prokaryotic genomes. Repeats of 21-37 bp typically show weak dyad symmetry and are separated by regularly sized, nonrepetitive spacer sequences. Four CRISPR-associated (Cas protein families, designated Cas1 to Cas4, are strictly associated with CRISPR elements and always occur near a repeat cluster. Some spacers originate from mobile genetic elements and are thought to confer "immunity" against the elements that harbor these sequences. In the present study, we have systematically investigated uncharacterized proteins encoded in the vicinity of these CRISPRs and found many additional protein families that are strictly associated with CRISPR loci across multiple prokaryotic species. Multiple sequence alignments and hidden Markov models have been built for 45 Cas protein families. These models identify family members with high sensitivity and selectivity and classify key regulators of development, DevR and DevS, in Myxococcus xanthus as Cas proteins. These identifications show that CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a repeat cluster or filling the region between two repeat clusters. Distinctive subsets of the collection of Cas proteins recur in phylogenetically distant species and correlate with characteristic repeat periodicity. The analyses presented here support initial proposals of mobility of these units, along with the likelihood that loci of different subtypes interact with one another as well as with host cell defensive, replicative, and regulatory systems. It is evident from this analysis that CRISPR/cas loci are larger, more complex, and more heterogeneous than previously appreciated.

  16. Managing a world that not exists never again. Are you ready to fight in the Information Society?

    Directory of Open Access Journals (Sweden)

    Yordan Sedeño

    2007-07-01

    Full Text Available While much is new and exciting, many of the changes that seem so profound are actually superficial. The principles of economics and wealth creation endure. However, the new business climate has undermined traditional management practices and it has made the economic management techniques of information technology more relevant than ever before. The bad or lack use of the information nowadays to know all happened, is happening and will happen in a future can drive you to bankrupts. That is why, in the Information Society, how it’s called, all you Information Technology have to work in function to manage all the information that is important for you organization to know all about your environment. The use of the Information technology is very important to keep alive in this competitive business world. For a lot of managers all this is no more than a new “Buzzword”; but this business era has taught us that all them is wrong.

  17. Integration of relational and hierarchical network information for protein function prediction

    Directory of Open Access Journals (Sweden)

    Jiang Xiaoyu

    2008-08-01

    Full Text Available Abstract Background In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most existing technologies pursue this task as a classification problem, on a term-by-term basis, for each term in a database, such as the Gene Ontology (GO database, a popular rigorous vocabulary for biological functions. However, ontology structures are essentially hierarchies, with certain top to bottom annotation rules which protein function predictions should in principle follow. Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions. Results We propose a probabilistic framework to integrate information in relational data, in the form of a protein-protein interaction network, and a hierarchically structured database of terms, in the form of the GO database, for the purpose of protein function prediction. At the heart of our framework is a factorization of local neighborhood information in the protein-protein interaction network across successive ancestral terms in the GO hierarchy. We introduce a classifier within this framework, with computationally efficient implementation, that produces GO-term predictions that naturally obey a hierarchical 'true-path' consistency from root to leaves, without the need for further post-processing. Conclusion A cross-validation study, using data from the yeast Saccharomyces cerevisiae, shows our method offers substantial improvements over both standard 'guilt-by-association' (i.e., Nearest-Neighbor and more refined Markov random field methods, whether in their original form or when post-processed to artificially impose 'true-path' consistency. Further analysis of the results indicates that these improvements are associated with increased predictive capabilities (i.e., increased

  18. Evidence for the Existence of One Antenna-Associated, Lipid-Dissolved and Two Protein-Bound Pools of Diadinoxanthin Cycle Pigments in Diatoms[C][W

    Science.gov (United States)

    Lepetit, Bernard; Volke, Daniela; Gilbert, Matthias; Wilhelm, Christian; Goss, Reimund

    2010-01-01

    We studied the localization of diadinoxanthin cycle pigments in the diatoms Cyclotella meneghiniana and Phaeodactylum tricornutum. Isolation of pigment protein complexes revealed that the majority of high-light-synthesized diadinoxanthin and diatoxanthin is associated with the fucoxanthin chlorophyll protein (FCP) complexes. The characterization of intact cells, thylakoid membranes, and pigment protein complexes by absorption and low-temperature fluorescence spectroscopy showed that the FCPs contain certain amounts of protein-bound diadinoxanthin cycle pigments, which are not significantly different in high-light and low-light cultures. The largest part of high-light-formed diadinoxanthin cycle pigments, however, is not bound to antenna apoproteins but located in a lipid shield around the FCPs, which is copurified with the complexes. This lipid shield is primarily composed of the thylakoid membrane lipid monogalactosyldiacylglycerol. We also show that the photosystem I (PSI) fraction contains a tightly connected FCP complex that is enriched in protein-bound diadinoxanthin cycle pigments. The peripheral FCP and the FCP associated with PSI are composed of different apoproteins. Tandem mass spectrometry analysis revealed that the peripheral FCP is composed mainly of the light-harvesting complex protein Lhcf and also significant amounts of Lhcr. The PSI fraction, on the other hand, shows an enrichment of Lhcr proteins, which are thus responsible for the diadinoxanthin cycle pigment binding. The existence of lipid-dissolved and protein-bound diadinoxanthin cycle pigments in the peripheral antenna and in PSI is discussed with respect to different specific functions of the xanthophylls. PMID:20935178

  19. Evidence for the existence of one antenna-associated, lipid-dissolved and two protein-bound pools of diadinoxanthin cycle pigments in diatoms.

    Science.gov (United States)

    Lepetit, Bernard; Volke, Daniela; Gilbert, Matthias; Wilhelm, Christian; Goss, Reimund

    2010-12-01

    We studied the localization of diadinoxanthin cycle pigments in the diatoms Cyclotella meneghiniana and Phaeodactylum tricornutum. Isolation of pigment protein complexes revealed that the majority of high-light-synthesized diadinoxanthin and diatoxanthin is associated with the fucoxanthin chlorophyll protein (FCP) complexes. The characterization of intact cells, thylakoid membranes, and pigment protein complexes by absorption and low-temperature fluorescence spectroscopy showed that the FCPs contain certain amounts of protein-bound diadinoxanthin cycle pigments, which are not significantly different in high-light and low-light cultures. The largest part of high-light-formed diadinoxanthin cycle pigments, however, is not bound to antenna apoproteins but located in a lipid shield around the FCPs, which is copurified with the complexes. This lipid shield is primarily composed of the thylakoid membrane lipid monogalactosyldiacylglycerol. We also show that the photosystem I (PSI) fraction contains a tightly connected FCP complex that is enriched in protein-bound diadinoxanthin cycle pigments. The peripheral FCP and the FCP associated with PSI are composed of different apoproteins. Tandem mass spectrometry analysis revealed that the peripheral FCP is composed mainly of the light-harvesting complex protein Lhcf and also significant amounts of Lhcr. The PSI fraction, on the other hand, shows an enrichment of Lhcr proteins, which are thus responsible for the diadinoxanthin cycle pigment binding. The existence of lipid-dissolved and protein-bound diadinoxanthin cycle pigments in the peripheral antenna and in PSI is discussed with respect to different specific functions of the xanthophylls.

  20. Modeling proteins using a super-secondary structure library and NMR chemical shift information.

    Science.gov (United States)

    Menon, Vilas; Vallat, Brinda K; Dybas, Joseph M; Fiser, Andras

    2013-06-04

    A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Protein in Urine: MedlinePlus Lab Test Information

    Science.gov (United States)

    ... this page: https://medlineplus.gov/labtests/proteininurine.html Protein in Urine To use the sharing features on this page, please enable JavaScript. What is a Protein in Urine Test? A protein in urine test ...

  2. Potential application of remote sensing in monitoring informal settlements in developing countries where complimentary data does not exist

    CSIR Research Space (South Africa)

    Busgeeth, K

    2008-04-01

    Full Text Available society. Factors that have led to the mushrooming of informal settlements in developing countries, most particularly in Africa, are massive rural urban migration, poverty and unequal distribution of wealth, poor land delivery systems, political...

  3. Summary of existing information pertinent to environmental contaminants and oil spills on breeding Atlantic Coast piping plovers

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Information regarding environmental contaminants and oil spills on breeding Atlantic Coast piping plovers (Charadrius melodus) was solicited from state and federal...

  4. Multi-crystallin complexes exist in the water-soluble high molecular weight protein fractions of aging normal and cataractous human lenses.

    Science.gov (United States)

    Srivastava, K; Chaves, J M; Srivastava, O P; Kirk, M

    2008-10-01

    The purpose of the study was to identify non-covalently held complexes that exist in the water-soluble high molecular weight (WS-HMW) protein fractions of normal human lenses of 20-year-old and 60- to 70-year-old, and in the age-matched 60- to 70-year-old cataractous lenses. The WS protein fractions were prepared from five pooled normal lenses of 20-year-old donors or five pooled lenses of 60- to 70-year-old donors or four pooled cataractous lenses (with nuclear opacity) of 60- to 70-year-old donors. Each WS protein fraction was subjected to size-exclusion chromatography using an Agarose A 5m column to recover the void volume WS-HMW protein fraction. A method known as blue-native polyacrylamide gel electrophoresis (BN-PAGE), which allows the isolation of large multi-protein complexes (MPCs) in their native state for further characterization, was used to separate such complexes from individual WS-HMW protein fractions. The protein species that existed as a complex were excised from a gel and trypsin-digested, and the amino acid sequences of the tryptic fragments analyzed by electrospray tandem mass spectrometry (ES-MS/MS). After the second-dimensional sodium dodecyl sulfate-PAGE during BN-PAGE, protein complexes containing a total of 16, 12, and 24 species with M(r) between 10 and 90 kDa were identified in the HMW protein fractions of normal lenses of 20-year-old, 60- to 70-year-old and cataractous lenses of 60- to 70-year-old donors, respectively. Based on the amino acid sequences of tryptic peptides of individual protein species in the complexes by the ES-MS/MS method, the presence of alpha-, beta-, and gamma-crystallin species along with beaded filament proteins (filensin and phakinin) was observed in the 20-year-old normal lenses. The 60- to 70-year-old normal lenses contained filensin and aldehyde dehydrogenase in addition to the above crystallins. Similarly, the age-matched cataractous lenses also contained the above crystallins and aldehyde dehydrogenase but

  5. Fission Meter Information Barrier Attribute Measurement System: Task 1 Report: Document existing Fission Meter neutron IB system

    Energy Technology Data Exchange (ETDEWEB)

    Kerr, P. L. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-02-28

    An SNM attribute Information Barrier (IB) system was developed for a 2011 US/UK Exercise. The system was modified and extensively tested in a 2013-2014 US-UK Measurement Campaign. This work demonstrated rapid deployment of an IB system for potential treaty use. The system utilizes an Ortec Fission Meter neutron multiplicity counter and custom computer code. The system demonstrates a proof-of-principle automated Pu-240 mass determination with an information barrier. After a software start command is issued, the system automatically acquires and downloads data, performs an analysis, and displays the results. This system conveys the results of a Pu mass threshold measurements in a way the does not reveal sensitive information. In full IB mode, only red/green ‘lights’ are displayed in the software. In test mode, more detailed information is displayed. The code can also read in, analyze, and display results from previously acquired or simulated data. Because the equipment is commercial-off-the-shelf (COTS), the system demonstrates a low-cost short-lead-time technology for treaty SNM attribute measurements. A deployed system will likely require integration of additional authentication and tamper-indicating technologies. This will be discussed for the project in this and future progress reports.

  6. Mapping geomorphology based on the information from existing geomorphological maps with a multiple-point geostatistics technique

    NARCIS (Netherlands)

    Babel, Lucie; Vannametee, Ekkamol; Hendriks, Martin; Schuur, Jasper; de Jong, Steven; Bierkens, Marinus; Karssenberg, Derek

    2014-01-01

    Geomorphological maps are valuable tools for studying land surfaceprocesses. Information obtained from the field geomorphological maps canbe, in turn, used in mapping geomorphology at another area. In thisstudy, we present an application of the multiple-point geostatistics(MPG) technique in

  7. Hydroxyl radical "footprinting": high-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein.

    OpenAIRE

    Tullius, T D; Dombroski, B A

    1986-01-01

    A method has been developed for making "footprints" of proteins bound to DNA. The hydroxyl radical, generated by reduction of hydrogen peroxide by iron(II), is the reagent used to cut the DNA. Hydroxyl radical breaks the backbone of DNA with almost no sequence dependence, so all backbone positions may be monitored for contact with protein. In addition to defining the DNA sequence in contact with the protein, hydroxyl radical footprints embody structural information about the DNA-protein compl...

  8. Implementation of an anonymisation tool for clinical trials using a clinical trial processor integrated with an existing trial patient data information system

    NARCIS (Netherlands)

    Aryanto, Kadek Y. E.; Broekema, Andre; Oudkerk, Matthijs; van Ooijen, Peter M. A.

    To present an adapted Clinical Trial Processor (CTP) test set-up for receiving, anonymising and saving Digital Imaging and Communications in Medicine (DICOM) data using external input from the original database of an existing clinical study information system to guide the anonymisation process. Two

  9. An Advancement To The Security Level Through Galois Field In The Existing Password Based Technique Of Hiding Classified Information In Images

    Directory of Open Access Journals (Sweden)

    Mita Kosode

    2015-06-01

    Full Text Available Abstract In this paper we are using the existing passcode based approach of hiding classified information in images with addition of the Galois field theorywhich is advancing the security level to make this combination method extremely difficult to intercept and useful for open channel communication while maintaining the losses and high speed transmission.

  10. Family planning 2011: better use of existing methods, new strategies and more informed choices for female contraception.

    Science.gov (United States)

    Crosignani, Pier Giorgio; Glasier, Anna

    2012-01-01

    BACKGROUND This paper explores recent developments in female contraception, using them to illustrate how adaptation of existing methods, improved service delivery and understanding contraceptive behaviour might increase contraceptive uptake and correct and consistent use, and how the development of new methods holds some promise for capitalizing on the potential non-contraceptive benefits. METHODS Searches were performed in Medline and other databases. Selection criteria included high-quality studies and studies relevant to clinical reproductive medicine. Summaries were presented and discussed by the European Society of Human Reproduction and Embryology (ESHRE) Workshop Group. RESULTS The topics discussed include: adapted regimens for combined oral contraceptive pills, non-invasive methods of female sterilization, the need to improve the awareness of pregnancy risk to increase the use of emergency contraception, improvements in the evidence base for the safety and service delivery of intrauterine methods, emphasis on the potential benefits of combined oral contraceptives for women with hirsutism and acne, the potential of female sterilization to prevent ovarian cancer, and the promise of anti-progesterones and new approaches to dual protection. CONCLUSIONS Although great strides have been made in recent years in increasing contraceptive use among women in many countries where contraceptive prevalence is low or there is a high unmet need for contraception, much more can, and needs to, be done.

  11. Indoor air quality in mechanically ventilated residential dwellings/low-rise buildings: A review of existing information

    DEFF Research Database (Denmark)

    Aganovic, Amar; Hamon, Mathieu; Kolarik, Jakub

    Mechanical ventilation has become a mandatory requirement in multiple European standards addressing indoor air quality (IAQ) and ventilation in residential dwellings (single family houses and low-rise apartment buildings). This article presents the state of the art study through a review of the e......Mechanical ventilation has become a mandatory requirement in multiple European standards addressing indoor air quality (IAQ) and ventilation in residential dwellings (single family houses and low-rise apartment buildings). This article presents the state of the art study through a review...... concentrations. The authors additionally noted that the literature frequently reported the role of improper maintenance and use on deterioration of IAQ in residential dwellings. The summarized data and comments may provide useful information for future guidelines related to ventilation strategies designed...

  12. Mapping geomorphology based on the information from existing geomorphological maps with a multiple-point geostatistics technique

    Science.gov (United States)

    Babel, Lucie; Vannametee, Ekkamol; Hendriks, Martin; Schuur, Jasper; de Jong, Steven; Bierkens, Marc; Karssenberg, Derek

    2014-05-01

    Geomorphological maps are valuable tools for studying land surface processes. Information obtained from the field geomorphological maps can be, in turn, used in mapping geomorphology at another area. In this study, we present an application of the multiple-point geostatistics (MPG) technique in geomorphological mapping. This technique makes use of the field geomorphological maps, together with the topographical data obtained from the Digital Elevation Model (DEM), to derive the knowledge on the formation of different geomorphological units in the landscape (e.g. river terrace, alluvial fan, badlands) as a basis in mapping areas with unknown geomorphology. This approach starts from characterizing the occurrence of each geomorphological class as a function of land surface attributes (i.e. attribute pattern), which consists of DEM derivatives discretized into classes (e.g. slope class) observed at that cell location, and geomorphology at multiple neighboring locations. The latter gives information on the spatial relation between geomorphological units. Number of cell occurrences per geomorphological class per attribute pattern is counted and stored in the frequency database, which will be subsequently used in the mapping. In the mapping stage, the algorithm assigns a realization of a geomorphological class to the target mapping cell, based on the probability function of geomorphological occurrences conditioned to the observed attribute pattern at the target mapping cell, as retrieved from the frequency database. The approach is tested to map the geomorphology in the 280 km2 Buëch catchment, French Alps. We use 4 morphometric attributes, extracted from a 37.5-m DEM resolution (i.e. height above the nearest drainage, slope gradient, profile curvature, and slope variability); and 2 non-morphometric attributes (i.e. geomorphology observed at 1-cell and 10-cells downstream from a cell of interest). Mapping is done using different frequency databases created from different

  13. GPCRDB: an information system for G protein-coupled receptors

    NARCIS (Netherlands)

    Isberg, V.; Vroling, B.; Kant, R.; Li, K.; Vriend, G.; Gloriam, D.

    2014-01-01

    For the past 20 years, the GPCRDB (G protein-coupled receptors database; http://www.gpcr.org/7tm/) has been a 'one-stop shop' for G protein-coupled receptor (GPCR)-related data. The GPCRDB contains experimental data on sequences, ligand-binding constants, mutations and oligomers, as well as many

  14. Representation of protein-sequence information by amino acid subalphabets

    DEFF Research Database (Denmark)

    Andersen, C.A.F.; Brunak, Søren

    2004-01-01

    Within computational biology, algorithms are constructed with the aim of extracting knowledge from biological data, in particular, data generated by the large genome projects, where gene and protein sequences are produced in high volume. In this article, we explore new ways of representing protei......-which now are common in proteins-might have emerged from simpler selections, or alphabets, in use earlier during the evolution of living organisms....

  15. Existing buildings

    DEFF Research Database (Denmark)

    Gram-Hanssen, Kirsten

    2014-01-01

    their homes. These policy measures include building regulations, energy tax and different types of incentives and information dissemination. The conclusion calls for new and innovative policy measures to cope with the realities of renovations of owner-occupied houses and how energy efficiency improvement...

  16. Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information

    Science.gov (United States)

    Lopes, Anne; Sacquin-Mora, Sophie; Dimitrova, Viktoriya; Laine, Elodie; Ponty, Yann; Carbone, Alessandra

    2013-01-01

    Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking simulations and binding site predictions resulting from evolutionary sequence analysis, are possible and realizable on hundreds of proteins with variate structures and interfaces. We demonstrated this on the 168 proteins of the Mintseris Benchmark 2.0. On the one hand, we evaluated the quality of the interaction signal and the contribution of docking information compared to evolutionary information showing that the combination of the two improves partner identification. On the other hand, since protein interactions usually occur in crowded environments with several competing partners, we realized a thorough analysis of the interactions of proteins with true partners but also with non-partners to evaluate whether proteins in the environment, competing with the true partner, affect its identification. We found three populations of proteins: strongly competing, never competing, and interacting with different levels of strength. Populations and levels of strength are numerically characterized and provide a signature for the behavior of a protein in the crowded environment. We showed that partner identification, to some extent, does not depend on the competing partners present in the environment, that certain biochemical classes of proteins are intrinsically easier to analyze than others, and that small proteins are not more promiscuous than large ones. Our approach brings to light that the knowledge of the binding site can be used to reduce the high computational cost of docking simulations with no consequence in the quality of the results, demonstrating the possibility to apply coarse-grain docking to datasets made of thousands of proteins. Comparison with all available large-scale analyses aimed to partner predictions is realized. We release the complete decoys set issued by coarse-grain docking simulations of both true and false interacting partners, and their evolutionary

  17. Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information

    Directory of Open Access Journals (Sweden)

    Pedamallu Chandra Sekhar

    2010-08-01

    Full Text Available Abstract Background Protein-protein interactions are crucially important for cellular processes. Knowledge of these interactions improves the understanding of cell cycle, metabolism, signaling, transport, and secretion. Information about interactions can hint at molecular causes of diseases, and can provide clues for new therapeutic approaches. Several (usually expensive and time consuming experimental methods can probe protein - protein interactions. Data sets, derived from such experiments make the development of prediction methods feasible, and make the creation of protein-protein interaction network predicting tools possible. Methods Here we report the development of a simple open source program module (OpenPPI_predictor that can generate a putative protein-protein interaction network for target genomes. This tool uses the orthologous interactome network data from a related, experimentally studied organism. Results Results from our predictions can be visualized using the Cytoscape visualization software, and can be piped to downstream processing algorithms. We have employed our program to predict protein-protein interaction network for the human parasite roundworm Brugia malayi, using interactome data from the free living nematode Caenorhabditis elegans. Availability The OpenPPI_predictor source code is available from http://tools.neb.com/~posfai/.

  18. A new computational strategy for identifying essential proteins based on network topological properties and biological information.

    Science.gov (United States)

    Qin, Chao; Sun, Yongqi; Dong, Yadong

    2017-01-01

    Essential proteins are the proteins that are indispensable to the survival and development of an organism. Deleting a single essential protein will cause lethality or infertility. Identifying and analysing essential proteins are key to understanding the molecular mechanisms of living cells. There are two types of methods for predicting essential proteins: experimental methods, which require considerable time and resources, and computational methods, which overcome the shortcomings of experimental methods. However, the prediction accuracy of computational methods for essential proteins requires further improvement. In this paper, we propose a new computational strategy named CoTB for identifying essential proteins based on a combination of topological properties, subcellular localization information and orthologous protein information. First, we introduce several topological properties of the protein-protein interaction (PPI) network. Second, we propose new methods for measuring orthologous information and subcellular localization and a new computational strategy that uses a random forest prediction model to obtain a probability score for the proteins being essential. Finally, we conduct experiments on four different Saccharomyces cerevisiae datasets. The experimental results demonstrate that our strategy for identifying essential proteins outperforms traditional computational methods and the most recently developed method, SON. In particular, our strategy improves the prediction accuracy to 89, 78, 79, and 85 percent on the YDIP, YMIPS, YMBD and YHQ datasets at the top 100 level, respectively.

  19. Conservation of Shannon's redundancy for proteins. [information theory applied to amino acid sequences

    Science.gov (United States)

    Gatlin, L. L.

    1974-01-01

    Concepts of information theory are applied to examine various proteins in terms of their redundancy in natural originators such as animals and plants. The Monte Carlo method is used to derive information parameters for random protein sequences. Real protein sequence parameters are compared with the standard parameters of protein sequences having a specific length. The tendency of a chain to contain some amino acids more frequently than others and the tendency of a chain to contain certain amino acid pairs more frequently than other pairs are used as randomness measures of individual protein sequences. Non-periodic proteins are generally found to have random Shannon redundancies except in cases of constraints due to short chain length and genetic codes. Redundant characteristics of highly periodic proteins are discussed. A degree of periodicity parameter is derived.

  20. NEP1 orthologs encoding necrosis and ethylene inducing proteins exist as a multigene family in Phytophthora megakarya, causal agent of black pod disease on cacao.

    Science.gov (United States)

    Bae, Hanhong; Bowers, John H; Tooley, Paul W; Bailey, Bryan A

    2005-12-01

    Phvytophthora megakarya is a devastating oomycete pathogen that causes black pod disease in cacao. Phytophthora species produce a protein that has a similar sequence to the necrosis and ethylene inducing protein (Nep1) of Fusarium oxysporum. Multiple copies of NEP1 orthologs (PmegNEP) have been identified in P. megakarya and four other Phytophthora species (P. citrophthora, P. capsici, P. palmivora, and P. sojae). Genome database searches confirmed the existence of multiple copies of NEP1 orthologs in P. sojae and P. ramorum. In this study, nine different PmegNEP orthologs from P. megakarya strain Mk-1 were identified and analyzed. Of these nine orthologs, six were expressed in mycelium and in P. megakarya zoospore-infected cacao leaf tissue. The remaining two clones are either regulated differently, or are nonfunctional genes. Sequence analysis revealed that six PmegNEP orthologs were organized in two clusters of three orthologs each in the P. megakarya genome. Evidence is presented for the instability in the P. megakarya genome resulting from duplications, inversions, and fused genes resulting in multiple NEP1 orthologs. Traits characteristic of the Phytophthora genome, such as the clustering of NEP1 orthologs, the lack of CATT and TATA boxes, the lack of introns, and the short distance between ORFs were also observed.

  1. Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection.

    Science.gov (United States)

    Liu, Bin; Zhang, Deyuan; Xu, Ruifeng; Xu, Jinghao; Wang, Xiaolong; Chen, Qingcai; Dong, Qiwen; Chou, Kuo-Chen

    2014-02-15

    Owing to its importance in both basic research (such as molecular evolution and protein attribute prediction) and practical application (such as timely modeling the 3D structures of proteins targeted for drug development), protein remote homology detection has attracted a great deal of interest. It is intriguing to note that the profile-based approach is promising and holds high potential in this regard. To further improve protein remote homology detection, a key step is how to find an optimal means to extract the evolutionary information into the profiles. Here, we propose a novel approach, the so-called profile-based protein representation, to extract the evolutionary information via the frequency profiles. The latter can be calculated from the multiple sequence alignments generated by PSI-BLAST. Three top performing sequence-based kernels (SVM-Ngram, SVM-pairwise and SVM-LA) were combined with the profile-based protein representation. Various tests were conducted on a SCOP benchmark dataset that contains 54 families and 23 superfamilies. The results showed that the new approach is promising, and can obviously improve the performance of the three kernels. Furthermore, our approach can also provide useful insights for studying the features of proteins in various families. It has not escaped our notice that the current approach can be easily combined with the existing sequence-based methods so as to improve their performance as well. For users' convenience, the source code of generating the profile-based proteins and the multiple kernel learning was also provided at http://bioinformatics.hitsz.edu.cn/main/~binliu/remote/

  2. Protein structure and evolution: are they constrained globally by a principle derived from information theory?

    Science.gov (United States)

    Hatton, Leslie; Warr, Gregory

    2015-01-01

    That the physicochemical properties of amino acids constrain the structure, function and evolution of proteins is not in doubt. However, principles derived from information theory may also set bounds on the structure (and thus also the evolution) of proteins. Here we analyze the global properties of the full set of proteins in release 13-11 of the SwissProt database, showing by experimental test of predictions from information theory that their collective structure exhibits properties that are consistent with their being guided by a conservation principle. This principle (Conservation of Information) defines the global properties of systems composed of discrete components each of which is in turn assembled from discrete smaller pieces. In the system of proteins, each protein is a component, and each protein is assembled from amino acids. Central to this principle is the inter-relationship of the unique amino acid count and total length of a protein and its implications for both average protein length and occurrence of proteins with specific unique amino acid counts. The unique amino acid count is simply the number of distinct amino acids (including those that are post-translationally modified) that occur in a protein, and is independent of the number of times that the particular amino acid occurs in the sequence. Conservation of Information does not operate at the local level (it is independent of the physicochemical properties of the amino acids) where the influences of natural selection are manifest in the variety of protein structure and function that is well understood. Rather, this analysis implies that Conservation of Information would define the global bounds within which the whole system of proteins is constrained; thus it appears to be acting to constrain evolution at a level different from natural selection, a conclusion that appears counter-intuitive but is supported by the studies described herein.

  3. Ebolavirus Database: Gene and Protein Information Resource for Ebolaviruses

    Directory of Open Access Journals (Sweden)

    Rayapadi G. Swetha

    2016-01-01

    Full Text Available Ebola Virus Disease (EVD is a life-threatening haemorrhagic fever in humans. Even though there are many reports on EVD, the protein precursor functions and virulent factors of ebolaviruses remain poorly understood. Comparative analyses of Ebolavirus genomes will help in the identification of these important features. This prompted us to develop the Ebolavirus Database (EDB and we have provided links to various tools that will aid researchers to locate important regions in both the genomes and proteomes of Ebolavirus. The genomic analyses of ebolaviruses will provide important clues for locating the essential and core functional genes. The aim of EDB is to act as an integrated resource for ebolaviruses and we strongly believe that the database will be a useful tool for clinicians, microbiologists, health care workers, and bioscience researchers.

  4. Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

    DEFF Research Database (Denmark)

    Lenaerts, Tom; Ferkinghoff-Borg, Jesper; Stricher, Francois

    2008-01-01

    Background: Efficient communication between distant sites within a protein is essential for cooperative biological response. Although often associated with large allosteric movements, more subtle changes in protein dynamics can also induce long-range correlations. However, an appropriate formalism...... that directly relates protein structural dynamics to information exchange between functional sites is still lacking. Results: Here we introduce a method to analyze protein dynamics within the framework of information theory and show that signal transduction within proteins can be considered as a particular...... distal communication is achieved. We illustrate the approach by analyzing information transfer by the SH2 domain of Fyn tyrosine kinase, obtained from Monte Carlo dynamics simulations. Our analysis reveals that the Fyn SH2 domain forms a noisy communication channel that couples residues located...

  5. Updating flood maps efficiently using existing hydraulic models, very-high-accuracy elevation data, and a geographic information system; a pilot study on the Nisqually River, Washington

    Science.gov (United States)

    Jones, Joseph L.; Haluska, Tana L.; Kresch, David L.

    2001-01-01

    A method of updating flood inundation maps at a fraction of the expense of using traditional methods was piloted in Washington State as part of the U.S. Geological Survey Urban Geologic and Hydrologic Hazards Initiative. Large savings in expense may be achieved by building upon previous Flood Insurance Studies and automating the process of flood delineation with a Geographic Information System (GIS); increases in accuracy and detail result from the use of very-high-accuracy elevation data and automated delineation; and the resulting digital data sets contain valuable ancillary information such as flood depth, as well as greatly facilitating map storage and utility. The method consists of creating stage-discharge relations from the archived output of the existing hydraulic model, using these relations to create updated flood stages for recalculated flood discharges, and using a GIS to automate the map generation process. Many of the effective flood maps were created in the late 1970?s and early 1980?s, and suffer from a number of well recognized deficiencies such as out-of-date or inaccurate estimates of discharges for selected recurrence intervals, changes in basin characteristics, and relatively low quality elevation data used for flood delineation. FEMA estimates that 45 percent of effective maps are over 10 years old (FEMA, 1997). Consequently, Congress has mandated the updating and periodic review of existing maps, which have cost the Nation almost 3 billion (1997) dollars. The need to update maps and the cost of doing so were the primary motivations for piloting a more cost-effective and efficient updating method. New technologies such as Geographic Information Systems and LIDAR (Light Detection and Ranging) elevation mapping are key to improving the efficiency of flood map updating, but they also improve the accuracy, detail, and usefulness of the resulting digital flood maps. GISs produce digital maps without manual estimation of inundated areas between

  6. Sequence coevolution between RNA and protein characterized by mutual information between residue triplets.

    Directory of Open Access Journals (Sweden)

    Relly Brandman

    Full Text Available Coevolving residues in a multiple sequence alignment provide evolutionary clues of biophysical interactions in 3D structure. Despite a rich literature describing amino acid coevolution within or between proteins and nucleic acid coevolution within RNA, to date there has been no direct evidence of coevolution between protein and RNA. The ribosome, a structurally conserved macromolecular machine composed of over 50 interacting protein and RNA chains, provides a natural example of RNA/protein interactions that likely coevolved. We provide the first direct evidence of RNA/protein coevolution by characterizing the mutual information in residue triplets from a multiple sequence alignment of ribosomal protein L22 and neighboring 23S RNA. We define residue triplets as three positions in the multiple sequence alignment, where one position is from the 23S RNA and two positions are from the L22 protein. We show that residue triplets with high mutual information are more likely than residue doublets to be proximal in 3D space. Some high mutual information residue triplets cluster in a connected series across the L22 protein structure, similar to patterns seen in protein coevolution. We also describe RNA nucleotides for which switching from one nucleotide to another (or between purines and pyrimidines results in a change in amino acid distribution for proximal amino acid positions. Multiple crystal structures for evolutionarily distinct ribosome species can provide structural evidence for these differences. For one residue triplet, a pyrimidine in one species is a purine in another, and RNA/protein hydrogen bonds are present in one species but not the other. The results provide the first direct evidence of RNA/protein coevolution by using higher order mutual information, suggesting that biophysical constraints on interacting RNA and protein chains are indeed a driving force in their evolution.

  7. Discovery of a novel functional leptin protein (LEP) in zebra finches: evidence for the existence of an authentic avian leptin gene predominantly expressed in the brain and pituitary.

    Science.gov (United States)

    Huang, Guian; Li, Juan; Wang, Hongning; Lan, Xinyu; Wang, Yajun

    2014-09-01

    Leptin (LEP) is reported to play important roles in controlling energy balance in vertebrates, including birds. However, it remains an open question whether an authentic "LEP gene" exists and functions in birds. Here, we identified and characterized a LEP gene (zebra finch LEP [zbLEP]) encoding a 172-amino acid precursor in zebra finches. Despite zbLEP showing limited amino acid sequence identity (26%-29%) to human and mouse LEPs, synteny analysis proved that zbLEP is orthologous to mammalian LEP. Using a pAH32 luciferase reporter system and Western blot analysis, we demonstrated that the recombinant zbLEP protein could potently activate finch and chicken LEP receptors (zbLEPR; cLEPR) expressed in human embryonic kidney 293 cells and enhance signal transducer and activator of transcription 3 phosphorylation, further indicating that zbLEP is a functional ligand for avian LEPRs. Interestingly, quantitative real-time RT-PCR revealed that zbLEP mRNA is expressed nearly exclusively in the pituitary and various brain regions but undetectable in adipose tissue and liver, whereas zbLEPR mRNA is widely expressed in adult finch tissues examined with abundant expression noted in pituitary, implying that unlike mammalian LEP, finch LEP may not act as an adipocyte-derived signal to control energy balance. As in finches, a LEP highly homologous to zbLEP was also identified in budgerigar genome. Strikingly, finch and budgerigar LEPs show little homology with chicken LEP (cLEP) previously reported, suggesting that the so-called cLEP is incorrect. Collectively, our data provide convincing evidence for the existence of an authentic functional LEP in avian species and suggest an important role of brain- and pituitary-derived LEP played in vertebrates.

  8. Antenatal care for healthy pregnant women: a mapping of interventions from existing guidelines to inform the development of new WHO guidance on antenatal care.

    Science.gov (United States)

    Abalos, E; Chamillard, M; Diaz, V; Tuncalp, Ӧ; Gülmezoglu, A M

    2016-03-01

    The World Health Organization (WHO) is in the process of updating antenatal care (ANC) guidelines. To map the existing clinical practice guidelines related to routine ANC for healthy women and to summarise all practices considered during routine ANC. A systematic search in four databases for all clinical practice guidelines published after January 2000. Two researchers independently assessed the list of potentially eligible publications. Information on scope of the guideline, type of practice, associated gestational age, recommendation type and the source of evidence were mapped. Of 1866 references, we identified 85 guidelines focusing on the ANC period: 15 pertaining to routine ANC and 70 pertaining to specific situations. A total of 135 interventions from routine ANC guidelines were extracted, and categorised as clinical interventions (n = 80), screening/diagnostic procedures (n = 47) and health systems related (n = 8). Screening interventions, (syphilis, anaemia) were the most common practices. Within the 70 specific situation guidelines, 102 recommendations were identified. Overall, for 33 (out of 171) interventions there were conflicting recommendations provided by the different guidelines. Mapping the current guidelines including practices related to routine ANC informed the scoping phase for the WHO guideline for ANC. Our analysis indicates that guideline development processes may lead to different recommendations, due to context, evidence base or assessment of evidence. It would be useful for guideline developers to map and refer to other similar guidelines and, where relevant, explore the discrepancies in recommendations and others. We identified existing ANC guidelines and mapped scope, practices, recommendations and source of evidence. © 2015 The Authors. BJOG An International Journal of Obstetrics and Gynaecology published by John Wiley & Sons Ltd on behalf of Royal College of Obstetricians and Gynaecologists.

  9. Deduction of structural information of interfacial proteins by combined vibrational spectroscopic methods.

    Science.gov (United States)

    Wang, Jie; Paszti, Zoltan; Clarke, Matthew L; Chen, Xiaoyun; Chen, Zhan

    2007-05-31

    We demonstrate both theoretically and experimentally that the combination of vibrational spectroscopic techniques on samples can be used to deduce more detailed structural information of interfacial proteins and peptides. Such an approach can be used to elucidate structures of proteins or peptides at interfaces, such as at the solid/liquid interface or in cell membranes. We also discuss that the controlled perturbations may provide more measured parameters for structural studies on such proteins and peptides. In this paper, we will demonstrate that optical spectroscopic techniques such as polarized Fourier transform infrared spectroscopy (FTIR), sum frequency generation (SFG) vibrational spectroscopy, and higher order nonlinear vibrational spectroscopies can be used to deduce different and complementary structural information of molecules at interfaces (e.g., orientation information of certain functional groups and secondary structures of interfacial proteins). Also, we believe that controlled perturbations on samples, such as variation of sample temperature, application of electrical fields, and alternation of substrate roughness, can provide more detailed information regarding the interfacial structures of proteins and peptides. The development of nonlinear vibrational spectroscopies, such as SFG and four-wave mixing vibrational spectroscopy, to examine interfacial protein and peptide structures, and introduction of external perturbations on samples should be able to substantially advance our knowledge in understanding structures and thus functions of proteins and peptides at interfaces.

  10. Prediction of hot spots in protein interfaces using extreme learning machines with the information of spatial neighbour residues.

    Science.gov (United States)

    Wang, Lin; Zhang, Wenjuan; Gao, Qiang; Xiong, Congcong

    2014-08-01

    The identification of hot spots, a small subset of protein interfaces that accounts for the majority of binding free energy, is becoming increasingly important for the research on protein-protein interaction and drug design. For each interface residue or target residue to be predicted, the authors extract hybrid features which incorporate a wide range of information of the target residue and its spatial neighbor residues, that is, the nearest contact residue in the other face (mirror-contact residue) and the nearest contact residue in the same face (intra-contact residue). Here, feature selection is performed using random forests to avoid over-fitting. Thereafter, the extreme learning machine is employed to effectively integrate these hybrid features for predicting hot spots in protein interfaces. By the 5-fold cross validation in the training set, their method can achieve accuracy (ACC) of 82.1% and Matthew's correlation coefficient (MCC) of 0.459, and outperforms some alternative machine learning methods in the comparison study. Furthermore, their method achieves ACC of 76.8% and MCC of 0.401 in the independent test set, and is more effective than the major existing hot spot predictors. Their prediction method offers a powerful tool for uncovering candidate residues in the studies of alanine scanning mutagenesis for functional protein interaction sites.

  11. RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information.

    Science.gov (United States)

    Ghosh, Pritha; Mathew, Oommen K; Sowdhamini, Ramanathan

    2016-10-07

    RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies. It will be useful to obtain an early understanding and association of RNA-binding property of sequences of gene products. Here, we report a web server, RStrucFam, to predict the structure, type of cognate RNA(s) and function(s) of proteins, where possible, from mere sequence information. The web server employs Hidden Markov Model scan (hmmscan) to enable association to a back-end database of structural and sequence families. The database (HMMRBP) comprises of 437 HMMs of RBP families of known structure that have been generated using structure-based sequence alignments and 746 sequence-centric RBP family HMMs. The input protein sequence is associated with structural or sequence domain families, if structure or sequence signatures exist. In case of association of the protein with a family of known structures, output features like, multiple structure-based sequence alignment (MSSA) of the query with all others members of that family is provided. Further, cognate RNA partner(s) for that protein, Gene Ontology (GO) annotations, if any and a homology model of the protein can be obtained. The users can also browse through the database for details pertaining to each family, protein or RNA and their related information based on keyword search or RNA motif search. RStrucFam is a web server that exploits structurally conserved features of RBPs, derived from known family members and imprinted in mathematical profiles, to predict putative RBPs from sequence information. Proteins that fail to associate with such structure-centric families are further queried against the sequence-centric RBP family HMMs in the HMMRBP database. Further, all other essential

  12. MIToS.jl: mutual information tools for protein sequence analysis in the Julia language

    DEFF Research Database (Denmark)

    Zea, Diego J.; Anfossi, Diego; Nielsen, Morten

    2017-01-01

    Motivation: MIToS is an environment for mutual information analysis and a framework for protein multiple sequence alignments (MSAs) and protein structures (PDB) management in Julia language. It integrates sequence and structural information through SIFTS, making Pfam MSAs analysis straightforward...... and Implementation: The software is totally implemented in Julia and supported for Linux, OS X and Windows. It’s freely available on GitHub under MIT license: http://mitos.leloir.org.ar. Contacts:diegozea@gmail.com or cmb@leloir.org.ar Supplementary information: Supplementary data are available at Bioinformatics...

  13. C-reactive protein is differentially modulated by co-existing infections, vitamin deficiencies and maternal factors in pregnant and lactating indigenous Panamanian women.

    Science.gov (United States)

    González-Fernández, Doris; Pons, Emérita Del Carmen; Rueda, Delfina; Sinisterra, Odalis Teresa; Murillo, Enrique; Scott, Marilyn E; Koski, Kristine G

    2017-06-02

    The usefulness of C-reactive protein (CRP) as a non-specific marker of inflammation during pregnancy and lactation is unclear in impoverished populations where co-existing infections and vitamin deficiencies are common. This cross-sectional study in Panama recruited 120 pregnant and 99 lactating Ngäbe-Buglé women from 14 communities in rural Panama. Obstetric history, indoor wood smoke exposure, fieldwork, BMI, vitamins A, B12, D, and folic acid, and inflammation markers (CRP, neutrophil/lymphocyte ratio (NLR), plateletcrit and cytokines) were measured. Multiple regressions explored both associations of CRP with other inflammatory markers and associations of CRP and elevated CRP based on trimester-specific cut-offs with maternal factors, infections and vitamin deficiencies. CRP was higher in pregnancy (51.4 ± 4.7 nmol/L) than lactation (27.8 ± 3.5 nmol/L) and was elevated above trimester specific cut-offs in 21% of pregnant and 30% of lactating women. Vitamin deficiencies were common (vitamin A 29.6%; vitamin D 68.5%; vitamin B12 68%; folic acid 25.5%) and over 50% of women had two or more concurrent deficiencies as well as multiple infections. Multiple regression models highlighted differences in variables associated with CRP between pregnancy and lactation. In pregnancy, CRP was positively associated with greater indoor wood smoke exposure, caries and hookworm and negatively associated with Ascaris and vaginal Lactobacillus and Bacteroides/Gardnerella scores. Consistent with this, greater wood smoke exposure, caries as well as higher diplococcal infection score increased the odds of trimester-elevated CRP concentrations whereas longer gestational age lowered the likelihood of a trimester-elevated CRP. During lactation, folic acid deficiency was associated with higher CRP whereas parity, number of eosinophils and Mobiluncus score were associated with lower CRP. Also, a higher BMI and Trichomonas vaginalis score increased the likelihood of an elevated

  14. ABIOGENIC INFORMATION COUPLING BETWEEN NUCLEIC ACID AND PROTEIN,OR, HOW PROTEIN AND DNA WERE MARRIED

    Energy Technology Data Exchange (ETDEWEB)

    Calvin, Melvin

    1968-12-01

    There is now experimental evidence for selectivity between the amino acid and the nucleic acid base which is the beginning of the chemical translation process from one linear system to the other. The linear system of the nucleic acid is, of course, an excellent place to store the information, whereas the linear system of the polypeptide, on the other hand, is the versatile system which can perform many different types of reactions but is unable to store information reliably. The experiments the author has described here may represent the beginning of the method of coupling of those two essential qualities which are required for the generation and evolution of a living organism.

  15. Synthesis and Comparison of Baseline Avian and Bat Use, Raptor Nesting and Mortality Information from Proposed and Existing Wind Developments: Final Report.

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, Wallace P.

    2002-12-01

    Primarily due to concerns generated from observed raptor mortality at the Altamont Pass (CA) wind plant, one of the first commercial electricity generating wind plants in the U.S., new proposed wind projects both within and outside of California have received a great deal of scrutiny and environmental review. A large amount of baseline and operational monitoring data have been collected at proposed and existing U.S. wind plants. The primary use of the avian baseline data collected at wind developments has been to estimate the overall project impacts (e.g., very low, low, moderate, and high relative mortality) on birds, especially raptors and sensitive species (e.g., state and federally listed species). In a few cases, these data have also been used for guiding placement of turbines within a project boundary. This new information has strengthened our ability to accurately predict and mitigate impacts from new projects. This report should assist various stakeholders in the interpretation and use of this large information source in evaluating new projects. This report also suggests that the level of baseline data (e.g., avian use data) required to adequately assess expected impacts of some projects may be reduced. This report provides an evaluation of the ability to predict direct impacts on avian resources (primarily raptors and waterfowl/waterbirds) using less than an entire year of baseline avian use data (one season, two seasons, etc.). This evaluation is important because pre-construction wildlife surveys can be one of the most time-consuming aspects of permitting wind power projects. For baseline data, this study focuses primarily on standardized avian use data usually collected using point count survey methodology and raptor nest survey data. In addition to avian use and raptor nest survey data, other baseline data is usually collected at a proposed project to further quantify potential impacts. These surveys often include vegetation mapping and state or

  16. Relating sequence encoded information to form and function of intrinsically disordered proteins.

    Science.gov (United States)

    Das, Rahul K; Ruff, Kiersten M; Pappu, Rohit V

    2015-06-01

    Intrinsically disordered proteins (IDPs) showcase the importance of conformational plasticity and heterogeneity in protein function. We summarize recent advances that connect information encoded in IDP sequences to their conformational properties and functions. We focus on insights obtained through a combination of atomistic simulations and biophysical measurements that are synthesized into a coherent framework using polymer physics theories. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. MIToS.jl: mutual information tools for protein sequence analysis in the Julia language.

    Science.gov (United States)

    Zea, Diego J; Anfossi, Diego; Nielsen, Morten; Marino-Buslje, Cristina

    2017-02-15

    MIToS is an environment for mutual information analysis and a framework for protein multiple sequence alignments (MSAs) and protein structures (PDB) management in Julia language. It integrates sequence and structural information through SIFTS, making Pfam MSAs analysis straightforward. MIToS streamlines the implementation of any measure calculated from residue contingency tables and its optimization and testing in terms of protein contact prediction. As an example, we implemented and tested a BLOSUM62-based pseudo-count strategy in mutual information analysis. The software is totally implemented in Julia and supported for Linux, OS X and Windows. It's freely available on GitHub under MIT license: http://mitos.leloir.org.ar . diegozea@gmail.com or cmb@leloir.org.ar. Supplementary data are available at Bioinformatics online.

  18. A reversible Renilla luciferase protein complementation assay for rapid identification of protein-protein interactions reveals the existence of an interaction network involved in xyloglucan biosynthesis in the plant Golgi apparatus.

    Science.gov (United States)

    Lund, Christian H; Bromley, Jennifer R; Stenbæk, Anne; Rasmussen, Randi E; Scheller, Henrik V; Sakuragi, Yumiko

    2015-01-01

    A growing body of evidence suggests that protein-protein interactions (PPIs) occur amongst glycosyltransferases (GTs) required for plant glycan biosynthesis (e.g. cell wall polysaccharides and N-glycans) in the Golgi apparatus, and may control the functions of these enzymes. However, identification of PPIs in the endomembrane system in a relatively fast and simple fashion is technically challenging, hampering the progress in understanding the functional coordination of the enzymes in Golgi glycan biosynthesis. To solve the challenges, we adapted and streamlined a reversible Renilla luciferase protein complementation assay (Rluc-PCA), originally reported for use in human cells, for transient expression in Nicotiana benthamiana. We tested Rluc-PCA and successfully identified luminescence complementation amongst Golgi-localizing GTs known to form a heterodimer (GAUT1 and GAUT7) and those which homooligomerize (ARAD1). In contrast, no interaction was shown between negative controls (e.g. GAUT7, ARAD1, IRX9). Rluc-PCA was used to investigate PPIs amongst Golgi-localizing GTs involved in biosynthesis of hemicelluloses. Although no PPI was identified among six GTs involved in xylan biosynthesis, Rluc-PCA confirmed three previously proposed interactions and identified seven novel PPIs amongst GTs involved in xyloglucan biosynthesis. Notably, three of the novel PPIs were confirmed by a yeast-based split-ubiquitin assay. Finally, Gateway-enabled expression vectors were generated, allowing rapid construction of fusion proteins to the Rluc reporters and epitope tags. Our results show that Rluc-PCA coupled with transient expression in N. benthamiana is a fast and versatile method suitable for analysis of PPIs between Golgi resident proteins in an easy and mid-throughput fashion in planta. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  19. Gene ontology-based protein function prediction by using sequence composition information.

    Science.gov (United States)

    Dong, Qiwen; Zhou, Shuigeng; Deng, Lei; Guan, Jihong

    2010-06-01

    The prediction of protein function is a difficult and important problem in computational biology. In this study, an efficient method is presented to predict protein function with sequence composition information. Four kinds of basic building blocks of protein sequences are investigated, including N-grams, binary profiles, PFAM domains and InterPro domains. The protein sequences are mapped into high-dimensional vectors by using the occurrence frequencies of each kind of building blocks. The resulting vectors are then taken as input to support vector machine to predict their function based on gene ontology. Experiments are conducted over the subset of GOA database. The experimental results show that the protein function can be predicted from primary sequence information. The method based on InterPro domains outperforms the other building blocks, and gets an overall accuracy of 0.87 and ROC score is 0.93. We also demonstrate that the use of feature extraction algorithms such as latent semantic analysis and nonnegative matrix factorization, can efficiently remove noise and improve the prediction efficiency without significantly degrading the performance. The results obtained here are helpful for the prediction of protein function by using only sequence information.

  20. Co-existence of scrapie prion protein types 1 and 2 in sporadic Creutzfeldt-Jakob disease: its effect on the phenotype and prion-type characteristics

    NARCIS (Netherlands)

    Cali, I.; Castellani, R.; Alshekhlee, A.; Cohen, Y.; Blevins, J.; Yuan, J.; Langeveld, J.P.M.; Parchi, P.; Safar, J.G.; Zou, W.Q.; Gambetti, P.

    2009-01-01

    Five phenotypically distinct subtypes have been identified in sporadic Creutzfeldt-Jakob disease (sCJD), based on the methionine/valine polymorphic genotype of codon 129 of the prion protein (PrP) gene and the presence of either one of the two protease K-resistant scrapie prion protein (PrPSc) types

  1. Minimum Information Loss Based Multi-kernel Learning for Flagellar Protein Recognition in Trypanosoma Brucei

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-12-01

    Trypanosma brucei (T. Brucei) is an important pathogen agent of African trypanosomiasis. The flagellum is an essential and multifunctional organelle of T. Brucei, thus it is very important to recognize the flagellar proteins from T. Brucei proteins for the purposes of both biological research and drug design. In this paper, we investigate computationally recognizing flagellar proteins in T. Brucei by pattern recognition methods. It is argued that an optimal decision function can be obtained as the difference of probability functions of flagella protein and the non-flagellar protein for the purpose of flagella protein recognition. We propose to learn a multi-kernel classification function to approximate this optimal decision function, by minimizing the information loss of such approximation which is measured by the Kull back-Leibler (KL) divergence. An iterative multi-kernel classifier learning algorithm is developed to minimize the KL divergence for the problem of T. Brucei flagella protein recognition, experiments show its advantage over other T. Brucei flagellar protein recognition and multi-kernel learning methods. © 2014 IEEE.

  2. Sedimentation velocity of intrinsically disordered proteins: what information can we actually obtain?

    Science.gov (United States)

    Scott, David J; Winzor, Donald J

    2012-01-01

    Intrinsically disordered proteins are a challenge to characterise structurally because of their innate flexibility. Hydrodynamic methods such as sedimentation velocity analytical ultracentrifugation have been proposed as methods for their characterisation. By examining in detail this assumption we show that although velocity measurements do yield information on gross conformation, the information is restricted to only the weight averaged sedimentation and diffusion coefficients of the conformational ensemble.

  3. PIE the search: searching PubMed literature for protein interaction information.

    Science.gov (United States)

    Kim, Sun; Kwon, Dongseop; Shin, Soo-Yong; Wilbur, W John

    2012-02-15

    Finding protein-protein interaction (PPI) information from literature is challenging but an important issue. However, keyword search in PubMed(®) is often time consuming because it requires a series of actions that refine keywords and browse search results until it reaches a goal. Due to the rapid growth of biomedical literature, it has become more difficult for biologists and curators to locate PPI information quickly. Therefore, a tool for prioritizing PPI informative articles can be a useful assistant for finding this PPI-relevant information. PIE (Protein Interaction information Extraction) the search is a web service implementing a competition-winning approach utilizing word and syntactic analyses by machine learning techniques. For easy user access, PIE the search provides a PubMed-like search environment, but the output is the list of articles prioritized by PPI confidence scores. By obtaining PPI-related articles at high rank, researchers can more easily find the up-to-date PPI information, which cannot be found in manually curated PPI databases. http://www.ncbi.nlm.nih.gov/IRET/PIE/.

  4. Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information.

    Science.gov (United States)

    Panwar, Bharat; Gupta, Sudheer; Raghava, Gajendra P S

    2013-02-07

    The vitamins are important cofactors in various enzymatic-reactions. In past, many inhibitors have been designed against vitamin binding pockets in order to inhibit vitamin-protein interactions. Thus, it is important to identify vitamin interacting residues in a protein. It is possible to detect vitamin-binding pockets on a protein, if its tertiary structure is known. Unfortunately tertiary structures of limited proteins are available. Therefore, it is important to develop in-silico models for predicting vitamin interacting residues in protein from its primary structure. In this study, first we compared protein-interacting residues of vitamins with other ligands using Two Sample Logo (TSL). It was observed that ATP, GTP, NAD, FAD and mannose preferred {G,R,K,S,H}, {G,K,T,S,D,N}, {T,G,Y}, {G,Y,W} and {Y,D,W,N,E} residues respectively, whereas vitamins preferred {Y,F,S,W,T,G,H} residues for the interaction with proteins. Furthermore, compositional information of preferred and non-preferred residues along with patterns-specificity was also observed within different vitamin-classes. Vitamins A, B and B6 preferred {F,I,W,Y,L,V}, {S,Y,G,T,H,W,N,E} and {S,T,G,H,Y,N} interacting residues respectively. It suggested that protein-binding patterns of vitamins are different from other ligands, and motivated us to develop separate predictor for vitamins and their sub-classes. The four different prediction modules, (i) vitamin interacting residues (VIRs), (ii) vitamin-A interacting residues (VAIRs), (iii) vitamin-B interacting residues (VBIRs) and (iv) pyridoxal-5-phosphate (vitamin B6) interacting residues (PLPIRs) have been developed. We applied various classifiers of SVM, BayesNet, NaiveBayes, ComplementNaiveBayes, NaiveBayesMultinomial, RandomForest and IBk etc., as machine learning techniques, using binary and Position-Specific Scoring Matrix (PSSM) features of protein sequences. Finally, we selected best performing SVM modules and obtained highest MCC of 0.53, 0.48, 0.61, 0

  5. Amino acid alphabet reduction preserves fold information contained in contact interactions in proteins.

    Science.gov (United States)

    Solis, Armando D

    2015-12-01

    To reduce complexity, understand generalized rules of protein folding, and facilitate de novo protein design, the 20-letter amino acid alphabet is commonly reduced to a smaller alphabet by clustering amino acids based on some measure of similarity. In this work, we seek the optimal alphabet that preserves as much of the structural information found in long-range (contact) interactions among amino acids in natively-folded proteins. We employ the Information Maximization Device, based on information theory, to partition the amino acids into well-defined clusters. Numbering from 2 to 19 groups, these optimal clusters of amino acids, while generated automatically, embody well-known properties of amino acids such as hydrophobicity/polarity, charge, size, and aromaticity, and are demonstrated to maintain the discriminative power of long-range interactions with minimal loss of mutual information. Our measurements suggest that reduced alphabets (of less than 10) are able to capture virtually all of the information residing in native contacts and may be sufficient for fold recognition, as demonstrated by extensive threading tests. In an expansive survey of the literature, we observe that alphabets derived from various approaches-including those derived from physicochemical intuition, local structure considerations, and sequence alignments of remote homologs-fare consistently well in preserving contact interaction information, highlighting a convergence in the various factors thought to be relevant to the folding code. Moreover, we find that alphabets commonly used in experimental protein design are nearly optimal and are largely coherent with observations that have arisen in this work. © 2015 Wiley Periodicals, Inc.

  6. Incorporating the type and direction information in predicting novel regulatory interactions between HIV-1 and human proteins using a biclustering approach

    Science.gov (United States)

    2014-01-01

    Background Discovering novel interactions between HIV-1 and human proteins would greatly contribute to different areas of HIV research. Identification of such interactions leads to a greater insight into drug target prediction. Some recent studies have been conducted for computational prediction of new interactions based on the experimentally validated information stored in a HIV-1-human protein-protein interaction database. However, these techniques do not predict any regulatory mechanism between HIV-1 and human proteins by considering interaction types and direction of regulation of interactions. Results Here we present an association rule mining technique based on biclustering for discovering a set of rules among human and HIV-1 proteins using the publicly available HIV-1-human PPI database. These rules are subsequently utilized to predict some novel interactions among HIV-1 and human proteins. For prediction purpose both the interaction types and direction of regulation of interactions, (i.e., virus-to-host or host-to-virus) are considered here to provide important additional information about the regulation pattern of interactions. We have also studied the biclusters and analyzed the significant GO terms and KEGG pathways in which the human proteins of the biclusters participate. Moreover the predicted rules have also been analyzed to discover regulatory relationship between some human proteins in course of HIV-1 infection. Some experimental evidences of our predicted interactions have been found by searching the recent literatures in PUBMED. We have also highlighted some human proteins that are likely to act against the HIV-1 attack. Conclusions We pose the problem of identifying new regulatory interactions between HIV-1 and human proteins based on the existing PPI database as an association rule mining problem based on biclustering algorithm. We discover some novel regulatory interactions between HIV-1 and human proteins. Significant number of predicted

  7. Prediction of membrane transport proteins and their substrate specificities using primary sequence information.

    Directory of Open Access Journals (Sweden)

    Nitish K Mishra

    Full Text Available Membrane transport proteins (transporters move hydrophilic substrates across hydrophobic membranes and play vital roles in most cellular functions. Transporters represent a diverse group of proteins that differ in topology, energy coupling mechanism, and substrate specificity as well as sequence similarity. Among the functional annotations of transporters, information about their transporting substrates is especially important. The experimental identification and characterization of transporters is currently costly and time-consuming. The development of robust bioinformatics-based methods for the prediction of membrane transport proteins and their substrate specificities is therefore an important and urgent task.Support vector machine (SVM-based computational models, which comprehensively utilize integrative protein sequence features such as amino acid composition, dipeptide composition, physico-chemical composition, biochemical composition, and position-specific scoring matrices (PSSM, were developed to predict the substrate specificity of seven transporter classes: amino acid, anion, cation, electron, protein/mRNA, sugar, and other transporters. An additional model to differentiate transporters from non-transporters was also developed. Among the developed models, the biochemical composition and PSSM hybrid model outperformed other models and achieved an overall average prediction accuracy of 76.69% with a Mathews correlation coefficient (MCC of 0.49 and a receiver operating characteristic area under the curve (AUC of 0.833 on our main dataset. This model also achieved an overall average prediction accuracy of 78.88% and MCC of 0.41 on an independent dataset.Our analyses suggest that evolutionary information (i.e., the PSSM and the AAIndex are key features for the substrate specificity prediction of transport proteins. In comparison, similarity-based methods such as BLAST, PSI-BLAST, and hidden Markov models do not provide accurate predictions

  8. The C proteins of HeLa 40S nuclear ribonucleoprotein particles exist as anisotropic tetramers of (C1)3 C2.

    OpenAIRE

    Barnett, S F; Friedman, D L; LeStourgeon, W M

    1989-01-01

    The C proteins (C1 and C2) of HeLa 40S heterogeneous nuclear ribonucleoprotein particles copurify under native conditions as a stable complex with a fixed molar protein ratio (S.F. Barnett, W.M. LeStourgeon, and D.L. Friedman, J. Biochem. Biophys. Methods 16:87-97, 1988). Gel filtration chromatography and velocity sedimentation analyses of these complexes revealed a large Stokes radius (6.2 nm) and a sedimentation coefficient of 5.8S. On the basis of these values and a partial specific volume...

  9. Unraveling the CHIP:Hsp70 complex as an information processor for protein quality control.

    Science.gov (United States)

    VanPelt, Jamie; Page, Richard C

    2017-02-01

    The CHIP:Hsp70 complex stands at the crossroads of the cellular protein quality control system. Hsp70 facilitates active refolding of misfolded client proteins, while CHIP directs ubiquitination of misfolded client proteins bound to Hsp70. The direct competition between CHIP and Hsp70 for the fate of misfolded proteins leads to the question: how does the CHIP:Hsp70 complex execute triage decisions that direct misfolded proteins for either refolding or degradation? The current body of literature points toward action of the CHIP:Hsp70 complex as an information processor that takes inputs in the form of client folding state, dynamics, and posttranslational modifications, then outputs either refolded or ubiquitinated client proteins. Herein we examine the CHIP:Hsp70 complex beginning with the structure and function of CHIP and Hsp70, followed by an examination of recent studies of the interactions and dynamics of the CHIP:Hsp70 complex. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Endogenous type II cGMP-dependent protein kinase exists as a dimer in membranes and can Be functionally distinguished from the type I isoforms

    NARCIS (Netherlands)

    A.B. Vaandrager (Arie); M.J. Edixhoven (Marcel); A.G. Bot (Alice); M.A. Kroos (Marian); T. Jarchau; S. Lohmann; H.G. Genieser; H.R. de Jonge (Hugo)

    1997-01-01

    textabstractIn mammalian tissues two types of cGMP-dependent protein kinase (cGK) have been identified. In contrast to the dimeric cGK I, cGK II purified from pig intestine was shown previously to behave as a monomer. However, recombinant rat cGK II was found to have

  11. Assessing Digital Information Literacy in Higher Education: A Review of Existing Frameworks and Assessments with Recommendations for Next-Generation Assessment. Research Report. ETS RR-16-32

    Science.gov (United States)

    Sparks, Jesse R.; Katz, Irvin R.; Beile, Penny M.

    2016-01-01

    Digital information literacy (DIL)--generally defined as the ability to obtain, understand, evaluate, and use information in a variety of digital technology contexts--is a critically important skill deemed necessary for success in higher education as well as in the global networked economy. To determine whether college graduates possess the…

  12. Towards an Online Bachelor of Information Science Degree Programme in a Nigerian University: Part 1--Lessons from the Literature and Existing Curricula

    Science.gov (United States)

    Ajiferuke, Isola; Tiamiyu, Mutawakilu; Longe, Folake; Nwagwu, Williams; Ogunsola, Kemi; Opesade, Adeola; Olatokun, Wole

    2012-01-01

    Training programmes for the information professions worldwide have been shifting and diversifying the scope of their claimed domains and curricula in order to empower their graduates with diverse knowledge and versatile technical skills required to compete successfully in the highly competitive job markets in the information industries. In line…

  13. Computing highly correlated positions using mutual information and graph theory for G protein-coupled receptors.

    Directory of Open Access Journals (Sweden)

    Sarosh N Fatakia

    Full Text Available G protein-coupled receptors (GPCRs are a superfamily of seven transmembrane-spanning proteins involved in a wide array of physiological functions and are the most common targets of pharmaceuticals. This study aims to identify a cohort or clique of positions that share high mutual information. Using a multiple sequence alignment of the transmembrane (TM domains, we calculated the mutual information between all inter-TM pairs of aligned positions and ranked the pairs by mutual information. A mutual information graph was constructed with vertices that corresponded to TM positions and edges between vertices were drawn if the mutual information exceeded a threshold of statistical significance. Positions with high degree (i.e. had significant mutual information with a large number of other positions were found to line a well defined inter-TM ligand binding cavity for class A as well as class C GPCRs. Although the natural ligands of class C receptors bind to their extracellular N-terminal domains, the possibility of modulating their activity through ligands that bind to their helical bundle has been reported. Such positions were not found for class B GPCRs, in agreement with the observation that there are not known ligands that bind within their TM helical bundle. All identified key positions formed a clique within the MI graph of interest. For a subset of class A receptors we also considered the alignment of a portion of the second extracellular loop, and found that the two positions adjacent to the conserved Cys that bridges the loop with the TM3 qualified as key positions. Our algorithm may be useful for localizing topologically conserved regions in other protein families.

  14. Computing highly correlated positions using mutual information and graph theory for G protein-coupled receptors.

    Science.gov (United States)

    Fatakia, Sarosh N; Costanzi, Stefano; Chow, Carson C

    2009-01-01

    G protein-coupled receptors (GPCRs) are a superfamily of seven transmembrane-spanning proteins involved in a wide array of physiological functions and are the most common targets of pharmaceuticals. This study aims to identify a cohort or clique of positions that share high mutual information. Using a multiple sequence alignment of the transmembrane (TM) domains, we calculated the mutual information between all inter-TM pairs of aligned positions and ranked the pairs by mutual information. A mutual information graph was constructed with vertices that corresponded to TM positions and edges between vertices were drawn if the mutual information exceeded a threshold of statistical significance. Positions with high degree (i.e. had significant mutual information with a large number of other positions) were found to line a well defined inter-TM ligand binding cavity for class A as well as class C GPCRs. Although the natural ligands of class C receptors bind to their extracellular N-terminal domains, the possibility of modulating their activity through ligands that bind to their helical bundle has been reported. Such positions were not found for class B GPCRs, in agreement with the observation that there are not known ligands that bind within their TM helical bundle. All identified key positions formed a clique within the MI graph of interest. For a subset of class A receptors we also considered the alignment of a portion of the second extracellular loop, and found that the two positions adjacent to the conserved Cys that bridges the loop with the TM3 qualified as key positions. Our algorithm may be useful for localizing topologically conserved regions in other protein families.

  15. Two applications of information extraction to biological science journal articles: enzyme interactions and protein structures.

    Science.gov (United States)

    Humphreys, K; Demetriou, G; Gaizauskas, R

    2000-01-01

    Information extraction technology, as defined and developed through the U.S. DARPA Message Understanding Conferences (MUCs), has proved successful at extracting information primarily from newswire texts and primarily in domains concerned with human activity. In this paper we consider the application of this technology to the extraction of information from scientific journal papers in the area of molecular biology. In particular, we describe how an information extraction system designed to participate in the MUC exercises has been modified for two bioinformatics applications: EMPathIE, concerned with enzyme and metabolic pathways; and PASTA, concerned with protein structure. Progress to date provides convincing grounds for believing that IE techniques will deliver novel and effective ways for scientists to make use of the core literature which defines their disciplines.

  16. Exploiting structural and topological information to improve prediction of RNA-protein binding sites

    Directory of Open Access Journals (Sweden)

    Yuan Zheng

    2009-10-01

    Full Text Available Abstract Background RNA-protein interactions are important for a wide range of biological processes. Current computational methods to predict interacting residues in RNA-protein interfaces predominately rely on sequence data. It is, however, known that interface residue propensity is closely correlated with structural properties. In this paper we systematically study information obtained from sequences and structures and compare their contributions in this prediction problem. Particularly, different geometrical and network topological properties of protein structures are evaluated to improve interface residue prediction accuracy. Results We have quantified the impact of structural information on the prediction accuracy in comparison to the purely sequence based approach using two machine learning techniques: Naïve Bayes classifiers and Support Vector Machines. The highest AUC of 0.83 was achieved by a Support Vector Machine, exploiting PSI-BLAST profile, accessible surface area, betweenness-centrality and retention coefficient as input features. Taking into account that our results are based on a larger non-redundant data set, the prediction accuracy is considerably higher than reported in previous, comparable studies. A protein-RNA interface predictor (PRIP and the data set have been made available at http://www.qfab.org/PRIP. Conclusion Graph-theoretic properties of residue contact maps derived from protein structures such as betweenness-centrality can supplement sequence or structure features to improve the prediction accuracy for binding residues in RNA-protein interactions. While Support Vector Machines perform better on this task, Naïve Bayes classifiers also have been found to achieve good prediction accuracies but require much less training time and are an attractive choice for large scale predictions.

  17. Discrepancy between mRNA and protein abundance: insight from information retrieval process in computers.

    Science.gov (United States)

    Wang, Degeng

    2008-12-01

    Discrepancy between the abundance of cognate protein and RNA molecules is frequently observed. A theoretical understanding of this discrepancy remains elusive, and it is frequently described as surprises and/or technical difficulties in the literature. Protein and RNA represent different steps of the multi-stepped cellular genetic information flow process, in which they are dynamically produced and degraded. This paper explores a comparison with a similar process in computers-multi-step information flow from storage level to the execution level. Functional similarities can be found in almost every facet of the retrieval process. Firstly, common architecture is shared, as the ribonome (RNA space) and the proteome (protein space) are functionally similar to the computer primary memory and the computer cache memory, respectively. Secondly, the retrieval process functions, in both systems, to support the operation of dynamic networks-biochemical regulatory networks in cells and, in computers, the virtual networks (of CPU instructions) that the CPU travels through while executing computer programs. Moreover, many regulatory techniques are implemented in computers at each step of the information retrieval process, with a goal of optimizing system performance. Cellular counterparts can be easily identified for these regulatory techniques. In other words, this comparative study attempted to utilize theoretical insight from computer system design principles as catalysis to sketch an integrative view of the gene expression process, that is, how it functions to ensure efficient operation of the overall cellular regulatory network. In context of this bird's-eye view, discrepancy between protein and RNA abundance became a logical observation one would expect. It was suggested that this discrepancy, when interpreted in the context of system operation, serves as a potential source of information to decipher regulatory logics underneath biochemical network operation.

  18. Proteomics informed by transcriptomics identifies novel secreted proteins in Dermacentor andersoni saliva

    Energy Technology Data Exchange (ETDEWEB)

    Mudenda, Lwiindi; Aguilar Pierle, Sebastian; Turse, Joshua E.; Scoles, Glen A.; Purvine, Samuel O.; Nicora, Carrie D.; Clauss, Therese RW; Ueti, Massaro W.; Brown, Wendy C.; Brayton, Kelly A.

    2014-08-07

    Dermacentor andersoni, known as the Rocky Mountain wood tick, is found in the western United States and transmits pathogens that cause diseases of veterinary and public health importance including Rocky Mountain spotted fever, tularemia, Colorado tick fever and bovine anaplasmosis. Tick saliva is known to modulate both innate and acquired immune responses, enabling ticks to feed for several days without detection. During feeding ticks subvert host defences such as hemostasis and inflammation, which would otherwise result in coagulation, wound repair and rejection of the tick. Molecular characterization of the proteins and pharmacological molecules secreted in tick saliva offers an opportunity to develop tick vaccines as an alternative to the use of acaricides, as well as new anti-inflammatory drugs. We performed proteomics informed by transcriptomics to identify D. andersoni saliva proteins that are secreted during feeding. The transcript data generated a database of 21,797 consensus sequences, which we used to identify 677 proteins secreted in the saliva of D. andersoni ticks fed for 2 and 5 days, following proteomic investigations of whole saliva using mass spectrometry. Salivary gland transcript levels of unfed ticks were compared with 2 and 5 day fed ticks to identify genes upregulated early during tick feeding. We cross-referenced the proteomic data with the transcriptomic data to identify 157 proteins of interest for immunomodulation and blood feeding. Proteins of unknown function as well as known immunomodulators were identified.

  19. Pathfinder to EXIST: ProtoEXIST

    Science.gov (United States)

    Garson, A. B., III; Allen, B.; Baker, R. G.; Barthelmy, S. D.; Burke, M.; Burnham, J.; Chammas, N.; Collins, J.; Cook, W. R.; Copete, A.; Gehrels, N.; Gauron, T.; Grindlay, J.; Harrison, F. A.; Hong, J.; Howell, J.; Krawczynski, H.; Labov, S.; Said, B.; Sheikh Sheikh, S.

    2008-04-01

    We describe the ProtoEXIST instrument, our fist-generation wide-field hard X-ray imaging (20 - 600 keV) balloon-borne telescope. The ProtoEXIST program is a pathfinder for the Energetic X-ray Imaging Survey Telescope (EXIST), a candidate for the Black Hole Finder Probe. ProtoEXIST consists of two independent coded-aperture telescopes using pixellated (2.5mm pitch) CZT detectors. The two telescopes will provide performance comparison of two shielding configurations, for optimization of the EXIST design. We report on the science goals and designs of both ProtoEXIST and EXIST and their implications for hard X-ray astronomy and astrophysics.

  20. The master two-dimensional gel database of human AMA cell proteins: towards linking protein and genome sequence and mapping information (update 1991)

    DEFF Research Database (Denmark)

    Celis, J E; Leffers, H; Rasmussen, H H

    1991-01-01

    autoantigens" and "cDNAs". For convenience we have included an alphabetical list of all known proteins recorded in this database. In the long run, the main goal of this database is to link protein and DNA sequencing and mapping information (Human Genome Program) and to provide an integrated picture...

  1. CROPCAST - A Review Of An Existing Remote Sensor-Based Agricultural Information System With A View Toward Future Remote Sensor Applications

    Science.gov (United States)

    Merritt, Earl S.; Heitkemper, Lawrence; Marcus, Kevin

    1984-08-01

    Global agricultural production information is the key to many economic decisions. National level planners use it to plan imports or to assess balance of payments, farmers use it to make planting decisions, lending and aid institutions use it to plan loans and aid needs, commodity buyers use it to plan purchases. Traditional information systems are slow, offer little confidence and may be inaccurate; systems based on the use of space remote sensor systems are, on the other hand, fast, provide good confidence and are demonstrating improving accuracies. The system structure for remote sensor assisted agricultural information systems is centered on a geobased structure, mapped outputs pinpoint locations where plant stress is impacting yields. Meteorological satellite assessments pinpoint where rainfall and significant solar radiation is impacting the plant environment. The CROPCAST Agricultural Information System offers an opportunity to examine an operating system which contains characteristics essential to all future systems. CROPCAST's use of a grid/cell geobased structure provides a mechanism to effectively use remote-sensor derived data of all types, i.e., Landsats, metsats, aircraft and human eyeball derived data. Predictive models operating in CROPCAST provide updated agricultural assessments in the time intervals when no Landsat or other field observation data are available. Economic models provide the opportunity to merge CROPCAST diagnostic and predictive output with the market place at both the cash and futures level. This presentation will examine the CROPCAST structure as a model for future uses of remote sensing data from civil remote sensing systems in assessing global agricultural production. A review of the future direction to be taken by the CROPCAST System will be included to identify new avenues for remote sensor-based agricultural information system growth over the coming decade of change in remote sensor systems.

  2. EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction.

    Science.gov (United States)

    Stahl, Kolja; Schneider, Michael; Brock, Oliver

    2017-06-17

    Accurately predicted contacts allow to compute the 3D structure of a protein. Since the solution space of native residue-residue contact pairs is very large, it is necessary to leverage information to identify relevant regions of the solution space, i.e. correct contacts. Every additional source of information can contribute to narrowing down candidate regions. Therefore, recent methods combined evolutionary and sequence-based information as well as evolutionary and physicochemical information. We develop a new contact predictor (EPSILON-CP) that goes beyond current methods by combining evolutionary, physicochemical, and sequence-based information. The problems resulting from the increased dimensionality and complexity of the learning problem are combated with a careful feature analysis, which results in a drastically reduced feature set. The different information sources are combined using deep neural networks. On 21 hard CASP11 FM targets, EPSILON-CP achieves a mean precision of 35.7% for top- L/10 predicted long-range contacts, which is 11% better than the CASP11 winning version of MetaPSICOV. The improvement on 1.5L is 17%. Furthermore, in this study we find that the amino acid composition, a commonly used feature, is rendered ineffective in the context of meta approaches. The size of the refined feature set decreased by 75%, enabling a significant increase in training data for machine learning, contributing significantly to the observed improvements. Exploiting as much and diverse information as possible is key to accurate contact prediction. Simply merging the information introduces new challenges. Our study suggests that critical feature analysis can improve the performance of contact prediction methods that combine multiple information sources. EPSILON-CP is available as a webservice: http://compbio.robotics.tu-berlin.de/epsilon/.

  3. Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information

    Science.gov (United States)

    2013-01-01

    Background The vitamins are important cofactors in various enzymatic-reactions. In past, many inhibitors have been designed against vitamin binding pockets in order to inhibit vitamin-protein interactions. Thus, it is important to identify vitamin interacting residues in a protein. It is possible to detect vitamin-binding pockets on a protein, if its tertiary structure is known. Unfortunately tertiary structures of limited proteins are available. Therefore, it is important to develop in-silico models for predicting vitamin interacting residues in protein from its primary structure. Results In this study, first we compared protein-interacting residues of vitamins with other ligands using Two Sample Logo (TSL). It was observed that ATP, GTP, NAD, FAD and mannose preferred {G,R,K,S,H}, {G,K,T,S,D,N}, {T,G,Y}, {G,Y,W} and {Y,D,W,N,E} residues respectively, whereas vitamins preferred {Y,F,S,W,T,G,H} residues for the interaction with proteins. Furthermore, compositional information of preferred and non-preferred residues along with patterns-specificity was also observed within different vitamin-classes. Vitamins A, B and B6 preferred {F,I,W,Y,L,V}, {S,Y,G,T,H,W,N,E} and {S,T,G,H,Y,N} interacting residues respectively. It suggested that protein-binding patterns of vitamins are different from other ligands, and motivated us to develop separate predictor for vitamins and their sub-classes. The four different prediction modules, (i) vitamin interacting residues (VIRs), (ii) vitamin-A interacting residues (VAIRs), (iii) vitamin-B interacting residues (VBIRs) and (iv) pyridoxal-5-phosphate (vitamin B6) interacting residues (PLPIRs) have been developed. We applied various classifiers of SVM, BayesNet, NaiveBayes, ComplementNaiveBayes, NaiveBayesMultinomial, RandomForest and IBk etc., as machine learning techniques, using binary and Position-Specific Scoring Matrix (PSSM) features of protein sequences. Finally, we selected best performing SVM modules and obtained highest MCC of

  4. Governance and Risk Management of Network and Information Security: The Role of Public Private Partnerships in Managing the Existing and Emerging Risks

    Science.gov (United States)

    Navare, Jyoti; Gemikonakli, Orhan

    Globalisation and new technology has opened the gates to more security risks. As the strategic importance of communication networks and information increased, threats to the security and safety of communication infrastructures, as well as information stored in and/or transmitted increased significantly. The development of the self replicating programmes has become a nightmare for Internet users. Leading companies, strategic organisations were not immune to attacks; they were also "hacked" and overtaken by intruders. Incidents of recent years have also shown that national/regional crisis may also trigger cyber attacks at large scale. Experts forecast that cyber wars are likely to take the stage as tension mounts between developed societies. New risks such as cyber-attacks, network terrorism and disintegration of traditional infrastructures has somewhat blurred the boundaries of operation and control. This paper seeks to consider the risk management and governance and looking more specifically at implications for emerging economies.

  5. RPPAML/RIMS: a metadata format and an information management system for reverse phase protein arrays.

    Science.gov (United States)

    Stanislaus, Romesh; Carey, Mark; Deus, Helena F; Coombes, Kevin; Hennessy, Bryan T; Mills, Gordon B; Almeida, Jonas S

    2008-12-22

    Reverse Phase Protein Arrays (RPPA) are convenient assay platforms to investigate the presence of biomarkers in tissue lysates. As with other high-throughput technologies, substantial amounts of analytical data are generated. Over 1,000 samples may be printed on a single nitrocellulose slide. Up to 100 different proteins may be assessed using immunoperoxidase or immunoflorescence techniques in order to determine relative amounts of protein expression in the samples of interest. In this report an RPPA Information Management System (RIMS) is described and made available with open source software. In order to implement the proposed system, we propose a metadata format known as reverse phase protein array markup language (RPPAML). RPPAML would enable researchers to describe, document and disseminate RPPA data. The complexity of the data structure needed to describe the results and the graphic tools necessary to visualize them require a software deployment distributed between a client and a server application. This was achieved without sacrificing interoperability between individual deployments through the use of an open source semantic database, S3DB. This data service backbone is available to multiple client side applications that can also access other server side deployments. The RIMS platform was designed to interoperate with other data analysis and data visualization tools such as Cytoscape. The proposed RPPAML data format hopes to standardize RPPA data. Standardization of data would result in diverse client applications being able to operate on the same set of data. Additionally, having data in a standard format would enable data dissemination and data analysis.

  6. Conceptual design report: Nuclear materials storage facility renovation. Part 5, Structural/seismic investigation. Section A report, existing conditions calculations/supporting information

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-07-14

    The Nuclear Materials Storage Facility (NMSF) at the Los Alamos National Laboratory (LANL) was a Fiscal Year (FY) 1984 line-item project completed in 1987 that has never been operated because of major design and construction deficiencies. This renovation project, which will correct those deficiencies and allow operation of the facility, is proposed as an FY 97 line item. The mission of the project is to provide centralized intermediate and long-term storage of special nuclear materials (SNM) associated with defined LANL programmatic missions and to establish a centralized SNM shipping and receiving location for Technical Area (TA)-55 at LANL. Based on current projections, existing storage space for SNM at other locations at LANL will be loaded to capacity by approximately 2002. This will adversely affect LANUs ability to meet its mission requirements in the future. The affected missions include LANL`s weapons research, development, and testing (WRD&T) program; special materials recovery; stockpile survelliance/evaluation; advanced fuels and heat sources development and production; and safe, secure storage of existing nuclear materials inventories. The problem is further exacerbated by LANL`s inability to ship any materials offsite because of the lack of receiver sites for mate rial and regulatory issues. Correction of the current deficiencies and enhancement of the facility will provide centralized storage close to a nuclear materials processing facility. The project will enable long-term, cost-effective storage in a secure environment with reduced radiation exposure to workers, and eliminate potential exposures to the public. Based upon US Department of Energy (DOE) Albuquerque Operations (DOE/Al) Office and LANL projections, storage space limitations/restrictions will begin to affect LANL`s ability to meet its missions between 1998 and 2002.

  7. What trial participants need to be told about placebo effects to give informed consent: a survey to establish existing knowledge among patients with back pain.

    Science.gov (United States)

    Hughes, John; Greville-Harris, Maddy; Graham, Cynthia A; Lewith, George; White, Peter; Bishop, Felicity L

    2017-12-01

    Patients require an accurate knowledge about placebos and their possible effects to ensure consent for placebo-controlled clinical trials is adequately informed. However, few previous studies have explored patients' baseline (ie, pretrial recruitment) levels of understanding and knowledge about placebos. The present online survey aimed to assess knowledge about placebos among patients with a history of back pain. A 15-item questionnaire was constructed to measure knowledge about placebos. Additional questions assessed sociodemographic characteristics, duration and severity of back pain, and previous experience of receiving placebos. Participants recruited from community settings completed the study online. 210 participants completed the questionnaire. 86.7% had back pain in the past 6 months, 44.3% currently had back pain. 4.3% had received a placebo intervention as part of a clinical trial and 68.1% had previously read or heard information about placebos. Overall knowledge of placebos was high, with participants on average answering 12.07 of 15 questions about placebos correctly (SD=2.35). However, few participants correctly answered questions about the nocebo effect (31.9% correct) and the impact of the colour of a placebo pill (55.2% correct). The findings identified key gaps in knowledge about placebos. The lack of understanding of the nocebo effect in particular has implications for the informed consent of trial participants. Research ethics committees and investigators should prioritise amending informed consent procedures to incorporate the fact that participants in the placebo arm might experience adverse side effects. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  8. Discerning tumor status from unstructured MRI reports--completeness of information in existing reports and utility of automated natural language processing.

    Science.gov (United States)

    Cheng, Lionel T E; Zheng, Jiaping; Savova, Guergana K; Erickson, Bradley J

    2010-04-01

    Information in electronic medical records is often in an unstructured free-text format. This format presents challenges for expedient data retrieval and may fail to convey important findings. Natural language processing (NLP) is an emerging technique for rapid and efficient clinical data retrieval. While proven in disease detection, the utility of NLP in discerning disease progression from free-text reports is untested. We aimed to (1) assess whether unstructured radiology reports contained sufficient information for tumor status classification; (2) develop an NLP-based data extraction tool to determine tumor status from unstructured reports; and (3) compare NLP and human tumor status classification outcomes. Consecutive follow-up brain tumor magnetic resonance imaging reports (2000--2007) from a tertiary center were manually annotated using consensus guidelines on tumor status. Reports were randomized to NLP training (70%) or testing (30%) groups. The NLP tool utilized a support vector machines model with statistical and rule-based outcomes. Most reports had sufficient information for tumor status classification, although 0.8% did not describe status despite reference to prior examinations. Tumor size was unreported in 68.7% of documents, while 50.3% lacked data on change magnitude when there was detectable progression or regression. Using retrospective human classification as the gold standard, NLP achieved 80.6% sensitivity and 91.6% specificity for tumor status determination (mean positive predictive value, 82.4%; negative predictive value, 92.0%). In conclusion, most reports contained sufficient information for tumor status determination, though variable features were used to describe status. NLP demonstrated good accuracy for tumor status classification and may have novel application for automated disease status classification from electronic databases.

  9. Improving the Accuracy of Fitted Atomic Models in Cryo-EM Density Maps of Protein Assemblies Using Evolutionary Information from Aligned Homologous Proteins.

    Science.gov (United States)

    Rakesh, Ramachandran; Srinivasan, Narayanaswamy

    2016-01-01

    Cryo-Electron Microscopy (cryo-EM) has become an important technique to obtain structural insights into large macromolecular assemblies. However the resolution of the density maps do not allow for its interpretation at atomic level. Hence they are combined with high resolution structures along with information from other experimental or bioinformatics techniques to obtain pseudo-atomic models. Here, we describe the use of evolutionary conservation of residues as obtained from protein structures and alignments of homologous proteins to detect errors in the fitting of atomic structures as well as improve accuracy of the protein-protein interfacial regions in the cryo-EM density maps.

  10. Minimal information: an urgent need to assess the functional reliability of recombinant proteins used in biological experiments

    Directory of Open Access Journals (Sweden)

    de Marco Ario

    2008-07-01

    Full Text Available Abstract Structural characterization of proteins used in biological experiments is largely neglected. In most publications, the information available is totally insufficient to judge the functionality of the proteins used and, therefore, the significance of identified protein-protein interactions (was the interaction specific or due to unspecific binding of misfolded protein regions? or reliability of kinetic and thermodynamic data (how much protein was in its native form?. As a consequence, the results of single experiments might not only become questionable, but the whole reliability of systems biology, built on these fundaments, would be weakened. The introduction of Minimal Information concerning purified proteins to add as metadata to the main body of a manuscript would render straightforward the assessment of their functional and structural qualities and, consequently, of results obtained using these proteins. Furthermore, accepted standards for protein annotation would simplify data comparison and exchange. This article has been envisaged as a proposal for aggregating scientists who share the opinion that the scientific community needs a platform for Minimum Information for Protein Functionality Evaluation (MIPFE.

  11. Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods

    Science.gov (United States)

    Sofia, Heidi J.; Chen, Guang; Hetzler, Beth G.; Reyes-Spindola, Jorge F.; Miller, Nancy E.

    2001-01-01

    A novel protein superfamily with over 600 members was discovered by iterative profile searches and analyzed with powerful bioinformatics and information visualization methods. Evidence exists that these proteins generate a radical species by reductive cleavage of S-adenosylmethionine (SAM) through an unusual Fe-S center. The superfamily (named here Radical SAM) provides evidence that radical-based catalysis is important in a number of previously well- studied but unresolved biochemical pathways and reflects an ancient conserved mechanistic approach to difficult chemistries. Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulfur insertion, ring formation, anaerobic oxidation and protein radical formation. They function in DNA precursor, vitamin, cofactor, antibiotic and herbicide biosynthesis and in biodegradation pathways. One eukaryotic member is interferon-inducible and is considered a candidate drug target for osteoporosis; another is observed to bind the neuronal Cdk5 activator protein. Five defining members not previously recognized as homologs are lysine 2,3-aminomutase, biotin synthase, lipoic acid synthase and the activating enzymes for pyruvate formate-lyase and anaerobic ribonucleotide reductase. Two functional predictions for unknown proteins are made based on integrating other data types such as motif, domain, operon and biochemical pathway into an organized view of similarity relationships. PMID:11222759

  12. VaProS: a database-integration approach for protein/genome information retrieval

    KAUST Repository

    Gojobori, Takashi

    2016-12-24

    Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3D) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3D structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://p4d-info.nig.ac.jp/vapros/.

  13. Proteomic amino-termini profiling reveals targeting information for protein import into complex plastids.

    Directory of Open Access Journals (Sweden)

    Pitter F Huesgen

    Full Text Available In organisms with complex plastids acquired by secondary endosymbiosis from a photosynthetic eukaryote, the majority of plastid proteins are nuclear-encoded, translated on cytoplasmic ribosomes, and guided across four membranes by a bipartite targeting sequence. In-depth understanding of this vital import process has been impeded by a lack of information about the transit peptide part of this sequence, which mediates transport across the inner three membranes. We determined the mature N-termini of hundreds of proteins from the model diatom Thalassiosira pseudonana, revealing extensive N-terminal modification by acetylation and proteolytic processing in both cytosol and plastid. We identified 63 mature N-termini of nucleus-encoded plastid proteins, deduced their complete transit peptide sequences, determined a consensus motif for their cleavage by the stromal processing peptidase, and found evidence for subsequent processing by a plastid methionine aminopeptidase. The cleavage motif differs from that of higher plants, but is shared with other eukaryotes with complex plastids.

  14. On the possible role of protein vibrations in information processing in the brain: three Russian dolls.

    Science.gov (United States)

    Smythies, John

    2015-01-01

    Until recently it was held that the neurocomputations conducted by the brain involved only whole neurons as the operating units. This may however represent only a part of the mechanism. This theoretical and academic position article reviews the considerable evidence that allosteric interactions between proteins (as extensively described by Fuxe et al., 2014), and in particular protein vibrations in neurons, form small scale codes that are involved as parts of the complex information processing systems of the brain. The argument is then developed to suggest that the protein allosteric and vibration codes (that operate at the molecular level) are nested within a medium scale coding system whose computational units are organelles (such as microtubules). This medium scale code is nested in turn inside a large scale coding system, whose computational units are individual neurons. The hypothesis suggests that these three levels interact vertically in both directions thus materially increasing the computational capacity of the brain. The whole hierarchy is thus similar to three nested Russian dolls. This theoretical development may be of use in the design of experiments to test it.

  15. Inferring protein function by domain context similarities in protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    Sun Zhirong

    2009-12-01

    Full Text Available Abstract Background Genome sequencing projects generate massive amounts of sequence data but there are still many proteins whose functions remain unknown. The availability of large scale protein-protein interaction data sets makes it possible to develop new function prediction methods based on protein-protein interaction (PPI networks. Although several existing methods combine multiple information resources, there is no study that integrates protein domain information and PPI networks to predict protein functions. Results The domain context similarity can be a useful index to predict protein function similarity. The prediction accuracy of our method in yeast is between 63%-67%, which outperforms the other methods in terms of ROC curves. Conclusion This paper presents a novel protein function prediction method that combines protein domain composition information and PPI networks. Performance evaluations show that this method outperforms existing methods.

  16. RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays

    Directory of Open Access Journals (Sweden)

    Hennessy Bryan T

    2008-12-01

    Full Text Available Abstract Background Reverse Phase Protein Arrays (RPPA are convenient assay platforms to investigate the presence of biomarkers in tissue lysates. As with other high-throughput technologies, substantial amounts of analytical data are generated. Over 1000 samples may be printed on a single nitrocellulose slide. Up to 100 different proteins may be assessed using immunoperoxidase or immunoflorescence techniques in order to determine relative amounts of protein expression in the samples of interest. Results In this report an RPPA Information Management System (RIMS is described and made available with open source software. In order to implement the proposed system, we propose a metadata format known as reverse phase protein array markup language (RPPAML. RPPAML would enable researchers to describe, document and disseminate RPPA data. The complexity of the data structure needed to describe the results and the graphic tools necessary to visualize them require a software deployment distributed between a client and a server application. This was achieved without sacrificing interoperability between individual deployments through the use of an open source semantic database, S3DB. This data service backbone is available to multiple client side applications that can also access other server side deployments. The RIMS platform was designed to interoperate with other data analysis and data visualization tools such as Cytoscape. Conclusion The proposed RPPAML data format hopes to standardize RPPA data. Standardization of data would result in diverse client applications being able to operate on the same set of data. Additionally, having data in a standard format would enable data dissemination and data analysis.

  17. A structurally informed autotransporter platform for efficient heterologous protein secretion and display

    Directory of Open Access Journals (Sweden)

    Jong Wouter SP

    2012-06-01

    Full Text Available Abstract Background The self-sufficient autotransporter (AT pathway, ubiquitous in Gram-negative bacteria, combines a relatively simple protein secretion mechanism with a high transport capacity. ATs consist of a secreted passenger domain and a β-domain that facilitates transfer of the passenger across the cell-envelope. They have a great potential for the extracellular expression of recombinant proteins but their exploitation has suffered from the limited structural knowledge of carrier ATs. Capitalizing on its crystal structure, we have engineered the Escherichia coli AT Hemoglobin protease (Hbp into a platform for the secretion and surface display of heterologous proteins, using the Mycobacterium tuberculosis vaccine target ESAT6 as a model protein. Results Based on the Hbp crystal structure, five passenger side domains were selected and one by one replaced by ESAT6, whereas a β-helical core structure (β-stem was left intact. The resulting Hbp-ESAT6 chimeras were efficiently and stably secreted into the culture medium of E. coli. On the other hand, Hbp-ESAT6 fusions containing a truncated β-stem appeared unstable after translocation, demonstrating the importance of an intact β-stem. By interrupting the cleavage site between passenger and β-domain, Hbp-ESAT6 display variants were constructed that remain cell associated and facilitate efficient surface exposure of ESAT6 as judged by proteinase K accessibility and whole cell immuno-EM analysis. Upon replacement of the passenger side domain of an alternative AT, EspC, ESAT6 was also efficiently secreted, showing the approach is more generally applicable to ATs. Furthermore, Hbp-ESAT6 was efficiently displayed in an attenuated Salmonella typhimurium strain upon chromosomal integration of a single encoding gene copy, demonstrating the potential of the Hbp platform for live vaccine development. Conclusions We developed the first structurally informed AT platform for efficient secretion and

  18. PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system

    Directory of Open Access Journals (Sweden)

    Picard-Cloutier Aude

    2007-12-01

    Full Text Available Abstract Background In the "post-genome" era, mass spectrometry (MS has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results in an increasing amount of proteome data. This data must be archived and analysed using specialized bioinformatics tools. Description We herein describe "PARPs database," a data analysis and management pipeline for liquid chromatography tandem mass spectrometry (LC-MS/MS proteomics. PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified. Conclusion Using this pipeline, we have successfully identified several interactions of biological significance between PARP-1 and other proteins, namely RFC-1, 2, 3, 4 and 5.

  19. EXIST Perspective for SFXTs

    Science.gov (United States)

    Ubertini, Pietro; Sidoli, L.; Sguera, V.; Bazzano, A.

    2009-12-01

    Supergiant Fast X-ray Transients (SFXTs) are one of the most interesting (and unexpected) results of the INTEGRAL mission. They are a new class of HMXBs displaying short hard X-ray outbursts (duration less tha a day) characterized by fast flares (few hours timescale) and large dinamic range (10E3-10E4). The physical mechanism driving their peculiar behaviour is still unclear and highly debated: some models involve the structure of the supergiant companion donor wind (likely clumpy, in a spherical or non spherical geometry) and the orbital properties (wide separation with eccentric or circular orbit), while others involve the properties of the neutron star compact object and invoke very low magnetic field values (B 1E14 G, magnetars). The picture is still highly unclear from the observational point of view as well: no cyclotron lines have been detected in the spectra, thus the strength of the neutron star magnetic field is unknown. Orbital periods have been measured in only 4 systems, spanning from 3.3 days to 165 days. Even the duty cycle seems to be quite different from source to source. The Energetic X-ray Imaging Survey Telescope (EXIST), with its hard X-ray all-sky survey and large improved limiting sensitivity, will allow us to get a clearer picture of SFXTs. A complete census of their number is essential to enlarge the sample. A long term and continuous as possible X-ray monitoring is crucial to -(1) obtain the duty cycle, -(2 )investigate their unknown orbital properties (separation, orbital period, eccentricity),- (3) to completely cover the whole outburst activity, (4)-to search for cyclotron lines in the high energy spectra. EXIST observations will provide crucial informations to test the different models and shed light on the peculiar behaviour of SFXTs.

  20. Requirements for existing buildings

    DEFF Research Database (Denmark)

    Thomsen, Kirsten Engelund; Wittchen, Kim Bjarne

    This report collects energy performance requirements for existing buildings in European member states by June 2012.......This report collects energy performance requirements for existing buildings in European member states by June 2012....

  1. DPRK Information Strategy - Does It Exist

    Science.gov (United States)

    2005-08-01

    that could be refurbished and recommence production for export of minerals such as magnesite and zinc. An example is given below in Figure 4.3...inefficient technology (such as making fertilizer from coal) should not

  2. A novel Multi-Agent Ada-Boost algorithm for predicting protein structural class with the information of protein secondary structure.

    Science.gov (United States)

    Fan, Ming; Zheng, Bin; Li, Lihua

    2015-10-01

    Knowledge of the structural class of a given protein is important for understanding its folding patterns. Although a lot of efforts have been made, it still remains a challenging problem for prediction of protein structural class solely from protein sequences. The feature extraction and classification of proteins are the main problems in prediction. In this research, we extended our earlier work regarding these two aspects. In protein feature extraction, we proposed a scheme by calculating the word frequency and word position from sequences of amino acid, reduced amino acid, and secondary structure. For an accurate classification of the structural class of protein, we developed a novel Multi-Agent Ada-Boost (MA-Ada) method by integrating the features of Multi-Agent system into Ada-Boost algorithm. Extensive experiments were taken to test and compare the proposed method using four benchmark datasets in low homology. The results showed classification accuracies of 88.5%, 96.0%, 88.4%, and 85.5%, respectively, which are much better compared with the existing methods. The source code and dataset are available on request.

  3. Allometry of Factor VIII and informed scaling of next generation therapeutic proteins

    Science.gov (United States)

    Kosloski, Matthew P.; Pisal, Dipak S.; Mager, Donald E.; Balu-Iyer, Sathy V.

    2013-01-01

    Allometric scaling has been applied to the pharmacokinetics (PK) of factor VIII (FVIII), but published relationships are based on relatively small subsets of available data. Numerous next generation forms of FVIII are being developed (e.g. Fc fusion, PEGylated, and liposomal formulations) and traditional pharmacokinetic scaling of these products would not incorporate the wealth of existing knowledge for current FVIII therapy in humans. We conducted a meta-analysis and developed allometric relationships of FVIII from over 100 PK studies collected from literature. Normalized Wajima curves were used to relate mean FVIII profiles between species. An ‘informed scaling’ approach was derived for predicting first-in-human PK parameters and demonstrated with a case study for an Fc fusion FVIII. NCA values for FVIII PK were well described by the allometric equations CL=6.59·W0.85 and Vss=65.0·W0.97. A subset of studies characterized by two compartment modeling showed strong linearity in scaling of total clearance and central volume, but more variability in distributional clearance and peripheral volume. Wajima curves for FVIII superimposed across species and the disposition of Fc fusion FVIII in humans was well predicted by ‘informed scaling.’ This approach might be generally applicable for predicting human PK of next generational therapeutics. PMID:23620343

  4. Relating diseases by integrating gene associations and information flow through protein interaction network.

    Science.gov (United States)

    Hamaneh, Mehdi Bagheri; Yu, Yi-Kuo

    2014-01-01

    Identifying similar diseases could potentially provide deeper understanding of their underlying causes, and may even hint at possible treatments. For this purpose, it is necessary to have a similarity measure that reflects the underpinning molecular interactions and biological pathways. We have thus devised a network-based measure that can partially fulfill this goal. Our method assigns weights to all proteins (and consequently their encoding genes) by using information flow from a disease to the protein interaction network and back. Similarity between two diseases is then defined as the cosine of the angle between their corresponding weight vectors. The proposed method also provides a way to suggest disease-pathway associations by using the weights assigned to the genes to perform enrichment analysis for each disease. By calculating pairwise similarities between 2534 diseases, we show that our disease similarity measure is strongly correlated with the probability of finding the diseases in the same disease family and, more importantly, sharing biological pathways. We have also compared our results to those of MimMiner, a text-mining method that assigns pairwise similarity scores to diseases. We find the results of the two methods to be complementary. It is also shown that clustering diseases based on their similarities and performing enrichment analysis for the cluster centers significantly increases the term association rate, suggesting that the cluster centers are better representatives for biological pathways than the diseases themselves. This lends support to the view that our similarity measure is a good indicator of relatedness of biological processes involved in causing the diseases. Although not needed for understanding this paper, the raw results are available for download for further study at ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/DiseaseRelations/.

  5. QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information

    Directory of Open Access Journals (Sweden)

    Schwede Torsten

    2009-05-01

    Full Text Available Abstract Background The selection of the most accurate protein model from a set of alternatives is a crucial step in protein structure prediction both in template-based and ab initio approaches. Scoring functions have been developed which can either return a quality estimate for a single model or derive a score from the information contained in the ensemble of models for a given sequence. Local structural features occurring more frequently in the ensemble have a greater probability of being correct. Within the context of the CASP experiment, these so called consensus methods have been shown to perform considerably better in selecting good candidate models, but tend to fail if the best models are far from the dominant structural cluster. In this paper we show that model selection can be improved if both approaches are combined by pre-filtering the models used during the calculation of the structural consensus. Results Our recently published QMEAN composite scoring function has been improved by including an all-atom interaction potential term. The preliminary model ranking based on the new QMEAN score is used to select a subset of reliable models against which the structural consensus score is calculated. This scoring function called QMEANclust achieves a correlation coefficient of predicted quality score and GDT_TS of 0.9 averaged over the 98 CASP7 targets and perform significantly better in selecting good models from the ensemble of server models than any other groups participating in the quality estimation category of CASP7. Both scoring functions are also benchmarked on the MOULDER test set consisting of 20 target proteins each with 300 alternatives models generated by MODELLER. QMEAN outperforms all other tested scoring functions operating on individual models, while the consensus method QMEANclust only works properly on decoy sets containing a certain fraction of near-native conformations. We also present a local version of QMEAN for the per

  6. A role for information collection, management, and integration in structure-function studies of G-protein coupled receptors.

    Science.gov (United States)

    Shi, Lei; Javitch, Jonathan A

    2006-01-01

    Elucidation of protein function is greatly facilitated by the availability of an atomic resolution structure or a reliable molecular model. The difficulty of obtaining atomic resolution structures of membrane proteins in general, and of G-protein coupled receptors (GPCRs) in particular, has made the information available from sequence analysis, mutagenesis, and the literature on related GPCRs exceptionally important. Here, we review previous studies of GPCR structure-function from the perspectives of sequence analysis, management of mutagenesis and ligand binding data, and literature data mining. The knowledge derived from these information resources not only constitutes the prerequisites for reliable molecular modeling, but also can provide other insights into GPCR functions. Finally, we review approaches for information integration and applying knowledge discovery techniques to structure-function studies of GPCRs, including molecular modeling itself.

  7. The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory.

    Science.gov (United States)

    Morris, Chris; Pajon, Anne; Griffiths, Susanne L; Daniel, Ed; Savitsky, Marc; Lin, Bill; Diprose, Jonathan M; da Silva, Alan Wilter; Pilicheva, Katya; Troshin, Peter; van Niekerk, Johannes; Isaacs, Neil; Naismith, James; Nave, Colin; Blake, Richard; Wilson, Keith S; Stuart, David I; Henrick, Kim; Esnouf, Robert M

    2011-04-01

    The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service.

  8. Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom

    Directory of Open Access Journals (Sweden)

    Echavarri-Erasun Carlos

    2007-08-01

    Full Text Available Abstract Background The construction of robust and well resolved phylogenetic trees is important for our understanding of many, if not all biological processes, including speciation and origin of higher taxa, genome evolution, metabolic diversification, multicellularity, origin of life styles, pathogenicity and so on. Many older phylogenies were not well supported due to insufficient phylogenetic signal present in the single or few genes used in phylogenetic reconstructions. Importantly, single gene phylogenies were not always found to be congruent. The phylogenetic signal may, therefore, be increased by enlarging the number of genes included in phylogenetic studies. Unfortunately, concatenation of many genes does not take into consideration the evolutionary history of each individual gene. Here, we describe an approach to select informative phylogenetic proteins to be used in the Tree of Life (TOL and barcoding projects by comparing the cophenetic correlation coefficients (CCC among individual protein distance matrices of proteins, using the fungi as an example. The method demonstrated that the quality and number of concatenated proteins is important for a reliable estimation of TOL. Approximately 40–45 concatenated proteins seem needed to resolve fungal TOL. Results In total 4852 orthologous proteins (KOGs were assigned among 33 fungal genomes from the Asco- and Basidiomycota and 70 of these represented single copy proteins. The individual protein distance matrices based on 531 concatenated proteins that has been used for phylogeny reconstruction before 14 were compared one with another in order to select those with the highest CCC, which then was used as a reference. This reference distance matrix was compared with those of the 70 single copy proteins selected and their CCC values were calculated. Sixty four KOGs showed a CCC above 0.50 and these were further considered for their phylogenetic potential. Proteins belonging to the cellular

  9. Mining disease genes using integrated protein-protein interaction and gene-gene co-regulation information.

    Science.gov (United States)

    Li, Jin; Wang, Limei; Guo, Maozu; Zhang, Ruijie; Dai, Qiguo; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Xuan, Ping; Zhang, Mingming

    2015-01-01

    In humans, despite the rapid increase in disease-associated gene discovery, a large proportion of disease-associated genes are still unknown. Many network-based approaches have been used to prioritize disease genes. Many networks, such as the protein-protein interaction (PPI), KEGG, and gene co-expression networks, have been used. Expression quantitative trait loci (eQTLs) have been successfully applied for the determination of genes associated with several diseases. In this study, we constructed an eQTL-based gene-gene co-regulation network (GGCRN) and used it to mine for disease genes. We adopted the random walk with restart (RWR) algorithm to mine for genes associated with Alzheimer disease. Compared to the Human Protein Reference Database (HPRD) PPI network alone, the integrated HPRD PPI and GGCRN networks provided faster convergence and revealed new disease-related genes. Therefore, using the RWR algorithm for integrated PPI and GGCRN is an effective method for disease-associated gene mining.

  10. A protocol for CABS-dock protein-peptide docking driven by side-chain contact information.

    Science.gov (United States)

    Kurcinski, Mateusz; Blaszczyk, Maciej; Ciemny, Maciej Pawel; Kolinski, Andrzej; Kmiecik, Sebastian

    2017-08-18

    The characterization of protein-peptide interactions is a challenge for computational molecular docking. Protein-peptide docking tools face at least two major difficulties: (1) efficient sampling of large-scale conformational changes induced by binding and (2) selection of the best models from a large set of predicted structures. In this paper, we merge an efficient sampling technique with external information about side-chain contacts to sample and select the best possible models. In this paper we test a new protocol that uses information about side-chain contacts in CABS-dock protein-peptide docking. As shown in our recent studies, CABS-dock enables efficient modeling of large-scale conformational changes without knowledge about the binding site. However, the resulting set of binding sites and poses is in many cases highly diverse and difficult to score. As we demonstrate here, information about a single side-chain contact can significantly improve the prediction accuracy. Importantly, the imposed constraints for side-chain contacts are quite soft. Therefore, the developed protocol does not require precise contact information and ensures large-scale peptide flexibility in the broad contact area. The demonstrated protocol provides the extension of the CABS-dock method that can be practically used in the structure prediction of protein-peptide complexes guided by the knowledge of the binding interface.

  11. The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Morris, Chris [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Pajon, Anne [Wellcome Trust Genome Campus, Hinxton CB10 1SD (United Kingdom); Griffiths, Susanne L. [University of York, Heslington, York YO10 5DD (United Kingdom); Daniel, Ed [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Savitsky, Marc [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Lin, Bill [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Diprose, Jonathan M. [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Wilter da Silva, Alan [Wellcome Trust Genome Campus, Hinxton CB10 1SD (United Kingdom); Pilicheva, Katya [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Troshin, Peter [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Niekerk, Johannes van [University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom); Isaacs, Neil [University of Glasgow, Glasgow G12 8QQ, Scotland (United Kingdom); Naismith, James [University of St Andrews, St Andrews, Fife KY16 9ST, Scotland (United Kingdom); Nave, Colin; Blake, Richard [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Wilson, Keith S. [University of York, Heslington, York YO10 5DD (United Kingdom); Stuart, David I. [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Henrick, Kim [Wellcome Trust Genome Campus, Hinxton CB10 1SD (United Kingdom); Esnouf, Robert M., E-mail: robert@strubi.ox.ac.uk [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom)

    2011-04-01

    The Protein Information Management System (PiMS) is described together with a discussion of how its features make it well suited to laboratories of all sizes. The techniques used in protein production and structural biology have been developing rapidly, but techniques for recording the laboratory information produced have not kept pace. One approach is the development of laboratory information-management systems (LIMS), which typically use a relational database schema to model and store results from a laboratory workflow. The underlying philosophy and implementation of the Protein Information Management System (PiMS), a LIMS development specifically targeted at the flexible and unpredictable workflows of protein-production research laboratories of all scales, is described. PiMS is a web-based Java application that uses either Postgres or Oracle as the underlying relational database-management system. PiMS is available under a free licence to all academic laboratories either for local installation or for use as a managed service.

  12. Identification of functionally diverse lipocalin proteins from sequence information using support vector machine.

    Science.gov (United States)

    Pugalenthi, Ganesan; Kandaswamy, Krishna Kumar; Suganthan, P N; Archunan, G; Sowdhamini, R

    2010-08-01

    Lipocalins are functionally diverse proteins that are composed of 120-180 amino acid residues. Members of this family have several important biological functions including ligand transport, cryptic coloration, sensory transduction, endonuclease activity, stress response activity in plants, odorant binding, prostaglandin biosynthesis, cellular homeostasis regulation, immunity, immunotherapy and so on. Identification of lipocalins from protein sequence is more challenging due to the poor sequence identity which often falls below the twilight zone. So far, no specific method has been reported to identify lipocalins from primary sequence. In this paper, we report a support vector machine (SVM) approach to predict lipocalins from protein sequence using sequence-derived properties. LipoPred was trained using a dataset consisting of 325 lipocalin proteins and 325 non-lipocalin proteins, and evaluated by an independent set of 140 lipocalin proteins and 21,447 non-lipocalin proteins. LipoPred achieved 88.61% accuracy with 89.26% sensitivity, 85.27% specificity and 0.74 Matthew's correlation coefficient (MCC). When applied on the test dataset, LipoPred achieved 84.25% accuracy with 88.57% sensitivity, 84.22% specificity and MCC of 0.16. LipoPred achieved better performance rate when compared with PSI-BLAST, HMM and SVM-Prot methods. Out of 218 lipocalins, LipoPred correctly predicted 194 proteins including 39 lipocalins that are non-homologous to any protein in the SWISSPROT database. This result shows that LipoPred is potentially useful for predicting the lipocalin proteins that have no sequence homologs in the sequence databases. Further, successful prediction of nine hypothetical lipocalin proteins and five new members of lipocalin family prove that LipoPred can be efficiently used to identify and annotate the new lipocalin proteins from sequence databases. The LipoPred software and dataset are available at http://www3.ntu.edu.sg/home/EPNSugan/index_files/lipopred.htm.

  13. Development of Computational Tools for the Inference of Protein Interaction Specificity Rules and Functional Annotation Using Structural Information

    Directory of Open Access Journals (Sweden)

    Manuela Helmer-Citterich

    2006-04-01

    Full Text Available Relatively few protein structures are known, compared to the enormous amount of sequence data produced in the sequencing of different genomes, and relatively few protein complexes are deposited in the PDB with respect to the great amount of interaction data coming from high-throughput experiments (two-hybrid or affinity purification of protein complexes and mass spectrometry. Nevertheless, we can rely on computational techniques for the extraction of high-quality and information-rich data from the known structures and for their spreading in the protein sequence space. We describe here the ongoing research projects in our group: we analyse the protein complexes stored in the PDB and, for each complex involving one domain belonging to a family of interaction domains for which some interaction data are available, we can calculate its probability of interaction with any protein sequence. We analyse the structures of proteins encoding a function specified in a PROSITE pattern, which exhibits relatively low selectivity and specificity, and build extended patterns. To this aim, we consider residues that are well-conserved in the structure, even if their conservation cannot easily be recognized in the sequence alignment of the proteins holding the function. We also analyse protein surface regions and, through the annotation of the solvent-exposed residues, we annotate protein surface patches via a structural comparison performed with stringent parameters and independently of the residue order in the sequence. Local surface comparison may also help in identifying new sequence patterns, which could not be highlighted with other sequence-based methods.

  14. The EXIST OIRT

    Science.gov (United States)

    Allen, Branden; Golisano, C.; Kutyrev, A.; Moseley, H.; Grindlay, J.; Hong, J.; EXIST Team

    2009-01-01

    The EXIST Optical / Infrared Telescope (OIRT) has been integrated into the EXIST concept design for the determination GRB redshifts on orbit and to preform follow up source identification and studies following the generation of a trigger from the EXIST high energy telescope (HET). The base OIRT main design has been inherited from the NextView OIRT has been operating in low earth orbit since September of 2007 and is currently being used for the acquisition of geospatial data. After reconfiguration of the instrumentation for astrophysical observations the OIRT will have an angular resolution of 0.15" and a 5'×5' field of view and be sensitive to emission in the range of 0.4 $\\mu$m - 2.2 $\\mu$m. Passive cooling of the tertiary, secondary, and primary mirrors will enable observation into the Ks$ band.

  15. Seven fundamental, unsolved questions in molecular biology. Cooperative storage and bi-directional transfer of biological information by nucleic acids and proteins: an alternative to "central dogma".

    Science.gov (United States)

    Biro, J C

    2004-01-01

    The Human Genome Mapping Project provided us a large amount of sequence data. However our understanding of these data did not grow proportionally, because old dogmas still set the limits of our thinking. The gene-centric, reductionistical side of molecular biology is reviewed and seven problems are formulated, each indicating the insufficiency of the "central dogma". The following is concluded and suggested: 1. Genes are located and expressed on both DNA strands; 2. Introns are the source of important biological regulation and diversity; 3. Repeats are the frame of the chromatin structure and participate in the chromatin regulation; 4. The molecular accessibility of the canonical dsDNA structure is poor; 5. The genetic code is co-evolved with the amino acids and there is a stereochemical matching between the codes andamino acids; 6. The flow of information between nucleic acids and proteins is bi-directional and reverse translation might exist; 7. Complex genetic information is always carried and stored by nucleic acids and proteins together.

  16. A multiple information fusion method for predicting subcellular locations of two different types of bacterial protein simultaneously.

    Science.gov (United States)

    Chen, Jing; Xu, Huimin; He, Ping-An; Dai, Qi; Yao, Yuhua

    2016-01-01

    Subcellular localization prediction of bacterial protein is an important component of bioinformatics, which has great importance for drug design and other applications. For the prediction of protein subcellular localization, as we all know, lots of computational tools have been developed in the recent decades. In this study, we firstly introduce three kinds of protein sequences encoding schemes: physicochemical-based, evolutionary-based, and GO-based. The original and consensus sequences were combined with physicochemical properties. And elements information of different rows and columns in position-specific scoring matrix were taken into consideration simultaneously for more core and essence information. Computational methods based on gene ontology (GO) have been demonstrated to be superior to methods based on other features. Then principal component analysis (PCA) is applied for feature selection and reduced vectors are input to a support vector machine (SVM) to predict protein subcellular localization. The proposed method can achieve a prediction accuracy of 98.28% and 97.87% on a stringent Gram-positive (Gpos) and Gram-negative (Gneg) dataset with Jackknife test, respectively. At last, we calculate "absolute true overall accuracy (ATOA)", which is stricter than overall accuracy. The ATOA obtained from the proposed method is also up to 97.32% and 93.06% for Gpos and Gneg. From both the rationality of testing procedure and the success rates of test results, the current method can improve the prediction quality of protein subcellular localization. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  17. The value of protein structure classification information-Surveying the scientific literature.

    Science.gov (United States)

    Fox, Naomi K; Brenner, Steven E; Chandonia, John-Marc

    2015-11-01

    The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP-extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012-2013 that cite SCOP, 439 actually use data from the resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non-SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

  18. Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Konuma, Tsuyoshi [Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology (United States); Harada, Erisa [Suntory Foundation for Life Sciences, Bioorganic Research Institute (Japan); Sugase, Kenji, E-mail: sugase@sunbor.or.jp, E-mail: sugase@moleng.kyoto-u.ac.jp [Kyoto University, Department of Molecular Engineering, Graduate School of Engineering (Japan)

    2015-12-15

    Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

  19. Does Unconscious Racism Exist?

    Science.gov (United States)

    Quillian, Lincoln

    2008-01-01

    This essay argues for the existence of a form of unconscious racism. Research on implicit prejudice provides good evidence that most persons have deeply held negative associations with minority groups that can lead to subtle discrimination without conscious awareness. The evidence for implicit attitudes is briefly reviewed. Criticisms of the…

  20. Hydrophobic cluster analysis of G protein-coupled receptors: a powerful tool to derive structural and functional information from 2D-representation of protein sequences.

    Science.gov (United States)

    Lentes, K U; Mathieu, E; Bischoff, R; Rasmussen, U B; Pavirani, A

    1993-01-01

    Current methods for comparative analyses of protein sequences are 1D-alignments of amino acid sequences based on the maximization of amino acid identity (homology) and the prediction of secondary structure elements. This method has a major drawback once the amino acid identity drops below 20-25%, since maximization of a homology score does not take into account any structural information. A new technique called Hydrophobic Cluster Analysis (HCA) has been developed by Lemesle-Varloot et al. (Biochimie 72, 555-574), 1990). This consists of comparing several sequences simultaneously and combining homology detection with secondary structure analysis. HCA is primarily based on the detection and comparison of structural segments constituting the hydrophobic core of globular protein domains, with or without transmembrane domains. We have applied HCA to the analysis of different families of G-protein coupled receptors, such as catecholamine receptors as well as peptide hormone receptors. Utilizing HCA the thrombin receptor, a new and as yet unique member of the family of G-protein coupled receptors, can be clearly classified as being closely related to the family of neuropeptide receptors rather than to the catecholamine receptors for which the shape of the hydrophobic clusters and the length of their third cytoplasmic loop are very different. Furthermore, the potential of HCA to predict relationships between new putative and already characterized members of this family of receptors will be presented.

  1. Computing highly correlated positions using mutual information and graph theory for G protein-coupled receptors

    National Research Council Canada - National Science Library

    Fatakia, Sarosh N; Costanzi, Stefano; Chow, Carson C

    2009-01-01

    .... A mutual information graph was constructed with vertices that corresponded to TM positions and edges between vertices were drawn if the mutual information exceeded a threshold of statistical significance...

  2. VT Existing Hydroelectric Sites

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) The Renewable Energy Atlas of Vermont and this dataset were created to assist town energy committees, the Clean Energy Development Fund and other...

  3. Background Studies for EXIST

    Science.gov (United States)

    Wilson, Colleen A.; Pendleton, G. N.; Fishman, G. J.

    2004-01-01

    We present results from a study of the trapped proton and electron background for several orbital inclinations and altitudes. This study includes time dependent effects. In addition we describe a 3 component cosmic background model developed at the University of Southampton, UK. The three components are cosmic diffuse gamma rays, atmospheric albedo gamma rays, and cosmic ray protons. We present examples of how this model was applied to BATSE and discuss its application to EXIST.

  4. Sensitivity enhancement and contrasting information provided by free radicals in oriented-sample NMR of bicelle-reconstituted membrane proteins

    Science.gov (United States)

    Tesch, Deanna M.; Nevzorov, Alexander A.

    2014-02-01

    Elucidating structure and topology of membrane proteins (MPs) is essential for unveiling functionality of these important biological constituents. Oriented-sample solid-state NMR (OS-NMR) is capable of providing such information on MPs under nearly physiological conditions. However, two dimensional OS-NMR experiments can take several days to complete due to long longitudinal relaxation times combined with the large number of scans to achieve sufficient signal sensitivity in biological samples. Here, free radicals 5-DOXYL stearic acid, TEMPOL, and CAT-1 were added to uniformly 15N-labeled Pf1 coat protein reconstituted in DMPC/DHPC bicelles, and their effect on the longitudinal relaxation times (T1Z) was investigated. The dramatically shortened T1Z's allowed for the signal gain per unit time to be used for either: (i) up to a threefold reduction of the total experimental time at 99% magnetization recovery or (ii) obtaining up to 74% signal enhancement between the control and radical samples during constant experimental time at “optimal” relaxation delays. In addition, through OS-NMR and high-field EPR studies, free radicals were able to provide positional constraints in the bicelle system, which provide a description of the location of each residue in Pf1 coat protein within the bicellar membranes. This information can be useful in the determination of oligomerization states and immersion depths of larger membrane proteins.

  5. Sensitivity enhancement and contrasting information provided by free radicals in oriented-sample NMR of bicelle-reconstituted membrane proteins.

    Science.gov (United States)

    Tesch, Deanna M; Nevzorov, Alexander A

    2014-02-01

    Elucidating structure and topology of membrane proteins (MPs) is essential for unveiling functionality of these important biological constituents. Oriented-sample solid-state NMR (OS-NMR) is capable of providing such information on MPs under nearly physiological conditions. However, two dimensional OS-NMR experiments can take several days to complete due to long longitudinal relaxation times combined with the large number of scans to achieve sufficient signal sensitivity in biological samples. Here, free radicals 5-DOXYL stearic acid, TEMPOL, and CAT-1 were added to uniformly (15)N-labeled Pf1 coat protein reconstituted in DMPC/DHPC bicelles, and their effect on the longitudinal relaxation times (T1Z) was investigated. The dramatically shortened T1Z's allowed for the signal gain per unit time to be used for either: (i) up to a threefold reduction of the total experimental time at 99% magnetization recovery or (ii) obtaining up to 74% signal enhancement between the control and radical samples during constant experimental time at "optimal" relaxation delays. In addition, through OS-NMR and high-field EPR studies, free radicals were able to provide positional constraints in the bicelle system, which provide a description of the location of each residue in Pf1 coat protein within the bicellar membranes. This information can be useful in the determination of oligomerization states and immersion depths of larger membrane proteins. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. Identification of DNA–protein Binding Sites through Multi-Scale Local Average Blocks on Sequence Information

    Directory of Open Access Journals (Sweden)

    Cong Shen

    2017-11-01

    Full Text Available DNA–protein interactions appear as pivotal roles in diverse biological procedures and are paramount for cell metabolism, while identifying them with computational means is a kind of prudent scenario in depleting in vitro and in vivo experimental charging. A variety of state-of-the-art investigations have been elucidated to improve the accuracy of the DNA–protein binding sites prediction. Nevertheless, structure-based approaches are limited under the condition without 3D information, and the predictive validity is still refinable. In this essay, we address a kind of competitive method called Multi-scale Local Average Blocks (MLAB algorithm to solve this issue. Different from structure-based routes, MLAB exploits a strategy that not only extracts local evolutionary information from primary sequences, but also using predicts solvent accessibility. Moreover, the construction about predictors of DNA–protein binding sites wields an ensemble weighted sparse representation model with random under-sampling. To evaluate the performance of MLAB, we conduct comprehensive experiments of DNA–protein binding sites prediction. MLAB gives M C C of 0.392 , 0.315 , 0.439 and 0.245 on PDNA-543, PDNA-41, PDNA-316 and PDNA-52 datasets, respectively. It shows that MLAB gains advantages by comparing with other outstanding methods. M C C for our method is increased by at least 0.053 , 0.015 and 0.064 on PDNA-543, PDNA-41 and PDNA-316 datasets, respectively.

  7. Bridging topological and functional information in protein interaction networks by short loops profiling

    Science.gov (United States)

    Chung, Sun Sook; Pandini, Alessandro; Annibale, Alessia; Coolen, Anthony C. C.; Thomas, N. Shaun B.; Fraternali, Franca

    2015-02-01

    Protein-protein interaction networks (PPINs) have been employed to identify potential novel interconnections between proteins as well as crucial cellular functions. In this study we identify fundamental principles of PPIN topologies by analysing network motifs of short loops, which are small cyclic interactions of between 3 and 6 proteins. We compared 30 PPINs with corresponding randomised null models and examined the occurrence of common biological functions in loops extracted from a cross-validated high-confidence dataset of 622 human protein complexes. We demonstrate that loops are an intrinsic feature of PPINs and that specific cell functions are predominantly performed by loops of different lengths. Topologically, we find that loops are strongly related to the accuracy of PPINs and define a core of interactions with high resilience. The identification of this core and the analysis of loop composition are promising tools to assess PPIN quality and to uncover possible biases from experimental detection methods. More than 96% of loops share at least one biological function, with enrichment of cellular functions related to mRNA metabolic processing and the cell cycle. Our analyses suggest that these motifs can be used in the design of targeted experiments for functional phenotype detection.

  8. Combining substrate specificity analysis with support vector classifiers reveals feruloyl esterase as a phylogenetically informative protein group

    DEFF Research Database (Denmark)

    Olivares Hernandez, Roberto; Sunner, Hampus; Frisvad, Jens Christian

    2010-01-01

    Background Our understanding of how fungi evolved to develop a variety of ecological niches, is limited but of fundamental biological importance. Specifically, the evolution of enzymes affects how well species can adapt to new environmental conditions. Feruloyl esterases (FAEs) are enzymes able...... defined via our phylogenetic analysis not only suggests that FAEs are phylogenetically informative proteins but it is also a considerable step towards improved FAEs functional prediction....

  9. The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone.

    Science.gov (United States)

    Roche, Daniel Barry; Brüls, Thomas

    2015-05-01

    As the largest fraction of any proteome does not carry out enzymatic functions, and in order to leverage 3D structural data for the annotation of increasingly higher volumes of sequence data, we wanted to assess the strength of the link between coarse grained structural data (i.e., homologous superfamily level) and the enzymatic versus non-enzymatic nature of protein sequences. To probe this relationship, we took advantage of 41 phylogenetically diverse (encompassing 11 distinct phyla) genomes recently sequenced within the GEBA initiative, for which we integrated structural information, as defined by CATH, with enzyme level information, as defined by Enzyme Commission (EC) numbers. This analysis revealed that only a very small fraction (about 1%) of domain sequences occurring in the analyzed genomes was found to be associated with homologous superfamilies strongly indicative of enzymatic function. Resorting to less stringent criteria to define enzyme versus non-enzyme biased structural classes or excluding highly prevalent folds from the analysis had only modest effect on this proportion. Thus, the low genomic coverage by structurally anchored protein domains strongly associated to catalytic activities indicates that, on its own, the power of coarse grained structural information to infer the general property of being an enzyme is rather limited. © 2015 The Protein Society.

  10. Existing chemicals: international activities.

    Science.gov (United States)

    Purchase, J F

    1989-01-01

    The standards of care used in the protection of the health and safety of people exposed to chemicals has increased dramatically in the last decade. Standards imposed by regulation and those adopted by industry have required a greater level of knowledge about the hazards of chemicals. In the E.E.C., the 6th amendment of the dangerous substances directive imposed the requirement that al new chemicals should be tested according to prescribed programme before introduction on to the market. The development of a European inventory of existing chemicals was an integral part of the 6th amendment. It has now become clear that increased standards of care referred to above must be applied to the chemicals on the inventory list. There is, however, a considerable amount of activity already under way in various international agencies. The OECD Chemicals Programme has been involved in considering the problem of existing chemicals for some time, and is producing a priority list and action programme. The International Programme on Chemical Safety produces international chemical safety cards, health and safety guides and environmental health criteria documents. The international register of potentially toxic compounds (part of UNEP) has prepared chemical data profiles on 990 compounds. The International Agency for Research on Cancer prepared monographs on the carcinogenic risk of chemicals to man. So far 42 volumes have been prepared covering about 900 substances. IARC and IPCS also prepare periodic reports on ongoing research on carcinogenicity or toxicity (respectively) of chemicals. The chemical industry through ECETOC (the European Chemical Industry Ecology and Toxicology Centre) has mounted a major initiative on existing chemicals. Comprehensive reviews of the toxicity of selected chemicals are published (Joint Assessment of Commodity Chemicals). In its technical report no. 30 ECETOC lists reviews and evaluations by major national and international organisations, which provides

  11. Do multiquark hadrons exist

    Energy Technology Data Exchange (ETDEWEB)

    Weinstein, J.; Isgur, N.

    1982-03-08

    The qqq-barq-bar system has been examined by solving the four-particle Schroedinger equation variationally. The main findings are that: (1) qqq-barq-bar bound states normally do not exist, (2) the cryptoexotic 0/sup + +/ sector of this system with KK-bar quantum numbers is probably the only exception to (1) and its bound states can be identified with the S* and delta just below KK-bar threshold, (3) qqq-barq-bar bound states provide a model for the weak binding and color-singlet clustering observed in nuclei, and (4) there is no indication that this system has strong resonances.

  12. Repowering existing plants

    Energy Technology Data Exchange (ETDEWEB)

    Steazel, W.C.; Sopocy, D.M.; Pace, S.E.

    1998-07-01

    Increased competition among power generation companies, changes in generating system load requirements, lower allowable plant emissions, and changes in fuel availability and cost accentuate the need to closely assess the economics and performances of older electric generation units. Generally, decisions must be made as to whether these units should be retired and replaced with new generation capacity, whether capacity should be purchased from other generation companies, or if these existing units should be repowered. These decisions usually require the evaluation of many factors including; environmental discharge limits, permitting requirements, generating load demand increases, options for increasing the benefits of using existing facilities (e.g.; increasing efficiency and output), fuel cost increases, transmission requirements and access, optional plant designs. Many of these factors need to be used in the analysis based on a range rather than one specific value to test for changes in the selection of the best option because of future uncertainties. Usually complicated analysis results because of all the factors involved. Computer products that integrate performance and financial analysis can provide substantial value by enabling the user to evaluate the applicable plant options and range of input. The SOAPP (State-of-the-Art Power Plant) family of software products provides easy to use tools for rapid, thorough and economical evaluation of plant option. Repowering evaluation methodology typically used in the US, technology options, and available SOAPP repowering software are reviewed in this paper.

  13. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.

    Science.gov (United States)

    Biasini, Marco; Bienert, Stefan; Waterhouse, Andrew; Arnold, Konstantin; Studer, Gabriel; Schmidt, Tobias; Kiefer, Florian; Gallo Cassarino, Tiziano; Bertoni, Martino; Bordoli, Lorenza; Schwede, Torsten

    2014-07-01

    Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. Here, we describe the latest version of the SWISS-MODEL expert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The improved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. The accuracy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states. SWISS-MODEL is available at http://swissmodel.expasy.org/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. ProtNA-ASA: Protein-nucleic acid structural database with information on accessible surface area

    Science.gov (United States)

    Tkachenko, M. Y.; Boryskina, O. P.; Shestopalova, A. V.; Tolstorukov, M. Y.

    The article describes a new database (ProtNA-ASA), which combines the data on conformational parameters of nucleic acids and calculations of the accessible surface area (ASA) of nucleic acid atoms in protein-DNA/RNA complexes. As for October 2008, the database contains 214 DNA-protein and 28 RNA-protein non-homologous complexes. The database provides structural parameters that describe local geometry of base pairs and base-pair steps as well as backbone torsion angles. Additionally, total ASA of DNA/RNA atoms and the accessible area of atoms in the minor and major grooves are calculated. ProtNA-ASA database facilitates studying the relationship between the DNA/RNA conformation and availability of atoms for contact with proteins either in major or in minor groove for different nucleotides. Such an analysis is important for understanding the principles of molecular recognition including indirect sequence readout. The database is publicly available for use at http://www.protna.bio-page.org.

  15. A structurally informed autotransporter platform for efficient heterologous protein secretion and display

    NARCIS (Netherlands)

    Jong, Wouter S. P.; Soprova, Zora; de Punder, Karin; ten Hagen-Jongman, Corinne M.; Wagner, Samuel; Wickström, David; de Gier, Jan-Willem; Andersen, Peter; van der Wel, Nicole N.; Luirink, Joen

    2012-01-01

    Background: The self-sufficient autotransporter (AT) pathway, ubiquitous in Gram-negative bacteria, combines a relatively simple protein secretion mechanism with a high transport capacity. ATs consist of a secreted passenger domain and a beta-domain that facilitates transfer of the passenger across

  16. Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information

    Directory of Open Access Journals (Sweden)

    Vullo Alessandro

    2007-06-01

    Full Text Available Abstract Background Structural properties of proteins such as secondary structure and solvent accessibility contribute to three-dimensional structure prediction, not only in the ab initio case but also when homology information to known structures is available. Structural properties are also routinely used in protein analysis even when homology is available, largely because homology modelling is lower throughput than, say, secondary structure prediction. Nonetheless, predictors of secondary structure and solvent accessibility are virtually always ab initio. Results Here we develop high-throughput machine learning systems for the prediction of protein secondary structure and solvent accessibility that exploit homology to proteins of known structure, where available, in the form of simple structural frequency profiles extracted from sets of PDB templates. We compare these systems to their state-of-the-art ab initio counterparts, and with a number of baselines in which secondary structures and solvent accessibilities are extracted directly from the templates. We show that structural information from templates greatly improves secondary structure and solvent accessibility prediction quality, and that, on average, the systems significantly enrich the information contained in the templates. For sequence similarity exceeding 30%, secondary structure prediction quality is approximately 90%, close to its theoretical maximum, and 2-class solvent accessibility roughly 85%. Gains are robust with respect to template selection noise, and significant for marginal sequence similarity and for short alignments, supporting the claim that these improved predictions may prove beneficial beyond the case in which clear homology is available. Conclusion The predictive system are publicly available at the address http://distill.ucd.ie.

  17. Existence of Minkowski space

    CERN Document Server

    Wagner, Serge

    2016-01-01

    Physics textbooks present Minkowski space as an almost pure mathematical construct, without any explicit restriction on a domain where it is applicable in physics. Meanwhile, its physical meaning cannot but follow the same premises as those which underlies the special relativity theory: motion of free point particles and propagation of electromagnetic waves. However, the common formalism of coordinate transformations between any two inertial frames appears too ponderous to infer the existence of Minkowski space. For this reason, the time dilation and retardation, the contraction of the length along and the spatial invariance across the direction of relative motion of two frames are presented in a coordinate-free manner. This results in the transformation between two frames in the form of relationships between the time moments and the components of the position vector of a given event, along and across the directions of the frames' motion. The obtained transformation rules for the components of the position ve...

  18. Lebesgue Sets Immeasurable Existence

    Directory of Open Access Journals (Sweden)

    Diana Marginean Petrovai

    2012-12-01

    Full Text Available It is well known that the notion of measure and integral were released early enough in close connection with practical problems of measuring of geometric figures. Notion of measure was outlined in the early 20th century through H. Lebesgue’s research, founder of the modern theory of measure and integral. It was developed concurrently a technique of integration of functions. Gradually it was formed a specific area todaycalled the measure and integral theory. Essential contributions to building this theory was made by a large number of mathematicians: C. Carathodory, J. Radon, O. Nikodym, S. Bochner, J. Pettis, P. Halmos and many others. In the following we present several abstract sets, classes of sets. There exists the sets which are not Lebesgue measurable and the sets which are Lebesgue measurable but are not Borel measurable. Hence B ⊂ L ⊂ P(X.

  19. Accurate refinement of docked protein complexes using evolutionary information and deep learning.

    Science.gov (United States)

    Akbal-Delibas, Bahar; Farhoodi, Roshanak; Pomplun, Marc; Haspel, Nurit

    2016-06-01

    One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining protein-protein complexes. Given a docked complex, the refinement tool produces a small set of refined versions of the input complex, with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work, we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 Å error margin on average, by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures.

  20. InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information

    Science.gov (United States)

    Yu, Jinchao; Vavrusa, Marek; Andreani, Jessica; Rey, Julien; Tufféry, Pierre; Guerois, Raphaël

    2016-01-01

    The structural modeling of protein–protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-body docking search is performed using the FRODOCK program and the resulting models are re-scored with InterEvScore and SOAP-PP statistical potentials. The InterEvScore potential was specifically designed to integrate co-evolutionary information in the docking process. InterEvDock server is thus particularly well suited in case homologous sequences are available for both binding partners. The server returns 10 structures of the most likely consensus models together with 10 predicted residues most likely involved in the interface. In 91% of all complexes tested in the benchmark, at least one residue out of the 10 predicted is involved in the interface, providing useful guidelines for mutagenesis. InterEvDock is able to identify a correct model among the top10 models for 49% of the rigid-body cases with evolutionary information, making it a unique and efficient tool to explore structural interactomes under an evolutionary perspective. The InterEvDock web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock/. PMID:27131368

  1. Existing Analytical Frameworks for Information Behaviour Don’t Fully Explain HIV/AIDS Information Exchange in Rural Communities in Ontario, Canada. A Review of: Veinot, T., Harris, R., Bella, L., Rootman, I., & Krajnak, J. (2006. HIV/AIDS Information exchange in rural communities: Preliminary findings from a three‐province study. Canadian Journal of Information and Library Science, 30(3/4, 271‐290.

    Directory of Open Access Journals (Sweden)

    Kate Kelly

    2010-03-01

    its presence supersedes the professional role of the provider (social workers and counsellors were identified as key information sources over medical professionals in this instance. Participants responded negatively to the perceived lack of support from providers including doubting the information provided.•PHAs monitor their worlds and keep up to date about HIV/AIDS.Inconsistent with theories:•Reliance on caregivers for information is not solely explained by fear of stigma or exposure. Rather, it is the specialized knowledge and immersion in HIV/AIDS which is valued.•The distinction between peer or kin sources of information and institutional information sources is less clear and relationships with professionals can turn personal over time.•Inter‐personal connections include organisations, not just individuals, particularly AIDS Service Organizations and HIV specialist clinics.•Relatively few incidents of finding useful information about HIV/AIDS incidentally were described. The concept of information just being “out there” was not really applicable to rural settings, likely due to the lack of discussion within participant communities and local media. When it was discussed, participants reported being more likely to gain misinformation through their personal networks.•Incidental information acquisition originates mostly from professional and organisational sources. Participants identified posters, leaflets, and, for those who interacted with organisations, information via mail as contributing to current awareness.•The gate keeping concept does not capture all the information sharing activities undertaken by “gate keepers” in rural areas, and neither does it include formal providers of information, yet all PHAs interviewed identified formal providers as key sources.Conclusion – The findings reinforce some of the existing analytical framework theories, particularly the importance of affective components (i.e. emotional supports of information

  2. Mauriac syndrome still exists.

    Science.gov (United States)

    Dias, Joana; Martins, Sofia; Carvalho, Susana; Marques, Olinda; Antunes, Ana

    2013-05-01

    Mauriac syndrome (MS) is a rare complication of type 1 diabetes mellitus (DM1). It is related to low insulin concentrations and is less common since longer-acting insulins became available. It is characterized by hepatomegaly, growth and puberty delay, and the presence of elevated transaminases and serum lipids. The aim of this study was to describe the patients from a pediatric diabetic population that fulfill the criteria of MS. A retrospective analysis of the pediatric diabetic population with diagnostic criteria of MS currently followed at Hospital de Braga, was performed. From a population of 91 patients with DM1 18 years, 6 patients with the criteria for MS were identified: 5 girls, and 1 boy. The age at presentation was 13-17 years, with a minimum interval between DM1 diagnosis and MS criteria of 4 years. All the patients were prescribed intensive insulin therapy (median daily insulin dose: 0.88 U/kg). All had a previous history of poor glycemic control before the diagnosis of MS with glycated hemoglobin (HbA1c) between 8.8 and 12.9%. Increase of hepatic enzymes was present in all the patients; 4 of them had associated hepatomegaly. All the girls presented puberty delay and cushingoid features. None of the patients presented short stature and 5 of them presented mixed dyslipidemia. Although MS is an ancient entity described in DM1, it still exists, particularly in adolescent females. Being aware of MS is of extreme importance since most of the clinical features are reversible with better glycemic control. Copyright © 2012 SEEN. Published by Elsevier Espana. All rights reserved.

  3. Discovery of new candidate genes related to brain development using protein interaction information.

    Science.gov (United States)

    Chen, Lei; Chu, Chen; Kong, Xiangyin; Huang, Tao; Cai, Yu-Dong

    2015-01-01

    Human brain development is a dramatic process composed of a series of complex and fine-tuned spatiotemporal gene expressions. A good comprehension of this process can assist us in developing the potential of our brain. However, we have only limited knowledge about the genes and gene functions that are involved in this biological process. Therefore, a substantial demand remains to discover new brain development-related genes and identify their biological functions. In this study, we aimed to discover new brain-development related genes by building a computational method. We referred to a series of computational methods used to discover new disease-related genes and developed a similar method. In this method, the shortest path algorithm was executed on a weighted graph that was constructed using protein-protein interactions. New candidate genes fell on at least one of the shortest paths connecting two known genes that are related to brain development. A randomization test was then adopted to filter positive discoveries. Of the final identified genes, several have been reported to be associated with brain development, indicating the effectiveness of the method, whereas several of the others may have potential roles in brain development.

  4. Exploiting Large-Scale Drug-Protein Interaction Information for Computational Drug Repurposing

    Science.gov (United States)

    2014-06-20

    burden, to Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington VA...number of on-bits, as the synthetic routes may be under patent coverage and, therefore, the compounds are less likely to be found in the catalogs of...Clotrimazole 22.6 For oropharyngeal candidiasis, vaginal yeast infections, and fungal infections. Ketoconazole 21.5 For fungal infections. Dexamethasone

  5. Does the mental lexicon exist?

    Directory of Open Access Journals (Sweden)

    Lucilene Bender de Sousa

    2015-09-01

    Full Text Available One of the central and mostintriguing components of language processing to researchers is the mentallexicon. The term was used for the first time by Ann Triesman in 1961 and westill do not have clear answers on how it is structured and how muchinformation it contains, or even if there is something to be called a mentallexicon. For some time, mental lexicon has been compared to a mental dictionaryboth storing and organizing word knowledge; however, they are surely differentin structure and quantity/quality of information. Neuroimaging studies havealso tried to bring contributions to these questions. Some researchers believethat there are many lexicons, one for each level of stored information (ULLMAN,2007: orthographic, phonological, semantic and syntactic lexicons. Another group of researchers (MCCLELLAND;ROGERS, 2003; SEIDENBERG, 1997, etc. postulates the existence of only onelexicon where all information levels are integrated. Recently, a new audaciousproposal has been done by Elman (2009, the inexistence of a mental lexicon. Inthis paper, we discuss the different views of mental lexicon structure andcontent. We try to proceed on the discussion of Elman’s new proposal andconfront it to data obtained by behavioral, neuroimaging and computationalstudies.

  6. Identification of Protein–Protein Interactions via a Novel Matrix-Based Sequence Representation Model with Amino Acid Contact Information

    Directory of Open Access Journals (Sweden)

    Yijie Ding

    2016-09-01

    Full Text Available Identification of protein–protein interactions (PPIs is a difficult and important problem in biology. Since experimental methods for predicting PPIs are both expensive and time-consuming, many computational methods have been developed to predict PPIs and interaction networks, which can be used to complement experimental approaches. However, these methods have limitations to overcome. They need a large number of homology proteins or literature to be applied in their method. In this paper, we propose a novel matrix-based protein sequence representation approach to predict PPIs, using an ensemble learning method for classification. We construct the matrix of Amino Acid Contact (AAC, based on the statistical analysis of residue-pairing frequencies in a database of 6323 protein–protein complexes. We first represent the protein sequence as a Substitution Matrix Representation (SMR matrix. Then, the feature vector is extracted by applying algorithms of Histogram of Oriented Gradient (HOG and Singular Value Decomposition (SVD on the SMR matrix. Finally, we feed the feature vector into a Random Forest (RF for judging interaction pairs and non-interaction pairs. Our method is applied to several PPI datasets to evaluate its performance. On the S . c e r e v i s i a e dataset, our method achieves 94 . 83 % accuracy and 92 . 40 % sensitivity. Compared with existing methods, and the accuracy of our method is increased by 0 . 11 percentage points. On the H . p y l o r i dataset, our method achieves 89 . 06 % accuracy and 88 . 15 % sensitivity, the accuracy of our method is increased by 0 . 76 % . On the H u m a n PPI dataset, our method achieves 97 . 60 % accuracy and 96 . 37 % sensitivity, and the accuracy of our method is increased by 1 . 30 % . In addition, we test our method on a very important PPI network, and it achieves 92 . 71 % accuracy. In the Wnt-related network, the accuracy of our method is increased by 16 . 67 % . The source code and all

  7. Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels

    Directory of Open Access Journals (Sweden)

    McDermott Drew

    2009-08-01

    Full Text Available Abstract Background Proteins interact through specific binding interfaces that contain many residues in domains. Protein interactions thus occur on three different levels of a concept hierarchy: whole-proteins, domains, and residues. Each level offers a distinct and complementary set of features for computationally predicting interactions, including functional genomic features of whole proteins, evolutionary features of domain families and physical-chemical features of individual residues. The predictions at each level could benefit from using the features at all three levels. However, it is not trivial as the features are provided at different granularity. Results To link up the predictions at the three levels, we propose a multi-level machine-learning framework that allows for explicit information flow between the levels. We demonstrate, using representative yeast interaction networks, that our algorithm is able to utilize complementary feature sets to make more accurate predictions at the three levels than when the three problems are approached independently. To facilitate application of our multi-level learning framework, we discuss three key aspects of multi-level learning and the corresponding design choices that we have made in the implementation of a concrete learning algorithm. 1 Architecture of information flow: we show the greater flexibility of bidirectional flow over independent levels and unidirectional flow; 2 Coupling mechanism of the different levels: We show how this can be accomplished via augmenting the training sets at each level, and discuss the prevention of error propagation between different levels by means of soft coupling; 3 Sparseness of data: We show that the multi-level framework compounds data sparsity issues, and discuss how this can be dealt with by building local models in information-rich parts of the data. Our proof-of-concept learning algorithm demonstrates the advantage of combining levels, and opens up

  8. Binomial probability distribution model-based protein identification algorithm for tandem mass spectrometry utilizing peak intensity information.

    Science.gov (United States)

    Xiao, Chuan-Le; Chen, Xiao-Zhou; Du, Yang-Li; Sun, Xuesong; Zhang, Gong; He, Qing-Yu

    2013-01-04

    Mass spectrometry has become one of the most important technologies in proteomic analysis. Tandem mass spectrometry (LC-MS/MS) is a major tool for the analysis of peptide mixtures from protein samples. The key step of MS data processing is the identification of peptides from experimental spectra by searching public sequence databases. Although a number of algorithms to identify peptides from MS/MS data have been already proposed, e.g. Sequest, OMSSA, X!Tandem, Mascot, etc., they are mainly based on statistical models considering only peak-matches between experimental and theoretical spectra, but not peak intensity information. Moreover, different algorithms gave different results from the same MS data, implying their probable incompleteness and questionable reproducibility. We developed a novel peptide identification algorithm, ProVerB, based on a binomial probability distribution model of protein tandem mass spectrometry combined with a new scoring function, making full use of peak intensity information and, thus, enhancing the ability of identification. Compared with Mascot, Sequest, and SQID, ProVerB identified significantly more peptides from LC-MS/MS data sets than the current algorithms at 1% False Discovery Rate (FDR) and provided more confident peptide identifications. ProVerB is also compatible with various platforms and experimental data sets, showing its robustness and versatility. The open-source program ProVerB is available at http://bioinformatics.jnu.edu.cn/software/proverb/ .

  9. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers. The bi...

  10. Improving protein function prediction using domain and protein complexes in PPI networks.

    Science.gov (United States)

    Peng, Wei; Wang, Jianxin; Cai, Juan; Chen, Lu; Li, Min; Wu, Fang-Xiang

    2014-03-24

    Characterization of unknown proteins through computational approaches is one of the most challenging problems in silico biology, which has attracted world-wide interests and great efforts. There have been some computational methods proposed to address this problem, which are either based on homology mapping or in the context of protein interaction networks. In this paper, two algorithms are proposed by integrating the protein-protein interaction (PPI) network, proteins' domain information and protein complexes. The one is domain combination similarity (DCS), which combines the domain compositions of both proteins and their neighbors. The other is domain combination similarity in context of protein complexes (DSCP), which extends the protein functional similarity definition of DCS by combining the domain compositions of both proteins and the complexes including them. The new algorithms are tested on networks of the model species of Saccharomyces cerevisiae to predict functions of unknown proteins using cross validations. Comparing with other several existing algorithms, the results have demonstrated the effectiveness of our proposed methods in protein function prediction. Furthermore, the algorithm DSCP using experimental determined complex data is robust when a large percentage of the proteins in the network is unknown, and it outperforms DCS and other several existing algorithms. The accuracy of predicting protein function can be improved by integrating the protein-protein interaction (PPI) network, proteins' domain information and protein complexes.

  11. Automated image analysis of cyclin D1 protein expression in invasive lobular breast carcinoma provides independent prognostic information.

    Science.gov (United States)

    Tobin, Nicholas P; Lundgren, Katja L; Conway, Catherine; Anagnostaki, Lola; Costello, Sean; Landberg, Göran

    2012-11-01

    The emergence of automated image analysis algorithms has aided the enumeration, quantification, and immunohistochemical analyses of tumor cells in both whole section and tissue microarray samples. To date, the focus of such algorithms in the breast cancer setting has been on traditional markers in the common invasive ductal carcinoma subtype. Here, we aimed to optimize and validate an automated analysis of the cell cycle regulator cyclin D1 in a large collection of invasive lobular carcinoma and relate its expression to clinicopathologic data. The image analysis algorithm was trained to optimally match manual scoring of cyclin D1 protein expression in a subset of invasive lobular carcinoma tissue microarray cores. The algorithm was capable of distinguishing cyclin D1-positive cells and illustrated high correlation with traditional manual scoring (κ=0.63). It was then applied to our entire cohort of 483 patients, with subsequent statistical comparisons to clinical data. We found no correlation between cyclin D1 expression and tumor size, grade, and lymph node status. However, overexpression of the protein was associated with reduced recurrence-free survival (P=.029), as was positive nodal status (Pinvasive lobular carcinoma. Finally, high cyclin D1 expression was associated with increased hazard ratio in multivariate analysis (hazard ratio, 1.75; 95% confidence interval, 1.05-2.89). In conclusion, we describe an image analysis algorithm capable of reliably analyzing cyclin D1 staining in invasive lobular carcinoma and have linked overexpression of the protein to increased recurrence risk. Our findings support the use of cyclin D1 as a clinically informative biomarker for invasive lobular breast cancer. Copyright © 2012 Elsevier Inc. All rights reserved.

  12. Existence and Detection of Fireballs,

    Science.gov (United States)

    An attempt is made to analyze critically the experimental proofs indicating the existence of fireballs. Some ideas are presented on methods of the...properties of fireballs if their existence will be checked by other methods. (Author)

  13. Pre-existing Antibody: Biotherapeutic Modality-Based Review

    OpenAIRE

    Gorovits, Boris; Clements-Egan, Adrienne; Birchler, Mary; Liang, Meina; Myler, Heather; Peng, Kun; Purushothama, Shobha; Rajadhyaksha, Manoj; Salazar-Fontana, Laura; Sung, Crystal; Xue, Li

    2016-01-01

    Pre-existing antibodies to biotherapeutic drugs have been detected in drug-naïve subjects for a variety of biotherapeutic modalities. Pre-existing antibodies are immunoglobulins that are either specific or cross-reacting with a protein or glycan epitopes on a biotherapeutic compound. Although the exact cause for pre-existing antibodies is often unknown, environmental exposures to non-human proteins, glycans, and structurally similar products are frequently proposed as factors. Clinical conseq...

  14. Predict protein structural class for low-similarity sequences by evolutionary difference information into the general form of Chou's pseudo amino acid composition.

    Science.gov (United States)

    Zhang, Lichao; Zhao, Xiqiang; Kong, Liang

    2014-08-21

    Knowledge of protein structural class plays an important role in characterizing the overall folding type of a given protein. At present, it is still a challenge to extract sequence information solely using protein sequence for protein structural class prediction with low similarity sequence in the current computational biology. In this study, a novel sequence representation method is proposed based on position specific scoring matrix for protein structural class prediction. By defined evolutionary difference formula, varying length proteins are expressed as uniform dimensional vectors, which can represent evolutionary difference information between the adjacent residues of a given protein. To perform and evaluate the proposed method, support vector machine and jackknife tests are employed on three widely used datasets, 25PDB, 1189 and 640 datasets with sequence similarity lower than 25%, 40% and 25%, respectively. Comparison of our results with the previous methods shows that our method may provide a promising method to predict protein structural class especially for low-similarity sequences. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Building and evaluation of a structured representation of pharmacokinetics information presented in SPCs: from existing conceptual views of pharmacokinetics associated with natural language processing to object-oriented design.

    Science.gov (United States)

    Duclos-Cartolano, Catherine; Venot, Alain

    2003-01-01

    Develop a detailed representation of pharmacokinetics (PK), derived from the information in Summaries of Product Characteristics (SPCs), for use in computerized systems to help practitioners in pharmaco-therapeutic reasoning. Available knowledge about PK was studied to identify main PK concepts and organize them in a preliminary generic model. The information from 1950 PK SPC-texts in the French language was studied using a morpho-syntactic analyzer. It produced a list of candidate terms (CTs) from which those describing main PK concepts were selected. The contexts in which they occurred were explored to discover co-occurring CTs. The regrouping according to CT semantic types led to a detailed object-oriented model of PK. The model was evaluated. A random sample of 100 PK texts structured according to the model was judged for completeness and semantic accuracy by 8 experts who were blinded to other experts' responses. The PK text file contained about 300000 words, and the morpho-syntactic analysis extracted 17520 different CTs. The context of 592 CTs was studied and used to deduce the PK model. It consists of four entities: the information about the real PK process, the experimental protocol, the mathematical modeling, and the influence of factors causing variation. Experts judged that the PK model represented the information in 100 sample PK texts completely in 89% of cases and nearly completely in the other 11%. There was no distortion of meaning in 98% of cases and little distortion in the remainder. The PK model seems to be applicable to all SPCs and can be used to retranscribe legal information from PK sections of SPCs into structured databases.

  16. Protein function prediction by collective classification with explicit and implicit edges in protein-protein interaction networks.

    Science.gov (United States)

    Xiong, Wei; Liu, Hui; Guan, Jihong; Zhou, Shuigeng

    2013-01-01

    Protein function prediction is an important problem in the post-genomic era. Recent advances in experimental biology have enabled the production of vast amounts of protein-protein interaction (PPI) data. Thus, using PPI data to functionally annotate proteins has been extensively studied. However, most existing network-based approaches do not work well when annotation and interaction information is inadequate in the networks. In this paper, we proposed a new method that combines PPI information and protein sequence information to boost the prediction performance based on collective classification. Our method divides function prediction into two phases: First, the original PPI network is enriched by adding a number of edges that are inferred from protein sequence information. We call the added edges implicit edges, and the existing ones explicit edges correspondingly. Second, a collective classification algorithm is employed on the new network to predict protein function. We conducted extensive experiments on two real, publicly available PPI datasets. Compared to four existing protein function prediction approaches, our method performs better in many situations, which shows that adding implicit edges can indeed improve the prediction performance. Furthermore, the experimental results also indicate that our method is significantly better than the compared approaches in sparsely-labeled networks, and it is robust to the change of the proportion of annotated proteins.

  17. Kierkegaardovo pojetí existence

    OpenAIRE

    Janatová, Kristýna

    2016-01-01

    The topic of the bachelor thesis is "Kierkegaard's conception of existence". There are both the life of the Danish philosopher Søren Kierkegaard and his philosophy discussed. The issue of human existence is analysed with its main three stages which are focused on aesthetics, ethics and religion. These stages of existence are at first described and afterwards compared with each other. The aesthetic represents the first stage of life and the religious stage is considered to be the highest aim o...

  18. What is the gold standard for comprehensive interinstitutional communication of perioperative information for thyroid cancer patients? A comparison of existing electronic health records with the current American Thyroid Association recommendations.

    Science.gov (United States)

    Dos Reis, Laura L; Tuttle, R Michael; Alon, Eran; Bergman, Donald A; Bernet, Victor; Brett, Elise M; Cobin, Rhoda; Doherty, Gerard; Harris, Jeffrey R; Klopper, Joshua; Lee, Stephanie L; Lupo, Mark; Milas, Mira; Machac, Josef; Mechanick, Jeffrey I; Orloff, Lisa; Randolph, Gregory; Ross, Douglas S; Smallridge, Robert C; Terris, David James; Tufano, Ralph P; Mehra, Saral; Scherl, Sophie; Clain, Jason B; Urken, Mark L

    2014-10-01

    Appropriate management of well-differentiated thyroid cancer requires treating clinicians to have access to critical elements of the patient's presentation, surgical management, postoperative course, and pathologic assessment. Electronic health records (EHRs) provide an effective method for the storage and transmission of patient information, although most commercially available EHRs are not intended to be disease-specific. In addition, there are significant challenges for the sharing of relevant clinical information when providers involved in the care of a patient with thyroid cancer are not connected by a common EHR. In 2012, the American Thyroid Association (ATA) defined the critical elements for optimal interclinician communication in a position paper entitled, "The Essential Elements of Interdisciplinary Communication of Perioperative Information for Patients Undergoing Thyroid Cancer Surgery." We present a field-by-field comparison of the ATA's essential elements as applied to three contemporary electronic reporting systems: the Thyroid Surgery e-Form from Memorial Sloan-Kettering Cancer Center (MSKCC), the Alberta WebSMR from the University of Calgary, and the Thyroid Cancer Care Collaborative (TCCC). The MSKCC e-form fulfills 21 of 32 intraoperative fields and includes an additional 14 fields not specifically mentioned in the ATA's report. The Alberta WebSMR fulfills 45 of 82 preoperative and intraoperative fields outlined by the ATA and includes 13 additional fields. The TCCC fulfills 117 of 120 fields outlined by the ATA and includes 23 additional fields. Effective management of thyroid cancer is a highly collaborative, multidisciplinary effort. The patient information that factors into clinical decisions about thyroid cancer is complex. For these reasons, EHRs are particularly favorable for the management of patients with thyroid cancer. The MSKCC Thyroid Surgery e-Form, the Alberta WebSMR, and the TCCC each meet all of the general recommendations for

  19. Geographic Information Systems for Assessing Existing and Potential Bio-energy Resources: Their Use in Determining Land Use and Management Options which Minimize Ecological and Landscape Impacts in Rural Areas

    Science.gov (United States)

    Jackman, A. E.; Fabos, J. G.; Carlozzi, C. C.

    1982-01-01

    A management construct is described which forms part of an overall landscape ecological planning model which has as a principal objective the extension of the traditional descriptive land use mapping capabilities of geographic information systems into land management realms. It is noted that geographic information systems appear to be moving to more comprehensive methods of data handling and storage, such as relational and hierarchical data management systems, and a clear need has simultaneously arisen therefore for planning assessment techniques and methodologies which can actually use such complex levels of data in a systematic, yet flexible and scenario dependent way. The descriptive of mapping method proposed broaches such issues and utilizes a current New England bioenergy scenario, stimulated by the use of hardwoods for household heating purposes established in the post oil crisis era and the increased awareness of the possible landscape and ecological ramifications of the continued increasing use of the resource.

  20. Behaviour of intrinsically disordered proteins in protein-protein complexes with an emphasis on fuzziness

    DEFF Research Database (Denmark)

    Olsen, Johan Gotthardt; Teilum, Kaare; Kragelund, Birthe Brandt

    2017-01-01

    Intrinsically disordered proteins (IDPs) do not, by themselves, fold into a compact globular structure. They are extremely dynamic and flexible, and are typically involved in signalling and transduction of information through binding to other macromolecules. The reason for their existence may lie...

  1. Molecular cloning, modeling and differential expression of a gene encoding a silent information regulator-like protein from Sporothrix schenckii.

    Science.gov (United States)

    Hou, Binbin; Liu, Xiaoming; Zheng, Fangliang; Xu, Xuezhu; Zhang, Zhenying

    2014-06-01

    Sporothrix schenckii (S. schenckii) is a dimorphic fungus that produces lymphocutaneous lesions. The signature characteristic of S. schenckii is a temperature-induced phase transition. Silent information regulator (Sir) has been proven to be involved in phenotypic switching in Saccharomyces cerevisiae (S. cerevisiae) and Candida albicans (C. albicans) by organizing chromatin structure. In this study, we isolated and characterized a Sir homologue gene, designated as SsSir2, from the yeast form of S. schenckii. The full-length SsSir2 cDNA sequence is 1753 bp in size and contains an open reading frame of 1329 bp encoding 442 amino acids. The predicted molecular mass of SsSir2 is 48.1 kDa with an estimated theoretical isoelectric point of 4.6. The SsSir2 kinase domain shows a 78% identity with that of Hst2, a Sir2 Ib gene from S. cerevisiae. Three exons and two introns were identified within the 1472‑bp SsSir2 genomic DNA sequence of S. schenckii. A three-dimensional model of SsSir2 was constructed using a homology modeling method, and its reliability was evaluated. The active site of SsSir2 was identified by docking simulation, which indicated that several important residues, such as Asn127 and Asp129, play an important role in the histone deacetylase activity of Sir2 family proteins. The differential expression of the SsSir2 in two stages was demonstrated by real-time RT-PCR. The expression of SsSir2 was higher in the yeast stage compared with that in the mycelial one, which indicated that SsSir2 may be involved in the phenotypic switching and morphogenesis of the yeast phase in S. schenckii.

  2. Can C-reactive protein inform antidepressant medication selection in depressed outpatients? Findings from the CO-MED trial.

    Science.gov (United States)

    Jha, Manish K; Minhajuddin, Abu; Gadad, Bharathi S; Greer, Tracy; Grannemann, Bruce; Soyombo, Abigail; Mayes, Taryn L; Rush, A John; Trivedi, Madhukar H

    2017-04-01

    Currently, no valid measures inform treatment selection for depressed patients. Whether C-reactive protein (CRP) in particular and two other acute phase reactants (inflammatory markers) could differentiate between patients responding to either of two treatments with different mechanisms of action was assessed. Subjects included Combining Medications to Enhance Depression Outcomes (CO-MED) trial participants randomly assigned to either escitalopram plus placebo (SSRI monotherapy, n=51) or bupropion plus escitalopram combination (bupropion-SSRI combination, n=55) with baseline plasma samples. CRP, serum amyloid P component, and alpha-2-macroglobulin were measured using the Bioplex Pro™ human acute-phase 4-plex panel. We conducted mixed model analyses of depressive symptom (Quick Inventory of Depressive Symptomatology Self-Report) and side-effect burden (Frequency, Intensity, and Burden of Side-Effects Rating Scale) obtained weekly or every other week over the 12-week acute-phase of CO-MED trial to evaluate the relationship between these outcomes and baseline CRP and other acute-phase reactants. The treatment arms did not differ in depressive symptom or side effect outcomes. Most participants (69.8%, 74/106) had baseline CRP levels greater than 1mg/L (indicative of systemic inflammatory activity). Higher baseline CRP levels were associated lower depression severity (correlation coefficient=-0.63) with bupropion-SSRI combination but not with SSRI monotherapy (correlation coefficient=0.40). The overall remission rate was 41.5%. The estimated remission rate with CRP threshold based assignment (SSRI monotherapy for <1mg/L and Bupropion-SSRI for ≥1mg/L) was 53.1%, with a number needed to treat of 8.6. Side effect burden was unrelated to any baseline inflammatory marker. Baseline CRP levels relate differentially to antidepressant treatment outcomes in persons with major depressive disorder. Clinicaltrials.gov identifier: NCT00590863. Copyright © 2017 Elsevier Ltd. All

  3. Protein-protein interaction predictions using text mining methods.

    Science.gov (United States)

    Papanikolaou, Nikolas; Pavlopoulos, Georgios A; Theodosiou, Theodosios; Iliopoulos, Ioannis

    2015-03-01

    It is beyond any doubt that proteins and their interactions play an essential role in most complex biological processes. The understanding of their function individually, but also in the form of protein complexes is of a great importance. Nowadays, despite the plethora of various high-throughput experimental approaches for detecting protein-protein interactions, many computational methods aiming to predict new interactions have appeared and gained interest. In this review, we focus on text-mining based computational methodologies, aiming to extract information for proteins and their interactions from public repositories such as literature and various biological databases. We discuss their strengths, their weaknesses and how they complement existing experimental techniques by simultaneously commenting on the biological databases which hold such information and the benchmark datasets that can be used for evaluating new tools. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Hydrophobic cluster analysis of G protein-coupled receptors: a powerful tool to derive structural and functional information from 2D-representation of protein sequences

    NARCIS (Netherlands)

    Lentes, K.U.; Mathieu, E.; Bischoff, Rainer; Rasmussen, U.B.; Pavirani, A.

    1993-01-01

    Current methods for comparative analyses of protein sequences are 1D-alignments of amino acid sequences based on the maximization of amino acid identity (homology) and the prediction of secondary structure elements. This method has a major drawback once the amino acid identity drops below 20-25%,

  5. Text Mining for Protein Docking.

    Science.gov (United States)

    Badal, Varsha D; Kundrotas, Petras J; Vakser, Ilya A

    2015-12-01

    The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking). Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu). The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features) approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound benchmark set

  6. Text Mining for Protein Docking.

    Directory of Open Access Journals (Sweden)

    Varsha D Badal

    2015-12-01

    Full Text Available The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking. Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu. The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound

  7. Existing Steel Railway Bridges Evaluation

    Directory of Open Access Journals (Sweden)

    Vičan Josef

    2016-12-01

    Full Text Available The article describes general principles and basis of evaluation of existing railway bridges based on the concept of load-carrying capacity determination. Compared to the design of a new bridge, the modified reliability level for existing bridges evaluation should be considered due to implementation of the additional data related to bridge condition and behaviour obtained from regular inspections. Based on those data respecting the bridge remaining lifetime, a modification of partial safety factors for actions and materials could be respected in the bridge evaluation process. A great attention is also paid to the specific problems of determination of load-caring capacity of steel railway bridges in service. Recommendation for global analysis and methodology for existing steel bridge superstructure load-carrying capacity determination are described too.

  8. Analysis and classification of DNA-binding sites in single-stranded and double-stranded DNA-binding proteins using protein information.

    Science.gov (United States)

    Wang, Wei; Liu, Juan; Xiong, Yi; Zhu, Lida; Zhou, Xionghui

    2014-08-01

    Single-stranded DNA-binding proteins (SSBs) and double-stranded DNA-binding proteins (DSBs) play different roles in biological processes when they bind to single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA). However, the underlying binding mechanisms of SSBs and DSBs have not yet been fully understood. Here, the authors firstly constructed two groups of ssDNA and dsDNA specific binding sites from two non-redundant sets of SSBs and DSBs. They further analysed the relationship between the two classes of binding sites and a newly proposed set of features (residue charge distribution, secondary structure and spatial shape). To assess and utilise the predictive power of these features, they trained a classification model using support vector machine to make predictions about the ssDNA and the dsDNA binding sites. The author's analysis and prediction results indicated that the two classes of binding sites can be distinguishable by the three types of features, and the final classifier using all the features achieved satisfactory performance. In conclusion, the proposed features will deepen their understanding of the specificity of proteins which bind to ssDNA or dsDNA.

  9. Existence of mesons after deconfinement

    NARCIS (Netherlands)

    F. Brau (Fabian); F. Buisseret

    2007-01-01

    textabstractWe investigate the possibility for a quark-antiquark pair to form a bound state at temperatures higher than the critical one ($T>T_c$), thus after deconfinement. Our main goal is to find analytical criteria constraining the existence of such mesons. Our formalism relies on a Schrödinger

  10. Limitations of existing web services

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Limitations of existing web services. Uploading or downloading large data. Serving too many user from single source. Difficult to provide computer intensive job. Depend on internet and its bandwidth. Security of data in transition. Maintain confidentiality of data ...

  11. Performance of Existing Hydrogen Stations

    Energy Technology Data Exchange (ETDEWEB)

    Sprik, Samuel [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Kurtz, Jennifer M [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Ainscough, Christopher D [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Saur, Genevieve [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Peters, Michael C [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-12-01

    In this presentation, the National Renewable Energy Laboratory presented aggregated analysis results on the performance of existing hydrogen stations, including performance, operation, utilization, maintenance, safety, hydrogen quality, and cost. The U.S. Department of Energy funds technology validation work at NREL through its National Fuel Cell Technology Evaluation Center (NFCTEC).

  12. Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures.

    Science.gov (United States)

    Maheshwari, Surabhi; Brylinski, Michal

    2015-11-23

    Protein-protein interactions (PPIs) mediate the vast majority of biological processes, therefore, significant efforts have been directed to investigate PPIs to fully comprehend cellular functions. Predicting complex structures is critical to reveal molecular mechanisms by which proteins operate. Despite recent advances in the development of new methods to model macromolecular assemblies, most current methodologies are designed to work with experimentally determined protein structures. However, because only computer-generated models are available for a large number of proteins in a given genome, computational tools should tolerate structural inaccuracies in order to perform the genome-wide modeling of PPIs. To address this problem, we developed eRank(PPI), an algorithm for the identification of near-native conformations generated by protein docking using experimental structures as well as protein models. The scoring function implemented in eRank(PPI) employs multiple features including interface probability estimates calculated by eFindSite(PPI) and a novel contact-based symmetry score. In comparative benchmarks using representative datasets of homo- and hetero-complexes, we show that eRank(PPI) consistently outperforms state-of-the-art algorithms improving the success rate by ~10 %. eRank(PPI) was designed to bridge the gap between the volume of sequence data, the evidence of binary interactions, and the atomic details of pharmacologically relevant protein complexes. Tolerating structure imperfections in computer-generated models opens up a possibility to conduct the exhaustive structure-based reconstruction of PPI networks across proteomes. The methods and datasets used in this study are available at www.brylinski.org/erankppi.

  13. Genome-Wide Prediction and Analysis of 3D-Domain Swapped Proteins in the Human Genome from Sequence Information.

    Science.gov (United States)

    Upadhyay, Atul Kumar; Sowdhamini, Ramanathan

    2016-01-01

    3D-domain swapping is one of the mechanisms of protein oligomerization and the proteins exhibiting this phenomenon have many biological functions. These proteins, which undergo domain swapping, have acquired much attention owing to their involvement in human diseases, such as conformational diseases, amyloidosis, serpinopathies, proteionopathies etc. Early realisation of proteins in the whole human genome that retain tendency to domain swap will enable many aspects of disease control management. Predictive models were developed by using machine learning approaches with an average accuracy of 78% (85.6% of sensitivity, 87.5% of specificity and an MCC value of 0.72) to predict putative domain swapping in protein sequences. These models were applied to many complete genomes with special emphasis on the human genome. Nearly 44% of the protein sequences in the human genome were predicted positive for domain swapping. Enrichment analysis was performed on the positively predicted sequences from human genome for their domain distribution, disease association and functional importance based on Gene Ontology (GO). Enrichment analysis was also performed to infer a better understanding of the functional importance of these sequences. Finally, we developed hinge region prediction, in the given putative domain swapped sequence, by using important physicochemical properties of amino acids.

  14. Information and Informality

    DEFF Research Database (Denmark)

    Larsson, Magnus; Segerstéen, Solveig; Svensson, Cathrin

    2011-01-01

    leaders were thus seen to function on the level of the organization as a whole, and in cooperation with formal leaders. Drawing on existing theory of leadership in creative and professional contexts, this cooperation can be specified to concern task structuring. The informal leaders in our study......The article presents an empirical study of informal leadership in an international high-tech company. The empirical work consisted of qualitative observation and shadowing of managers in the company, and a total of 14 interviews. The transcribed fieldnotes and audio recordings of observations...... and interviews were analyzed thematically, resulting in three central themes: informality, information based authority, and information brokering. The general informal character of interactions at work included a network based information dissemination. In these networks, persons were percieved as informal...

  15. What is information?

    Science.gov (United States)

    Barbieri, Marcello

    2016-03-13

    Molecular biology is based on two great discoveries: the first is that genes carry hereditary information in the form of linear sequences of nucleotides; the second is that in protein synthesis a sequence of nucleotides is translated into a sequence of amino acids, a process that amounts to a transfer of information from genes to proteins. These discoveries have shown that the information of genes and proteins is the specific linear order of their sequences. This is a clear definition of information and there is no doubt that it reflects an experimental reality. What is not clear, however, is the ontological status of information, and the result is that today we have two conflicting paradigms in biology. One is the 'chemical paradigm', the idea that 'life is chemistry', or, more precisely, that 'life is an extremely complex form of chemistry'. The other is the 'information paradigm', the view that chemistry is not enough, that 'life is chemistry plus information'. This implies that there is an ontological difference between information and chemistry, a difference which is often expressed by saying that information-based processes like heredity and natural selection simply do not exist in the world of chemistry. Against this conclusion, the supporters of the chemical paradigm have argued that the concept of information is only a linguistic metaphor, a word that summarizes the result of countless underlying chemical reactions. The supporters of the information paradigm insist that information is a real and fundamental component of the living world, but have not been able to prove this point. As a result, the chemical view has not been abandoned and the two paradigms both coexist today. Here, it is shown that a solution to the ontological problem of information does exist. It comes from the idea that life is artefact-making, that genes and proteins are molecular artefacts manufactured by molecular machines and that artefacts necessarily require sequences and coding

  16. Serum peptide/protein profiling by mass spectrometry provides diagnostic information independently of CA125 in women with an ovarian tumor

    DEFF Research Database (Denmark)

    Callesen, Anne; Madsen, Jonna S; Iachina, Maria

    2010-01-01

    In the present study, the use of a robust and sensitive mass spectrometry based protein profiling analysis was tested as diagnostic tools for women with an ovarian tumor. The potential additional diagnostic value of serum protein profiles independent of the information provided by CA125 were also...... investigated. Protein profiles of 113 serum samples from women with an ovarian tumor (54 malign and 59 benign) were generated using MALDI-TOF MS. A total of 98 peaks with a significant difference (povarian tumors were identified. After...... average linkage clustering, a profile of 46 statistical significant mass peaks was identified to distinguish malignant tumors and benign tumors/cysts. In the subgroup of women with normal CA125 values (

  17. Human Rights Being and Existence

    Directory of Open Access Journals (Sweden)

    Xabier Etexeberria

    2013-05-01

    Full Text Available The ontological perspective in the approach to human rights is subject to different traps,against which measures must be taken. But it also faces us to the challenge of precisely specifying what they are and how are they to be based. In this paper we try to face this challenge, paying attention to avoid the traps above mentioned. The first part of it is focused on being-existence of human rights,trying to specify critically their «places»: social reality, laws and, in a founding sense, human dignity.The second part takes the category being-essence as reference, asking about the kind of being of humanrights in their different types. This «kind» will show itself densely mediated by cultural diversity andtemporality-historicity. What is really pretended with this reflection is to contribute to the cause of thesocial existence of human rights.

  18. The EXIST Mission Concept Study

    Science.gov (United States)

    Fishman, Gerald J.; Grindlay, J.; Hong, J.

    2008-01-01

    EXIST is a mission designed to find and study black holes (BHs) over a wide range of environments and masses, including: 1) BHs accreting from binary companions or dense molecular clouds throughout our Galaxy and the Local Group, 2) supermassive black holes (SMBHs) lying dormant in galaxies that reveal their existence by disrupting passing stars, and 3) SMBHs that are hidden from our view at lower energies due to obscuration by the gas that they accrete. 4) the birth of stellar mass BHs which is accompanied by long cosmic gamma-ray bursts (GRBs) which are seen several times a day and may be associated with the earliest stars to form in the Universe. EXIST will provide an order of magnitude increase in sensitivity and angular resolution as well as greater spectral resolution and bandwidth compared with earlier hard X-ray survey telescopes. With an onboard optical-infra red (IR) telescope, EXIST will measure the spectra and redshifts of GRBs and their utility as cosmological probes of the highest z universe and epoch of reionization. The mission would retain its primary goal of being the Black Hole Finder Probe in the Beyond Einstein Program. However, the new design for EXIST proposed to be studied here represents a significant advance from its previous incarnation as presented to BEPAC. The mission is now less than half the total mass, would be launched on the smallest EELV available (Atlas V-401) for a Medium Class mission, and most importantly includes a two-telescope complement that is ideally suited for the study of both obscured and very distant BHs. EXIST retains its very wide field hard X-ray imaging High Energy Telescope (HET) as the primary instrument, now with improved angular and spectral resolution, and in a more compact payload that allows occasional rapid slews for immediate optical/IR imaging and spectra of GRBs and AGN as well as enhanced hard X-ray spectra and timing with pointed observations. The mission would conduct a 2 year full sky survey in

  19. Application of information theory to a three-body coarse-grained representation of proteins in the PDB: insights into the structural and evolutionary roles of residues in protein structure.

    Science.gov (United States)

    Thompson, Jared J; Tabatabaei Ghomi, Hamed; Lill, Markus A

    2014-12-01

    Knowledge-based methods for analyzing protein structures, such as statistical potentials, primarily consider the distances between pairs of bodies (atoms or groups of atoms). Considerations of several bodies simultaneously are generally used to characterize bonded structural elements or those in close contact with each other, but historically do not consider atoms that are not in direct contact with each other. In this report, we introduce an information-theoretic method for detecting and quantifying distance-dependent through-space multibody relationships between the sidechains of three residues. The technique introduced is capable of producing convergent and consistent results when applied to a sufficiently large database of randomly chosen, experimentally solved protein structures. The results of our study can be shown to reproduce established physico-chemical properties of residues as well as more recently discovered properties and interactions. These results offer insight into the numerous roles that residues play in protein structure, as well as relationships between residue function, protein structure, and evolution. The techniques and insights presented in this work should be useful in the future development of novel knowledge-based tools for the evaluation of protein structure. © 2014 Wiley Periodicals, Inc.

  20. Differential denaturation of serum proteome reveals a significant amount of hidden information in complex mixtures of proteins.

    Science.gov (United States)

    Verdoliva, Vincenzo; Senatore, Cinzia; Polci, Maria Letizia; Rossi, Stefania; Cordella, Martina; Carlucci, Giuseppe; Marchetti, Paolo; Antonini-Cappellini, Giancarlo; Facchiano, Antonio; D'Arcangelo, Daniela; Facchiano, Francesco

    2013-01-01

    Recently developed proteomic technologies allow to profile thousands of proteins within a high-throughput approach towards biomarker discovery, although results are not as satisfactory as expected. In the present study we demonstrate that serum proteome denaturation is a key underestimated feature; in fact, a new differential denaturation protocol better discriminates serum proteins according to their electrophoretic mobility as compared to single-denaturation protocols. Sixty nine different denaturation treatments were tested and the 3 most discriminating ones were selected (TRIDENT analysis) and applied to human sera, showing a significant improvement of serum protein discrimination as confirmed by MALDI-TOF/MS and LC-MS/MS identification, depending on the type of denaturation applied. Thereafter sera from mice and patients carrying cutaneous melanoma were analyzed through TRIDENT. Nine and 8 protein bands were found differentially expressed in mice and human melanoma sera, compared to healthy controls (pdenaturation may significantly improve analytical procedures involving complex protein mixtures; iii) serum differential denaturation protocol highlights interesting proteomic differences between cancer and healthy sera.

  1. Information on existing monitoring practices for Harmful Algal ...

    African Journals Online (AJOL)

    spamer

    Food Hygiene Control Agency, the Oceanographic Company of Norway, the Institute of Marine Research and the Directorate for Fisheries, is reviewed. Potentially harmful algae on the Norwegian coast are found primarily in four classes of phytoplankton, dinoflagellates, prymnesiophytes, diatoms and raphidophytes.

  2. Modeling Truth Existence in Truth Discovery.

    Science.gov (United States)

    Zhi, Shi; Zhao, Bo; Tong, Wenzhu; Gao, Jing; Yu, Dian; Ji, Heng; Han, Jiawei

    2015-08-01

    When integrating information from multiple sources, it is common to encounter conflicting answers to the same question. Truth discovery is to infer the most accurate and complete integrated answers from conflicting sources. In some cases, there exist questions for which the true answers are excluded from the candidate answers provided by all sources. Without any prior knowledge, these questions, named no-truth questions, are difficult to be distinguished from the questions that have true answers, named has-truth questions. In particular, these no-truth questions degrade the precision of the answer integration system. We address such a challenge by introducing source quality, which is made up of three fine-grained measures: silent rate, false spoken rate and true spoken rate. By incorporating these three measures, we propose a probabilistic graphical model, which simultaneously infers truth as well as source quality without any a priori training involving ground truth answers. Moreover, since inferring this graphical model requires parameter tuning of the prior of truth, we propose an initialization scheme based upon a quantity named truth existence score, which synthesizes two indicators, namely, participation rate and consistency rate. Compared with existing methods, our method can effectively filter out no-truth questions, which results in more accurate source quality estimation. Consequently, our method provides more accurate and complete answers to both has-truth and no-truth questions. Experiments on three real-world datasets illustrate the notable advantage of our method over existing state-of-the-art truth discovery methods.

  3. Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models.

    Directory of Open Access Journals (Sweden)

    2005-08-01

    Full Text Available The bias in protein structure and function space resulting from experimental limitations and targeting of particular functional classes of proteins by structural biologists has long been recognized, but never continuously quantified. Using the Enzyme Commission and the Gene Ontology classifications as a reference frame, and integrating structure data from the Protein Data Bank (PDB, target sequences from the structural genomics projects, structure homology derived from the SUPERFAMILY database, and genome annotations from Ensembl and NCBI, we provide a quantified view, both at the domain and whole-protein levels, of the current and projected coverage of protein structure and function space relative to the human genome. Protein structures currently provide at least one domain that covers 37% of the functional classes identified in the genome; whole structure coverage exists for 25% of the genome. If all the structural genomics targets were solved (twice the current number of structures in the PDB, it is estimated that structures of one domain would cover 69% of the functional classes identified and complete structure coverage would be 44%. Homology models from existing experimental structures extend the 37% coverage to 56% of the genome as single domains and 25% to 31% for complete structures. Coverage from homology models is not evenly distributed by protein family, reflecting differing degrees of sequence and structure divergence within families. While these data provide coverage, conversely, they also systematically highlight functional classes of proteins for which structures should be determined. Current key functional families without structure representation are highlighted here; updated information on the "most wanted list" that should be solved is available on a weekly basis from http://function.rcsb.org:8080/pdb/function_distribution/index.html.

  4. Identification of co-evolving sites in the ligand binding domain of G protein-coupled receptors using mutual information

    Science.gov (United States)

    Fatakia, Sarosh N.; Costanzi, Stefano; Chow, Carson C.

    2008-03-01

    G protein-coupled receptors (GPCRs) are the largest superfamily of membrane proteins in humans. They are involved in signal transduction in numerous cellular processes and are the most common target for pharmacological intervention via activation or inhibition. Identification of functionally important sites is relevant for better understanding the ligand-receptor interaction and therefore for drug delivery. In a superfamily of proteins, functionally important but co-evolving sites are not easily identified in a multiple sequence alignment (MSA). Using a MSA of trans-membrane (TM) domains of GPCR superfamily, we identify sites which co-evolve, and may therefore be functionally important. Assigning the TM site as a node and the MI of site pairs as an inverse inter-node distance, a MI graph is established. Co-evolving sites are then identified via this graph. Nodes characterized by high connectivity are located within the commonly accepted ligand binding site of GPCRs, suggesting that concerted co-evolution of a number of neighboring residues gave rise to a multitude of subfamilies each recognizing a specific set of ligands. MI and graph analysis may serve as a tool for the identification of topologically conserved binding pockets in the families of evolutionarily related proteins.

  5. OPMSP: A Computational Method Integrating Protein Interaction and Sequence Information for the Identification of Novel Putative Oncogenes.

    Science.gov (United States)

    Chen, Lei; Wang, Baoman; Wang, ShaoPeng; Yang, Jing; Hu, Jerry; Xie, ZhiQun; Wang, Yuwei; Huang, Tao; Cai, Yu-Dong

    2016-01-01

    Oncogenes are genes that have the potential to cause cancer. Oncogene research can provide insight into the occurrence and development of cancer, thereby helping to prevent cancer and to design effective treatments. This study proposes a network method called the oncogene prediction method based on shortest path algorithm (OPMSP) for the identification of novel oncogenes in a large protein network built using protein-protein interaction data. Novel putative genes were extracted from the shortest paths connecting any two known oncogenes. Then, they were filtered by a randomization test, and the linkages among them and known oncogenes were measured by protein interaction and sequence data. Thirty-seven new putative oncogenes were identified by this method. The enrichment analysis of the 37 putative oncogenes indicated that they are highly associated with several biological processes related to the initiation, progression and metastasis of tumors. Six of these genes-ESR1, CDK9, SEPT2, HOXA10, LMX1B, and NR2C2-are extensively discussed. Several lines of evidence indicate that they may be novel oncogenes.

  6. Turbulence: does energy cascade exist?

    CERN Document Server

    Josserand, Christophe; Lehner, Thierry; Pomeau, Yves

    2016-01-01

    To answer the question whether a cascade of energy exists or not in turbulence, we propose a set of correlation functions able to test if there is an irreversible transfert of energy, step by step, from large to small structures. These tests are applied to real Eulerian data of a turbulent velocity flow, taken in the wind grid tunnel of Modane, and also to a prototype model equation for wave turbulence. First we demonstrate the irreversible character of the flow by using multi-time correlation function at a given point of space. Moreover the unexpected behavior of the test function leads us to connect irreversibility and finite time singularities (intermittency). Secondly we show that turbulent cascade exists, and is a dynamical process, by using a test function depending on time and frequency. The cascade shows up only in the inertial domain where the kinetic energy is transferred more rapidly (on average) from the wavenumber $k_{1}$ to $k_{2}$ than from $k_{1}$ to $k'_{2}$ larger than $k_{2}$.

  7. A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities

    Directory of Open Access Journals (Sweden)

    Maréchal Eric

    2005-03-01

    Full Text Available Abstract Background Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons and be the basis for a novel method of consistent and stable phylogenetic reconstruction. Results We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. Conclusion The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

  8. Protein immobilization strategies for protein biochips

    NARCIS (Netherlands)

    Rusmini, F.; Rusmini, Federica; Zhong, Zhiyuan; Feijen, Jan

    2007-01-01

    In the past few years, protein biochips have emerged as promising proteomic and diagnostic tools for obtaining information about protein functions and interactions. Important technological innovations have been made. However, considerable development is still required, especially regarding protein

  9. LANGUAGE SYSTEM: INFORMATION, INFORMATIONAL CONTENT, INFORMATION TRANSFERITY

    Directory of Open Access Journals (Sweden)

    Elvira Galievna Zarifullina

    2014-10-01

    Full Text Available The article is devoted to research of language system as information system. To this point of view informational content and information transferity are properties of language as main and the most fail-safe communication instrument in human society.  In whole, informational content and information transferity are aspects of information. In that meaning the language realizes function that associated with database of information system: realization of information in formalized form, accumulation, storage and information transfer.But language itself is not an information. Information is language and speech, created with language. Language should be defined as database, because in human thought language doesn’t present as information, but as the formalized model, the system, which elements are bounded with each other and united by the algorithms. The modern forms of language existence are distributed database with multiple accesses, because language belongs to language native bearers, which use it simultaneously.

  10. Straightening: existence, uniqueness and stability

    Science.gov (United States)

    Destrade, M.; Ogden, R. W.; Sgura, I.; Vergori, L.

    2014-01-01

    One of the least studied universal deformations of incompressible nonlinear elasticity, namely the straightening of a sector of a circular cylinder into a rectangular block, is revisited here and, in particular, issues of existence and stability are addressed. Particular attention is paid to the system of forces required to sustain the large static deformation, including by the application of end couples. The influence of geometric parameters and constitutive models on the appearance of wrinkles on the compressed face of the block is also studied. Different numerical methods for solving the incremental stability problem are compared and it is found that the impedance matrix method, based on the resolution of a matrix Riccati differential equation, is the more precise. PMID:24711723

  11. EXIST OIRT Camera and Spectrometer

    Science.gov (United States)

    Kutyrev, Alexander; Moseley, S. H.; Golisano, C.; Gong, Q.; Allen, B.; Grindlay, J.; Hong, J.; Woodgate, B.; EXIST Team

    2009-01-01

    The EXIST mission includes a 1.1m infrared and visible telescope which provides the capability to locate, identify, and obtain spectra of GRB afterglows at redshifts up to z 20. To allow rapid identification and spectroscopic follow up, the instruments will provide wide band imaging, covering the full error circle of the Gamma Ray Telescope (GRT), low spectral resolution slitless spectroscopy, and high resolution integral field spectroscopy. The integral field unit will have a small field of view of 2" x 2" to study diffuse objects, e.g. GRB host galaxies. The instrumentation capabilities will allow this telescope quickly identify the afterglow, measure its brightness curves, redshift, measure spectral characteristics of the GRBs, and measure absorption spectra of the intervening intergalactic medium. With this instrument, high redshift GRBs become important tools for observing the processes through which the universe is ionized.

  12. Why do interstellar grains exist?

    Science.gov (United States)

    Seab, C. G.; Hollenbach, D. J.; Mckee, C. F.; Tielens, Alexander G. G. M.

    1986-01-01

    There exists a discrepancy between calculated destruction rates of grains in the interstellar medium and postulated sources of new grains. This problem was examined by modelling the global life cycle of grains in the galaxy. The model includes: grain destruction due to supernovae shock waves; grain injection from cool stars, planetary nebulae, star formation, novae, and supernovae; grain growth by accretion in dark clouds; and a mixing scheme between phases of the interstellar medium. Grain growth in molecular clouds is considered as a mechanism or increasing the formation rate. To decrease the shock destruction rate, several new physical processes, such as partial vaporization effects in grain-grain collisions, breakdown of the small Larmor radius approximation for betatron acceleration, and relaxation of the steady-state shock assumption are included.

  13. EXOSOMES: CAN DOCTORS STILL IGNORE THEIR EXISTENCE?

    Directory of Open Access Journals (Sweden)

    Celeste Caruso Bavisotto

    2013-04-01

    Full Text Available With this invited commentary we want to draw the attention of young medical doctors, the main readers of this journal, towards the existence and importance of a group of nanovesicles released by human cells: the exosomes. These vesicles are incontinently secreted as a mean of cell-to-cell communication. They are involved in a number of physiologic processes as well as in the pathogenesis of, virtually, all human diseases. They can be isolated from all biological fluids, like blood, urine, sweat, sperm, crevicular fluid, bile, etc., and their composition in terms of proteins, RNA and lipids is different in pathology that in physiologic conditions. It is therefore possible to predict that they will become an important diagnostic and therapeutic tool in medicine.

  14. NetTurnP – Neural Network Prediction of Beta-turns by Use of Evolutionary Information and Predicted Protein Sequence Features

    DEFF Research Database (Denmark)

    Petersen, Bent; Lundegaard, Claus; Petersen, Thomas Nordahl

    2010-01-01

    is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino......β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method...... NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which...

  15. Predictive characterization of hypothetical proteins in Staphylococcus aureus NCTC 8325.

    Science.gov (United States)

    School, Kuana; Marklevitz, Jessica; K Schram, William; K Harris, Laura

    2016-01-01

    Staphylococcus aureus is one of the most common hospital acquired infections. It colonizes immunocompromised patients and with the number of antibiotic resistant strains increasing, medicine needs new treatment options. Understanding more about the proteins this organism uses would further this goal. Hypothetical proteins are sequences thought to encode a functional protein but for which little to no evidence of that function exists. About half of the genomic proteins in reference strain S. aureus NCTC 8325 are hypothetical. Since annotation of these proteins can lead to new therapeutic targets, a high demand to characterize hypothetical proteins is present. This work examines 35 hypothetical proteins from the chromosome of S. aureus NCTC 8325. Examination includes physiochemical characterization; sequence homology; structural homology; domain recognition; structure modeling; active site depiction; predicted protein-protein interactions; protein-chemical interactions; protein localization; protein stability; and protein solubility. The examination revealed some hypothetical proteins related to virulent domains and protein-protein interactions including superoxide dismutase, O-antigen, bacterial ferric iron reductase and siderophore synthesis. Yet other hypothetical proteins appear to be metabolic or transport proteins including ABC transporters, major facilitator superfamily, S-adenosylmethionine decarboxylase, and GTPases. Progress evaluating some hypothetical proteins, particularly the smaller ones, was incomplete due to limited homology and structural information in public repositories. These data characterizing hypothetical proteins will contribute to the scientific understanding of S. aureus by identifying potential drug targets and aiding in future drug discovery.

  16. Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis.

    Science.gov (United States)

    Miotto, Olivo; Heiny, At; Tan, Tin Wee; August, J Thomas; Brusic, Vladimir

    2008-01-01

    The identification of mutations that confer unique properties to a pathogen, such as host range, is of fundamental importance in the fight against disease. This paper describes a novel method for identifying amino acid sites that distinguish specific sets of protein sequences, by comparative analysis of matched alignments. The use of mutual information to identify distinctive residues responsible for functional variants makes this approach highly suitable for analyzing large sets of sequences. To support mutual information analysis, we developed the AVANA software, which utilizes sequence annotations to select sets for comparison, according to user-specified criteria. The method presented was applied to an analysis of influenza A PB2 protein sequences, with the objective of identifying the components of adaptation to human-to-human transmission, and reconstructing the mutation history of these components. We compared over 3,000 PB2 protein sequences of human-transmissible and avian isolates, to produce a catalogue of sites involved in adaptation to human-to-human transmission. This analysis identified 17 characteristic sites, five of which have been present in human-transmissible strains since the 1918 Spanish flu pandemic. Sixteen of these sites are located in functional domains, suggesting they may play functional roles in host-range specificity. The catalogue of characteristic sites was used to derive sequence signatures from historical isolates. These signatures, arranged in chronological order, reveal an evolutionary timeline for the adaptation of the PB2 protein to human hosts. By providing the most complete elucidation to date of the functional components participating in PB2 protein adaptation to humans, this study demonstrates that mutual information is a powerful tool for comparative characterization of sequence sets. In addition to confirming previously reported findings, several novel characteristic sites within PB2 are reported. Sequence signatures

  17. The allometric partition of whole body protein in lean fraction of growing pigs using information from three different datasets

    Directory of Open Access Journals (Sweden)

    A. Piva

    2010-04-01

    Full Text Available The hypothesis that a single allometric relationship relating carcass lean protein (CLP to whole body protein (WBP can allow accurate estimates of CLP on pigs of different populations, sex and nutritional history, was tested. Three datasets of different origins were used. Data were representative of 548 pigs, castrated males and females, of 8 pig populations, serially slaughtered over ample empty body weight (EBW ranges (from 22 to 217 kg. WBP and CLP ranged, respectively, from 2 to 28 and from 1 to 16 kg. The pooled data were run and the following relationship was found: CLP=0.497*WBP1.021 (CV=0.062; rsd=0.501 kg. The residuals were subjected to ANOVA to test the effects due to dataset, pig population within dataset and sex; significant differences between datasets mean residuals (+0.095, SE=0.041; -0.258, SE=0.094; -0.116, SE=0.055 kg, P<0.001 were observed. No differences due to sex and pig populations were found. The average residuals were low and only in few cases they differed from zero. Conclusions: CLP can be accurately predicted from WBP; the coefficients of this function are mainly influenced by the procedures of slaughtering, dissection, sampling and analysis.

  18. iPhos-PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory.

    Science.gov (United States)

    Qiu, Wang-Ren; Sun, Bi-Qian; Xiao, Xuan; Xu, Dong; Chou, Kuo-Chen

    2017-05-01

    Protein phosphorylation plays a critical role in human body by altering the structural conformation of a protein, causing it to become activated/deactivated, or functional modification. Given an uncharacterized protein sequence, can we predict whether it may be phosphorylated or may not? This is no doubt a very meaningful problem for both basic research and drug development. Unfortunately, to our best knowledge, so far no high throughput bioinformatics tool whatsoever has been developed to address such a very basic but important problem due to its extremely complexity and lacking sufficient training data. Here we proposed a predictor called iPhos-PseEvo by (1) incorporating the protein sequence evolutionary information into the general pseudo amino acid composition (PseAAC) via the grey system theory, (2) balancing out the skewed training datasets by the asymmetric bootstrap approach, and (3) constructing an ensemble predictor by fusing an array of individual random forest classifiers thru a voting system. Rigorous jackknife tests have indicated that very promising success rates have been achieved by iPhos-PseEvo even for such a difficult problem. A user-friendly web-server for iPhos-PseEvo has been established at http://www.jci-bioinfo.cn/iPhos-PseEvo, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved. It has not escaped our notice that the formulation and approach presented here can be used to analyze many other problems in protein science as well. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Canola/rapeseed protein-functionality and nutrition

    Directory of Open Access Journals (Sweden)

    Wanasundara Janitha P.D.

    2016-07-01

    Full Text Available Protein rich meal is a valuable co-product of canola/rapeseed oil extraction. Seed storage proteins that include cruciferin (11S and napin (2S dominate the protein complement of canola while oleosins, lipid transfer proteins and other minor proteins of non-storage nature are also found. Although oil-free canola meal contains 36–40% protein on a dry weight basis, non-protein components including fibre, polymeric phenolics, phytates and sinapine, etc. of the seed coat and cellular components make protein less suitable for food use. Separation of canola protein from non-protein components is a technical challenge but necessary to obtain full nutritional and functional potential of protein. Process conditions of raw material and protein preparation are critical of nutritional and functional value of the final protein product. The storage proteins of canola can satisfy many nutritional and functional requirements for food applications. Protein macromolecules of canola also provide functionalities required in applications beyond edible uses; there exists substantial potential as a source of plant protein and a renewable biopolymer. Available information at present is mostly based on the protein products that can be obtained as mixtures of storage protein types and other chemical constituents of the seed; therefore, full potential of canola storage proteins is yet to be revealed.

  20. Green fluorescent protein (GFP) leakage from microbial biosensors provides useful information for the evaluation of the scale-down effect

    DEFF Research Database (Denmark)

    Delvigne, Frank; Brognaux, Alison; Francis, Frédéric

    2011-01-01

    Mixing deficiencies can be potentially detected by the use of a dedicated whole cell microbial biosensor. In this work, a csiE promoter induced under carbon-limited conditions was involved in the elaboration of such biosensor. The cisE biosensor exhibited interesting response after up and down......-shift of the dilution rate in chemostat mode. Glucose limitation was accompanied by green fluorescent protein (GFP) leakage to the extracellular medium. In order to test the responsiveness of microbial biosensors to substrate fluctuations in large-scale, a scale-down reactor (SDR) experiment was performed. The glucose...... fluctuations were characterized at the single cell level and tend to decrease the induction of GFP. Simulations run on the basis of a stochastic hydrodynamic model have shown the variability and the frequencies at which biosensors are exposed to glucose gradient in the SDR. GFP leakage was observed to a great...

  1. Pre-existing Antibody: Biotherapeutic Modality-Based Review.

    Science.gov (United States)

    Gorovits, Boris; Clements-Egan, Adrienne; Birchler, Mary; Liang, Meina; Myler, Heather; Peng, Kun; Purushothama, Shobha; Rajadhyaksha, Manoj; Salazar-Fontana, Laura; Sung, Crystal; Xue, Li

    2016-03-01

    Pre-existing antibodies to biotherapeutic drugs have been detected in drug-naïve subjects for a variety of biotherapeutic modalities. Pre-existing antibodies are immunoglobulins that are either specific or cross-reacting with a protein or glycan epitopes on a biotherapeutic compound. Although the exact cause for pre-existing antibodies is often unknown, environmental exposures to non-human proteins, glycans, and structurally similar products are frequently proposed as factors. Clinical consequences of the pre-existing antibodies vary from an adverse effect on patient safety to no impact at all and remain highly dependent on the biotherapeutic drug modality and therapeutic indication. As such, pre-existing antibodies are viewed as an immunogenicity risk factor requiring a careful evaluation. Herein, the relationships between biotherapeutic modalities to the nature, prevalence, and clinical consequences of pre-existing antibodies are reviewed. Initial evidence for pre-existing antibody is often identified during anti-drug antibody (ADA) assay development. Other interfering factors known to cause false ADA positive signal, including circulating multimeric drug target, rheumatoid factors, and heterophilic antibodies, are discussed.

  2. Pre-existing biotherapeutic-reactive antibodies: survey results within the American Association of Pharmaceutical Scientists.

    Science.gov (United States)

    Xue, Li; Fiscella, Michele; Rajadhyaksha, Manoj; Goyal, Jaya; Holland, Claire; Gorovits, Boris; Morimoto, Alyssa

    2013-07-01

    The immunogenicity profile of a biotherapeutic is determined by a multitude of product and patient-related risk factors that can influence the observed incidence and clinical consequences of immunogenicity. Pre-existing antibodies, i.e., biotherapeutic-reactive antibodies present in samples from treatment-naïve subjects, have been commonly observed during immunogenicity assessments; however their relevance in terms of the safety and efficacy of a biotherapeutic is poorly understood. An American Association of Pharmaceutical Scientists-sponsored survey was conducted to gather information about the prevalence, nature, and consequences of pre-existing antibodies in clinical and nonclinical studies. The survey results indicate that pre-existing antibodies against a variety of biotherapeutics (e.g., mAbs, fusion proteins) are frequently encountered, especially in the context of autoimmune diseases, but that the methods and approaches used to detect, characterize, and report these antibodies vary. In most cases, pre-existing antibodies did not appear to have clinical consequences; however, a few of the respondents reported having observed an effect on pharmacokinetic, pharmacodynamic, safety, and/or efficacy parameters. The findings from this survey are an important first step in evaluating the potential risks associated with the presence of pre-existing antibodies and highlight the importance of standardizing the approaches for detection and characterization of these antibodies. Cross-industry sharing of case studies and relevant data collection will help better inform biotherapeutic risk/benefit profiles and provide deeper understanding of the biological consequences of pre-existing antibodies.

  3. Exploring hepsin functional genetic variation association with disease specific protein expression in bipolar disorder: Applications of a proteomic informed genomic approach.

    Science.gov (United States)

    Nassan, Malik; Jia, Yun-Fang; Jenkins, Greg; Colby, Colin; Feeder, Scott; Choi, Doo-Sup; Veldic, Marin; McElroy, Susan L; Bond, David J; Weinshilboum, Richard; Biernacka, Joanna M; Frye, Mark A

    2017-12-01

    In a prior discovery study, increased levels of serum Growth Differentiation Factor 15 (GDF15), Hepsin (HPN), and Matrix Metalloproteinase-7 (MMP7) were observed in bipolar depressed patients vs controls. This exploratory post-hoc analysis applied a proteomic-informed genomic research strategy to study the potential functional role of these proteins in bipolar disorder (BP). Utilizing the Genotype-Tissue Expression (GTEx) database to identify cis-acting blood expression quantitative trait loci (cis-eQTLs), five eQTL variants from the HPN gene were analyzed for association with BP cases using genotype data of cases from the discovery study (n = 58) versus healthy controls (n = 777). After adjusting for relevant covariates, we analyzed the relationship between these 5 cis-eQTLs and HPN serum level in the BP cases. All 5 cis-eQTL minor alleles were significantly more frequent in BP cases vs controls [(rs62122114, OR = 1.6, p = 0.02), (rs67003112, OR = 1.6, p = 0.02), (rs4997929, OR = 1.7, p = 0.01), (rs12610663, OR = 1.7, p = 0.01), (rs62122148, OR = 1.7, P = 0.01)]. The minor allele (A) in rs62122114 was significantly associated with increased serum HPN level in BP cases (Beta = 0.12, P = 0.049). However, this same minor allele was associated with reduced gene expression in GTEx controls. These exploratory analyses suggest that genetic variation in/near the gene encoding for hepsin protein may influence risk of bipolar disorder. This genetic variation, at least for the rs62122114-A allele, may have functional impact (i.e. differential expression) as evidenced by serum HPN protein expression. Although limited by small sample size, this study highlights the merits of proteomic informed functional genomic studies as a tool to investigate with greater precision the genetic risk of bipolar disorder and secondary relationships to protein expression recognizing, and encouraging in subsequent studies, high likelihood of epigenetic modification of

  4. Use of evolutionary information in the fitting of atomic level protein models in low resolution cryo-EM map of a protein assembly improves the accuracy of the fitting.

    Science.gov (United States)

    Joseph, Agnel P; Swapna, Lakshmipuram S; Rakesh, Ramachandran; Srinivasan, Narayanaswamy

    2016-09-01

    Protein-protein interface residues, especially those at the core of the interface, exhibit higher conservation than residues in solvent exposed regions. Here, we explore the ability of this differential conservation to evaluate fittings of atomic models in low-resolution cryo-EM maps and select models from the ensemble of solutions that are often proposed by different model fitting techniques. As a prelude, using a non-redundant and high-resolution structural dataset involving 125 permanent and 95 transient complexes, we confirm that core interface residues are conserved significantly better than nearby non-interface residues and this result is used in the cryo-EM map analysis. From the analysis of inter-component interfaces in a set of fitted models associated with low-resolution cryo-EM maps of ribosomes, chaperones and proteasomes we note that a few poorly conserved residues occur at interfaces. Interestingly a few conserved residues are not in the interface, though they are close to the interface. These observations raise the potential requirement of refitting the models in the cryo-EM maps. We show that sampling an ensemble of models and selection of models with high residue conservation at the interface and in good agreement with the density helps in improving the accuracy of the fit. This study indicates that evolutionary information can serve as an additional input to improve and validate fitting of atomic models in cryo-EM density maps. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Adaptation of Impact Questions from an Existing Toolkit Provided Clear Assessment of Valued Service Elements and Desirable Service Improvements in a Primary Health Care Library and Information Service. A Review of: Urquhart, C., Thomas, R., Ovens, J., Lucking, W., & Villa, J. (2010. Planning changes to health library services on the basis of impact assessment. Health Information and Libraries Journal, 27(4, 277-285. doi: 10.1111/j.1471-1842.2010.00900.x

    Directory of Open Access Journals (Sweden)

    Kate Kelly

    2011-01-01

    resources for loan (n=57, 37.5% were the top two service elements used, with literature searching third (n=46, 30.3%.The service completely met the needs of 93% (n=141 of respondents, with 97.4% (n=148 reporting being wholly satisfied that information was delivered in time.In terms of the immediate cognitive impact of the information obtained, 93% (n=141 reported obtaining relevant information, 76% (n=115 current information, and 72% (n=109 accurate information. Nearly 70% were distributing information or resources to other people, and 68% were sharing or discussing information provided with colleagues. Nobody claimed that they had found little or nothing of value.Advice to patients, clients or carers was the most frequently cited impact category (n=104, 68%, followed by advice to colleagues (n=84, 55.3%.The main strengths of the service were the perceived reliability of the service, the current awareness and alerting service run from one site, and literature searching support for commissioning and public health enquiries. Respondents reported saving time, and the main cognitive impact was the perceived relevance of the information obtained. Service weaknesses identified related to accessibility issues such as parking, opening hours, and staff coverage, and outreach was identified as the main service development opportunity.Conclusion – The adaptation of an existing questionnaire provided a clear assessment of the effectiveness of a primary health care information service to a broad spectrum of users. Respondents identified what they valued about the service and how it could be improved.

  6. Reversible unfolding of infectious prion assemblies reveals the existence of an oligomeric elementary brick.

    Directory of Open Access Journals (Sweden)

    Angélique Igel-Egalon

    2017-09-01

    Full Text Available Mammalian prions, the pathogens that cause transmissible spongiform encephalopathies, propagate by self-perpetuating the structural information stored in the abnormally folded, aggregated conformer (PrPSc of the host-encoded prion protein (PrPC. To date, no structural model related to prion assembly organization satisfactorily describes how strain-specified structural information is encoded and by which mechanism this information is transferred to PrPC. To achieve progress on this issue, we correlated the PrPSc quaternary structural transition from three distinct prion strains during unfolding and refolding with their templating activity. We reveal the existence of a mesoscopic organization in PrPSc through the packing of a highly stable oligomeric elementary subunit (suPrP, in which the strain structural determinant (SSD is encoded. Once kinetically trapped, this elementary subunit reversibly loses all replicative information. We demonstrate that acquisition of the templating interface and infectivity requires structural rearrangement of suPrP, in concert with its condensation. The existence of such an elementary brick scales down the SSD support to a small oligomer and provide a basis of reflexion for prion templating process and propagation.

  7. Transfer of Dorsoventral and Terminal Information from the Ovary to the Embryo by a Common Group of Eggshell Proteins in Drosophila.

    Science.gov (United States)

    Mineo, Alessandro; Furriols, Marc; Casanova, Jordi

    2017-04-01

    The Drosophila eggshell is an extracellular matrix that confers protection to the egg and also plays a role in transferring positional information from the ovary to pattern the embryo. Among the constituents of the Drosophila eggshell, Nasrat, Polehole, and Closca form a group of proteins related by sequence, secreted by the oocyte, and mutually required for their incorporation into the eggshell. Besides their role in eggshell integrity, Nasrat, Polehole, and Closca are also required for embryonic terminal patterning by anchoring or stabilizing Torso-like at the eggshell. Here, we show that they are also required for dorsoventral patterning, thereby unveiling that the dorsoventral and terminal systems, hitherto considered independent, share a common extracellular step. Furthermore, we show that Nasrat, Polehole, and Closca are required for proper Nudel activity, a protease acting both in embryonic dorsoventral patterning and eggshell integrity, thus providing a means to account for the role of Nasrat, Polehole, and Closca. We propose that a Nasrat/Polehole/Closca complex acts as a multifunctional hub to anchor various proteins synthesized at oogenesis, ensuring their spatial and temporal restricted function. Copyright © 2017 by the Genetics Society of America.

  8. Information processing

    NARCIS (Netherlands)

    Jong, de Peter J.; Emmelkamp, Paul; Ehring, Thomas

    2014-01-01

    Cognitive models imply that emotional disorders critically depend on the existence of maladaptive cognitive structures in memory. These so-called schemas are assumed to automatically influence all stages of individuals' information processing. The basic assumption of the information-processing

  9. Rationale and design of the Baptist Employee Healthy Heart Study: a randomized trial assessing the efficacy of the addition of an interactive, personalized, web-based, lifestyle intervention tool to an existing health information web platform in a high-risk employee population.

    Science.gov (United States)

    Post, Janisse M; Ali, Shozab S; Roberson, Lara L; Aneni, Ehimen C; Shaharyar, Sameer; Younus, Adnan; Jamal, Omar; Ahmad, Rameez; Aziz, Muhammad A; Malik, Rehan; Spatz, Erica S; Feldman, Theodore; Fialkow, Jonathan; Veledar, Emir; Cury, Ricardo C; Agatston, Arthur S; Nasir, Khurram

    2016-07-01

    Metabolic syndrome (MetS) and diabetes confer a high risk for developing subsequent cardiovascular disease (CVD). Persons with MetS constitute 24-34 % of the employee population at Baptist Health South Florida (BHSF), a self-insured healthcare organization. The Baptist Employee Healthy Heart Study (BEHHS) aims to assess the addition of a personalized, interactive, web-based, nutrition-management and lifestyle-management program to the existing health-expertise web platform available to BHSF employees in reducing and/or stabilizing CVD and lifestyle risk factors and markers of subclinical CVD. Subjects with MetS or Type II Diabetes will be recruited from an employee population at BHSF and randomized to either an intervention or a control arm. The intervention arm will be given access to a web-based personalized diet-modification and weight-modification program. The control arm will be reminded to use the standard informational health website available and accessible to all BHSF employees. Subjects will undergo coronary calcium testing, carotid intima-media thickness scans, peripheral arterial tonometry, and advanced lipid panel testing at visit 1, in addition to lifestyle and medical history questionnaires. All tests will be repeated at visits 2 and 4 with the exception of the coronary calcium test, which will only be performed at baseline and visit 4. Visit 3 will capture vitals, anthropometrics, and responses to the questionnaires only. Results of this study will provide information on the effectiveness of personalized, web-based, lifestyle-management tools in reducing healthcare costs, promoting healthy choices, and reducing cardiovascular risk in an employee population. It will also provide information about the natural history of carotid atherosclerosis and endothelial dysfunction in asymptomatic but high-risk populations. ClinicalTrials.gov registry, NCT01912209 . Registered on 3 July 2013.

  10. Evidence Based Research Activities, Interests and Opportunities Exist for Practitioners in all Library Sectors in the British Isles. A review of: McNicol, Sarah. “Is Research an Untapped Resource in the Library and Information Profession?” Journal of Librarianship and Information Science 36.3 (September 2004:119-26.

    Directory of Open Access Journals (Sweden)

    Julie McKenna

    2006-03-01

    Full Text Available Objective – To scope the range, nature and challenges of present, planned and future research by practitioners within libraries in the British Isles. Design – A series of survey questionnaires sent by mail. Setting – Public, academic, health, special and school libraries of the British Isles. Subjects – A total of 2384 questionnaires were sent out and 334 responses were received. 62 academic libraries, 83 health libraries, 78 public libraries, 63 school libraries and 48 special libraries participated in the study. Methods – This study was undertaken in 2003 by a research team at the University of Central England. Survey questionnaires were sent by mail to library directors in all public library authorities, academic libraries, health libraries and special libraries in England, Wales, Scotland, Northern Ireland and the Republic of Ireland. In addition, questionnaires were sent to the librarians in all state and independent schools within a sample of nine local education authorities. Each participant was asked to identify past and future research issues of interest and the barriers to research practice within their library. Research was defined to include work on both externally funded and inhouse projects and examples of the types of activities that this might include were provided. Main results – Half the respondents reported that they had been involved in some form of research in the past two years, with the lowest level of involvement from school libraries and the highest in public libraries. Generally, only the library directly involved in conducting the research made use of the findings and a gap in the dissemination of results was identified across sectors. User surveys were the most common form of research undertaken across libraries and slightly fewer respondents intended to carry out research in the coming twelve months than had in the past (the area most commonly mentioned was user surveys. Information and communications

  11. Dynamically searching for a domain for protein function prediction.

    Science.gov (United States)

    Hou, Jingyu; Jiang, Yongqing

    2013-08-01

    The availability of large amounts of protein-protein interaction (PPI) data makes it feasible to use computational approaches to predict protein functions. The base of existing computational approaches is to exploit the known function information of annotated proteins in the PPI data to predict functions of un-annotated proteins. However, these approaches consider the prediction domain (i.e. the set of proteins from which the functions are predicted) as unchangeable during the prediction procedure. This may lead to valuable information being overwhelmed by the unavoidable noise information in the PPI data when predicting protein functions, and in turn, the prediction results will be distorted. In this paper, we propose a novel method to dynamically predict protein functions from the PPI data. Our method regards the function prediction as a dynamic process of finding a suitable prediction domain, from which representative functions of the domain are selected to predict functions of un-annotated proteins. Our method exploits the topological structural information of a PPI network and the semantic relationship between protein functions to measure the relationship between proteins, dynamically select a suitable prediction domain and predict functions. The evaluation on real PPI datasets demonstrated the effectiveness of our proposed method, and generated better prediction results.

  12. NetTurnP--neural network prediction of beta-turns by use of evolutionary information and predicted protein sequence features.

    Directory of Open Access Journals (Sweden)

    Bent Petersen

    Full Text Available UNLABELLED: β-turns are the most common type of non-repetitive structures, and constitute on average 25% of the amino acids in proteins. The formation of β-turns plays an important role in protein folding, protein stability and molecular recognition processes. In this work we present the neural network method NetTurnP, for prediction of two-class β-turns and prediction of the individual β-turn types, by use of evolutionary information and predicted protein sequence features. It has been evaluated against a commonly used dataset BT426, and achieves a Matthews correlation coefficient of 0.50, which is the highest reported performance on a two-class prediction of β-turn and not-β-turn. Furthermore NetTurnP shows improved performance on some of the specific β-turn types. In the present work, neural network methods have been trained to predict β-turn or not and individual β-turn types from the primary amino acid sequence. The individual β-turn types I, I', II, II', VIII, VIa1, VIa2, VIba and IV have been predicted based on classifications by PROMOTIF, and the two-class prediction of β-turn or not is a superset comprised of all β-turn types. The performance is evaluated using a golden set of non-homologous sequences known as BT426. Our two-class prediction method achieves a performance of: MCC=0.50, Qtotal=82.1%, sensitivity=75.6%, PPV=68.8% and AUC=0.864. We have compared our performance to eleven other prediction methods that obtain Matthews correlation coefficients in the range of 0.17-0.47. For the type specific β-turn predictions, only type I and II can be predicted with reasonable Matthews correlation coefficients, where we obtain performance values of 0.36 and 0.31, respectively. CONCLUSION: The NetTurnP method has been implemented as a webserver, which is freely available at http://www.cbs.dtu.dk/services/NetTurnP/. NetTurnP is the only available webserver that allows submission of multiple sequences.

  13. Bioinformatics and moonlighting proteins

    Directory of Open Access Journals (Sweden)

    Sergio eHernández

    2015-06-01

    Full Text Available Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyse and describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are: a remote homology searches using Psi-Blast, b detection of functional motifs and domains, c analysis of data from protein-protein interaction databases (PPIs, d match the query protein sequence to 3D databases (i.e., algorithms as PISITE, e mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs have the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations –it requires the existence of multialigned family protein sequences - but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/, previously published by our group, has been used as a benchmark for the all of the analyses.

  14. State of the Art Manufacturing of Protein Hydrolysates

    Science.gov (United States)

    Pasupuleti, Vijai K.; Braun, Steven

    The use of protein hydrolysates in microbiological media has been in existence for several decades and the basic manufacturing process of protein hydrolysates has remained the same. However, with increasing use of protein hydrolysates in specialized applications such as animal cell culture processes, the manufacturing of protein hydrolysates has dramatically improved and is still in its infancy to uncover the specific peptide, peptides and combination of individual amino acids that produce intended effects for that application. This will change as the protein hydrolysate manufacturers and end-users exchange information and work towards the common goal of developing the best protein hydrolysates for specific applications. This chapter will review the generic manufacturing of protein hydrolysates describing individual unit operations, problems faced by manufacturers and suggestions for obtaining consistent product and guidelines for the end-users in getting regulatory support and setting up reliable specifications. Finally the chapter concludes with future trends of protein hydrolysates.

  15. Does occupational health nursing exist in India?

    Science.gov (United States)

    Tiwari, Rajnarayan R; Sharma, Anjali; Zodpey, Sanjay P; Khandare, Shobha M

    2014-01-01

    Occupational health services are important to develop healthy and productive work forces, which should be delivered through occupational health team. Occupational health nurse (OHN) is an important member of this team and is required to apply nursing principles in conserving the health of workers in occupational settings. This article attempts to map the occupational health nursing courses in India and design competencies and curriculum for such a course. Information through the Internet, printed journals, and perspectives of the key stakeholders were the principal sources of data. In India, there is a need to initiate a course on occupational health nursing to provide occupational health services for the organized and unorganized sector workforce. A certificate course for occupational health nursing for 3-4 months duration offered through contact session mode can be an opportune beginning. However, to cater employed nurses an online course can be another effective alternative. The theoretical part should essentially include modules on occupational diseases, industrial hygiene, and occupational health legislation, whereas the modules on practical aspects can include visits to industries. Taking into account the existing norms of Indian Factories Act for hazardous units of organized sector an estimated 1,34,640 OHNs are required. There is a need-supply gap in the number of occupational health nursing manpower in India, which can be attributed to the absence of any course to train such manpower.

  16. GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction

    Directory of Open Access Journals (Sweden)

    Zheng Huiru

    2009-01-01

    Full Text Available Abstract Background Information about protein interaction networks is fundamental to understanding protein function and cellular processes. Interaction patterns among proteins can suggest new drug targets and aid in the design of new therapeutic interventions. Efforts have been made to map interactions on a proteomic-wide scale using both experimental and computational techniques. Reference datasets that contain known interacting proteins (positive cases and non-interacting proteins (negative cases are essential to support computational prediction and validation of protein-protein interactions. Information on known interacting and non interacting proteins are usually stored within databases. Extraction of these data can be both complex and time consuming. Although, the automatic construction of reference datasets for classification is a useful resource for researchers no public resource currently exists to perform this task. Results GRIP (Gold Reference dataset constructor from Information on Protein complexes is a web-based system that provides researchers with the functionality to create reference datasets for protein-protein interaction prediction in Saccharomyces cerevisiae. Both positive and negative cases for a reference dataset can be extracted, organised and downloaded by the user. GRIP also provides an upload facility whereby users can submit proteins to determine protein complex membership. A search facility is provided where a user can search for protein complex information in Saccharomyces cerevisiae. Conclusion GRIP is developed to retrieve information on protein complex, cellular localisation, and physical and genetic interactions in Saccharomyces cerevisiae. Manual construction of reference datasets can be a time consuming process requiring programming knowledge. GRIP simplifies and speeds up this process by allowing users to automatically construct reference datasets. GRIP is free to access at http://rosalind.infj.ulst.ac.uk/GRIP/.

  17. GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction.

    Science.gov (United States)

    Browne, Fiona; Wang, Haiying; Zheng, Huiru; Azuaje, Francisco

    2009-01-26

    Information about protein interaction networks is fundamental to understanding protein function and cellular processes. Interaction patterns among proteins can suggest new drug targets and aid in the design of new therapeutic interventions. Efforts have been made to map interactions on a proteomic-wide scale using both experimental and computational techniques. Reference datasets that contain known interacting proteins (positive cases) and non-interacting proteins (negative cases) are essential to support computational prediction and validation of protein-protein interactions. Information on known interacting and non interacting proteins are usually stored within databases. Extraction of these data can be both complex and time consuming. Although, the automatic construction of reference datasets for classification is a useful resource for researchers no public resource currently exists to perform this task. GRIP (Gold Reference dataset constructor from Information on Protein complexes) is a web-based system that provides researchers with the functionality to create reference datasets for protein-protein interaction prediction in Saccharomyces cerevisiae. Both positive and negative cases for a reference dataset can be extracted, organised and downloaded by the user. GRIP also provides an upload facility whereby users can submit proteins to determine protein complex membership. A search facility is provided where a user can search for protein complex information in Saccharomyces cerevisiae. GRIP is developed to retrieve information on protein complex, cellular localisation, and physical and genetic interactions in Saccharomyces cerevisiae. Manual construction of reference datasets can be a time consuming process requiring programming knowledge. GRIP simplifies and speeds up this process by allowing users to automatically construct reference datasets. GRIP is free to access at http://rosalind.infj.ulst.ac.uk/GRIP/.

  18. The contribution of Toll-like receptor 2 to the innate recognition of a Leishmania infantum silent information regulator 2 protein.

    Science.gov (United States)

    Silvestre, Ricardo; Silva, Ana M; Cordeiro-da-Silva, Anabela; Ouaissi, Ali

    2009-12-01

    We have characterized a Leishmania protein belonging to the silent information regulator 2 (SIR2) family [SIR2 related protein 1 (SIR2RP1)] that might play an immunoregulatory role during infection through its capacity to trigger B-cell effector functions. We report here that SIR2RP1 leads to the proliferation of activated B cells, causing increased expression of major histocompatibility complex (MHC) II and the costimulatory molecules CD40 and CD86, which are critical ligands for T-cell cross-talk during the development of adaptive immune responses. In contrast, B cells isolated from Toll-like receptor 2 (TLR2) knockout mice were unable to respond to the SIR2RP1 stimulus. Similarly, SIR2RP1 induced the maturation of dendritic cells (DCs) in a TLR2-dependent manner with the secretion of pro-inflammatory cytokines [interleukin (IL)-12 and tumour necrosis factor (TNF)-alpha] and enhanced the costimulatory properties of DCs. Nevertheless, immunization assays demonstrated that TLR2-deficient mice were able to mount a specific humoral response to SIR2RP1. Interestingly, further investigations showed that macrophages were activated by SIR2RP1 even in the absence of TLR2. Therefore, a different type of interplay between SIR2RP1 and the major antigen-presenting cells in vivo could explain the immune response observed in TLR2-deficient mice. Together, these results demonstrate that TLR2 signalling contributes to SIR2RP1 recognition by innate immune host cells.

  19. Tau protein

    DEFF Research Database (Denmark)

    Frederiksen, Jette Lautrup Battistini; Kristensen, Kim; Bahl, Jmc

    2011-01-01

    Background: Tau protein has been proposed as biomarker of axonal damage leading to irreversible neurological impairment in MS. CSF concentrations may be useful when determining risk of progression from ON to MS. Objective: To investigate the association between tau protein concentration and 14......-3-3 protein in the cerebrospinal fluid (CSF) of patients with monosymptomatic optic neuritis (ON) versus patients with monosymptomatic onset who progressed to multiple sclerosis (MS). To evaluate results against data found in a complete literature review. Methods: A total of 66 patients with MS and/or ON from...... the Department of Neurology of Glostrup Hospital, University of Copenhagen, Denmark, were included. CSF samples were analysed for tau protein and 14-3-3 protein, and clinical and paraclinical information was obtained from medical records. Results: The study shows a significantly increased concentration of tau...

  20. Intrinsically disordered proteins in the nucleus of human cells.

    Science.gov (United States)

    Frege, Telma; Uversky, Vladimir N

    2015-05-01

    Intrinsically disordered proteins are known to perform a variety of important functions such as macromolecular recognition, promiscuous binding, and signaling. They are crucial players in various cellular pathway and processes, where they often have key regulatory roles. Among vital cellular processes intimately linked to the intrinsically disordered proteins is transcription, an intricate biological performance predominantly developing inside the cell nucleus. With this work, we gathered information about proteins that exist in various compartments and sub-nuclear bodies of the nucleus of the human cells, with the goal of identifying which ones are highly disordered and which functions are ascribed to the disordered nuclear proteins.

  1. SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces

    Directory of Open Access Journals (Sweden)

    Schroeder Michael

    2006-03-01

    Full Text Available Abstract Background Currently there is a strong need for methods that help to obtain an accurate description of protein interfaces in order to be able to understand the principles that govern molecular recognition and protein function. Many of the recent efforts to computationally identify and characterize protein networks extract protein interaction information at atomic resolution from the PDB. However, they pay none or little attention to small protein ligands and solvent. They are key components and mediators of protein interactions and fundamental for a complete description of protein interfaces. Interactome profiling requires the development of computational tools to extract and analyze protein-protein, protein-ligand and detailed solvent interaction information from the PDB in an automatic and comparative fashion. Adding this information to the existing one on protein-protein interactions will allow us to better understand protein interaction networks and protein function. Description SCOWLP (Structural Characterization Of Water, Ligands and Proteins is a user-friendly and publicly accessible web-based relational database for detailed characterization and visualization of the PDB protein interfaces. The SCOWLP database includes proteins, peptidic-ligands and interface water molecules as descriptors of protein interfaces. It contains currently 74,907 protein interfaces and 2,093,976 residue-residue interactions formed by 60,664 structural units (protein domains and peptidic-ligands and their interacting solvent. The SCOWLP web-server allows detailed structural analysis and comparisons of protein interfaces at atomic level by text query of PDB codes and/or by navigating a SCOP-based tree. It includes a visualization tool to interactively display the interfaces and label interacting residues and interface solvent by atomic physicochemical properties. SCOWLP is automatically updated with every SCOP release. Conclusion SCOWLP enriches

  2. Inhibition of existing denitrification enzyme activity by chloramphenicol

    Science.gov (United States)

    Brooks, M.H.; Smith, R.L.; Macalady, D.L.

    1992-01-01

    Chloramphenicol completely inhibited the activity of existing denitrification enzymes in acetylene-block incubations with (i) sediments from a nitrate-contaminated aquifer and (ii) a continuous culture of denitrifying groundwater bacteria. Control flasks with no antibiotic produced significant amounts of nitrous oxide in the same time period. Amendment with chloramphenicol after nitrous oxide production had begun resulted in a significant decrease in the rate of nitrous oxide production. Chloramphenicol also decreased (>50%) the activity of existing denitrification enzymes in pure cultures of Pseudomonas denitrificans that were harvested during log- phase growth and maintained for 2 weeks in a starvation medium lacking electron donor. Short-term time courses of nitrate consumption and nitrous oxide production in the presence of acetylene with P. denitrificans undergoing carbon starvation were performed under optimal conditions designed to mimic denitrification enzyme activity assays used with soils. Time courses were linear for both chloramphenicol and control flasks, and rate estimates for the two treatments were significantly different at the 95% confidence level. Complete or partial inhibition of existing enzyme activity is not consistent with the current understanding of the mode of action of chloramphenicol or current practice, in which the compound is frequently employed to inhibit de novo protein synthesis during the course of microbial activity assays. The results of this study demonstrate that chloramphenicol amendment can inhibit the activity of existing denitrification enzymes and suggest that caution is needed in the design and interpretation of denitrification activity assays in which chloramphenicol is used to prevent new protein synthesis.

  3. Diving with pre-existing medical conditions.

    Science.gov (United States)

    Lippmann, John; McD Taylor, David; Stevenson, Christopher; Williams, Jo; Mitchell, Simon J

    2017-09-01

    This is the second report based on a survey of Divers Alert Network Asia-Pacific (DAN AP) members who dive with cardiovascular and respiratory conditions and diabetes. It examines the medical management of the divers' conditions, any diving modifications used to mitigate the risk and outcomes. An online cross-sectional survey was sent to 833 divers who had declared a targeted medical condition when applying for DAN AP membership between July 2009 and August 2013. Two-hundred-and-sixty-eight respondents (32%) provided sufficient information on their conditions to be included in the analyses. These included ischaemic heart disease (31), arrhythmias (20), cardiac septal defects (31), other cardiac conditions (10), hypertension (127), diabetes (25), asthma (40) and pneumothorax (5). Forty-nine per cent had sought specialist diving medical advice about their condition and 23% reported modifying their diving practices to mitigate their risk. The cohort had completed 183,069 career dives, 57,822 of these since being diagnosed with their medical condition. There were 27 individuals who reported having decompression illness (25 of whom were subsequently diagnosed with a persistent foramen ovale), and two individuals who experienced an arrhythmia during diving. Some DAN AP members are diving with medical conditions which could potentially impact the safety of their diving. A minority modified their diving practices to mitigate the risk of their condition and approximately half sought specialist diving medical advice. The incidence of diving-related problems precipitated by known and managed pre-existing health conditions seems low but further studies of larger cohorts and incorporating fatality data would be necessary to confirm this. These results are limited by the 32% response rate and potential for bias towards selection of those most careful with their health.

  4. Does Glocal Political Power Already Exist?

    Directory of Open Access Journals (Sweden)

    Lorenzo Ornaghi

    2017-05-01

    Full Text Available Large periods of history are usually characterized by equally important moments of change in scientific knowledge and, in particular, in the understanding of political power. We still need to study in depth whether the former provokes (almost of out necessity the latter, or whether they are “great” because they are favored by the innovation of the paradigms of knowledge. The passage from medieval universalism to the particularism of the modern age represents an extremely interesting analogy when compared to the transformations that are now underway. The example of John of Salisbury’s Policratus, the starting point of this article, is illuminating in our comprehension of the relevance of the interweaving between the persistence of the ancient forms of recognition of power and the search for new forms. The existence of glocal realities is already a fact. Even if it is relatively easy to recognize these realities (a business, a university, a humanitarian association, not a few of the same “parts” which constitute the traditional organization of the State, it is more difficult to define the specific characteristics of the power at their disposal. Moving from the widening gap between “actual” power and “potential” power, the article examines the motives for which the classical definitions of power are always becoming more insufficient in understanding the role now emerging from glocal realities. And, in particular, by looking at how the “command-obedience” relationship is changing also as a consequence of communication networks and information technology, the article analyzes that specific “contamination” within global elements and local elements, which seems to be the main base of glocal political power.

  5. Protein kinesis: The dynamics of protein trafficking and stability

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-12-31

    The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.

  6. 77 FR 34052 - Agency Information Collection Activities: Form I-102; Revision of an Existing Information...

    Science.gov (United States)

    2012-06-08

    .... Written comments and/or suggestions regarding the item(s) contained in this notice, especially regarding... Policy and Strategy, Clearance ] Office, 20 Massachusetts Avenue, Washington, DC 20529. Comments may also... please make sure to add OMB Control Number 1615-0079 in the subject box. Written comments and suggestions...

  7. 75 FR 78263 - Agency Information Collection Activities: Extension of an Existing Information Collection...

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    2010-12-15

    ... under review; Form G- 646, Sworn Statement of Refugee Applying for Admission to the United States; OMB... Refugee Applying for Admission to the United States. (3) Agency form number, if any, and the applicable... determine eligibility for the admission of the applicants to the United States as refugees. (5) An estimate...

  8. 77 FR 14407 - Agency Information Collection Activities: Extension of an Existing Information Collection...

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    2012-03-09

    ... under review; Form G- 646, Sworn Statement of Refugee Applying for Admission to the United States. The...: Sworn Statement of Refugee Applying for Admission to the United States. (3) Agency form number, if any... States as refugees. (5) An estimate of the total number of respondents and the amount of time estimated...

  9. 77 FR 37063 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-06-20

    .... Immigration and Customs Enforcement, 500 12th Street SW., Stop 5705, Washington, DC 20536; (202) 732-4356.... Form I- 312); U.S. Immigration and Customs Enforcement. (4) Affected public who will be asked or... Mattison, Chief, Records Management, U.S. Immigration and Customs Enforcement, Department of Homeland...

  10. Interaction entropy for protein-protein binding

    Science.gov (United States)

    Sun, Zhaoxi; Yan, Yu N.; Yang, Maoyou; Zhang, John Z. H.

    2017-03-01

    Protein-protein interactions are at the heart of signal transduction and are central to the function of protein machine in biology. The highly specific protein-protein binding is quantitatively characterized by the binding free energy whose accurate calculation from the first principle is a grand challenge in computational biology. In this paper, we show how the interaction entropy approach, which was recently proposed for protein-ligand binding free energy calculation, can be applied to computing the entropic contribution to the protein-protein binding free energy. Explicit theoretical derivation of the interaction entropy approach for protein-protein interaction system is given in detail from the basic definition. Extensive computational studies for a dozen realistic protein-protein interaction systems are carried out using the present approach and comparisons of the results for these protein-protein systems with those from the standard normal mode method are presented. Analysis of the present method for application in protein-protein binding as well as the limitation of the method in numerical computation is discussed. Our study and analysis of the results provided useful information for extracting correct entropic contribution in protein-protein binding from molecular dynamics simulations.

  11. The protein side of the central dogma: permanence and change.

    Science.gov (United States)

    Morange, Michel

    2006-01-01

    There are two facets to the central dogma proposed by Francis Crick in 1957. One concerns the relation between the sequence of nucleotides and the sequence of amino acids, the second is devoted to the relation between the sequence of amino acids and the native three-dimensional structure of proteins. 'Folding is simply a function of the order of the amino acids,' i.e. no information is required for the proper folding of a protein other than the information contained in its sequence. This protein side of the central dogma was elaborated in a scientific context in which the characteristics and functions of proteins, and the mechanisms of protein folding, were seen very differently. This context, which made the folding problem a simple one, supported the bold proposition of Francis Crick. The protein side of the central dogma was not challenged by the discovery of prions if one adopts the definition of information given by Francis Crick. It might have been challenged by the discovery that regulatory enzymes exist in different conformations, and the evidence for the existence of chaperones assisting protein folding. But it was not, and folding remains what it was for Francis Crick, 'simply a function of the order of amino acids'. But the meaning of 'function' has dramatically changed. It is no longer the result of simple physicochemical laws, but that of a long evolutionary process which has optimized protein folding. Molecular mechanistic explanations have to be allied with evolutionary explanations, in a way characteristic of present biology.

  12. Diffusion of information throughout the host interactome reveals gene expression variations in network proximity to target proteins of hepatitis C virus.

    Directory of Open Access Journals (Sweden)

    Ettore Mosca

    Full Text Available Hepatitis C virus infection is one of the most common and chronic in the world, and hepatitis associated with HCV infection is a major risk factor for the development of cirrhosis and hepatocellular carcinoma (HCC. The rapidly growing number of viral-host and host protein-protein interactions is enabling more and more reliable network-based analyses of viral infection supported by omics data. The study of molecular interaction networks helps to elucidate the mechanistic pathways linking HCV molecular activities and the host response that modulates the stepwise hepatocarcinogenic process from preneoplastic lesions (cirrhosis and dysplasia to HCC. Simulating the impact of HCV-host molecular interactions throughout the host protein-protein interaction (PPI network, we ranked the host proteins in relation to their network proximity to viral targets. We observed that the set of proteins in the neighborhood of HCV targets in the host interactome is enriched in key players of the host response to HCV infection. In opposition to HCV targets, subnetworks of proteins in network proximity to HCV targets are significantly enriched in proteins reported as differentially expressed in preneoplastic and neoplastic liver samples by two independent studies. Using multi-objective optimization, we extracted subnetworks that are simultaneously "guilt-by-association" with HCV proteins and enriched in proteins differentially expressed. These subnetworks contain established, recently proposed and novel candidate proteins for the regulation of the mechanisms of liver cells response to chronic HCV infection.

  13. Diffusion of Information throughout the Host Interactome Reveals Gene Expression Variations in Network Proximity to Target Proteins of Hepatitis C Virus

    Science.gov (United States)

    Milanesi, Luciano

    2014-01-01

    Hepatitis C virus infection is one of the most common and chronic in the world, and hepatitis associated with HCV infection is a major risk factor for the development of cirrhosis and hepatocellular carcinoma (HCC). The rapidly growing number of viral-host and host protein-protein interactions is enabling more and more reliable network-based analyses of viral infection supported by omics data. The study of molecular interaction networks helps to elucidate the mechanistic pathways linking HCV molecular activities and the host response that modulates the stepwise hepatocarcinogenic process from preneoplastic lesions (cirrhosis and dysplasia) to HCC. Simulating the impact of HCV-host molecular interactions throughout the host protein-protein interaction (PPI) network, we ranked the host proteins in relation to their network proximity to viral targets. We observed that the set of proteins in the neighborhood of HCV targets in the host interactome is enriched in key players of the host response to HCV infection. In opposition to HCV targets, subnetworks of proteins in network proximity to HCV targets are significantly enriched in proteins reported as differentially expressed in preneoplastic and neoplastic liver samples by two independent studies. Using multi-objective optimization, we extracted subnetworks that are simultaneously “guilt-by-association” with HCV proteins and enriched in proteins differentially expressed. These subnetworks contain established, recently proposed and novel candidate proteins for the regulation of the mechanisms of liver cells response to chronic HCV infection. PMID:25461596

  14. 7 CFR 1718.52 - Existing mortgages.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 11 2010-01-01 2010-01-01 false Existing mortgages. 1718.52 Section 1718.52... AGRICULTURE LOAN SECURITY DOCUMENTS FOR ELECTRIC BORROWERS Mortgage for Distribution Borrowers § 1718.52 Existing mortgages. Nothing contained in this subpart amends, invalidates, terminates or rescinds any...

  15. Structural reliability of existing city bridges

    NARCIS (Netherlands)

    Hellebrandt, L.; Steenbergen, R.; Vrouwenvelder, T.; Blom, K.

    2015-01-01

    Full probabilistic reliability analysis may be valuable for assessing existing structures. Measures for increasing the safety level are quite costly for existing structures and may be unnecessary when such a decision is grounded on a conservative analysis for determining the structural reliability.

  16. Existence of solutions of functional differential inclusions

    Directory of Open Access Journals (Sweden)

    A. Anguraj

    1992-01-01

    Full Text Available We prove the existence of solutions of a functional differential inclusion. By using the variation of parameters formula we convert the functional differential inclusion into an integral inclusion and prove the existence of a fixed point of the set-valued mapping with the help of the Kakutani-Bohnenblust-Karlin fixed point theorem.

  17. On determining if a specular point exists

    DEFF Research Database (Denmark)

    Rusch, W; Sørensen, O

    1979-01-01

    A technique is presented whereby the existence of a specular point on a convex surface of revolution can be determined without actually finding it. Only the evaluation of two simple algebraic expressions is involved. Should a specular point be found not to exist, a search procedure has been thereby...

  18. On the existence of consistent price systems

    DEFF Research Database (Denmark)

    Bayraktar, Erhan; Pakkanen, Mikko S.; Sayit, Hasanjan

    2014-01-01

    We formulate a sufficient condition for the existence of a consistent price system (CPS), which is weaker than the conditional full support condition (CFS). We use the new condition to show the existence of CPSs for certain processes that fail to have the CFS property. In particular this condition...

  19. Protein domain recurrence and order can enhance prediction of protein functions.

    Science.gov (United States)

    Messih, Mario Abdel; Chitale, Meghana; Bajic, Vladimir B; Kihara, Daisuke; Gao, Xin

    2012-09-15

    Burgeoning sequencing technologies have generated massive amounts of genomic and proteomic data. Annotating the functions of proteins identified in this data has become a big and crucial problem. Various computational methods have been developed to infer the protein functions based on either the sequences or domains of proteins. The existing methods, however, ignore the recurrence and the order of the protein domains in this function inference. We developed two new methods to infer protein functions based on protein domain recurrence and domain order. Our first method, DRDO, calculates the posterior probability of the Gene Ontology terms based on domain recurrence and domain order information, whereas our second method, DRDO-NB, relies on the naïve Bayes methodology using the same domain architecture information. Our large-scale benchmark comparisons show strong improvements in the accuracy of the protein function inference achieved by our new methods, demonstrating that domain recurrence and order can provide important information for inference of protein functions. The new models are provided as open source programs at http://sfb.kaust.edu.sa/Pages/Software.aspx. dkihara@cs.purdue.edu, xin.gao@kaust.edu.sa Supplementary data are available at Bioinformatics Online.

  20. Protein domain recurrence and order can enhance prediction of protein functions

    KAUST Repository

    Abdel Messih, Mario A.

    2012-09-07

    Motivation: Burgeoning sequencing technologies have generated massive amounts of genomic and proteomic data. Annotating the functions of proteins identified in this data has become a big and crucial problem. Various computational methods have been developed to infer the protein functions based on either the sequences or domains of proteins. The existing methods, however, ignore the recurrence and the order of the protein domains in this function inference. Results: We developed two new methods to infer protein functions based on protein domain recurrence and domain order. Our first method, DRDO, calculates the posterior probability of the Gene Ontology terms based on domain recurrence and domain order information, whereas our second method, DRDO-NB, relies on the nave Bayes methodology using the same domain architecture information. Our large-scale benchmark comparisons show strong improvements in the accuracy of the protein function inference achieved by our new methods, demonstrating that domain recurrence and order can provide important information for inference of protein functions. The Author(s) 2012. Published by Oxford University Press.

  1. Existence test for asynchronous interval iterations

    DEFF Research Database (Denmark)

    Madsen, Kaj; Caprani, O.; Stauning, Ole

    1997-01-01

    In the search for regions that contain fixed points ofa real function of several variables, tests based on interval calculationscan be used to establish existence ornon-existence of fixed points in regions that are examined in the course ofthe search. The search can e.g. be performed...... as a synchronous (sequential) interval iteration:In each iteration step all components of the iterate are calculatedbased on the previous iterate. In this case it is straight forward to base simple interval existence and non-existencetests on the calculations done in each step of the iteration. The search can also...... be performed as an asynchronous (parallel) iteration: Only a few components are changed in each stepand this calculation is in general based on components from differentprevious iterates. For the asynchronous iteration it turns out thatsimple tests of existence and non-existence can be based...

  2. EXIST's Gamma-Ray Burst Sensitivity

    Science.gov (United States)

    Band, D. L.; Grindlay, J. E.; Hong, J.; Fishman, G.; Hartmann, D. H.; Garson, A., III; Krawczynski, H.; Barthelmy, S.; Gehrels, N.; Skinner, G.

    2008-02-01

    We use semianalytic techniques to evaluate the burst sensitivity of designs for the EXIST hard X-ray survey mission. Applying these techniques to the mission design proposed for the Beyond Einstein program, we find that with its very large field of view and faint gamma-ray burst detection threshold, EXIST will detect and localize approximately two bursts per day, a large fraction of which may be at high redshift. We estimate that EXIST's maximum sensitivity will be ~4 times greater than that of Swift's Burst Alert Telescope. Bursts will be localized to better than 40'' at threshold, with a burst position as good as a few arcseconds for strong bursts. EXIST's combination of three different detector systems will provide spectra from 3 keV to more than 10 MeV. Thus, EXIST will enable a major leap in the understanding of bursts, their evolution, environment, and utility as cosmological probes.

  3. Wykrzyknik - istnienie - zmiana (Exclamation - Existence - Change

    Directory of Open Access Journals (Sweden)

    Maciej Karpiński

    2011-06-01

    Full Text Available It, what exists, so to say, demands for the addressee – the thing exists in the face of (for something (or somebody. In other words, the existence is the relation. The competitive conception of the existence outside the relation (existence isolated leads to the contradiction. The existential proposition ‘Some A exists’, understoodliterally, is the pleonasm. It tends to treat the existential proposition as the conventional figure, expressing the simple act of an A affirmation (the exclamation ‘A!’. The existence’s relation should not be narrowed down only to the relation of perception(esse est percipi. It is needed to be understood widely, as every relation, in which something influences on whatever (that is, some change occurs. This influence (change can take place both inside or outside the consciousness. The existing thing, the influence exerted by it, and the change, occurred as the result of this influence, are identical. Thanks to it, we can eliminate difficulties connected withfinding ‘the point of contact’ between modules of the existence’s relation (that is, ‘the place’ where existing thing and its addressee are connected. The existence, as the relation of influence-change, is modal and gradual (as regards both intensity and extensiveness: the thing, in different aspects, can exist more or less. Theoretically, discussed relation can be symmetrical or antisymmetrical. The concept of error should be redefined. The error concerning the existence (resp. the nonexistence of specified thing, must not mean the incompatibility between this thing and the perception (widely: between this thing and the change causedby this thing in its addressee. The existence is the unity of the thing-perception (resp. the thing-influence-change. That is why the incompatibility can occur only between the state of thing-perception (resp. the thing-influence-change and the related state of duty. The conception of the existence as the relation

  4. Protein Data Bank (PDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and...

  5. EXIST: The Next Large GRB Observatory

    Science.gov (United States)

    Fishman, Gerald J.

    2003-01-01

    Studies have begun on the EXIST (Energetic X-ray Imaging Survey Telescope) Mission as a Black Hole Survey 'Einstein Probe', a major element in the new NASA Beyond Einstein Program in the Office of Space Science. This program was approved by the US Congress, in February 2003 as part of the NASA FY2004 NASA budget. EXIST is planned as a very wide-field coded aperture telescope and a positional accuracy for GRBs better than one arc-minute. The baseline detectors are Cadmium-Zinc-Telluride (CZT), with a total sensitive area of approximately 8 m2. EXIST will use SWIFT as a pathfinder mission; the findings of SWIFT will refine the scientific objectives of EXIST and will help to determine many of its design parameters. EXIST will study early star and galaxy formation at high redshifts through observations of thousands of GRBs, their afterglows and host galaxies. It is intended that the international GRB community will play a large role in EXIST through direct participation as well as with complementary observational programs, both space-based and ground-based. Some preliminary design features and capabilities of the EXIST Mission will be presented.

  6. EXISTENCE OF MATTER IN THE UNIVERSE

    OpenAIRE

    Aksakallı, Cengiz

    2016-01-01

    This study was conducted as an attempt to determine the process of existence of the universe  and whether there is another volume that restricts the universe because of the metric expansion of space, and to determine whether there may be a new universe or existence  in the case of extinction of all the universe by way of mathematical and physical functions.This study was conducted as an attempt to determine the process of existence of the universe  and whether there is another volume that res...

  7. Existing and Expected Service Quality of Grameenphone Users in Bangladesh

    Directory of Open Access Journals (Sweden)

    Azmat Ullah

    2015-12-01

    Full Text Available The Grameenphone (GP is a market leader in the telecommunication industry in Bangladesh. This study investigates the existing and expected service quality of Grameenphone users in Bangladesh. The Study reveals that there are significant gap between existing and expected perceived service network, 3G, customer care, physical facilities, billing cost, information service, mobile banking and GP offers. The study concludes that customer satisfaction is a dynamic phenomenon. Maintaining desired level of customer satisfaction requires corporate proactive responsiveness in accessing, building & retaining satisfied customers for sustainable competitive advantages in the marketplace.

  8. Optimized purification of a fusion protein by reversed-phase high performance liquid chromatography informed by the linear solvent strength model.

    Science.gov (United States)

    Falconer, Isaac B; Mant, Colin T; McKnight, C James; Vugmeyster, Liliya; Hodges, Robert

    2017-10-27

    Fusion protein systems are commonly used for expression of small proteins and peptides. An important criterion for a fusion protein system to be useful is the ability to separate the protein of interest from the tag. Additionally, because no protease cleaves fusion proteins with 100% efficiency, the ability to separate the desired peptide from any remaining uncleaved protein is also necessary. This is likely to be the more difficult task as at least a portion of the sequence of the fusion protein is identical to that of the protein of interest. When a high level of purity is required, gradient elution reversed-phase HPLC is frequently used as a final purification step. Shallow gradients are often advantageous for maximizing both the purity and yield of the final product; however, the relationship between relative retention times at shallow gradients and those at steeper gradients typically used for analytical HPLC are not always straightforward. In this work, we report reversed-phase HPLC results for the fusion protein system consisting of the N-terminal domain of ribosomal protein L9 (NTL9) and the 36-residue villin headpiece subdomain (HP36) linked by a recognition sequence for the protease factor Xa. This system represents an excellent example of the difficulties in purification that may arise from this unexpected elution behavior at shallow gradients. Additionally, we report on the sensitivity of this elution behavior to the concentration of the additive trifluoroacetic acid in the mobile phase and present optimized conditions for separating HP36 from the full fusion protein by reversed-phase HPLC using a shallow gradient. Finally, we suggest that these findings are relevant to the purification of other fusion protein systems, for which similar problems may arise, and support this suggestion using insights from the linear solvent strength model of gradient elution liquid chromatography. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Pre-Existing Condition Insurance Plan Data

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Affordable Care Act created the new Pre-Existing Condition Insurance Plan (PCIP) program to make health insurance available to Americans denied coverage by...

  10. LANDFIRE (90m) Existing Vegetation Type

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This map depicts the distribution of existing vegetation types contained in the LANDFIRE dataset. All 30-meter EVT grids were resampled to 90-meter grids and merged...

  11. Policy on Existing Stocks of Pesticide Products

    Science.gov (United States)

    This statement establishes general principles the Agency generally will apply in determining whether and under what conditions to allow the sale and use of existing stocks of pesticides for which the registration has been amended, canceled, or suspended.

  12. Functional interpretation and the existence property

    DEFF Research Database (Denmark)

    Jørgensen, Klaus Frovin

    2004-01-01

    It is shown that functional interpretation can be used to show the existence property of intuitionistic number theory. On the basis of truth variants a comparison is then made between realisability and functional interpretation showing a structural difference between the two.......It is shown that functional interpretation can be used to show the existence property of intuitionistic number theory. On the basis of truth variants a comparison is then made between realisability and functional interpretation showing a structural difference between the two....

  13. Optimality and existence for Lipschitz equations

    Directory of Open Access Journals (Sweden)

    Johnny Henderson

    1988-01-01

    Full Text Available Solutions of certain boundary value problems are shown to exist for the nth order differential equation y(n=f(t,y,y′,…,y(n−1, where f is continuous on a slab (a,b×Rn and f satisfies a Lipschitz condition on the slab. Optimal length subintervals of (a,b are determined, in terms of the Lipschitz coefficients, on which there exist unique solutions.

  14. Year 2 Report: Protein Function Prediction Platform

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, C E

    2012-04-27

    Upon completion of our second year of development in a 3-year development cycle, we have completed a prototype protein structure-function annotation and function prediction system: Protein Function Prediction (PFP) platform (v.0.5). We have met our milestones for Years 1 and 2 and are positioned to continue development in completion of our original statement of work, or a reasonable modification thereof, in service to DTRA Programs involved in diagnostics and medical countermeasures research and development. The PFP platform is a multi-scale computational modeling system for protein structure-function annotation and function prediction. As of this writing, PFP is the only existing fully automated, high-throughput, multi-scale modeling, whole-proteome annotation platform, and represents a significant advance in the field of genome annotation (Fig. 1). PFP modules perform protein functional annotations at the sequence, systems biology, protein structure, and atomistic levels of biological complexity (Fig. 2). Because these approaches provide orthogonal means of characterizing proteins and suggesting protein function, PFP processing maximizes the protein functional information that can currently be gained by computational means. Comprehensive annotation of pathogen genomes is essential for bio-defense applications in pathogen characterization, threat assessment, and medical countermeasure design and development in that it can short-cut the time and effort required to select and characterize protein biomarkers.

  15. Sensitive red protein calcium indicators for imaging neural activity

    OpenAIRE

    Dana, Hod; Mohar, Boaz; Sun, Yi; Narayan, Sujatha; Gordus, Andrew; Hasseman, Jeremy P; Tsegaye, Getahun; Holt, Graham T.; Hu, Amy; Walpita, Deepika; Patel, Ronak; Macklin, John J.; Bargmann, Cornelia I; Ahrens, Misha B.; Schreiter, Eric R

    2016-01-01

    eLife digest Neurons encode information with brief electrical pulses called spikes. Monitoring spikes in large populations of neurons is a powerful method for studying how networks of neurons process information and produce behavior. This activity can be detected using fluorescent protein indicators, or ?probes?, which light up when neurons are active. The best existing probes produce green fluorescence. However, red fluorescent probes would allow us to see deeper into the brain, and could al...

  16. Green fluorescent protein as a reporter of prion protein folding

    Directory of Open Access Journals (Sweden)

    Dalton Kevin

    2006-08-01

    Full Text Available Abstract Background The amino terminal half of the cellular prion protein PrPc is implicated in both the binding of copper ions and the conformational changes that lead to disease but has no defined structure. However, as some structure is likely to exist we have investigated the use of an established protein refolding technology, fusion to green fluorescence protein (GFP, as a method to examine the refolding of the amino terminal domain of mouse prion protein. Results Fusion proteins of PrPc and GFP were expressed at high level in E.coli and could be purified to near homogeneity as insoluble inclusion bodies. Following denaturation, proteins were diluted into a refolding buffer whereupon GFP fluorescence recovered with time. Using several truncations of PrPc the rate of refolding was shown to depend on the prion sequence expressed. In a variation of the format, direct observation in E.coli, mutations introduced randomly in the PrPc protein sequence that affected folding could be selected directly by recovery of GFP fluorescence. Conclusion Use of GFP as a measure of refolding of PrPc fusion proteins in vitro and in vivo proved informative. Refolding in vitro suggested a local structure within the amino terminal domain while direct selection via fluorescence showed that as little as one amino acid change could significantly alter folding. These assay formats, not previously used to study PrP folding, may be generally useful for investigating PrPc structure and PrPc-ligand interaction.

  17. DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

    Directory of Open Access Journals (Sweden)

    Vakser Ilya A

    2011-07-01

    Full Text Available Abstract Background Computational approaches to protein-protein docking typically include scoring aimed at improving the rank of the near-native structure relative to the false-positive matches. Knowledge-based potentials improve modeling of protein complexes by taking advantage of the rapidly increasing amount of experimentally derived information on protein-protein association. An essential element of knowledge-based potentials is defining the reference state for an optimal description of the residue-residue (or atom-atom pairs in the non-interaction state. Results The study presents a new Distance- and Environment-dependent, Coarse-grained, Knowledge-based (DECK potential for scoring of protein-protein docking predictions. Training sets of protein-protein matches were generated based on bound and unbound forms of proteins taken from the DOCKGROUND resource. Each residue was represented by a pseudo-atom in the geometric center of the side chain. To capture the long-range and the multi-body interactions, residues in different secondary structure elements at protein-protein interfaces were considered as different residue types. Five reference states for the potentials were defined and tested. The optimal reference state was selected and the cutoff effect on the distance-dependent potentials investigated. The potentials were validated on the docking decoys sets, showing better performance than the existing potentials used in scoring of protein-protein docking results. Conclusions A novel residue-based statistical potential for protein-protein docking was developed and validated on docking decoy sets. The results show that the scoring function DECK can successfully identify near-native protein-protein matches and thus is useful in protein docking. In addition to the practical application of the potentials, the study provides insights into the relative utility of the reference states, the scope of the distance dependence, and the coarse-graining of

  18. Review of existing residential energy efficiency certification and rating programs

    Energy Technology Data Exchange (ETDEWEB)

    Hendrickson, P.L.

    1986-11-01

    This report was prepared for the Office of Buildings and Community Systems, US Department of Energy (DOE). The principal objective of the report is to present information on existing Home Energy Rating Systems (HERS) and their features. Much of the information in this report updates a 1982 report (PNL-4359), also prepared by the Pacific Northwest Laboratory (PNL) for DOE. Secondary objectives of the report are to qualitatively examine the benefits and costs of HERS programs, review survey results on the attitudes of various user groups toward the programs, and discuss selected design and implementation issues.

  19. Structural behaviour characterization of existing adobe constructions in Aveiro

    OpenAIRE

    H. Varum; Costa, A; Martins, T.(); Pereira, H; Almeida, J; Rodrigues, H.; D. Silveira

    2007-01-01

    Adobe was a widely used construction material in Aveiro, Portugal, till the middle of the 20th century. Nowadays, adobe can still be found in varied types of constructions, many of which are of cultural, historical, and also architectural recognized value. The existing adobe buildings present an important level of structural damage and, in many cases, are even near to ruin, having the majority a high vulnerability to seismic actions. To face the lack of information concerning the mechanica...

  20. Transcendental Self and the Feeling of Existence

    Directory of Open Access Journals (Sweden)

    Apaar Kumar

    2016-06-01

    Full Text Available In this essay, I investigate one aspect of Kant’s larger theory of the transcendental self. In the Prolegomena, Kant says that the transcendental self can be represented as a feeling of existence. In contrast to the view that Kant errs in describing the transcendental self in this fashion, I show that there exists a strand in Kant’s philosophy that permits us to interpret the representation of the transcendental self as a feeling of existence—as the obscurely conscious and temporally inaccessible modification of the state of the discursive subject, which is built into all the representations of such a subject. I also provide an account of how the transcendental self can be legitimately understood both as an epistemic condition for the possibility of experience as well as the representation of a non-naturalistic feeling of existence.

  1. The Existence of Public Protection Unit

    Directory of Open Access Journals (Sweden)

    Moh. Ilham A. Hamudy

    2014-12-01

    Full Text Available This article is about the Public Protection Unit (Satlinmas formerly known as civil defence (Hansip. This article is a summary of the results of the desk study and fieldwork conducted in October-November 2013 in the town of Magelang and Surabaya. This study used descriptive qualitative approach to explore the combined role and existence Satlinmas. The results of the study showed, the existence of the problem Satlinmas still leave many, including, first, the legal basis for the establishment of Satlinmas. Until now, there has been no new regulations governing Satlinmas. Existing regulations are too weak and cannot capture the times. Second, the formulation of concepts and basic tasks and functions Satlinmas overlap with other institutions. Third, Satlinmas image in society tend to fade and abused. Fourth, Satlinmas incorporation into the Municipal Police deemed not appropriate, because different philosophy.

  2. Existing bridge evaluation using deficiency point method

    Directory of Open Access Journals (Sweden)

    Vičan Josef

    2016-01-01

    Full Text Available In the transforming EU countries, transportation infrastructure has a prominent position in advancing industry and society. Recent developments show, that attention should be moved from the design of new structures towards the repair and reconstruction of existing ones to ensure and increase their satisfactory structural reliability and durability. The problem is very urgent because many construction projects, especially transport infrastructure, in most European countries are more than 50-60 years old and require rehabilitations based on objective evaluations. Therefore, the paper presents methodology of existing bridge evaluation based on reliability concept using Deficiency Point Method. The methodology was prepared from the viewpoint to determine the priority order for existing bridge rehabilitation.

  3. Robustness and health monitoring of existing bridges

    OpenAIRE

    Casas Rius, Joan Ramon

    2015-01-01

    The paper shows how the robustness concept, mainly developed and thought for the design of new structures, and the monitoring by suitable sensors based on fiber optics can also play a relevant role in the safety and management of existing bridges. A new approach of robustness more related to the long-term and service life of bridges is presented and its advantages in the decision-making process during the management of existing bridges are highlighted and afterwards applied on a real brid...

  4. Informing the Human Plasma Protein Binding of Environmental Chemicals by Machine Learning in the Pharmaceutical Space: Applicability Domain and Limits of Predictability

    Science.gov (United States)

    The free fraction of a xenobiotic in plasma (Fub) is an important determinant of chemical adsorption, distribution, metabolism, elimination, and toxicity, yet experimental plasma protein binding data is scarce for environmentally relevant chemicals. The presented work explores th...

  5. Foucault, Counselling and the Aesthetics of Existence

    Science.gov (United States)

    Peters, Michael A.

    2005-01-01

    Michel Foucault was drawn late in life to study the "arts of the self" in Greco-Roman culture as a basis, following Nietzsche, for what he called an "aesthetics of existence." By this, he meant a set of creative and experimental processes and techniques by which an individual turns him- or herself into a work of art. For Nietzsche, it was above…

  6. Proof That Chronic Lyme Disease Exists

    Directory of Open Access Journals (Sweden)

    Daniel J. Cameron

    2010-01-01

    Full Text Available The evidence continues to mount that Chronic Lyme Disease (CLD exists and must be addressed by the medical community if solutions are to be found. Four National Institutes of Health (NIH trials validated the existence and severity of CLD. Despite the evidence, there are physicians who continue to deny the existence and severity of CLD, which can hinder efforts to find a solution. Recognizing CLD could facilitate efforts to avoid diagnostic delays of two years and durations of illness of 4.7 to 9 years described in the NIH trials. The risk to society of emerging antibiotic-resistant organisms should be weighed against the societal risks associated with failing to treat an emerging population saddled with CLD. The mixed long-term outcome in children could also be examined. Once we accept the evidence that CLD exists, the medical community should be able to find solutions. Medical professionals should be encouraged to examine whether: (1 innovative treatments for early LD might prevent CLD, (2 early diagnosis of CLD might result in better treatment outcomes, and (3 more effective treatment regimens can be developed for CLD patients who have had prolonged illness and an associated poor quality of life.

  7. Conservation and Development Options existing on Uluguru ...

    African Journals Online (AJOL)

    Conservation and Development Options existing on Uluguru Mountains, Tanzania. ... Tanzania Journal of Forestry and Nature Conservation ... Abstract. Effective management of projects on Uluguru Mountains requires that both development and conservation options are weighed and that opportunities and challenges are ...

  8. 36 CFR 9.33 - Existing operations.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Existing operations. 9.33 Section 9.33 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR... permit may be continued for the term of that permit, exclusive of any renewal period whether mandatory or...

  9. Factorial Structure of the Existence Scale

    NARCIS (Netherlands)

    Brouwers, Tomic, W. A.

    2015-01-01

    Existential meaning in life is becoming an increasingly important measure of personal assessment. In search of a suitable instrument to measure existential meaning, the authors reviewed several measures. Eventually, they selected the Existence Scale (ES), doing so on theoretical grounds. The ES is a

  10. Transforming existing content into reusable Learning Objects

    NARCIS (Netherlands)

    Doorten, Monique; Giesbers, Bas; Janssen, José; Daniels, Jan; Koper, Rob

    2003-01-01

    Please cite as: Doorten, M., Giesbers, B., Janssen, J., Daniëls, J, & Koper, E.J.R., (2004). Transforming existing content into reusable learning objects. In R. McGreal, Online Education using Learning Objects (pp. 116-127). London: RoutledgeFalmer.

  11. 7 CFR 15b.18 - Existing facilities.

    Science.gov (United States)

    2010-01-01

    ... access to otherwise inaccessible areas or features of historic properties; (ii) Using audio-visual... visits, delivery of services at alternate accessible sites, alteration of exiting facilities and... significant alteration in its existing facilities, the recipient may, as an alternative, refer the handicapped...

  12. Implementation of ventilation in existing schools

    DEFF Research Database (Denmark)

    Hviid, Christian Anker; Petersen, Steffen

    ; they evaluate both scientific and practical implementation The analyses lead to a list of criteria associated with the implementation of ventilation in existing schools. Generic retrofitting scenarios which prioritize energy savings, indoor climate and building/facade integration are assembled and illustrated...

  13. Human organisms begin to exist at fertilization.

    Science.gov (United States)

    Miller, Calum; Pruss, Alexander

    2017-09-01

    Eugene Mills has recently argued that human organisms cannot begin to exist at fertilization because the evidence suggests that egg cells persist through fertilization and simply turn into zygotes. He offers two main arguments for this conclusion: that 'fertilized egg' commits no conceptual fallacy, and that on the face of it, it looks as though egg cells survive fertilization when the process is watched through a microscope. We refute these arguments and offer several reasons of our own to think that egg cells do not survive fertilization, appealing to various forms of essentialism regarding persons, fission cases, and a detailed discussion of the biological facts relevant to fertilization and genetics. We conclude that it is plausible, therefore, that human organisms begin to exist at fertilization - or, at the very least, that there are grounds for thinking that they existed as zygotes which do not apply to the prior egg cells. While this does not entail that human persons begin to exist at this point, it nevertheless has considerable significance for this latter question. © 2017 John Wiley & Sons Ltd.

  14. "Giftedness Science": Does It Exist at All?

    Science.gov (United States)

    David, Hanna

    2012-01-01

    In this commentary, the author finds that the target article, "Cultural Variation and Dominance in a Globalised Knowledge-Economy: Towards a Culture-Sensitive Research Paradigm in the Science of Giftedness", has three substantial failures: (1) an unproven, even incorrect assumption about the existence of bias in the "science of giftedness" due to…

  15. Existing data sources for clinical epidemiology:

    DEFF Research Database (Denmark)

    Schiodt, Morten; Larsson Wexell, Cecilia; Herlofson, Bente Brokstad

    2015-01-01

    registration form has been developed, and the relevant medical community has been informed either directly or through presentations at professional meetings. A website with study information is published in each country, and data entry is ongoing. This large-scale systematic uniform registration of ONJ cases...

  16. ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval

    Directory of Open Access Journals (Sweden)

    Wang Jingyan

    2012-05-01

    Full Text Available Abstract Background The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. Traditional protein search methods rely on a pairwise dissimilarity/similarity measure for comparing a pair of proteins. This kind of pairwise measures suffer from the limitation of neglecting the distribution of other proteins and thus cannot satisfy the need for high accuracy of the retrieval systems. Recent work in the machine learning community has shown that exploiting the global structure of the database and learning the contextual dissimilarity/similarity measures can improve the retrieval performance significantly. However, most existing contextual dissimilarity/similarity learning algorithms work in an unsupervised manner, which does not utilize the information of the known class labels of proteins in the database. Results In this paper, we propose a novel protein-protein dissimilarity learning algorithm, ProDis-ContSHC. ProDis-ContSHC regularizes an existing dissimilarity measure dij by considering the contextual information of the proteins. The context of a protein is defined by its neighboring proteins. The basic idea is, for a pair of proteins (i, j, if their context N(i and N(j is similar to each other, the two proteins should also have a high similarity. We implement this idea by regularizing dij by a factor learned from the context N(i and N(j. Moreover, we divide the context to hierarchial sub-context and get the contextual dissimilarity vector for each protein pair. Using the class label information of the proteins, we select the relevant (a pair of proteins that has the same class labels and irrelevant (with different labels protein pairs, and train an SVM model to distinguish between their contextual dissimilarity vectors. The SVM model is further used to learn a supervised regularizing factor. Finally, with the new Supervised learned Dissimilarity

  17. ProDis-ContSHC: Learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval

    KAUST Repository

    Wang, Jim Jing-Yan

    2012-05-08

    Background: The need to retrieve or classify protein molecules using structure or sequence-based similarity measures underlies a wide range of biomedical applications. Traditional protein search methods rely on a pairwise dissimilarity/similarity measure for comparing a pair of proteins. This kind of pairwise measures suffer from the limitation of neglecting the distribution of other proteins and thus cannot satisfy the need for high accuracy of the retrieval systems. Recent work in the machine learning community has shown that exploiting the global structure of the database and learning the contextual dissimilarity/similarity measures can improve the retrieval performance significantly. However, most existing contextual dissimilarity/similarity learning algorithms work in an unsupervised manner, which does not utilize the information of the known class labels of proteins in the database.Results: In this paper, we propose a novel protein-protein dissimilarity learning algorithm, ProDis-ContSHC. ProDis-ContSHC regularizes an existing dissimilarity measure dij by considering the contextual information of the proteins. The context of a protein is defined by its neighboring proteins. The basic idea is, for a pair of proteins (i, j), if their context N (i) and N (j) is similar to each other, the two proteins should also have a high similarity. We implement this idea by regularizing dij by a factor learned from the context N (i) and N (j). Moreover, we divide the context to hierarchial sub-context and get the contextual dissimilarity vector for each protein pair. Using the class label information of the proteins, we select the relevant (a pair of proteins that has the same class labels) and irrelevant (with different labels) protein pairs, and train an SVM model to distinguish between their contextual dissimilarity vectors. The SVM model is further used to learn a supervised regularizing factor. Finally, with the new Supervised learned Dissimilarity measure, we update

  18. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... for the vegetarian proteins, whether they have carbohydrate. Protein Choices Plant-Based Proteins Plant-based protein foods ...

  19. An incremental approach to automated protein localisation

    Directory of Open Access Journals (Sweden)

    Kummert Franz

    2008-10-01

    Full Text Available Abstract Background The subcellular localisation of proteins in intact living cells is an important means for gaining information about protein functions. Even dynamic processes can be captured, which can barely be predicted based on amino acid sequences. Besides increasing our knowledge about intracellular processes, this information facilitates the development of innovative therapies and new diagnostic methods. In order to perform such a localisation, the proteins under analysis are usually fused with a fluorescent protein. So, they can be observed by means of a fluorescence microscope and analysed. In recent years, several automated methods have been proposed for performing such analyses. Here, two different types of approaches can be distinguished: techniques which enable the recognition of a fixed set of protein locations and methods that identify new ones. To our knowledge, a combination of both approaches – i.e. a technique, which enables supervised learning using a known set of protein locations and is able to identify and incorporate new protein locations afterwards – has not been presented yet. Furthermore, associated problems, e.g. the recognition of cells to be analysed, have usually been neglected. Results We introduce a novel approach to automated protein localisation in living cells. In contrast to well-known techniques, the protein localisation technique presented in this article aims at combining the two types of approaches described above: After an automatic identification of unknown protein locations, a potential user is enabled to incorporate them into the pre-trained system. An incremental neural network allows the classification of a fixed set of protein location as well as the detection, clustering and incorporation of additional patterns that occur during an experiment. Here, the proposed technique achieves promising results with respect to both tasks. In addition, the protein localisation procedure has been adapted

  20. Gambling on the existence of other universes

    CERN Document Server

    Sangalli, Arturo

    2016-01-01

    Speculations and theories about the existence of other worlds have a long history. In recent times, the arguments have shifted away from their typical philosophical and theological character to supposedly become more objective thanks to their scientific underpinnings. A prime example of this is the current parallel universes or multiverse theory, which has the support of a number of famous cosmologists. In this article, we contend that the claim for the existence of those parallel universes, as presented in Max Tegmark's book "Our Mathematical Universe", rests crucially on some questionable probability arguments involving infinity. As a result, a doubt is cast over the multiverse hypothesis: Is it more credible than the counterarguments based on philosophical and metaphysical considerations?

  1. Co-existence in multispecies biofilm communities

    DEFF Research Database (Denmark)

    Røder, Henriette Lyng

    environment to evaluate their biofilm formation capability. It was found that multispecies consortia could lead to increased biofilm formation compared to mono species growth. This shows how co-localized isolates are able to influence biofilm production in a community with high relevance for food safety...... and production. The analysis was further extended in manuscript 3, in which the effect of social interac-tions on biofilm formation in multispecies co-cultures isolated from a diverse range of environments was examined. The question raised was whether the interspecific interactions of co-existing bacteria...... generally lead to enhanced biofilm formation in complex communities. We showed that bacteria, expected to have co-existed for a long time, generated more biofilm biomass in co-culture. This was further tested against random co-cultures of bacteria, which supported the conclusion. Discovering that some...

  2. Overview of Existing Wind Energy Ordinances

    Energy Technology Data Exchange (ETDEWEB)

    Oteri, F.

    2008-12-01

    Due to increased energy demand in the United States, rural communities with limited or no experience with wind energy now have the opportunity to become involved in this industry. Communities with good wind resources may be approached by entities with plans to develop the resource. Although these opportunities can create new revenue in the form of construction jobs and land lease payments, they also create a new responsibility on the part of local governments to ensure that ordinances will be established to aid the development of safe facilities that will be embraced by the community. The purpose of this report is to educate and engage state and local governments, as well as policymakers, about existing large wind energy ordinances. These groups will have a collection of examples to utilize when they attempt to draft a new large wind energy ordinance in a town or county without existing ordinances.

  3. Sustainability in the existing building stock

    DEFF Research Database (Denmark)

    Elle, Morten; Nielsen, Susanne Balslev; Hoffmann, Birgitte

    2005-01-01

    sustainable building. In other words: the question is if it sensible to talk about a ‘sustainable building’ without taking the activities in the building into account? In many contexts, maintenance of the existing building stock is not a hot political topic. Facilities management can, however, be a vehicle......This paper explores the role of Facilities Management in the relation to sustainable development in the existing building stock. Facilities management is a concept still developing as the management of buildings are becoming more and more professional. Many recognize today that facilities......, QRWfacilities management’s most important contribution to sustainable development in the built environment. Space management is an essential tool in facilities management – and it could be considered a powerful tool in sustainable development; remembering that the building not being built is perhaps the most...

  4. Co-existence of agricultural production systems.

    Science.gov (United States)

    Jank, Bernhard; Rath, Johannes; Gaugitsch, Helmut

    2006-05-01

    Strategies and best practices for the co-existence of GM and non-GM crops need to be developed and implemented with the participation of farmers and other stakeholders. According to the principle of 'subsidiarity', decisions should be made by the lowest authority possible. When applying this concept to the case of GM crops, the affected society should determine their use and management in a regional decision-making process. Public participation is better accomplished at a lower level, and democratic deficits in decision-making on GMOs are better resolved, enabling farmers to manage or avoid GM crops. Ultimately, voluntary GMO-free zones might be a tool for sustainable co-existence and GM-free production and GMO-free zones might create a specific image for marketing regional products and services, such as tourism.

  5. LOVE’S SYMPHONY: MULTIPLICITY OF EXISTENCE

    Directory of Open Access Journals (Sweden)

    CHRISTINE McNEILL-MATTESON

    2016-05-01

    Full Text Available Love, although universal in thought, is explicitly complex and articulately multi-defined in almost every idea and expression. Love written is timeless from the molecules we possess within us, to the cosmos we study and explore. We can only exist and continue to exist in harmony with creation. Harmony reaches far beyond galaxies and universes, flowing backinto the most separate of the smallest molecules. Within all common denominators of harmony there is love: the very catalyst of harmony itself. This paper will look at harmony from a poetic point of view and examine how it is expressed always in the context of the mystery of sentience and conscience from human biology to the divine cosmos

  6. Does H4SO5 exist?

    Science.gov (United States)

    Murillo, Fernando; Vargas-Caamal, Alba; Pan, Sudip; Cabellos, José Luis; Mora-Fonz, Miguel J; Muñoz-Castro, Alvaro; Restrepo, Albeiro; Merino, Gabriel

    2017-07-14

    The possible existence of H4SO5 in aqueous sulfuric acid is analyzed in detail. For bare H4SO5, the computed free energy barrier for the exergonic transformation of H4SO5 into the H2SO4H2O complex is only 3.8 kcal mol-1. The presence of water or sulfuric acid catalyzes the dehydration to such an extent that it becomes almost a barrierless process. In the gas phase, dehydration of H4SO5 is an autocatalytic reaction as the water molecule produced by the decomposition of one H4SO5 molecule induces further dissociation. Thus, in solution, the surrounding water molecules make the para-sulfuric acid a very vulnerable species to exist. The simulated Raman spectra also corroborate the absence of H4SO5 in solution.

  7. The Italian contribution to the EXIST mission

    Science.gov (United States)

    Natalucci, L.; Tagliaferri, G.; Caraveo, P.; Pareschi, G.; Ubertini, P.; Villa, G.

    The EXIST Mission is a proposed multi-wavelength observatory to carry out the most sensitive hard X-ray survey and census of SMBH as well as the most powerful follow-up of Gamma Ray Bursts (GRBs). This mission will carry a large area (4.5m2) CdZnTe modular detector with an angular resolution of ˜2arcmin, sensitive in the energy range 5-600 keV, and a near infrared telescope with cooled mirror with outstanding sensitivity and capability of measuring onboard the redshift of many GRBs. Italy will contribute to EXIST with the provision of a soft X-ray telescope sensitive in the energy range 0.1-10 keV with an effective area approximately equivalent to one mirror module of XMM-Newton. We will describe hereafter the characteristics and performance of this instrument together with its capability of performing serendipitous surveys.

  8. Existing right-of-way plats database.

    Science.gov (United States)

    2010-02-01

    The Maryland State Highway Administrations Office of Real Estate processes a high volume of plat information and research : requests on a daily basis. This is a lengthy process which is completed manually. The Office of Real Estate intends to impr...

  9. Existing data sources for clinical epidemiology

    DEFF Research Database (Denmark)

    Johannesdottir, Sigrun Alba; Horváth-Puhó, Erzsébet; Ehrenstein, Vera

    2012-01-01

    The Danish health care system provides partial reimbursement of most prescription medications in Denmark. The dispensation of prescription medications is registered in administrative databases. Each time a prescription is redeemed at a pharmacy, an electronic record is generated with information ...

  10. A General Existence Thorem of Zero Points

    NARCIS (Netherlands)

    Herings, P.J.J.; Koshevoy, G.A.; Talman, A.J.J.; Yang, Z.F.

    2002-01-01

    Let X be a non-empty, compact, convex set in Rn and ° an upper semi-continuous mapping from X to the collection of non-empty, compact, convex subsets of Rn.It is well known that such a mapping has a stationary point on X, i.e. there exists a point in X satisfying that its image under ° has a

  11. Maximising the value of existing buildings.

    Science.gov (United States)

    McCorkindale, Graham

    2012-10-01

    Graham McCorkindale, who heads the Health and Wellbeing strand at multi-disciplinary architecture, town planning, interior design, and landscape architecture practice, Keppie Design, examines how architects can best support the NHS at a time of major change by refocusing design skills hitherto focused on creating new healthcare facilities on the need to work within the existing estate--'maximising utilisation and getting best value from any available spend'.

  12. Business Plan for Existing Venture: Papu Cafe

    OpenAIRE

    Truc, Nha

    2017-01-01

    Finland is considered as one of the potential markets for specialty coffee industry with the high amount of coffee consumption. The aim of this research is developing a business plan for existing business – Papu Cafe in the center of Helsinki, Finland. In this research, the author focuses on investigating the entrepreneurship and coffee industry in Finland, the characteristics of coffee drinking trends. Besides, it is essential to understand the purpose of conducting a business plan for ...

  13. On the existence of persistently outperforming firms

    OpenAIRE

    Capasso, M.; Cefis, E.; Frenken, K.

    2014-01-01

    This study analyses persistence in growth rates for a data set of manufacturing firms of all sizes. Previous quantile autoregressions of firm growth rates show that extreme growth events are likely to be negatively correlated over time, thus questioning the existence of persistent outperformers. By supplementing the quantile regression analyses with transition probability matrices, our study shows that "bouncing" firms coexist with persistent outperformers. This result is shown to be robust f...

  14. Partial Cooperative Equilibria: Existence and Characterization

    Directory of Open Access Journals (Sweden)

    Amandine Ghintran

    2010-09-01

    Full Text Available We study the solution concepts of partial cooperative Cournot-Nash equilibria and partial cooperative Stackelberg equilibria. The partial cooperative Cournot-Nash equilibrium is axiomatically characterized by using notions of rationality, consistency and converse consistency with regard to reduced games. We also establish sufficient conditions for which partial cooperative Cournot-Nash equilibria and partial cooperative Stackelberg equilibria exist in supermodular games. Finally, we provide an application to strategic network formation where such solution concepts may be useful.

  15. The slowdown in existing home sales

    OpenAIRE

    Krainer, John

    2014-01-01

    Sales of existing homes slowed noticeably over the second half of 2013, reflecting a more drawn-out recovery than expected for housing markets. A main reason for the slowdown is higher mortgage rates that have made financing more costly nationwide. Sales appear to be slowing even more in distressed markets, where real estate investors had bought up single-family homes to convert into rental properties following the housing bust. Evidence suggests that investors may be retreating from these ma...

  16. Does evaporation paradox exist in China?

    Directory of Open Access Journals (Sweden)

    Z. T. Cong

    2009-03-01

    Full Text Available One expected consequence of global warming is the increase in evaporation. However, lots of observations show that the rate of evaporation from open pans of water has been steadily decreasing all over the world in the past 50 years. The contrast between expectation and observation is called "evaporation paradox". Based on data from 317 weather stations in China from 1956 to 2005, the trends of pan evaporation and air temperature were obtained and evaporation paradox was analyzed. The conclusions include: (1 From 1956 to 2005, pan evaporation paradox existed in China as a whole while pan evaporation kept decreasing and air temperature became warmer and warmer, but it does not apply to Northeast and Southeast China; (2 From 1956 to 1985, pan evaporation paradox existed narrowly as a whole with unobvious climate warming trend, but it does not apply to Northeast China; (3 From 1986 to 2005, in the past 20 years, pan evaporation paradox did not exist for the whole period while pan evaporation kept increasing, although it existed in South China. Furthermore, the trend of other weather factors including sunshine duration, windspeed, humidity and vapor pressure deficit, and their relations with pan evaporation are discussed. As a result, it can be concluded that pan evaporation decreasing is caused by the decreasing in radiation and wind speed before 1985 and pan evaporation increasing is caused by the decreasing in vapor pressure deficit due to strong warming after 1986. With the Budyko curve, it can be concluded that the actual evaporation decreased in the former 30 years and increased in the latter 20 year for the whole China.

  17. Dark Matter RNA: Existence, function, and controversy

    Directory of Open Access Journals (Sweden)

    Philipp eKapranov

    2012-04-01

    Full Text Available The mysteries surrounding the ~97-98% of the human genome that does not encode proteins have long captivated imagination of scientists. Does the protein coding, 2-3% of the genome carry the 97-98% as a mere passenger and neutral cargo on the evolutionary path, or does the latter have biological function? On one side of the debate, many commentaries have referred to the non-coding portion of the genome as selfish or junk DNA (Orgel and Crick, 1980, while on the other side, authors have argued that it contains the real blueprint for organismal development (Penman, 1995;Mattick, 2003, and the mechanisms of developmental complexity. Thus, this question could be referred to without much exaggeration as the most important issue in genetics today.

  18. Inform@ed space

    DEFF Research Database (Denmark)

    Bjerrum, Peter; Olsen, Kasper Nefer

    2001-01-01

    Inform@ed space Sensorial Perception And Computer Enchancement - bidrag til Nordisk Arkitekturforskningsforenings IT-konference, AAA april 2001.......Inform@ed space Sensorial Perception And Computer Enchancement - bidrag til Nordisk Arkitekturforskningsforenings IT-konference, AAA april 2001....

  19. Overview of EXIST mission science and implementation

    Science.gov (United States)

    Grindlay, J.; Gehrels, N.; Bloom, J.; Coppi, P.; Soderberg, Al.; Hong, J.; Allen, B.; Barthelmy, S.; Tagliaferri, G.; Moseley, H.; Kutyrev, A.; Fabbiano, G.; Fishman, G.; Ramsey, B.; Della Ceca, R.; Natalucci, L.; Ubertini, P., III

    2010-07-01

    The Energetic X-ray Imaging Survey Telescope (EXIST) is designed to i) use the birth of stellar mass black holes, as revealed by cosmic Gamma-Ray Bursts (GRBs), as probes of the very first stars and galaxies to exist in the Universe. Both their extreme luminosity (~104 times larger than the most luminous quasars) and their hard X-ray detectability over the full sky with wide-field imaging make them ideal "back-lights" to measure cosmic structure with X-ray, optical and near-IR (nIR) spectra over many sight lines to high redshift. The full-sky imaging detection and rapid followup narrowfield imaging and spectroscopy allow two additional primary science objectives: ii) novel surveys of supermassive black holes (SMBHs) accreting as very luminous but rare quasars, which can trace the birth and growth of the first SMBHs as well as quiescent SMBHs (non-accreting) which reveal their presence by X-ray flares from the tidal disruption of passing field stars; and iii) a multiwavelength Time Domain Astrophysics (TDA) survey to measure the temporal variability and physics of a wide range of objects, from birth to death of stars and from the thermal to non-thermal Universe. These science objectives are achieved with the telescopes and mission as proposed for EXIST described here.

  20. Do retroperitoneal extragonadal germ cell tumours exist?

    Science.gov (United States)

    Punjani, Nahid; Winquist, Eric; Power, Nicholas

    2015-01-01

    Extragonadal germ cell tumours (GCTs) have been described arising in midline structures. Although primary retroperitoneal extragonadal GCTs (RPGCTs) comprise 30% to 40% of these, their existence as a genuine disease has been questioned. Our study evaluated clinicopathological findings to examine this question in RPGCT patients at our centre. Data from 414 men between 1980 and 2014 treated at London Health Sciences Centre with chemotherapy for testicular GCTs were reviewed retrospectively. Primary RPGCT was defined as pathologically diagnosed GCT with no evidence of GCT in the testes by physical exam or ultrasound. Patients thought to have primary RPGCT at the time of initial diagnosis were identified from an electronic database and data were extracted. In total, 18 men with a diagnosis of metastatic RPGCT were identified. Four were excluded due to ultrasound reports that were incomplete or suggested malignancy. The remaining 14 patients had negative or non-specific ultrasounds, and all received platinum-based combination chemotherapy. Ten patients (71%) underwent post-chemotherapy RP lymph node dissections; of those 8 (57%) who underwent orchiectomy, none had corresponding pathologically normal testicular tissue. RPGCT patients present with more advanced disease stage. Our study sample size is limited, but the findings are consistent with existing literature suggesting that primary RPGCTs may not exist as a unique disease, but instead may represent metastatic disease from a clinically occult testicular primary. By corollary, viable malignant germ cells may be present in testes of patients with presumed primary RPGCT, and may persist as a site of residual malignant disease after chemotherapy.

  1. Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue.

    Science.gov (United States)

    Chavez, Juan D; Lee, Chi Fung; Caudal, Arianne; Keller, Andrew; Tian, Rong; Bruce, James E

    2017-11-24

    While modern structural biology technologies have greatly expanded the size and type of protein complexes that can now be studied, the ability to derive large-scale structural information on proteins and complexes as they exist within tissues is practically nonexistent. Here, we demonstrate the application of crosslinking mass spectrometry to identify protein structural features and interactions in tissue samples, providing systems structural biology insight into protein complexes as they exist in the mouse heart. This includes insights into multiple conformational states of sarcomere proteins, as well as interactions among OXPHOS complexes indicative of supercomplex assembly. The extension of crosslinking mass spectrometry analysis into the realm of tissues opens the door to increasing our understanding of protein structures and interactions within the context of the greater biological system. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Multi-iPPseEvo: A Multi-label Classifier for Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into Chou's General PseAAC via Grey System Theory.

    Science.gov (United States)

    Qiu, Wang-Ren; Zheng, Quan-Shu; Sun, Bi-Qian; Xiao, Xuan

    2017-03-01

    Predicting phosphorylation protein is a challenging problem, particularly when query proteins have multi-label features meaning that they may be phosphorylated at two or more different type amino acids. In fact, human protein usually be phosphorylated at serine, threonine and tyrosine. By introducing the "multi-label learning" approach, a novel predictor has been developed that can be used to deal with the systems containing both single- and multi-label phosphorylation protein. Here we proposed a predictor called Multi-iPPseEvo by (1) incorporating the protein sequence evolutionary information into the general pseudo amino acid composition (PseAAC) via the grey system theory, (2) balancing out the skewed training datasets by the asymmetric bootstrap approach, and (3) constructing an ensemble predictor by fusing an array of individual random forest classifiers thru a voting system. Rigorous cross-validations via a set of multi-label metrics indicate that the multi-label phosphorylation predictor is very promising and encouraging. The current approach represents a new strategy to deal with the multi-label biological problems, and the software is freely available for academic use at http://www.jci-bioinfo.cn/Multi-iPPseEvo. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. The application, benefits and challenges of retrofitting the existing buildings

    Science.gov (United States)

    Khairi, Muhammad; Jaapar, Aini; Yahya, Zaharah

    2017-11-01

    Sustainable development has been the main topic of debate for years in some countries such as United Kingdom, United State of America and Malaysia. Depletion of natural resources, global warming, economics uncertainty and health issues are some of the reasons behind sustainable development movements, it is not just a political debate in the parliament but more towards collective works among sectors in order to minimizing the negative impact of development to the environment and other living organism. Retrofit an existing building is one of the solutions to reduce the dependency on constructing new buildings. There are huge numbers of existing building stocks that suitable to be retrofitted such as historical buildings, offices, residential, warehouse, factories, vacant buildings and other historical buildings. Therefore, the aim of this research is to provide information on the application, benefits and challenges of retrofitting an existing building. Two buildings were chosen as case studies following by site visits and observation to the buildings. The data were then compared in a table form. Primary and secondary sources were also used for this research. The application of retrofit should be promoted across the construction and conservation industries since it has significant tangible and intangible benefits. It is one of the most environmentally friendly and efficient solutions to optimize the energy performance and could also helps to extend the life of the existing building or historical buildings while ensuring optimum thermal comfort for the occupants which leads to higher productivity.

  4. Conditions for the existence of clines.

    Science.gov (United States)

    Nagylaki, T

    1975-07-01

    A very general partial differential equation in space and time satisfied by the gene frequency in a monoecious population distributed continuously over an arbitrary habitat is derived. The treatment is restricted to a single diallelic locus in the absence of mutation and random drift, and it is supposed that time is continuous, births and deaths occur at random, and migration is independent of genotype. With the further assumptions that migration is isotropic and homogeneous, the population density is constant and uniform (as permitted by the population regulation mechanism included in the formulation), and Hardy-Weinberg proportions obtain locally, this partial differential equation reduces to the simplest multidimensional generalization of the classical Fisher-Haldane cline model. The efficacy of migration and selection in maintaining genetic variability at equilibrium in this model is investigated by deducing conditions for the existence of clines under various circumstances. The effects of the degree of dominance, a neutral belt between the regions where a particular allele is advantageous and deleterious, finiteness of the habitat, and habitat dimensionality are evaluated. Provided at least one of the alleles is favored only in a finite region, excluding the special case in which its total effective selective coefficient is zero, if conditions for supporting a cline are too unfavorable because migration is too strong, selection is too weak, or both, a cline cannot exist at all. Thus, unless there is overdominance, the population must be monomorphic. It is possible for a cline which can barely exist under the prevailing ecological circumstances to show a large amount of variation in gene frequency.

  5. Toward the Automated Generation of Components from Existing Source Code

    Energy Technology Data Exchange (ETDEWEB)

    Quinlan, D; Yi, Q; Kumfert, G; Epperly, T; Dahlgren, T; Schordan, M; White, B

    2004-12-02

    A major challenge to achieving widespread use of software component technology in scientific computing is an effective migration strategy for existing, or legacy, source code. This paper describes initial work and challenges in automating the identification and generation of components using the ROSE compiler infrastructure and the Babel language interoperability tool. Babel enables calling interfaces expressed in the Scientific Interface Definition Language (SIDL) to be implemented in, and called from, an arbitrary combination of supported languages. ROSE is used to build specialized source-to-source translators that (1) extract a SIDL interface specification from information implicit in existing C++ source code and (2) transform Babel's output to include dispatches to the legacy code.

  6. Expression of Epitope-Tagged Proteins in Mammalian Cells in Culture.

    Science.gov (United States)

    Bhatt, Jay M; Styers, Melanie L; Sztul, Elizabeth

    2016-01-01

    Before the advent of molecular methods to tag proteins, visualization of proteins within cells required the use of antibodies directed against the protein of interest. Thus, only proteins for which antibodies were available could be visualized. Epitope tagging allows the detection of all proteins with existing sequence information, irrespective of the availability of antibodies directed against them. This technique involves the generation of DNA constructs that express the protein of interest tagged with an epitope that can be recognized by a commercially available antibody. Proteins can be tagged with a wide variety of epitopes using commercially available vectors that allow expression in mammalian cells. Epitope-tagged proteins are easily transfected into mammalian cell lines and, in most cases, tightly mimic the behavior of the endogenous protein. Tagged proteins exogenously expressed in cells provide different types of information depending on the subsequent detection approaches. Using immunofluorescence and immunoelectron microscopy with anti-tag antibodies, relative to known markers of cellular organelles, can provide information on the subcellular localization of the tagged protein and may provide clues regarding the protein's function. Immunofluorescence with anti-tag antibodies can also be utilized to assess the tagged protein's responses to cellular signals and pharmacological treatments. Immunoprecipitations with anti-tag antibodies can recover protein complexes containing the protein of interest, resulting in the identification of interacting proteins. Recovery of tagged proteins on affinity matrices allows their purification for use in biochemical assays. In addition, specialized fluorescent tags, such as the green fluorescent protein (GFP) allow the analysis of cellular dynamics in live cells in real time.

  7. Existence of collateral Equilibrium without survival assumption

    Directory of Open Access Journals (Sweden)

    Jaime Orrillo

    2011-03-01

    Full Text Available This paper shows the existence of a collateral equilibrium without assuming any hypotheses on the strict positivity, be they individual initial endowments, including the ex post initial endowments, or aggregated initial endowments. Because of dropping the strict positivity of social initial endowment we fail to get an equilibrium. Instead, we get a quasi-equilibrium. Then, appealing to the concept of irreducibility (introduced by McKenzie in 1959 which is adapted to the collateral model, we show that the quasi-equilibrium is indeed a legitime equilibrium.

  8. Existing cometary data and future needs

    Science.gov (United States)

    Rahe, J.

    1981-01-01

    To assist scientists studying comets and their interaction with the interplanetary medium, compilations of existing cometary observations and data plans for additional publication are reported. The works cited include updates and/or supplements to: (1) the Catalogue of Cometary Orbits, (2) Physical Characteristics of Comets, (3) the Atlas of Representative Cometary Spectra, (4) the Atlas Cometas-Viento Solar, (5) the Isophotometrischer Atlas der Kometen, and (6) the Atlas of Cometary Forms. An Atlas of Cometary Spectra and an Atlas of Comet Halley 1910 (II) photographs and spectra are in preparation.

  9. Does the Kuleshov Effect really Exist?

    DEFF Research Database (Denmark)

    Barratt, Daniel; Cabak Rédei, Anna

    2013-01-01

    , sadness, and hunger/neutral conditions with equivalent stimuli. For each film sequence, the participant was asked: to rate the valence of the depicted person’s emotion; to rate how aroused the person appeared to be; and to identify the type of emotion that the person was feeling. The participant’s eye...... movements were recorded throughout the experiment using a remote eye-tracker (SMI iView X RED). A preliminary analysis of the results suggests that some sort of Kuleshov effect does in fact exist. For the different emotional conditions, the participants tended to choose the appropriate emotion more...

  10. Does the Kuleshov Effect Really Exist?

    DEFF Research Database (Denmark)

    Barratt, Daniel; Rédei, Anna Cabak; Innes-Ker, Åse

    2016-01-01

    to replicate Kuleshov’s original experiment using an improved experimental design. In a behavioral and eye tracking study, 36 participants were each presented with 24 film sequences of neutral faces across six emotional conditions. For each film sequence, the participants were asked to evaluate the emotion...... of the target person in terms of valence, arousal, and category. The participants’ eye movements were recorded throughout. The results suggest that some sort of Kuleshov effect does in fact exist. For each emotional condition, the participants tended to choose the appropriate category more frequently than...... between the emotional conditions....

  11. Do ‘African’ universities exist?

    DEFF Research Database (Denmark)

    2015-01-01

    This chapter provides a background for understanding the book. We outline some of the debates in which the individual chapters are situated and thereby show how the book contributes to and fills gaps in existing research. After providing a short history of African universities, the chapter...... by arguing that it is incorrect to talk about African universities as a certain type of university due to the different colonial heritage. However, universities in Africa are facing a number of similar challenges related to the European heritage of the university for instance what counts as legitimate...

  12. Energy Savings Measure Packages. Existing Homes

    Energy Technology Data Exchange (ETDEWEB)

    Casey, Sean [National Renewable Energy Lab. (NREL), Golden, CO (United States); Booten, Chuck [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2011-11-01

    This document presents the most cost effective Energy Savings Measure Packages (ESMP) for existing mixed-fuel and all electric homes to achieve 15% and 30% savings for each BetterBuildings grantee location across the United States. These packages are optimized for minimum cost to homeowners for source energy savings given the local climate and prevalent building characteristics (i.e. foundation types). Maximum cost savings are typically found between 30% and 50% energy savings over the reference home; this typically amounts to $300 - $700/year.

  13. Weighing Supermassive Black Holes with EXIST

    Science.gov (United States)

    Coppi, Paolo S.; Pappadakis, I.; ScienceTeam, EXIST

    2009-12-01

    The EXIST mission concept features a wide field of view telescope that scans the full sky every two orbits at hard X-ray energies (5-600 keV) as well as a high resolution (R 3000) near infrared/optical spectrograph that can be quickly slewed to new targets. These two instruments will enable us to extend supermassive black hole timing studies (reverberation mapping and power spectrum break determination) from the current sample of 30 objects to well over 300, including highly obscured ones. We present examples of the direct black hole mass determinations such studies will enable.

  14. Black Hole Caught Zapping Galaxy into Existence?

    Science.gov (United States)

    2009-11-01

    across the whole electromagnetic spectrum; particularly spectacular is the case of quasars, where the active core is so overwhelmingly bright that it outshines the luminosity of the host galaxy. [2] This part of the study is based on observations performed at mid-infrared wavelengths, with the powerful VLT spectrometer and imager for the mid-infrared (VISIR) instrument at the VLT, combined with additional data including: spectra acquired using VLT-FORS, optical and infrared images from the NASA/ESA Hubble Space Telescope, and radio observations from the Australia Telescope National Facility. [3] Most galaxies in the local Universe contain a supermassive black hole with a mass about 1/700th the mass of the stellar bulge. The origin of this black hole mass versus stellar mass relation is one of the most debated subjects in modern astrophysics. More information This research was presented in papers published in the journal Astronomy & Astrophysics: "Quasar induced galaxy formation: a new paradigm?" by Elbaz et al., and in the Astrophysical Journal "The QSO HE0450-2958: Scantily dressed or heavily robed? A normal quasar as part of an unusual ULIRG" by Jahnke et al. The team is composed of David Elbaz (Service d'Astrophysique, CEA Saclay, France), Knud Jahnke (Max Planck Institute for Astronomy, Heidelberg, Germany), Eric Pantin (Service d'Astrophysique, CEA Saclay, France), Damien Le Borgne (Paris University 6 and CNRS, Institut d'Astrophysique de Paris, France) and Géraldine Letawe (Institut d'Astrophysique et de Géophysique, Université de Liège, Belgium). ESO, the European Southern Observatory, is the foremost intergovernmental astronomy organisation in Europe and the world's most productive astronomical observatory. It is supported by 14 countries: Austria, Belgium, the Czech Republic, Denmark, France, Finland, Germany, Italy, the Netherlands, Portugal, Spain, Sweden, Switzerland and the United Kingdom. ESO carries out an ambitious programme focused on the design

  15. Protein Degradation Rate in Arabidopsis thaliana Leaf Growth and Development.

    Science.gov (United States)

    Li, Lei; Nelson, Clark J; Trösch, Josua; Castleden, Ian; Huang, Shaobai; Millar, A Harvey

    2017-02-01

    We applied 15N labeling approaches to leaves of the Arabidopsis thaliana rosette to characterize their protein degradation rate and understand its determinants. The progressive labeling of new peptides with 15N and measuring the decrease in the abundance of >60,000 existing peptides over time allowed us to define the degradation rate of 1228 proteins in vivo. We show that Arabidopsis protein half-lives vary from several hours to several months based on the exponential constant of the decay rate for each protein. This rate was calculated from the relative isotope abundance of each peptide and the fold change in protein abundance during growth. Protein complex membership and specific protein domains were found to be strong predictors of degradation rate, while N-end amino acid, hydrophobicity, or aggregation propensity of proteins were not. We discovered rapidly degrading subunits in a variety of protein complexes in plastids and identified the set of plant proteins whose degradation rate changed in different leaves of the rosette and correlated with leaf growth rate. From this information, we have calculated the protein turnover energy costs in different leaves and their key determinants within the proteome. © 2017 American Society of Plant Biologists. All rights reserved.

  16. SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds

    Directory of Open Access Journals (Sweden)

    Schreiber Sven

    2011-10-01

    Full Text Available Abstract Background Protein interactions are essential for coordinating cellular functions. Proteomic studies have already elucidated a huge amount of protein-protein interactions that require detailed functional analysis. Understanding the structural basis of each individual interaction through their structural determination is necessary, yet an unfeasible task. Therefore, computational tools able to predict protein binding regions and recognition modes are required to rationalize putative molecular functions for proteins. With this aim, we previously created SCOWLP, a structural classification of protein binding regions at protein family level, based on the information obtained from high-resolution 3D protein-protein and protein-peptide complexes. Description We present here a new version of SCOWLP that has been enhanced by the inclusion of protein-nucleic acid and protein-saccharide interactions. SCOWLP takes interfacial solvent into account for a detailed characterization of protein interactions. In addition, the binding regions obtained per protein family have been enriched by the inclusion of predicted binding regions, which have been inferred from structurally related proteins across all existing folds. These inferences might become very useful to suggest novel recognition regions and compare structurally similar interfaces from different families. Conclusions The updated SCOWLP has new functionalities that allow both, detection and comparison of protein regions recognizing different types of ligands, which include other proteins, peptides, nucleic acids and saccharides, within a solvated environment. Currently, SCOWLP allows the analysis of predicted protein binding regions based on structure-based inferences across fold space. These predictions may have a unique potential in assisting protein docking, in providing insights into protein interaction networks, and in guiding rational engineering of protein ligands. The newly designed

  17. Neutralino dark matter stars can not exist

    Science.gov (United States)

    Dai, De-Chang; Stojkovic, Dejan

    2009-08-01

    Motivated by the recent ``Cosmos Project" observation of dark-matter concentrations with no ordinary matter in the same place, we study the question of the existence of compact objects made of pure dark matter. We assume that the dark matter is neutralino, and compare its elastic and annihilation cross sections. We find that the two cross sections are of the same order of magnitude. This result has a straightforward and important consequence that neutralinos comprising a compact object can not achieve thermal equilibrium. To substantiate our arguments, by solving Oppenheimer-Volkoff equation we constructed a model of the star made of pure neutralinos. We explicitly showed that the condition for the thermal equilibrium supported by the Fermi pressure is never fulfilled inside the star. This neutralino state can not be described by the Fermi-Dirac distribution. Thus, a stable neutralino star, which is supported by the Fermi pressure, can not exist. We also estimated that a stable star can not contain more than a few percents of neutralinos, most of the mass must be in the form of the standard model particles.

  18. Existence families, functional calculi and evolution equations

    CERN Document Server

    deLaubenfels, Ralph

    1994-01-01

    This book presents an operator-theoretic approach to ill-posed evolution equations. It presents the basic theory, and the more surprising examples, of generalizations of strongly continuous semigroups known as 'existent families' and 'regularized semigroups'. These families of operators may be used either to produce all initial data for which a solution in the original space exists, or to construct a maximal subspace on which the problem is well-posed. Regularized semigroups are also used to construct functional, or operational, calculi for unbounded operators. The book takes an intuitive and constructive approach by emphasizing the interaction between functional calculus constructions and evolution equations. One thinks of a semigroup generated by A as etA and thinks of a regularized semigroup generated by A as etA g(A), producing solutions of the abstract Cauchy problem for initial data in the image of g(A). Material that is scattered throughout numerous papers is brought together and presented in a fresh, ...

  19. Repowering existing coal fired power plants

    Energy Technology Data Exchange (ETDEWEB)

    Stenzel, W.C.; Sopocy, E.M.; Pace, S.E.

    1997-12-31

    Increased competition among power generating companies, changes in generating system load requirements, lower allowable plant emissions, and changes in fuel availability and cost accentuate the need to closely assess the economics and performance of older electric generating units. Generally, decisions must be made as to whether these units should be retired and replaced with new generation capacity, whether capacity should be purchased from other generation companies, or if these existing units should be repowered. These decisions usually require the evaluation of many factors including: environmental discharge limits, permitting requirements, generating load demand increases, options for increasing the benefits of using existing facilities (e.g., increasing efficiency and output), fuel cost increases, transmission requirements and access, and optional plant designs. Many of these factors need to be used in the analysis based on a range rather than one specific value to test for changes in the selection of the best option because of future uncertainties. Usually complicated analysis results because of all the factors involved. Computer products that integrate performance and financial analysis can provide substantial value by enabling the user to evaluate the applicable plant options and range of input. The SOAPP (State-of-the-Art Power Plant) family of software products provides easy-to-use tools for rapid, thorough and economical evaluation of plant options. Repowering evaluation methodology typically used in the United States, technology options, and available SOAPP repowering software are reviewed in this paper. 14 figs.

  20. The existence of cords in olecranon bursae.

    Science.gov (United States)

    Ecker, Jeff; Ebert, Jay R; Taheri, Arash; Mathew, Ravi K; Chee, Derserri Y; Breidahl, William

    2015-10-01

    The purpose of this study was to document the existence of transverse cords in olecranon bursae in patients undergoing excision of the bursa and to describe the unique clinical presentation of patients with these cords. A retrospective study was performed on 24 patients who had surgery to excise an olecranon bursa between 2006 and 2011. The patient's history, preoperative radiographs, ultrasound images, intraoperative photographs, and findings on histologic analysis were reviewed in all cases. Nine olecranon bursae had cords (cord group) and 15 did not have cords (noncord group). All patients in the cord group were male manual laborers, and nearly all had olecranon enthesophytes (n = 8). Patients in the noncord group had associated medical conditions or an infection. A higher level of satisfaction was reported in the noncord group after surgical excision. This study documents the existence of transverse cords oriented at right angles to the long axis of the olecranon. Olecranon bursae with cords have a unique presentation and are found in male manual workers, are nearly always associated with an olecranon enthesophyte, and do not present with infections. Copyright © 2015 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

  1. Lessons learned from existing biomass power plants

    Energy Technology Data Exchange (ETDEWEB)

    Wiltsee, G.

    2000-02-24

    This report includes summary information on 20 biomass power plants, which represent some of the leaders in the industry. In each category an effort is made to identify plants that illustrate particular points. The project experiences described capture some important lessons learned that lead in the direction of an improved biomass power industry.

  2. Data Systems vs. Information Systems

    OpenAIRE

    Amatayakul, Margret K.

    1982-01-01

    This paper examines the current status of “hospital information systems” with respect to the distinction between data systems and information systems. It is proposed that the systems currently existing are incomplete data dystems resulting in ineffective information systems.

  3. A Review of Stapled Peptides and Small Molecules to Inhibit Protein-Protein Interactions in Cancer.

    Science.gov (United States)

    Iyer, Vidhya V

    2016-01-01

    Disruption of binding of two or more molecules to a protein surface is a common basis of inhibition of many biological activities. Smallmolecule inhibitors, antibodies, proteins, and peptidomimetics have been examined as ways to antagonize receptor activity. The peptide α-helix plays a crucial role in the function of many proteins. Hence, much effort has been invested in mimicking α-helices at the binding interface of two proteins to competitively inhibit their interactions. Peptide stapling involves choosing two amino acids on the same face of a native peptide sequence for substitution with non-native amino acids whose side chains can be "stapled" together. The focus of this review is to survey the prevalence in literature of stapled peptides and small-molecule antagonists of interactions of selected mammalian cancer targets, such as β-catenin, BH3-only members of the Bcl-2 family of proteins, eIF4E/G, estrogen receptor complexes, EZH2, Mdm2, Notch, p110α, and survivin. The increasing interest in protein targets currently considered to be "undruggable" with greater selectivity for existing targets, with the goal of overcoming the omnipresent problem of resistance, could be served well by utilizing information about protein-protein interactions to develop both small-molecule and stapled peptide inhibitors.

  4. Sequence-based prediction of protein-protein interaction sites with L1-logreg classifier.

    Science.gov (United States)

    Dhole, Kaustubh; Singh, Gurdeep; Pai, Priyadarshini P; Mondal, Sukanta

    2014-05-07

    Protein-protein interactions are of central importance for virtually every process in a living cell. Information about the interaction sites in proteins improves our understanding of disease mechanisms and can provide the basis for new therapeutic approaches. Since a multitude of unique residue-residue contacts facilitate the interactions, protein-protein interaction sites prediction has become one of the most important and challenging problems of computational biology. Although much progress in this field has been reported, this problem is yet to be satisfactorily solved. Here, a novel method (LORIS: L1-regularized LOgistic Regression based protein-protein Interaction Sites predictor) is proposed, that identifies interaction residues, using sequence features and is implemented via the L1-logreg classifier. Results show that LORIS is not only quite effective, but also, performs better than existing state-of-the art methods. LORIS, available as standalone package, can be useful for facilitating drug-design and targeted mutation related studies, which require a deeper knowledge of protein interactions sites. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Protein engineering techniques gateways to synthetic protein universe

    CERN Document Server

    Poluri, Krishna Mohan

    2017-01-01

    This brief provides a broad overview of protein-engineering research, offering a glimpse of the most common experimental methods. It also presents various computational programs with applications that are widely used in directed evolution, computational and de novo protein design. Further, it sheds light on the advantages and pitfalls of existing methodologies and future perspectives of protein engineering techniques.

  6. Worldwide overview of existing haemovigilance systems.

    Science.gov (United States)

    Faber, Jean-Claude

    2004-10-01

    Haemovigilance is a "quality process" with the aim to improve quality and increase safety of blood transfusion, taking into account that haemovigilance covers and surveys all activities of the blood transfusion chain from donors to recipients. Haemovigilance is indispensable when it comes to safety and quality of blood transfusions. Within the European Union (EU), the European Blood Directive requires haemovigilance in each Member State: the intention has been to rely on the existing or developing national systems. There are significant differences in haemovigilance around the world, in terms of definition, organisational schemes, state of development and implementation. These differences are more pronounced outside the EU: in some countries, even basic traceability causes a problem while in others systems similar as the most developed ones in the EU are implemented.

  7. The enhancement of existing DES Maplet interface

    Science.gov (United States)

    Abdullah, Nur Lina; Mutalip, Rasidah Abdull; Abdullah, Kamilah

    2014-07-01

    This study pertains to the process of Data Encryption Standard, DES. DES consists of encryption and decryption processes linked with mathematical elements such as algebra and number theory. Preliminary, studies revealed that most of mathematics students face a problem in understanding the complicated process of DES. In modern learning methods, learning environment becomes more interesting with the use of computer and a variety of mathematical software packages. Several mathematical softwares such as Maple, Mathematica, Mathlab and Sage were developed in order to fulfill the specific calculation requirements. Correspondingly, motivated from that, this study incorporated with Maple to enhance the existing DES Maplet interface to be more interactive and user-friendly compared to the original version.

  8. On the existence of Levi Foliations

    Directory of Open Access Journals (Sweden)

    RENATA N. OSTWALD

    2001-03-01

    Full Text Available Let L be a real 3 dimensional analytic variety. For each regular point p L there exists a unique complex line l p on the space tangent to L at p. When the field of complex line p l p is completely integrable, we say that L is Levi variety. More generally; let L M be a real subvariety in an holomorphic complex variety M. If there exists a real 2 dimensional integrable distribution on L which is invariant by the holomorphic structure J induced by M, we say that L is a Levi variety. We shall prove: Theorem. Let be a Levi foliation and let be the induced holomorphic foliation. Then, admits a Liouvillian first integral. In other words, if is a 3 dimensional analytic foliation such that the induced complex distribution defines an holomorphic foliation ; that is, if is a Levi foliation; then admits a Liouvillian first integral--a function which can be constructed by the composition of rational functions, exponentiation, integration, and algebraic functions (Singer 1992. For example, if f is an holomorphic function and if theta is real a 1-form on ; then the pull-back of theta by f defines a Levi foliation : f*theta = 0 which is tangent to the holomorphic foliation : df = 0. This problem was proposed by D. Cerveau in a meeting (see Fernandez 1997.Seja L Ì uma variedade real de dimensão 3. Para todo ponto regular p Î L existe uma única reta complexa l p no espaço tangente à L em p. Quando o campo de linhas complexas p l p é completamente integrável, dizemos que L é uma variedade de Levi. Mais geralmente, seja L Ì M uma subvariedade real em uma variedade analítica complexa. Se existe uma distribuição real integrável de dimensão 2 em L que é invariante pela estrutura holomorfa J induzida pela variedade complexa M, dizemos que L é uma variedade de Levi. Vamos provar: Teorema. Seja uma folheação de Levi e seja a folheação holomorfa induzida. Então tem integral primeira Liouvilliana. Em outras palavras, se é uma folheação real de

  9. Synaesthesia: the existing state of affairs.

    Science.gov (United States)

    Hochel, Matej; Milán, Emilio G

    2008-02-01

    In synaesthesia one type of stimulation evokes the sensation of another, such as when hearing a sound produces photisms--that is, mental percepts of colours. In the past, the idiosyncrasy of this phenomenon, as well as the natural mistrust of scientists towards the subjective, consigned synaesthesia to the periphery of scientific interest. However, the landscape has changed radically in the last two decades. The labour of many researchers, inside as well as outside of cognitive neuroscience, has transformed synaesthesia into a scientific reality whose existence can be demonstrated and studied empirically. The present paper summarizes and reflects on our current knowledge concerning synaesthesia in all its aspects (cognition, behaviour, neurology, genetics, and demographics).

  10. Compilation of Existing Neutron Screen Technology

    Directory of Open Access Journals (Sweden)

    N. Chrysanthopoulou

    2014-01-01

    Full Text Available The presence of fast neutron spectra in new reactors is expected to induce a strong impact on the contained materials, including structural materials, nuclear fuels, neutron reflecting materials, and tritium breeding materials. Therefore, introduction of these reactors into operation will require extensive testing of their components, which must be performed under neutronic conditions representative of those expected to prevail inside the reactor cores when in operation. Due to limited availability of fast reactors, testing of future reactor materials will mostly take place in water cooled material test reactors (MTRs by tailoring the neutron spectrum via neutron screens. The latter rely on the utilization of materials capable of absorbing neutrons at specific energy. A large but fragmented experience is available on that topic. In this work a comprehensive compilation of the existing neutron screen technology is attempted, focusing on neutron screens developed in order to locally enhance the fast over thermal neutron flux ratio in a reactor core.

  11. Gender Existence: Correlation between Equality and Identity

    Directory of Open Access Journals (Sweden)

    Svitlana Storozhuk

    2017-02-01

    Full Text Available The article deals with the conceptual vision of gender content in its relation to sex taking into account the extremes to which researchers of gender issues and social movements have resorted to and considering the role and place of men and women in social and cultural life. On this background wrongfulness of such approaches is justified, according to which gender and sex are identified. It is shown in this article that these notions have different meanings and represent different dimensions of human existence. Thus, in contrast to sex, which reveals the physiological differences between men and women, gender is a socio cultural construct which sets the «matrix» of gender interaction at every historical stage of social and cultural life by offering their own vision of gender equality. Alongside with other ideas we substantiate the idea that gender equality is possible only in the social aspect.

  12. Review of existing reactive transport software

    Energy Technology Data Exchange (ETDEWEB)

    Glassley, W., LLNL

    1998-02-03

    Simulations of thermal and hydrological evolution following the potential emplacement of a subterranean nuclear waste repository at Yucca Mountain, NV provide data that suggest the inevitability of dependent, simultaneous chemical evolution in this system. These chemical changes will modify significantly both the magnitude and structure of local porosity and permeability; hence, they will have a dynamic feedback effect on the evolving thermal and hydrological regime. Yet, despite this intimate interdependence of transport and chemical processes, a rigorous quantitative analysis of the post- emplacement environment that incorporates this critical feedback mechanism has not been completed to date. As an initial step in this direction, the present document outlines the fundamental chemical and transport processes that must be accounted for in such an analysis, and reviews the inventory of existing software that encodes these processed in explicitly coupled form. A companion report describes the prioritization of specific capabilities that are needed for modeling post-emplacement reactive transport at Yucca Mountain.

  13. Welfare Economics: A Story of Existence

    Directory of Open Access Journals (Sweden)

    Khalid Iqbal

    2017-06-01

    Full Text Available The purpose of this study is to explore that, despite severe challenges, welfare economics still exists. This descriptive study is conducted through some specific time line developments in this field. Economists are divided over the veracity and survival of the welfare economics. Welfare economics emphasizes on the optimum resource and goods allocation with the objective of better living standard, materialistic gains, social welfare and ethical decisions. It origins back to the political economics and utilitarianism. Adam Smith, Irving Fisher and Pareto contributed significantly towards it. During 1930 to 1940, American and British approaches were developed. Many economists tried to explore the relationship between level of income and happiness. Amartya Sen gave the comparative approach and Tinbergen pioneered the theory of equity. Contemporarily the futuristic restoration of welfare economics is on trial and hopes are alive. This study may be useful to understand the transitional and survival process of welfare economics.

  14. Testing Metadata Existence of Web Map Services

    Directory of Open Access Journals (Sweden)

    Jan Růžička

    2011-05-01

    Full Text Available For a general user is quite common to use data sources available on WWW. Almost all GIS software allow to use data sources available via Web Map Service (ISO/OGC standard interface. The opportunity to use different sources and combine them brings a lot of problems that were discussed many times on conferences or journal papers. One of the problem is based on non existence of metadata for published sources. The question was: were the discussions effective? The article is partly based on comparison of situation for metadata between years 2007 and 2010. Second part of the article is focused only on 2010 year situation. The paper is created in a context of research of intelligent map systems, that can be used for an automatic or a semi-automatic map creation or a map evaluation.

  15. [The depression epidemic does not exist].

    Science.gov (United States)

    van der Feltz-Cornelis, Christina M

    2009-01-01

    There has been much discussion in the media about the question of the existence of a depression epidemic. This leads on to the questions of whether the social and economic approaches are adequate, and what the alternatives are. The concept of the disease 'depression' can be defined using a medical model, or from a patient's or a societal perspective. From a medical perspective, indeed a depression epidemic has ensued from the increased prosperity and the associated decompression of the mortality rate. Society responded with preventative measures and policies aimed at improving functioning in the workplace. However, patients with a major depressive disorder (MDD) who are eligible for treatment are often not motivated to take it up, or are undertreated. Research is necessary in order to explore what patients think about the identification and treatment of depression. The confusion regarding the concept of depression found in the media, needs to be cleared.

  16. Do Bare Rocks Exist on the Moon?

    Science.gov (United States)

    Allen, Carlton; Bandfield, Joshua; Greenhagen, Benjamin; Hayne, Paul; Leader, Frank; Paige, David

    2017-01-01

    Astronaut surface observations and close-up images at the Apollo and Chang'e 1 landing sites confirm that at least some lunar rocks have no discernable dust cover. However, ALSEP (Apollo Lunar Surface Experiments Package) measurements as well as astronaut and LADEE (Lunar Atmosphere and Dust Environment Explorer) orbital observations and laboratory experiments possibly suggest that a fine fraction of dust is levitated and moves across and above the lunar surface. Over millions of years such dust might be expected to coat all exposed rock surfaces. This study uses thermal modeling, combined with Diviner (a Lunar Reconnaissance Orbiter experiment) orbital lunar eclipse temperature data, to further document the existence of bare rocks on the lunar surface.

  17. The pastor as model for peaceful existence

    Directory of Open Access Journals (Sweden)

    Terence Cooke

    2011-06-01

    Full Text Available Many people are disillusioned in the democratic South Africa. That is because they went out from the assumption that with the dawn of democracy, violence would disappear. Unfortunately this did not happen. As with most things in life it is not an either � or, but a both � and scenario. In fact, violence is part of the democratic system. Real peace between men and powers can only be the peace of God, the peace which alone heals all disorder. The peace of the world is at best peaceful coexistence, not peace.In South Africa we have a negotiated agreement to peaceful coexistence, and sometimes, for example, after the miracle of the 1994 election and the euphoria of the World Cups of 1995, 2007 and 2010, we may even think we have achieved real peace. It is indeed in these times of euphoria that the people of South Africa may be tempted to lower our aim and settle for second best thinking that we have arrived.Model is used not in the sense of the pastor being an example of a peaceful existence to be followed. It is rather used in the sense that a pastor in his or her professional capacity has the knowledge of the meaning of the term �peaceful existence� and also the hermeneutic competency to apply that knowledge in concrete situations. This opens the exiting possibility that pastors can become travel companions on the road to real peace.The different aspects of being a pastor, office bearer, professional and person, each contribute to the pastor being a model for peace. It must be emphasised that the different aspects always work together as a unity and the strength of the pastor as a model for a peaceful existence is in the simultaneous application of these aspects in the context in which the pastor lives.

  18. The high energy telescope on EXIST

    Science.gov (United States)

    Hong, J.; Grindlay, J. E.; Allen, B.; Barthelmy, S. D.; Skinner, G. K.; Gehrels, N.

    2009-08-01

    The Energetic X-ray Imaging Survey Telescope (EXIST) is a proposed next generation multi-wavelength survey mission. The primary instrument is a High Energy telescope (HET) that conducts the deepest survey for Gamma-ray Bursts (GRBs), obscured-accreting and dormant Supermassive Black Holes and Transients of all varieties for immediate followup studies by the two secondary instruments: a Soft X-ray Imager (SXI) and an Optical/Infrared Telescope (IRT). EXIST will explore the early Universe using high redshift GRBs as cosmic probes and survey black holes on all scales. The HET is a coded aperture telescope employing a large array of imaging CZT detectors (4.5 m2, 0.6 mm pixel) and a hybrid Tungsten mask. We review the current HET concept which follows an intensive design revision by the HET imaging working group and the recent engineering studies in the Instrument and Mission Design Lab at the Goddard Space Flight Center. The HET will locate GRBs and transients quickly (<10-30 sec) and accurately (< 20") for rapid (< 1-3 min) onboard followup soft X-ray and optical/IR (0.3-2.2 μm) imaging and spectroscopy. The broad energy band (5-600 keV) and the wide field of view (~90° × 70&° at 10% coding fraction) are optimal for capturing GRBs, obscured AGNs and rare transients. The continuous scan of the entire sky every 3 hours will establish a finely-sampled long-term history of many X-ray sources, opening up new possibilities for variability studies.

  19. Energy consumptions in existing buildings; Les consommations d'energie des batiments existants

    Energy Technology Data Exchange (ETDEWEB)

    Nuss, St. [Ecole Nationale Superieure des Arts et Industries de Strasbourg, 78 - Saint-Remy-Les-Chevreuse (France)]|[Costic, 78 - Sainte Remy les Chevreuses (France)

    2002-05-01

    This document presents a sectoral analysis of the energy consumptions in existing French buildings: 1) - residential sector: social buildings, private dwellings; 2) - tertiary sector: office buildings, hotels, commercial buildings, school buildings, hospitals; 3) - industry; 4) - general status. (J.S.)

  20. Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein.

    Science.gov (United States)

    Buffalo, Cosmo Z; Bahn-Suh, Adrian J; Hirakis, Sophia P; Biswas, Tapan; Amaro, Rommie E; Nizet, Victor; Ghosh, Partho

    2016-09-05

    No vaccine exists against group A Streptococcus (GAS), a leading cause of worldwide morbidity and mortality. A severe hurdle is the hypervariability of its major antigen, the M protein, with >200 different M types known. Neutralizing antibodies typically recognize M protein hypervariable regions (HVRs) and confer narrow protection. In stark contrast, human C4b-binding protein (C4BP), which is recruited to the GAS surface to block phagocytic killing, interacts with a remarkably large number of M protein HVRs (apparently ∼90%). Such broad recognition is rare, and we discovered a unique mechanism for this through the structure determination of four sequence-diverse M proteins in complexes with C4BP. The structures revealed a uniform and tolerant 'reading head' in C4BP, which detected conserved sequence patterns hidden within hypervariability. Our results open up possibilities for rational therapies that target the M-C4BP interaction, and also inform a path towards vaccine design.

  1. Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein

    Energy Technology Data Exchange (ETDEWEB)

    Buffalo, Cosmo Z.; Bahn-Suh, Adrian J.; Hirakis, Sophia P.; Biswas, Tapan; Amaro, Rommie E.; Nizet, Victor; Ghosh, Partho

    2016-09-05

    No vaccine exists against group A Streptococcus (GAS), a leading cause of worldwide morbidity and mortality. A severe hurdle is the hypervariability of its major antigen, the M protein, with >200 different M types known. Neutralizing antibodies typically recognize M protein hypervariable regions (HVRs) and confer narrow protection. In stark contrast, human C4b-binding protein (C4BP), which is recruited to the GAS surface to block phagocytic killing, interacts with a remarkably large number of M protein HVRs (apparently ~90%). Such broad recognition is rare, and we discovered a unique mechanism for this through the structure determination of four sequence-diverse M proteins in complexes with C4BP. The structures revealed a uniform and tolerant ‘reading head’ in C4BP, which detected conserved sequence patterns hidden within hypervariability. Our results open up possibilities for rational therapies that target the M–C4BP interaction, and also inform a path towards vaccine design.

  2. Discovering protein complexes in protein interaction networks via exploring the weak ties effect.

    Science.gov (United States)

    Ma, Xiaoke; Gao, Lin

    2012-01-01

    Studying protein complexes is very important in biological processes since it helps reveal the structure-functionality relationships in biological networks and much attention has been paid to accurately predict protein complexes from the increasing amount of protein-protein interaction (PPI) data. Most of the available algorithms are based on the assumption that dense subgraphs correspond to complexes, failing to take into account the inherence organization within protein complex and the roles of edges. Thus, there is a critical need to investigate the possibility of discovering protein complexes using the topological information hidden in edges. To provide an investigation of the roles of edges in PPI networks, we show that the edges connecting less similar vertices in topology are more significant in maintaining the global connectivity, indicating the weak ties phenomenon in PPI networks. We further demonstrate that there is a negative relation between the weak tie strength and the topological similarity. By using the bridges, a reliable virtual network is constructed, in which each maximal clique corresponds to the core of a complex. By this notion, the detection of the protein complexes is transformed into a classic all-clique problem. A novel core-attachment based method is developed, which detects the cores and attachments, respectively. A comprehensive comparison among the existing algorithms and our algorithm has been made by comparing the predicted complexes against benchmark complexes. We proved that the weak tie effect exists in the PPI network and demonstrated that the density is insufficient to characterize the topological structure of protein complexes. Furthermore, the experimental results on the yeast PPI network show that the proposed method outperforms the state-of-the-art algorithms. The analysis of detected modules by the present algorithm suggests that most of these modules have well biological significance in context of complexes, suggesting

  3. Protein docking prediction using predicted protein-protein interface

    Directory of Open Access Journals (Sweden)

    Li Bin

    2012-01-01

    Full Text Available Abstract Background Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. Results We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm, is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. Conclusion We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

  4. Unintentional formation and emission of the persistent organic pollutants HCB and PCBs in the Nordic countries. Documentation of existing information regarding sources and emissions to air, water and soil, with focus on reporting obligations according to the Stockholm Convention, the UNECE POP protocol, and PRTR registers

    Energy Technology Data Exchange (ETDEWEB)

    2009-07-01

    In recent years reporting requirements regarding emissions and releases of unintentionally formed persistent organic pollutants (POPs) have been laid on parties to international agreements and members of the EU. Such obligations include those under the Stockholm Convention on Persistent Organic Pollutants, the UNECE POP and PRTR protocols and the EU PRTR regulation. The aim of this project has been to assess, whether existing knowledge and data are adequate for the Nordic countries to be able to estimate the emissions eventually to be reported. The project reveals that there is a substantial lack of knowledge related to potential sources in the Nordic countries. It also suggests that even though many of the main potential sources are the same, the relative importance of them differs between countries. (au)

  5. ECOLOGICAL CONDITIONS OF EXISTENCE OF MYCOBACTERIA POPULATIONS

    Directory of Open Access Journals (Sweden)

    R. A. Nuratinov

    2014-01-01

    Full Text Available Abstract. Aim. Adaptation possibilities of mycobacteria in the conditions of existence in the external environment and habitats of animals and man are studied. Adaptation mechanisms, which have pathogenic mycobacteria, allow them to survive long and circulate in the environment, which leads to special sanitary and epidemiological value of pathogens of tuberculosis. Location. Russia, Dagestan.Results. Mycobacterium tuberculosis has a high resistance to influence of cold, heat, chemical and physical factors, moisture and light. They carry high and low temperatures, while more than a year pathogenic properties, and even more in the dark and without sunlight. It should be noted that the stability of pathogenic species of mycobacteria in the external environment is relatively lower than that of saprophytes, capable of quickly adapting to the external environment. Raonin’s groups have more widespread in environment, in water, soil, air, plants, and habitats of animals, products of plant and animal origin and their often isolated from clinical samples.Main conclusions. Environmental conditions define the intensity of habitats of any species of mycobacteria in certain landscapes and their circulation in macroorganism. The impact of the various elements of the environment both in the macro- and microorganisms is a response that was the basis for the development of the doctrine about “limiting factors”. This concept applies not only to the necessary for mycobacteria chemical elements, but also to all the other environmental factors (temperature, humidity, aeration conditions etc. Minimum and maximum intensity factors determine the limits of endurance species. Beyond these limits, due to sharply expressed extreme conditions and is portable microorganism existence of species is not possible. The most favorable for the species optimum intensity of environmental factors, usually occupied a middle position. This provision is significantly

  6. Measuring Input Thresholds on an Existing Board

    Science.gov (United States)

    Kuperman, Igor; Gutrich, Daniel G.; Berkun, Andrew C.

    2011-01-01

    A critical PECL (positive emitter-coupled logic) interface to Xilinx interface needed to be changed on an existing flight board. The new Xilinx input interface used a CMOS (complementary metal-oxide semiconductor) type of input, and the driver could meet its thresholds typically, but not in worst-case, according to the data sheet. The previous interface had been based on comparison with an external reference, but the CMOS input is based on comparison with an internal divider from the power supply. A way to measure what the exact input threshold was for this device for 64 inputs on a flight board was needed. The measurement technique allowed an accurate measurement of the voltage required to switch a Xilinx input from high to low for each of the 64 lines, while only probing two of them. Directly driving an external voltage was considered too risky, and tests done on any other unit could not be used to qualify the flight board. The two lines directly probed gave an absolute voltage threshold calibration, while data collected on the remaining 62 lines without probing gave relative measurements that could be used to identify any outliers. The PECL interface was forced to a long-period square wave by driving a saturated square wave into the ADC (analog to digital converter). The active pull-down circuit was turned off, causing each line to rise rapidly and fall slowly according to the input s weak pull-down circuitry. The fall time shows up as a change in the pulse width of the signal ready by the Xilinx. This change in pulse width is a function of capacitance, pulldown current, and input threshold. Capacitance was known from the different trace lengths, plus a gate input capacitance, which is the same for all inputs. The pull-down current is the same for all inputs including the two that are probed directly. The data was combined, and the Excel solver tool was used to find input thresholds for the 62 lines. This was repeated over different supply voltages and

  7. Effectiveness of Existing International Nuclear Liability Regime

    Energy Technology Data Exchange (ETDEWEB)

    Al-Doais, Salwa; Kessel, Daivd [KEPCO International Nuclear Graduate School, Daejeon (Korea, Republic of)

    2015-10-15

    The first convention was the Paris Convention on Third Party Liability in the Field of Nuclear Energy (the Paris Convention) had been adopted on 29 July 1960 under the auspices of the OECD, and entered into force on 1 April 1968. In 1963,the Brussels Convention - supplementary to the Paris Convention- was adopted in to provide additional funds to compensate damage as a result of a nuclear incident where Paris Convention funds proved to be insufficient. The IAEA's first convention was the Vienna Convention on Civil Liability for Nuclear Damage (the Vienna Convention) which adopted on 21 May 1963,and entered into force in 1977. Both the Paris Convention and the Vienna Convention laid down very similar nuclear liability rules based on the same general principles. The broad principles in these conventions can be summarized as follows: 1- The no-fault liability principle (strict liability) 2- Liability is channeled exclusively to the operator of the nuclear installation (legal channeling) 3- Only courts of the state in which the nuclear accident occurs would have jurisdiction (exclusive jurisdiction) 4- Limitation of the amount of liability and the time frame for claiming damages (limited liability) 5- The operator is required to have adequate insurance or financial guarantees to the extent of its liability amount (liability must be financially secured). 6- Liability is limited in time. Compensation rights are extinguished after specific time. 7- Non-discrimination of victims on the grounds of nationality, domicile or residence. Nuclear liability conventions objective is to provide adequate compensation payments to victims of a nuclear accident. Procedures for receiving these compensation are controlled by some rules such as exclusive jurisdiction, that rule need a further amendment to ensure the effectiveness of the exiting nuclear liability regime . Membership of the Conventions is a critical issue, because the existence of the conventions without being party to

  8. Upgrading existing evaporators to reduce energy consumption

    Energy Technology Data Exchange (ETDEWEB)

    1977-01-01

    This manual is intended to assist the evaporator engineer who will be performing the technical and economic analyses to determine the most suitable evaporator upgrading technique for his particular plant. Information is included on potentials for upgrading evaporators; correctable operating factors; heat recovery and other improvements in energy use with minor capital investments; upgrading through major capital investments; guidelines for formulating an upgrading program; and new technologies encompassing advanced designs, use of solar and low-grade heat sources, and heat transfer enhancement. A 36 item bibliography is included. (LCL)

  9. Information resources

    Science.gov (United States)

    Friend, Milton; Franson, J. Christian; Friend, Milton; Gibbs, Samantha E.J.; Wild, Margaret A.

    2015-10-19

    During recent decades, natural resources agency personnel and others involved with the management and stewardship of wildlife have experienced an increasing need to access information and obtain technical assistance for addressing a diverse array of wildlife disease issues. This Chapter provides a broad overview of selected sources for obtaining supplemental information and technical assistance for addressing wildlife disease issues in North America. Specifically, examples of existing major wildlife disease programs focusing on free-ranging wildlife populations are highlighted; training opportunities for enhancing within-agency wildlife disease response are identified; a selected reading list of wildlife disease references is provided; and selected Web sites providing timely information on wildlife disease are highlighted. No attempt is made to detail all the North American programs and capabilities that address disease in free-ranging wildlife populations. Instead, this Chapter is focused on enhancing awareness of the types of capabilities that exist as potential sources for assistance and collaboration between wildlife conservation agency personnel and others in addressing wildlife disease issues.

  10. LEVERAGING EXISTING HERITAGE DOCUMENTATION FOR ANIMATIONS: SENATE VIRTUAL TOUR

    Directory of Open Access Journals (Sweden)

    A. Dhanda

    2017-08-01

    Full Text Available The use of digital documentation techniques has led to an increase in opportunities for using documentation data for valorization purposes, in addition to technical purposes. Likewise, building information models (BIMs made from these data sets hold valuable information that can be as effective for public education as it is for rehabilitation. A BIM can reveal the elements of a building, as well as the different stages of a building over time. Valorizing this information increases the possibility for public engagement and interest in a heritage place. Digital data sets were leveraged by the Carleton Immersive Media Studio (CIMS for parts of a virtual tour of the Senate of Canada. For the tour, workflows involving four different programs were explored to determine an efficient and effective way to leverage the existing documentation data to create informative and visually enticing animations for public dissemination: Autodesk Revit, Enscape, Autodesk 3ds Max, and Bentley Pointools. The explored workflows involve animations of point clouds, BIMs, and a combination of the two.

  11. Leveraging Existing Heritage Documentation for Animations: Senate Virtual Tour

    Science.gov (United States)

    Dhanda, A.; Fai, S.; Graham, K.; Walczak, G.

    2017-08-01

    The use of digital documentation techniques has led to an increase in opportunities for using documentation data for valorization purposes, in addition to technical purposes. Likewise, building information models (BIMs) made from these data sets hold valuable information that can be as effective for public education as it is for rehabilitation. A BIM can reveal the elements of a building, as well as the different stages of a building over time. Valorizing this information increases the possibility for public engagement and interest in a heritage place. Digital data sets were leveraged by the Carleton Immersive Media Studio (CIMS) for parts of a virtual tour of the Senate of Canada. For the tour, workflows involving four different programs were explored to determine an efficient and effective way to leverage the existing documentation data to create informative and visually enticing animations for public dissemination: Autodesk Revit, Enscape, Autodesk 3ds Max, and Bentley Pointools. The explored workflows involve animations of point clouds, BIMs, and a combination of the two.

  12. ProtoEXIST: advanced prototype CZT coded aperture telescopes for EXIST

    Science.gov (United States)

    Allen, Branden; Hong, Jaesub; Grindlay, Josh; Barthelmy, Scott D.; Baker, Robert G.; Gehrels, Neil A.; Garson, Trey; Krawczynski, Henric S.; Cook, Walter R.; Harrison, Fiona A.; Apple, Jeffrey A.; Ramsey, Brian D.

    2010-07-01

    ProtoEXIST1 is a pathfinder for the EXIST-HET, a coded aperture hard X-ray telescope with a 4.5 m2 CZT detector plane a 90x70 degree field of view to be flown as the primary instrument on the EXIST mission and is intended to monitor the full sky every 3 h in an effort to locate GRBs and other high energy transients. ProtoEXIST1 consists of a 256 cm2 tiled CZT detector plane containing 4096 pixels composed of an 8x8 array of individual 1.95 cm x 1.95 cm x 0.5 cm CZT detector modules each with a 8 x 8 pixilated anode configured as a coded aperture telescope with a fully coded 10° x 10° field of view employing passive side shielding and an active CsI anti-coincidence rear shield, recently completed its maiden flight out of Ft. Sumner, NM on the 9th of October 2009. During the duration of its 6 hour flight on-board calibration of the detector plane was carried out utilizing a single tagged 198.8 nCi Am-241 source along with the simultaneous measurement of the background spectrum and an observation of Cygnus X-1. Here we recount the events of the flight and report on the detector performance in a near space environment. We also briefly discuss ProtoEXIST2: the next stage of detector development which employs the NuSTAR ASIC enabling finer (32×32) anode pixilation. When completed ProtoEXIST2 will consist of a 256 cm2 tiled array and be flown simultaneously with the ProtoEXIST1 telescope.

  13. On the Existence of Evolutionary Learning Equilibriums

    Directory of Open Access Journals (Sweden)

    Masudul Alam Choudhury

    2011-12-01

    Full Text Available The usual kinds of Fixed-Point Theorems formalized on the existence of competitive equilibrium that explain much of economic theory at the core of economics can operate only on bounded and closed sets with convex mappings. But these conditions are hardly true of the real world of economic and financial complexities and perturbations. The category of learning sets explained by continuous fields of interactive, integrative and evolutionary behaviour caused by dynamic preferences at the individual and institutional and social levels cannot maintain the assumption of closed, bounded and convex sets. Thus learning sets and multi-system inter-temporal relations explained by pervasive complementarities and  participation between variables and entities, and evolution by learning, have evolutionary equilibriums. Such a study requires a new methodological approach. This paper formalizes such a methodology for evolutionary equilibriums in learning spaces. It briefly points out the universality of learning equilibriums in all mathematical structures. For a particular case though, the inter-systemic interdependence between sustainable development and ethics and economics in the specific understanding of learning domain is pointed out.

  14. Evaluation and modification of existing CETP.

    Science.gov (United States)

    Sharma, Bhavisha; Shah, A R

    2013-07-01

    For the development of small and medium scale industries in various Gujarat industrial development corporation (GIDC) areas and in clusters of industrial areas, the common effluent treatment plant (CETP) has always been found advantageous in view of cost of treatment, operation and maintenance and disposal of residues being produced. In small scale industrial units due to market requirement, product changes and quantity enhancement are taking place. Due to such changes, the effluent characteristics are continuously changing which affects performance of CETP. Hence it has been found necessary to study continuously the performance, evaluation and modification in the working of the CETP. This paper contains a case study of one of the existing CETP near Baroda which is facing the problem of disposal of treated effluent in which the important parameters like COD, BOD, Suspended Solid, NH3-N and oil and grease were analyzed. Based on the characterization of wastewater, the various treatability studies were carried out on CETP wastewater. To comply with disposal standard prescribed by Effluent Channel Project Ltd.(ECPL)* and Gujarat Pollution Control Board (GPCB) for discharge of industrial effluent into channel, various treatments in form of ammonia stripping, coagulation and flocculation, biological treatment, filtration and chlorination are suggested.

  15. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

    Science.gov (United States)

    Di Tommaso, Paolo; Moretti, Sebastien; Xenarios, Ioannis; Orobitg, Miquel; Montanyola, Alberto; Chang, Jia-Ming; Taly, Jean-François; Notredame, Cedric

    2011-07-01

    This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

  16. A protein-dependent side-chain rotamer library.

    KAUST Repository

    Bhuyan, M.S.

    2011-12-14

    Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, side-chain conformations are determined by spatially local information, rather than sequentially local information. Since in the side-chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries. In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities. Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the side-chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the side-chain prediction power of the protein-dependent library is still comparable to the global-search-based side-chain prediction methods.

  17. Preferences for new and existing contraceptive products.

    Science.gov (United States)

    Fiebig, Denzil G; Knox, Stephanie; Viney, Rosalie; Haas, Marion; Street, Deborah J

    2011-09-01

    New contraceptive methods provide greater choice in terms of effectiveness, management of side-effects, convenience and frequency of administration and flexibility, but make the decisions about contraception more complex. There are limited data on the factors that determine women's choices among these alternatives, to inform providers about the factors which are most important to women, or to predict uptake of new products. This paper reports on a choice experiment designed to elicit women's preferences in relation to prescribed contraception and to forecast the impact of the introduction of two new products into the Australian market. A generalised multinomial logit model is estimated and used in the simulation exercise. The model forecasts that the hormonal patch would be well received among women, achieving a greater market share than current non-pill products, but the vaginal ring would have limited appeal. Copyright © 2011 John Wiley & Sons, Ltd.

  18. David Barker: the revolution that anticipates existence

    Directory of Open Access Journals (Sweden)

    Italo Farnetani

    2014-01-01

    Full Text Available David Barker is the man who “anticipated" the existence of babies by focusing attention on the importance of the fetus and what takes place during intrauterine life. Barker was one of the physicians who in the last decades brought about the greatest changes in medicine, changes so important as to represent a veritable revolution in medical thought. According to Barker's studies, the embryo obviously has a genetic complement coming from the mother and father, but from the very first stages of development it begins to undergo the influence of the outside environment, just as occurs for adults whose biological, psychological and pathological aspects are influenced by the environment to a not well-established percentage between genetic complement and epigenetics. Much of our future lives as adults is decided in our mothers' wombs. If Barker's discovery was revolutionary from the cultural standpoint, it was even more so from the strictly medical one. Barker's research method was rigid from the methodological standpoint, but innovative and speculative in its working hypotheses, with a humanistic slant. Barker's idea has another practical corollary: it is evident that the role of obstetricians, perinatologists and neonatologists is more and more relevant in medicine and future prevention. Unquestionably, besides the enormous merits of his clinical research, among the benefits that Barker has contributed there is that of having helped us to see things from new points of view. Not only is the neonate (and even more so the fetus not an adult of reduced proportions, but perhaps the neonate is the "father" of the adult person.

  19. A local average connectivity-based method for identifying essential proteins from the network level.

    Science.gov (United States)

    Li, Min; Wang, Jianxin; Chen, Xiang; Wang, Huan; Pan, Yi

    2011-06-01

    Identifying essential proteins is very important for understanding the minimal requirements of cellular survival and development. Fast growth in the amount of available protein-protein interactions has produced unprecedented opportunities for detecting protein essentiality from the network level. Essential proteins have been found to be more abundant among those highly connected proteins. However, there exist a number of highly connected proteins which are not essential. By analyzing these proteins, we find that few of their neighbors interact with each other. Thus, we propose a new local method, named LAC, to determine a protein's essentiality by evaluating the relationship between a protein and its neighbors. The performance of LAC is validated based on the yeast protein interaction networks obtained from two different databases: DIP and BioGRID. The experimental results of the two networks show that the number of essential proteins predicted by LAC clearly exceeds that explored by Degree Centrality (DC). More over, LAC is also compared with other seven measures of protein centrality (Neighborhood Component (DMNC), Betweenness Centrality (BC), Closeness Centrality (CC), Bottle Neck (BN), Information Centrality (IC), Eigenvector Centrality (EC), and Subgraph Centrality (SC)) in identifying essential proteins. The comparison results based on the validations of sensitivity, specificity, F-measure, positive predictive value, negative predictive value, and accuracy consistently show that LAC outweighs these seven previous methods. Copyright © 2011 Elsevier Ltd. All rights reserved.

  20. FireProt: web server for automated design of thermostable proteins

    Science.gov (United States)

    Musil, Milos; Stourac, Jan; Brezovsky, Jan; Prokop, Zbynek; Zendulka, Jaroslav; Martinek, Tomas

    2017-01-01

    Abstract There is a continuous interest in increasing proteins stability to enhance their usability in numerous biomedical and biotechnological applications. A number of in silico tools for the prediction of the effect of mutations on protein stability have been developed recently. However, only single-point mutations with a small effect on protein stability are typically predicted with the existing tools and have to be followed by laborious protein expression, purification, and characterization. Here, we present FireProt, a web server for the automated design of multiple-point thermostable mutant proteins that combines structural and evolutionary information in its calculation core. FireProt utilizes sixteen tools and three protein engineering strategies for making reliable protein designs. The server is complemented with interactive, easy-to-use interface that allows users to directly analyze and optionally modify designed thermostable mutants. FireProt is freely available at http://loschmidt.chemi.muni.cz/fireprot. PMID:28449074