WorldWideScience

Sample records for existing protein information

  1. Sharing information among existing data sources

    Science.gov (United States)

    Ashley, W. R., III

    1999-01-01

    The sharing of information between law enforcement agencies is a premise for the success of all jurisdictions. A wealth of information resides in both the databases and infrastructures of local, state, and regional agencies. However, this information is often not available to the law enforcement professionals who require it. When the information is, available, individual investigators must not only know that it exists, but where it resides, and how to retrieve it. In many cases, these types of cross-jurisdictional communications are limited to personal relationships that result from telephone calls, faxes, and in some cases, e-mail. As criminal elements become more sophisticated and distributed, law enforcement agencies must begin to develop infrastructures and common sharing mechanisms that address a constantly evolving criminal threat. Historically, criminals have taken advantage of the lack of communication between law enforcement agencies. Examples of this are evident in the search for stolen property and monetary dealings. Pawned property, cash transactions, and failure to supply child support are three common cross- jurisdictional crimes that could be better enforced by strengthening the lines of communication. Criminal behavior demonstrates that it is easier to profit from their actions by dealing in separate jurisdictions. For example, stolen property is sold outside of the jurisdiction of its origin. In most cases, simply traveling a short distance to the adjoining county or municipality is sufficient to ensure that apprehension of the criminal or seizure of the stolen property is highly unlikely. In addition to the traditional burglar, fugitives often sell or pawn property to finance their continued evasion from the law. Sharing of information in a rapid manner would increase the ability of law enforcement personnel to track and capture fugitives, as well as criminals. In an example to combat this threat, the State of Florida recently acted on the need to

  2. 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.

  3. 76 FR 9376 - Proposed Extension of Existing Information Collection;

    Science.gov (United States)

    2011-02-17

    ... Extension of Existing Information Collection; Refuse Piles and Impoundment Structures, Recordkeeping and... surface installations. More specifically, these sections address refuse piles (30 CFR 77.215), and... combination of materials; and refuse piles are deposits of coal mine waste (other than overburden or spoil...

  4. 78 FR 18620 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2013-03-27

    ... information technology, e.g., permitting electronic submission of responses. Overview of This Information... enforcement authority under the 287(g) program. This information is used by program managers and trainers in... Information Collection Activities: Extension, Without Change, of an Existing Information Collection; Comment...

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

    Science.gov (United States)

    2012-03-14

    ..., mechanical, or other technological collection techniques or other forms of information technology, e.g...; or inquiries for additional information should be directed to: John Ramsay, Forms Program Manager, U... Information Collection Activities: Extension, without Change, of an Existing Information Collection; Comment...

  6. 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.

  7. Learning to leverage existing information systems: Part 1. Principles.

    Science.gov (United States)

    Neil, Nancy; Nerenz, David

    2003-10-01

    The success of performance improvement efforts depends on effective measurement and feedback regarding clinical processes and outcomes. Yet most health care organizations have fragmented rather than integrated data systems. Methods and practical guidance are provided for leveraging available information sources to obtain and create valid performance improvement-related information for use by clinicians and administrators. At Virginia Mason Health System (VMHS; Seattle), a vertically integrated hospital and multispecialty group practice, patient records are paper based and are supplemented with electronic reporting for laboratory and radiology services. Despite growth in the resources and interest devoted to organization-wide performance measurement, quality improvement, and evidence-based tools, VMHS's information systems consist of largely stand-alone, legacy systems organized around the ability to retrieve information on patients, one at a time. By 2002, without any investment in technology, VMHS had developed standardized, clinic-wide key indicators of performance updated and reported regularly at the patient, provider, site, and organizational levels. On the basis of VHMS's experience, principles can be suggested to guide other organizations to explore solutions using their own information systems: for example, start simply, but start; identify information needs; tap multiple data streams; and improve incrementally.

  8. Fast mapping rapidly integrates information into existing memory networks.

    Science.gov (United States)

    Coutanche, Marc N; Thompson-Schill, Sharon L

    2014-12-01

    Successful learning involves integrating new material into existing memory networks. A learning procedure known as fast mapping (FM), thought to simulate the word-learning environment of children, has recently been linked to distinct neuroanatomical substrates in adults. This idea has suggested the (never-before tested) hypothesis that FM may promote rapid incorporation into cortical memory networks. We test this hypothesis here in 2 experiments. In our 1st experiment, we introduced 50 participants to 16 unfamiliar animals and names through FM or explicit encoding (EE) and tested participants on the training day, and again after sleep. Learning through EE produced strong declarative memories, without immediate lexical competition, as expected from slow-consolidation models. Learning through FM, however, led to almost immediate lexical competition, which continued to the next day. Additionally, the learned words began to prime related concepts on the day following FM (but not EE) training. In a 2nd experiment, we replicated the lexical integration results and determined that presenting an already-known item during learning was crucial for rapid integration through FM. The findings presented here indicate that learned items can be integrated into cortical memory networks at an accelerated rate through fast mapping. The retrieval of a related known concept, in order to infer the target of the FM question, is critical for this effect. PsycINFO Database Record (c) 2014 APA, all rights reserved.

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

    OpenAIRE

    Chéreau Denis; Videcoq Pauline; Ruffieux Cécile; Pichon Lisa; Motte Jean-Charles; Belaid Saliha; Ventureira Jorge; Lopez Michel

    2016-01-01

    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 con...

  10. 76 FR 3178 - Proposed Extension of Existing Information Collection; Rock Burst Control Plan, Metal and...

    Science.gov (United States)

    2011-01-19

    ... Extension of Existing Information Collection; Rock Burst Control Plan, Metal and Nonmetal Mines AGENCY: Mine... extension of the information collection for 30 CFR 57.3461 Rock Bursts. DATES: All comments must be received... contains the request for an extension of the existing collection of information in 30 CFR 57.3461 Rock...

  11. Information assessment on predicting protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Gerstein Mark

    2004-10-01

    Full Text Available Abstract Background Identifying protein-protein interactions is fundamental for understanding the molecular machinery of the cell. Proteome-wide studies of protein-protein interactions are of significant value, but the high-throughput experimental technologies suffer from high rates of both false positive and false negative predictions. In addition to high-throughput experimental data, many diverse types of genomic data can help predict protein-protein interactions, such as mRNA expression, localization, essentiality, and functional annotation. Evaluations of the information contributions from different evidences help to establish more parsimonious models with comparable or better prediction accuracy, and to obtain biological insights of the relationships between protein-protein interactions and other genomic information. Results Our assessment is based on the genomic features used in a Bayesian network approach to predict protein-protein interactions genome-wide in yeast. In the special case, when one does not have any missing information about any of the features, our analysis shows that there is a larger information contribution from the functional-classification than from expression correlations or essentiality. We also show that in this case alternative models, such as logistic regression and random forest, may be more effective than Bayesian networks for predicting interactions. Conclusions In the restricted problem posed by the complete-information subset, we identified that the MIPS and Gene Ontology (GO functional similarity datasets as the dominating information contributors for predicting the protein-protein interactions under the framework proposed by Jansen et al. Random forests based on the MIPS and GO information alone can give highly accurate classifications. In this particular subset of complete information, adding other genomic data does little for improving predictions. We also found that the data discretizations used in the

  12. Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols.

    Science.gov (United States)

    Li, Minghui; Goncearenco, Alexander; Panchenko, Anna R

    2017-01-01

    In this review we describe a protocol to annotate the effects of missense mutations on proteins, their functions, stability, and binding. For this purpose we present a collection of the most comprehensive databases which store different types of sequencing data on missense mutations, we discuss their relationships, possible intersections, and unique features. Next, we suggest an annotation workflow using the state-of-the art methods and highlight their usability, advantages, and limitations for different cases. Finally, we address a particularly difficult problem of deciphering the molecular mechanisms of mutations on proteins and protein complexes to understand the origins and mechanisms of diseases.

  13. 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.

  14. 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...

  15. IGF-Binding Proteins: Why Do They Exist and Why Are There So Many?

    Directory of Open Access Journals (Sweden)

    John B. Allard

    2018-04-01

    Full Text Available Insulin-like growth factors (IGFs are key growth-promoting peptides that act as both endocrine hormones and autocrine/paracrine growth factors. In the bloodstream and in local tissues, most IGF molecules are bound by one of the members of the IGF-binding protein (IGFBP family, of which six distinct types exist. These proteins bind to IGF with an equal or greater affinity than the IGF1 receptor and are thus in a key position to regulate IGF signaling globally and locally. Binding to an IGFBP increases the half-life of IGF in the circulation and blocks its potential binding to the insulin receptor. In addition to these classical roles, IGFBPs have been shown to modulate IGF signaling locally under various conditions. Although members of the IGFBP family share significant sequence homology, they each have unique structural features and play distinct roles. These IGFBP genes also have different modes of regulation and distinct expression patterns. Some IGFBPs have been found to bind to their own receptors or to translocate into the interior compartments of cells where they may execute IGF-independent actions. In spite of this functional and regulatory diversity, it has been puzzling that loss-of-function studies have yielded relatively little information about the physiological functions of IGFBPs. In this review, we suggest that evolution has tended to retain an array of IGFBPs in order to facilitate fine-tuning of IGF signaling. We explore the emerging explanation that many IGFBP functions have evolved to allow the targeted adjustment of IGF signaling under stressful or irregular conditions, which would likely not be revealed in a standard laboratory setting.

  16. 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.

  17. 77 FR 4574 - Agency Information Collection Activities: USCIS Case Status Online; Extension of an Existing...

    Science.gov (United States)

    2012-01-30

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information Collection Activities: USCIS Case Status Online; Extension of an Existing Information Collection; Comment Request ACTION: 60-Day Notice of Information Collection Under Review: USCIS Case Status Online. The...

  18. 78 FR 28894 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2013-05-16

    ... evaluate the company for inclusion in the IMAGE program. The information provided by the company plays a... entity in the private sector to participate in the program and the information obtained from the company... collection of information is necessary for the proper performance of the functions of the agency, including...

  19. 76 FR 81517 - Agency Information Collection Activities: Form I-131, Revision of an Existing Information...

    Science.gov (United States)

    2011-12-28

    ... information collection. (2) Title of the Form/Collection: Application for Travel Document. (3) Agency form... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information...-Day Notice of Information Collection Under Review: Form I- 131, Application for Travel Document. The...

  20. 76 FR 10609 - Agency Information Collection Activities: Form I-290B, Revision of an Existing Information...

    Science.gov (United States)

    2011-02-25

    ...: 30-Day Notice of Information Collection Under Review: Form I- 290B, Notice of Appeal to the Office of Administrative Appeals (AAO); OMB Control No. 1615-0095. The Department of Homeland Security, U.S. Citizenship... submission of responses. Overview of this information collection: (1) Type of Information Collection...

  1. Identification of energy information needs and existing information sources for Pennsylvania

    Energy Technology Data Exchange (ETDEWEB)

    Wisch, A.; Kunzier, J.; Limaye, D.; Orlando, J.

    1976-01-01

    Through use of a comprehensive interviewing schedule designed to elicit information needs from state policymakers, this study has shown a statewide need for a workable energy information network. As a counterpoint to this needs survey, it was also demonstrated that many of the components of such an information base already are available at the state and Federal levels. In order to assure that Pennsylvania's decision makers have access to this required information in a current and useful format at a minimal cost, this study has suggested a three-pronged action program: (1) In order to construct a workable energy information network for use by the Commonwealth, a liaison should be established with the Governor's Energy Council and the various national and regional energy information sources as cited in this report. (2) An information directory on State, Federal and private sources should be maintained and distributed on a continuing basis. An assessment of each source should be included with information on ease of access and relevance of the source to Pennsylvania. (3) After an information need is unable to be met through use of (1) the state energy information network and/or (2) the state energy information directory, effort should be initiated to satisfy that specific requirement.

  2. 76 FR 30741 - Agency Information Collection Activities: Existing Collection; Comments Requested: Prison...

    Science.gov (United States)

    2011-05-26

    ..., practitioners, researchers, students, the media, and others interested in criminal justice statistics. (5) An... DEPARTMENT OF JUSTICE Office of Justice Programs [OMB Number 1121-0102] Agency Information Collection Activities: Existing Collection; Comments Requested: Prison Population Reports: Summary of...

  3. 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.

  4. 77 FR 15787 - Agency Information Collection Activities: Form I-131, Revision of an Existing Information...

    Science.gov (United States)

    2012-03-16

    ... the Form/Collection: Application for Travel Document. (3) Agency Form Number, if any, and the... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information...-Day Notice of Information Collection Under Review: Form I- 131, Application for Travel Document. The...

  5. 77 FR 6134 - Agency Information Collection Activities: Form I-290B, Extension of an Existing Information...

    Science.gov (United States)

    2012-02-07

    ...: 60-Day Notice of Information Collection Under Review: Form I- 290B, Notice of Appeal or Motion...., permitting electronic submission of responses. Overview of this information collection: (1) Type of...: Notice of Appeal or Motion. (3) Agency form number, if any, and the applicable component of the...

  6. 77 FR 33002 - Proposed Extension of Existing Information Collection; Health Standards for Diesel Particulate...

    Science.gov (United States)

    2012-06-04

    ... information in accordance with the Paperwork Reduction Act of 1995. This program helps to assure that requested data can be provided in the desired format, reporting burden (time and financial resources) is... Extension of Existing Information Collection; Health Standards for Diesel Particulate Matter Exposure...

  7. 77 FR 58173 - Proposed Extension of Existing Information Collection; Explosive Materials and Blasting Units...

    Science.gov (United States)

    2012-09-19

    ... information in accordance with the Paperwork Reduction Act of 1995. This program helps to assure that requested data can be provided in the desired format, reporting burden (time and financial resources) is... Extension of Existing Information Collection; Explosive Materials and Blasting Units (Pertains to Metal and...

  8. 75 FR 79030 - Proposed Extension of Existing Information Collection; Training Plans and Records of Training

    Science.gov (United States)

    2010-12-17

    ... Extension of Existing Information Collection; Training Plans and Records of Training AGENCY: Mine Safety and... extension of the information collection for Training Plans and Records of Training, 30 CFR 48.3, 48.9, 48.23... require training plans for underground and surface mines, respectively. The standards are intended to...

  9. 77 FR 58170 - Proposed Renewal of Existing Information Collection; Fire Protection (Underground Coal Mines)

    Science.gov (United States)

    2012-09-19

    ... Renewal of Existing Information Collection; Fire Protection (Underground Coal Mines) AGENCY: Mine Safety... INFORMATION: I. Background Fire protection standards for underground coal mines are based on section 311(a) of the Federal Mine Safety and Health Act of 1977 (Mine Act). 30 CFR 75.1100 requires that each coal mine...

  10. Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations.

    Science.gov (United States)

    Ozgur, Beytullah; Ozdemir, E Sila; Gursoy, Attila; Keskin, Ozlem

    2017-04-20

    Intrinsic fluctuations of a protein enable it to sample a large repertoire of conformers including the open and closed forms. These distinct forms of the protein called conformational substates pre-exist together in equilibrium as an ensemble independent from its ligands. The role of ligand might be simply to alter the equilibrium toward the most appropriate form for binding. Normal mode analysis is proved to be useful in identifying the directions of conformational changes between substates. In this study, we demonstrate that the ratios of normalized weights of a few normal modes driving the protein between its substates can give insights about the ratios of kinetic conversion rates of the substates, although a direct relation between the eigenvalues and kinetic conversion rates or populations of each substate could not be observed. The correlation between the normalized mode weight ratios and the kinetic rate ratios is around 83% on a set of 11 non-enzyme proteins and around 59% on a set of 17 enzymes. The results are suggestive that mode motions carry intrinsic relations with thermodynamics and kinetics of the proteins.

  11. 76 FR 72209 - Agency Information Collection Activities: Form N-300; Revision of an Existing Information...

    Science.gov (United States)

    2011-11-22

    ...) will be submitting the following information collection request to the Office of Management and Budget... Security (DHS), and to the Office of Management and Budget (OMB) USCIS Desk Officer. Comments may be... documentary requirements for those seeking to work in certain occupations [[Page 72210

  12. 75 FR 32800 - Agency Information Collection Activities: Form N-300; Extension of an Existing Information...

    Science.gov (United States)

    2010-06-09

    ... Services (USCIS) has submitted the following information collection request to the Office of Management and... Homeland Security (DHS), and to the Office of Management and Budget (OMB) USCIS Desk Officer. Comments may... citizen of the United States. This collection is also used to satisfy documentary requirements for those...

  13. 75 FR 37815 - Agency Information Collection Activities: Two-Year Extension of an Existing Information...

    Science.gov (United States)

    2010-06-30

    ... health professions and nursing education and training programs. The reporting system measures the grantee... developed for the Bureau of Health Professions' Title VII and VIII health professions and nursing education... and Results Act (GPRA). The Bureau will be making minor changes to the previously approved information...

  14. 75 FR 51094 - Agency Information Collection Activities: Form N-600; Extension of an Existing Information...

    Science.gov (United States)

    2010-08-18

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services [OMB Control No. 1615..., Application for Certificate of Citizenship; OMB Control No. 1615- 0057. The Department of Homeland Security, U.S. Citizenship and Immigration Services (USCIS) will be submitting the following information...

  15. 77 FR 34052 - Agency Information Collection Activities: Form I-102; Revision of an Existing Information...

    Science.gov (United States)

    2012-06-08

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information... Nonimmigrant Arrival-Departure Document. The Department of Homeland Security, U.S. Citizenship and Immigration...-102; U.S. Citizenship and Immigration Services (USCIS). (4) Affected public who will be asked or...

  16. 77 FR 23270 - Agency Information Collection Activities: Form I-290B, Extension of an Existing Information...

    Science.gov (United States)

    2012-04-18

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information... Department of Homeland Security, U.S. Citizenship and Immigration Services (USCIS) will be [[Page 23271...: Form I-290B. U.S. Citizenship and Immigration Services. (4) Affected public who will be asked or...

  17. 76 FR 17144 - Agency Information Collection Activities: Form N-300; Extension of an Existing Information...

    Science.gov (United States)

    2011-03-28

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information... Intention; OMB Control No. 1615-0078. The Department Homeland Security, U.S. Citizenship and Immigration... the Department of Homeland Security sponsoring the collection: Form N-300; U.S. Citizenship and...

  18. 77 FR 14535 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2012-03-12

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information... Department of Homeland Security, U.S. Citizenship and Immigration Services (USCIS) will be submitting the...; U.S. Citizenship and Immigration Services (USCIS). (4) Affected public who will be asked or required...

  19. 75 FR 51096 - Agency Information Collection Activities: Form N-470; Extension of an Existing Information...

    Science.gov (United States)

    2010-08-18

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information... for Naturalization; OMB Control No. 1615-0056. The Department of Homeland Security, U.S. Citizenship... of Homeland Security sponsoring the collection: Form N-470; U.S. Citizenship and Immigration Services...

  20. 76 FR 55081 - Agency Information Collection Activities: Form I-129S; Extension of an Existing Information...

    Science.gov (United States)

    2011-09-06

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information... Blanket L Petition. The Department Homeland Security, U.S. Citizenship and Immigration Services (USCIS... of the Department of Homeland Security sponsoring the collection: Form I-129S; U.S. Citizenship and...

  1. 75 FR 30050 - Agency Information Collection Activities: Form N-648, Revision of an Existing Information...

    Science.gov (United States)

    2010-05-28

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information... Disability Exceptions. OMB Control No. 1615-0060. The Department of Homeland Security, U.S. Citizenship and...-648. U.S. Citizenship and Immigration Services (USCIS). (4) Affected public who will be asked or...

  2. 75 FR 51096 - Agency Information Collection Activities: Form N-400; Extension of an Existing Information...

    Science.gov (United States)

    2010-08-18

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information...; OMB Control No. 1615-0052. The Department of Homeland Security, U.S. Citizenship and Immigration.... Citizenship and Immigration Services (USCIS). (4) Affected public who will be asked or required to respond, as...

  3. 75 FR 6212 - Agency Information Collection Activities: Form I-129, Revision of an Existing Information...

    Science.gov (United States)

    2010-02-08

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information... Control Number 1615-0009. The Department of Homeland Security, U.S. Citizenship and Immigration Services... the Department of Homeland Security sponsoring the collection: Form I-129. U.S. Citizenship and...

  4. 76 FR 4930 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2011-01-27

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... addressed to OMB Desk Officer, for United States Immigration and Customs Enforcement, Department of Homeland...-Day Notice of Information Collection for Review; Immigration Bond; OMB Control No. 1653-0022. The...

  5. 77 FR 35991 - Agency Information Collection Activities: Form I-829, Extension of an Existing Information...

    Science.gov (United States)

    2012-06-15

    ... Entrepreneur to Remove Conditions. On June 7, 2012, the Department of Homeland Security (DHS), U.S. Citizenship... information collection. (2) Title of the Form/Collection: Petition by Entrepreneur to Remove Conditions. (3.... This form is used by a conditional resident alien entrepreneur who obtained such status through a...

  6. 76 FR 12750 - Agency Information Collection Activities: Form I-829, Extension of an Existing Information...

    Science.gov (United States)

    2011-03-08

    ... ACTION: 30-Day Notice of Information Collection Under Review: Form I- 829, Petition by Entrepreneur to... the Form/Collection: Petition by Entrepreneur to Remove Conditions. (3) Agency form number, if any... conditional resident alien entrepreneur who obtained such status through a qualifying investment, to apply to...

  7. 78 FR 69447 - Agency Information Collection Activities; Existing Collection, Comments Requested: Friction Ridge...

    Science.gov (United States)

    2013-11-19

    ... DEPARTMENT OF JUSTICE Federal Bureau of Investigation [OMB Number 1110-0046] Agency Information Collection Activities; Existing Collection, Comments Requested: Friction Ridge Cards: Arrest and Institution... expired. Reference: OMB control number of 1110-0046. (2) The title of the form/collection: Friction Ridge...

  8. 76 FR 9376 - Proposed Extension of Existing Information Collection on Qualification/Certification Program and...

    Science.gov (United States)

    2011-02-17

    ... Extension of Existing Information Collection on Qualification/Certification Program and Man Hoist Operators... 77.107-1 on Qualification/Certification Program and Man Hoist Operators Physical Fitness. DATES: All... Labor or Secretary of Health and Human Services must make frequent inspections and investigations in...

  9. 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 This paper looks at the residential dynamics in Khartoum, Sudan. Some patterns demonstrate that formal and informal systems co-exist and are mutually supportive. There are also particular spatial manifestations that have resulted from a unique socio...

  10. 76 FR 3175 - Proposed Extension of Existing Information Collection; Hoist Operators' Physical Fitness

    Science.gov (United States)

    2011-01-19

    ... Extension of Existing Information Collection; Hoist Operators' Physical Fitness AGENCY: Mine Safety and... fitness. DATES: All comments must be received by midnight Eastern Standard Time on March 21, 2011... 56.19057 and 57.19057 require the annual examination and certification of hoist operators' fitness by...

  11. 77 FR 42004 - Proposed Extension of Existing Information Collection; Main Fan Operation and Inspection in Gassy...

    Science.gov (United States)

    2012-07-17

    ... Extension of Existing Information Collection; Main Fan Operation and Inspection in Gassy Underground Metal...) conditions in underground metal and nonmetal mines are largely controlled by the main mine fans. When accumulations of explosive gases, such as methane, are not swept from the mine by the main fans, they may...

  12. 75 FR 79031 - Proposed Extension of Existing Information, Collection; Representative of Miners; Legal Identity...

    Science.gov (United States)

    2010-12-17

    ... Extension of Existing Information, Collection; Representative of Miners; Legal Identity Report; Opening and....2, 40.3, 40.4, and 40.5, Representative of Miners; 30 CFR 41.20, Legal Identity Report; 30 CFR 56... designation. Legal Identity Report Section 109(d) of the Mine Act requires each operator of a coal or other...

  13. Plutonium matters (Basic information about its creation, properties, uses and the quantities that exist)

    International Nuclear Information System (INIS)

    Meadley, T.

    1995-01-01

    Plutonium is almost unknown in nature and this, combined with the fact that it is ''man made'' in nuclear reactors, doubtless accounts for at least some of its notoriety as the world's most dangerous and poisonous substance. The purpose of this article is to demystify plutonium by providing some basic information about its creation, properties, uses and the quantities that exist. (Author)

  14. 77 FR 26046 - Proposed Extension of Existing Information Collection; Ground Control for Surface Coal Mines and...

    Science.gov (United States)

    2012-05-02

    ... Extension of Existing Information Collection; Ground Control for Surface Coal Mines and Surface Work Areas of Underground Coal Mines AGENCY: Mine Safety and Health Administration, Labor. ACTION: Request for... inspections and investigations in coal or other mines shall be made each year for the purposes of, among other...

  15. 77 FR 4834 - Proposed Extension of Existing Information Collection; Refuge Alternatives for Underground Coal...

    Science.gov (United States)

    2012-01-31

    ... Extension of Existing Information Collection; Refuge Alternatives for Underground Coal Mines AGENCY: Mine... Underground Coal Mines DATES: Submit comments on or before April 2, 2012. ADDRESSES: Comments must be.... Title: Refuge Alternatives for Underground Coal Mines. OMB Number: 1219-0146. Affected Public: Business...

  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. Mapping protein information to disease terminologies

    Directory of Open Access Journals (Sweden)

    Mottaz Anaïs

    2007-12-01

    Full Text Available In order to improve the accessibility of genomic and proteomic information to medical researchers, we have developed a procedure to link biological information on proteins involved in diseases to the MeSH and ICD-10 disease terminologies. For this purpose, we took advantage of the manually curated disease annotations in more than 2,000 human protein entries of the UniProt KnowledgeBase. We mapped disease names extracted from the entry comment lines or from the corresponding OMIM entry to the MeSH. The method was assessed on a benchmark set of 200 manually mapped disease comment lines. We obtained a recall of 54% for 91% precision. The same procedure was used to map the more than 3,000 diseases in Swiss-Prot to MeSH with comparable efficiency. Tested on ICD-10, the coverage of the mapped terms was lower, which could be explained by the coarse-grained structure of this terminology for hereditary disease description. The mapping is provided as supplementary material at http://research.isbsib.ch/unimed.

  19. Can infrared spectroscopy provide information on protein-protein interactions?

    Science.gov (United States)

    Haris, Parvez I

    2010-08-01

    For most biophysical techniques, characterization of protein-protein interactions is challenging; this is especially true with methods that rely on a physical phenomenon that is common to both of the interacting proteins. Thus, for example, in IR spectroscopy, the carbonyl vibration (1600-1700 cm(-1)) associated with the amide bonds from both of the interacting proteins will overlap extensively, making the interpretation of spectral changes very complicated. Isotope-edited infrared spectroscopy, where one of the interacting proteins is uniformly labelled with (13)C or (13)C,(15)N has been introduced as a solution to this problem, enabling the study of protein-protein interactions using IR spectroscopy. The large shift of the amide I band (approx. 45 cm(-1) towards lower frequency) upon (13)C labelling of one of the proteins reveals the amide I band of the unlabelled protein, enabling it to be used as a probe for monitoring conformational changes. With site-specific isotopic labelling, structural resolution at the level of individual amino acid residues can be achieved. Furthermore, the ability to record IR spectra of proteins in diverse environments means that isotope-edited IR spectroscopy can be used to structurally characterize difficult systems such as protein-protein complexes bound to membranes or large insoluble peptide/protein aggregates. In the present article, examples of application of isotope-edited IR spectroscopy for studying protein-protein interactions are provided.

  20. 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

    In vivo turnover rates of proteins covering the processes of protein synthesis and breakdown rates have been measured in many tissues and protein pools using various techniques. Connective tissue and collagen protein turnover is of specific interest since existing results are rather diverging. Th...... 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.......In vivo turnover rates of proteins covering the processes of protein synthesis and breakdown rates have been measured in many tissues and protein pools using various techniques. Connective tissue and collagen protein turnover is of specific interest since existing results are rather diverging....... 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...

  1. 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.

  2. Improving rates of screening and prevention by leveraging existing information systems.

    Science.gov (United States)

    Neil, Nancy

    2003-11-01

    In 1997 Virginia Mason Health System (VMMC), a vertically integrated hospital and multispecialty group practice, had no process or system to deliver the right patient clinical data, in the right form, at the right place--when providers needed it for effective patient care. Without any new investment in technology, a work group of five individuals leveraged existing, primarily paper-based information systems to launch development and implementation of a provider prompting tool--a primary care and prevention (PCP) report--which prompted providers to complete screening, prevention, and disease management services at every patient appointment. The work group developed and pilot tested the report and created a mechanism by which the report could be delivered just in time before each patient's appointment. The report integrated information from independent appointment scheduling, laboratory results reporting, patient demographics, and billing data sources. MEASURING THE PCP REPORT'S IMPACT: The results of two separate analyses demonstrate improvement in rates of screening and prevention across VMMC soon after the PCP report became available. These results led senior leadership to make the PCP report's utilization a systemwide imperative. The PCP report is used by nearly all primary care providers as a prompt to complete screening, prevention, and disease management services at every patient appointment.

  3. Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure.

    Science.gov (United States)

    Li, Tao; Li, Qian-Zhong

    2012-11-07

    RNA-protein interactions play important roles in various biological processes. The precise detection of RNA-protein interaction sites is very important for understanding essential biological processes and annotating the function of the proteins. In this study, based on various features from amino acid sequence and structure, including evolutionary information, solvent accessible surface area and torsion angles (φ, ψ) in the backbone structure of the polypeptide chain, a computational method for predicting RNA-binding sites in proteins is proposed. When the method is applied to predict RNA-binding sites in three datasets: RBP86 containing 86 protein chains, RBP107 containing 107 proteins chains and RBP109 containing 109 proteins chains, better sensitivities and specificities are obtained compared to previously published methods in five-fold cross-validation tests. In order to make further examination for the efficiency of our method, the RBP107 dataset is used as training set, RBP86 and RBP109 datasets are used as the independent test sets. In addition, as examples of our prediction, RNA-binding sites in a few proteins are presented. The annotated results are consistent with the PDB annotation. These results show that our method is useful for annotating RNA binding sites of novel proteins.

  4. 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

  5. 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

  6. 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

  7. Informal waste collection and its co-existence with the formal waste sector: The case of Kampala, Uganda

    NARCIS (Netherlands)

    Katusiimeh, M.W.; Burger, C.P.J.; Mol, A.P.J.

    2013-01-01

    We analyze how the informal collectors and the formal sector co-exist in solid waste collection in Kampala. We rely on household surveys and a small survey among the informal collectors in Kampala. Findings suggest that informal collectors play a substantial role in the first stage – collecting

  8. 77 FR 17098 - Proposed Extension of Existing Information Collection; Independent Contractor Registration and...

    Science.gov (United States)

    2012-03-23

    ... Information Collection; Independent Contractor Registration and Identification AGENCY: Mine Safety and Health...-00040, Independent Contractor Register. OMB last approved this information collection request (ICR) on...); or 202-693-9441 (facsimile). SUPPLEMENTARY INFORMATION: I. Background Independent contractors...

  9. On the existence of optimal contract mechanisms for incomplete information principal-agent models

    NARCIS (Netherlands)

    Balder, E.J.

    1997-01-01

    Two abstract results are given for the existence of optimal contract selection mechanisms in principal-agent models; by a suitable reformulation of the (almost) incentive compatibility constraint, they deal with both single- and multi-agent models. In particular, it is shown that the existence

  10. Exist and grow under internet world in the information manage office of the unit with R and D

    International Nuclear Information System (INIS)

    Chen Suyan

    2010-01-01

    In comprehensive research institutes, there exist information centers in addition to the main libraries. These information centers are either the branches of a main library or the units belonging to the research divisions. Compared to the main libraries, the information centers provide scientists with more professional, well targeted and applicable research resources. Their contribution to the successful research and development activities are essential and should not be ignored. In the computer age, people rely more on the Internet to obtain the information. Commercialized information service providers challenge the existence of the traditional information centers and even libraries are at risk of being obsolete. This paper reviewed the characteristics, current status and challenges of the information centers. We shared the successful experience of the Department of Reactor Engineering Research and Design and proposed the development strategies for information centers under the new environment. (author)

  11. 77 FR 51578 - Agency Information Collection Activities: Existing Collection; Comments Requested: Extension of a...

    Science.gov (United States)

    2012-08-24

    ... First and last names Demographic information: Sex; race; Hispanic origin; education level Offense type... military service, date and type of last discharge BJS uses the information gathered in NCRP in published...

  12. Protein Annotators' Assistant: A Novel Application of Information Retrieval Techniques.

    Science.gov (United States)

    Wise, Michael J.

    2000-01-01

    Protein Annotators' Assistant (PAA) is a software system which assists protein annotators in assigning functions to newly sequenced proteins. PAA employs a number of information retrieval techniques in a novel setting and is thus related to text categorization, where multiple categories may be suggested, except that in this case none of the…

  13. 75 FR 41244 - Proposed Collection; Request for Comments on an Existing Information Collection: (OMB Control No...

    Science.gov (United States)

    2010-07-15

    ... information collection. ``Self-Certification of Full-Time School Attendance for the School Year'' (OMB Control... other forms of information technology. We estimate 14,000 RI 25-14s will be processed annually. We... Information Collection: (OMB Control No. 3206-0032; RI 25-14 and RI 25- 14A) AGENCY: Office of Personnel...

  14. 75 FR 63180 - Agency Information Collection Activities: Existing Collection; Emergency Extension

    Science.gov (United States)

    2010-10-14

    ... be effective after the current October 31, 2010 expiration date. FOR FURTHER INFORMATION CONTACT... collected information from State and local governments with 100 or more full-time employees since 1974... governments and to provide information on the employment status of minorities and women. The data are shared...

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

    Science.gov (United States)

    2010-07-14

    ... be effective after the current July 31, 2010 expiration date. FOR FURTHER INFORMATION CONTACT: Ronald... information from State and local governments with 100 or more full-time employees since 1974 (biennially in... information on the employment status of minorities and women. The data are shared with several other Federal...

  16. 76 FR 58301 - Proposed Extension of Existing Information Collection; Automatic Fire Sensor and Warning Device...

    Science.gov (United States)

    2011-09-20

    ... Information Collection; Automatic Fire Sensor and Warning Device Systems; Examination and Test Requirements ACTION: Notice of request for public comments. SUMMARY: The Mine Safety and Health Administration (MSHA... public comment version of this information collection package. FOR FURTHER INFORMATION CONTACT: Roslyn B...

  17. 30 CFR 778.9 - Certifying and updating existing permit application information.

    Science.gov (United States)

    2010-07-01

    ... you have previously applied for a permit and the required information is already in AVS, then you may... information already in AVS is accurate and complete may certify to us by swearing or affirming, under oath and in writing, that the relevant information in AVS is accurate, complete, and up to date. (2) Part of...

  18. 77 FR 62267 - Proposed Extension of Existing Information Collection; Gamma Radiation Surveys

    Science.gov (United States)

    2012-10-12

    ... debilitating occupational diseases. Natural sources include rocks, soils, and ground water. Gamma radiation..., electronic, mechanical, or other technological collection techniques or other forms of information technology...

  19. 77 FR 16865 - Proposed Extension of Existing Information Collection; Occupational Noise Exposure

    Science.gov (United States)

    2012-03-22

    ... harmful physical agent and one of the most pervasive health hazards in mining. Repeated exposure to high... employees working nearby. The Mine Safety and Health Administration (MSHA), the Occupational Safety and... DEPARTMENT OF LABOR Mine Safety and Health Administration Proposed Extension of Existing...

  20. 77 FR 25205 - Proposed Extension of Existing Information Collection; Roof Control Plans for Underground Coal Mines

    Science.gov (United States)

    2012-04-27

    ... collections of information in accordance with the Paperwork Reduction Act of 1995. This program helps to assure that requested data can be provided in the desired format, reporting burden (time and financial... Information Collection; Roof Control Plans for Underground Coal Mines AGENCY: Mine Safety and Health...

  1. 77 FR 25206 - Proposed Extension of Existing Information Collection; Underground Retorts

    Science.gov (United States)

    2012-04-27

    ... information in accordance with the Paperwork Reduction Act of 1995. This program helps to ensure that requested data can be provided in the desired format, reporting burden (time and financial resources) is... Information Collection; Underground Retorts AGENCY: Mine Safety and Health Administration, Labor. ACTION...

  2. 75 FR 18833 - Agency Information Collection Activities: Existing Collection; Emergency Extension

    Science.gov (United States)

    2010-04-13

    ... be effective after the current April 30, 2010 expiration date. FOR FURTHER INFORMATION CONTACT... collected information from State and local governments with 100 or more full-time employees since 1974... minorities and women. The data are shared with several other Federal agencies. Pursuant to section 709(d) of...

  3. 77 FR 38323 - Proposed Extension of Existing Information Collection; Respirable Coal Mine Dust Sampling

    Science.gov (United States)

    2012-06-27

    ... Information Collection; Respirable Coal Mine Dust Sampling AGENCY: Mine Safety and Health Administration... Sampling'' to more accurately reflect the type of information that is collected. Chronic exposure to... dust levels since 1970 and, consequently, the prevalence rate of black lung among coal miners, severe...

  4. 76 FR 14073 - Agency Information Collection Activities: Existing Collection; Comments Requested

    Science.gov (United States)

    2011-03-15

    ... forms to replace the NPS-1A which will collect data on special topics, such as mental health, medical... information collection is published to obtain comments from the public and affected agencies. Comments are... or additional information, please contact Paul Guerino by e-mail at paul[email protected] or at (202...

  5. 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

  6. Regulator of G Protein Signaling 7 (RGS7) Can Exist in a Homo-oligomeric Form That Is Regulated by Gαo and R7-binding Protein.

    Science.gov (United States)

    Tayou, Junior; Wang, Qiang; Jang, Geeng-Fu; Pronin, Alexey N; Orlandi, Cesare; Martemyanov, Kirill A; Crabb, John W; Slepak, Vladlen Z

    2016-04-22

    RGS (regulator of G protein signaling) proteins of the R7 subfamily (RGS6, -7, -9, and -11) are highly expressed in neurons where they regulate many physiological processes. R7 RGS proteins contain several distinct domains and form obligatory dimers with the atypical Gβ subunit, Gβ5 They also interact with other proteins such as R7-binding protein, R9-anchoring protein, and the orphan receptors GPR158 and GPR179. These interactions facilitate plasma membrane targeting and stability of R7 proteins and modulate their activity. Here, we investigated RGS7 complexes using in situ chemical cross-linking. We found that in mouse brain and transfected cells cross-linking causes formation of distinct RGS7 complexes. One of the products had the apparent molecular mass of ∼150 kDa on SDS-PAGE and did not contain Gβ5 Mass spectrometry analysis showed no other proteins to be present within the 150-kDa complex in the amount close to stoichiometric with RGS7. This finding suggested that RGS7 could form a homo-oligomer. Indeed, co-immunoprecipitation of differentially tagged RGS7 constructs, with or without chemical cross-linking, demonstrated RGS7 self-association. RGS7-RGS7 interaction required the DEP domain but not the RGS and DHEX domains or the Gβ5 subunit. Using transfected cells and knock-out mice, we demonstrated that R7-binding protein had a strong inhibitory effect on homo-oligomerization of RGS7. In contrast, our data indicated that GPR158 could bind to the RGS7 homo-oligomer without causing its dissociation. Co-expression of constitutively active Gαo prevented the RGS7-RGS7 interaction. These results reveal the existence of RGS protein homo-oligomers and show regulation of their assembly by R7 RGS-binding partners. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  7. 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...

  8. 75 FR 80072 - Proposed Extension of Existing Information Collection; Radiation Sampling and Exposure Records

    Science.gov (United States)

    2010-12-21

    ... radon daughters are invisible and odorless. Decay of radon and its daughters results in emissions of... INFORMATION CONTACT section of this notice, or viewed on the Internet by selecting ``Rules & Regs'', and then...

  9. 78 FR 41062 - Agency Information Collection Activities: Existing Collection; Emergency Extension

    Science.gov (United States)

    2013-07-09

    ... Collection Title: Demographic Information on Federal Job Applicants. OMB Control No.: 3046-0046. Description... agencies to evaluate their employment practices through the collection and analysis of data on the race...

  10. 78 FR 56940 - Agency Information Collection Activities; Existing Collection-Reinstatement, Comments Requested...

    Science.gov (United States)

    2013-09-16

    ... Services Division (CJIS), Biometric Services Section, Customer Support Unit, Module E-1, 1000 Custer Hollow... techniques of other forms of information technology, e.g., permitting electronic submission of responses...

  11. 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.

  12. Crowdsourcing step-by-step information extraction to enhance existing how-to videos

    OpenAIRE

    Nguyen, Phu Tran; Weir, Sarah; Guo, Philip J.; Miller, Robert C.; Gajos, Krzysztof Z.; Kim, Ju Ho

    2014-01-01

    Millions of learners today use how-to videos to master new skills in a variety of domains. But browsing such videos is often tedious and inefficient because video player interfaces are not optimized for the unique step-by-step structure of such videos. This research aims to improve the learning experience of existing how-to videos with step-by-step annotations. We first performed a formative study to verify that annotations are actually useful to learners. We created ToolScape, an interac...

  13. Advances in Remote Sensing of Agriculture: Context Description, Existing Operational Monitoring Systems and Major Information Needs

    Directory of Open Access Journals (Sweden)

    Clement Atzberger

    2013-02-01

    Full Text Available Many remote sensing applications are devoted to the agricultural sector. Representative case studies are presented in the special issue “Advances in Remote Sensing of Agriculture”. To complement the examples published within the special issue, a few main applications with regional to global focus were selected for this review, where remote sensing contributions are traditionally strong. The selected applications are put in the context of the global challenges the agricultural sector is facing: minimizing the environmental impact, while increasing production and productivity. Five different applications have been selected, which are illustrated and described: (1 biomass and yield estimation, (2 vegetation vigor and drought stress monitoring, (3 assessment of crop phenological development, (4 crop acreage estimation and cropland mapping and (5 mapping of disturbances and land use/land cover (LULC changes. Many other applications exist, such as precision agriculture and irrigation management (see other special issues of this journal, but were not included to keep the paper concise. The paper starts with an overview of the main agricultural challenges. This section is followed by a brief overview of existing operational monitoring systems. Finally, in the main part of the paper, the mentioned applications are described and illustrated. The review concludes with some key recommendations.

  14. 77 FR 39238 - Agency Information Collection Activities: Existing Collection; Emergency Extension

    Science.gov (United States)

    2012-07-02

    ... requirements for elementary and secondary public school districts. The EEOC uses EEO-5 data to investigate charges of employment discrimination against elementary and secondary public school districts. The data... Information Collection--Emergency Request--Revision of a Currently Approved Collection: Elementary-Secondary...

  15. 77 FR 32698 - Proposed Extension of Existing Information Collection; Safety Standards for Roof Bolts in Metal...

    Science.gov (United States)

    2012-06-01

    ... are used to prevent the fall of roof, face, and rib. Advancements in technology of roof and rock bolts... information technology (e.g., permitting electronic submissions of responses), to minimize the burden of the...-0121. Affected Public: Business or other for-profit. Cite/Reference/Form/ etc. 30 CFR 56.3203, 57.3203...

  16. 76 FR 589 - Proposed Extension of Existing Information Collection; Mine Accident, Injury, Illness, Mine...

    Science.gov (United States)

    2011-01-05

    ... requires mine operators and independent contractors to immediately notify MSHA in the event of an accident... provides for uniform information gathering across the mining industry. Section 50.30 requires mine... types. These rates are used to analyze trends and to assess the degree of success of the health and...

  17. 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...

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

    Directory of Open Access Journals (Sweden)

    Serrano Luis

    2008-10-01

    Full Text Available Abstract 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 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. Conclusion 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.

  19. Smartphone applications for communicating avalanche risk information - a review of existing practices

    Science.gov (United States)

    Charrière, M. K. M.; Bogaard, T. A.

    2015-11-01

    Every year, in all mountainous regions, people are victims of avalanches. One way to decrease those losses is believed to be informing about danger levels. The paper presents a study on current practices in the development of smartphones applications that are dedicated to avalanche risk communication. The analysis based on semi-structured interviews with developers of smartphone apps highlights the context of their development, how choices of content and visualization were made as well as how their effectiveness is evaluated. It appears that although the communicators agree on the message to disseminate, its representation triggers debate. Moreover, only simple evaluation processes are conducted but there is a clear awareness that further scientific efforts are needed to analyze the effectiveness of the smartphone apps. Finally, the current or planned possibility for non-experts users to report feedback on the snow and avalanches conditions open the doors to a transition of these apps from one-way communication tools to two-ways communication platforms. This paper also indicates the remaining challenges that avalanche risk communication is facing, although it is disputably the most advanced and standardized practice compared to other natural hazards. Therefore, this research is of interest for the entire field of natural hazards related risk communication.

  20. Making the pediatric perioperative surgical home come to life by leveraging existing health information technology.

    Science.gov (United States)

    Leahy, Izabela C; Borczuk, Rachel; Ferrari, Lynne R

    2017-06-01

    To design a patient data dashboard for the Department of Anesthesiology, Perioperative and Pain Medicine at Boston Children's Hospital that supports care integration across the healthcare system as described by the pediatric perioperative surgical home (PPSH) initiative. By using 360 Technology, patient data was automatically pulled from all available Electronic Health Record sources from 2005 to the present. The PPSH dashboard described in this report provides a guide for implementation of PPSH Clinical Care Pathways. The dashboard integrates several databases to allow for visual longitudinal tracking of patient care, outcomes, and cost. The integration of electronic information provided the ability to display, compare, and analyze selected PPSH metrics in real time. By utilizing the PPSH dashboard format the use of an automated, integrated clinical, and financial health data profile for a specific patient population may improve clinicians' ability to have a comprehensive assessment of all care elements. This more global clinical thinking has the potential to produce bottom-up, evidence-based healthcare reform. The experience with the PPSH dashboard provides solid evidence for the use of integrated Electronic Health Record to improve patient outcomes and decrease cost.

  1. Experimental model considerations for the study of protein-energy malnutrition co-existing with ischemic brain injury.

    Science.gov (United States)

    Prosser-Loose, Erin J; Smith, Shari E; Paterson, Phyllis G

    2011-05-01

    Protein-energy malnutrition (PEM) affects ~16% of patients at admission for stroke. We previously modeled this in a gerbil global cerebral ischemia model and found that PEM impairs functional outcome and influences mechanisms of ischemic brain injury and recovery. Since this model is no longer reliable, we investigated the utility of the rat 2-vessel occlusion (2-VO) with hypotension model of global ischemia for further study of this clinical problem. Male, Sprague-Dawley rats were exposed to either control diet (18% protein) or PEM induced by feeding a low protein diet (2% protein) for 7d prior to either global ischemia or sham surgery. PEM did not significantly alter the hippocampal CA1 neuron death (p = 0.195 by 2-factor ANOVA) or the increase in dendritic injury caused by exposure to global ischemia. Unexpectedly, however, a strong trend was evident for PEM to decrease the consistency of hippocampal damage, as shown by an increased incidence of unilateral or no hippocampal damage (p=0.069 by chi-square analysis). Although PEM caused significant changes to baseline arterial blood pH, pO(2), pCO(2), and fasting glucose (p0.269). Intra-ischemic tympanic temperature and blood pressure were strictly and equally controlled between ischemic groups. We conclude that co-existing PEM confounded the consistency of hippocampal injury in the 2-VO model. Although the mechanisms responsible were not identified, this model of brain ischemia should not be used for studying this co-morbidity factor. © 2011 Bentham Science Publishers Ltd.

  2. Senescence marker protein 30 (SMP30 expression in eukaryotic cells: existence of multiple species and membrane localization.

    Directory of Open Access Journals (Sweden)

    Peethambaran Arun

    Full Text Available Senescence marker protein (SMP30, also known as regucalcin, is a 34 kDa cytosolic marker protein of aging which plays an important role in intracellular Ca(2+ homeostasis, ascorbic acid biosynthesis, oxidative stress, and detoxification of chemical warfare nerve agents. In our goal to investigate the activity of SMP30 for the detoxification of nerve agents, we have produced a recombinant adenovirus expressing human SMP30 as a fusion protein with a hemaglutinin tag (Ad-SMP30-HA. Ad-SMP30-HA transduced the expression of SMP30-HA and two additional forms of SMP30 with molecular sizes ∼28 kDa and 24 kDa in HEK-293A and C3A liver cells in a dose and time-dependent manner. Intravenous administration of Ad-SMP30-HA in mice results in the expression of all the three forms of SMP30 in the liver and diaphragm. LC-MS/MS results confirmed that the lower molecular weight 28 kDa and 24 kDa proteins are related to the 34 kDa SMP30. The 28 kDa and 24 kDa SMP30 forms were also detected in normal rat liver and mice injected with Ad-SMP30-HA suggesting that SMP30 does exist in multiple forms under physiological conditions. Time course experiments in both cell lines suggest that the 28 kDa and 24 kDa SMP30 forms are likely generated from the 34 kDa SMP30. Interestingly, the 28 kDa and 24 kDa SMP30 forms appeared initially in the cytosol and shifted to the particulate fraction. Studies using small molecule inhibitors of proteolytic pathways revealed the potential involvement of β and γ-secretases but not calpains, lysosomal proteases, proteasome and caspases. This is the first report describing the existence of multiple forms of SMP30, their preferential distribution to membranes and their generation through proteolysis possibly mediated by secretase enzymes.

  3. Identifying essential proteins based on sub-network partition and prioritization by integrating subcellular localization information.

    Science.gov (United States)

    Li, Min; Li, Wenkai; Wu, Fang-Xiang; Pan, Yi; Wang, Jianxin

    2018-06-14

    Essential proteins are important participants in various life activities and play a vital role in the survival and reproduction of living organisms. Identification of essential proteins from protein-protein interaction (PPI) networks has great significance to facilitate the study of human complex diseases, the design of drugs and the development of bioinformatics and computational science. Studies have shown that highly connected proteins in a PPI network tend to be essential. A series of computational methods have been proposed to identify essential proteins by analyzing topological structures of PPI networks. However, the high noise in the PPI data can degrade the accuracy of essential protein prediction. Moreover, proteins must be located in the appropriate subcellular localization to perform their functions, and only when the proteins are located in the same subcellular localization, it is possible that they can interact with each other. In this paper, we propose a new network-based essential protein discovery method based on sub-network partition and prioritization by integrating subcellular localization information, named SPP. The proposed method SPP was tested on two different yeast PPI networks obtained from DIP database and BioGRID database. The experimental results show that SPP can effectively reduce the effect of false positives in PPI networks and predict essential proteins more accurately compared with other existing computational methods DC, BC, CC, SC, EC, IC, NC. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. Utilization of information technology in eastern North Carolina physician practices: determining the existence of a digital divide.

    Science.gov (United States)

    Rosenthal, David A; Layman, Elizabeth J

    2008-02-13

    The United States Department of Health and Human Services (DHHS) has emphasized the importance of utilizing health information technologies, thus making the availability of electronic resources critical for physicians across the country. However, few empirical assessments exist regarding the current status of computerization and utilization of electronic resources in physician offices and physicians' perceptions of the advantages and disadvantages of computerization. Through a survey of physicians' utilization and perceptions of health information technology, this study found that a "digital divide" existed for eastern North Carolina physicians in smaller physician practices. The physicians in smaller practices were less likely to utilize or be interested in utilizing electronic health records, word processing applications, and the Internet.

  5. 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

  6. Predicting protein complexes using a supervised learning method combined with local structural information.

    Science.gov (United States)

    Dong, Yadong; Sun, Yongqi; Qin, Chao

    2018-01-01

    The existing protein complex detection methods can be broadly divided into two categories: unsupervised and supervised learning methods. Most of the unsupervised learning methods assume that protein complexes are in dense regions of protein-protein interaction (PPI) networks even though many true complexes are not dense subgraphs. Supervised learning methods utilize the informative properties of known complexes; they often extract features from existing complexes and then use the features to train a classification model. The trained model is used to guide the search process for new complexes. However, insufficient extracted features, noise in the PPI data and the incompleteness of complex data make the classification model imprecise. Consequently, the classification model is not sufficient for guiding the detection of complexes. Therefore, we propose a new robust score function that combines the classification model with local structural information. Based on the score function, we provide a search method that works both forwards and backwards. The results from experiments on six benchmark PPI datasets and three protein complex datasets show that our approach can achieve better performance compared with the state-of-the-art supervised, semi-supervised and unsupervised methods for protein complex detection, occasionally significantly outperforming such methods.

  7. 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.

  8. Analysis of informational redundancy in the protein-assembling machinery

    Science.gov (United States)

    Berkovich, Simon

    2004-03-01

    Entropy analysis of the DNA structure does not reveal a significant departure from randomness indicating lack of informational redundancy. This signifies the absence of a hidden meaning in the genome text and supports the 'barcode' interpretation of DNA given in [1]. Lack of informational redundancy is a characteristic property of an identification label rather than of a message of instructions. Yet randomness of DNA has to induce non-random structures of the proteins. Protein synthesis is a two-step process: transcription into RNA with gene splicing and formation a structure of amino acids. Entropy estimations, performed by A. Djebbari, show typical values of redundancy of the biomolecules along these pathways: DNA gene 4proteins 15-40in gene expression, the RNA copy carries the same information as the original DNA template. Randomness is essentially eliminated only at the step of the protein creation by a degenerate code. According to [1], the significance of the substitution of U for T with a subsequent gene splicing is that these transformations result in a different pattern of RNA oscillations, so the vital DNA communications are protected against extraneous noise coming from the protein making activities. 1. S. Berkovich, "On the 'barcode' functionality of DNA, or the Phenomenon of Life in the Physical Universe", Dorrance Publishing Co., Pittsburgh, 2003

  9. 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.

  10. 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.; Koh, Y. J.; Kim, H. S.; Koh, S. H.; Kang, D. H.; Kang, T. W. [Cheju National Univ., Jeju (Korea, Republic of)

    2004-02-15

    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. Also the recent trends of the individual technologies regarding the RI-PBR and RIA are summarized.

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

    DEFF Research Database (Denmark)

    Andersen, C.A.F.; Brunak, Søren

    2004-01-01

    -sequence information, using machine learning strategies, where the primary goal is the discovery of novel powerful representations for use in AI techniques. In the case of proteins and the 20 different amino acids they typically contain, it is also a secondary goal to discover how the current selection of amino acids...

  12. 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.

  13. 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.

  14. 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.

  15. Exhaustive search of linear information encoding protein-peptide recognition.

    Science.gov (United States)

    Kelil, Abdellali; Dubreuil, Benjamin; Levy, Emmanuel D; Michnick, Stephen W

    2017-04-01

    High-throughput in vitro methods have been extensively applied to identify linear information that encodes peptide recognition. However, these methods are limited in number of peptides, sequence variation, and length of peptides that can be explored, and often produce solutions that are not found in the cell. Despite the large number of methods developed to attempt addressing these issues, the exhaustive search of linear information encoding protein-peptide recognition has been so far physically unfeasible. Here, we describe a strategy, called DALEL, for the exhaustive search of linear sequence information encoded in proteins that bind to a common partner. We applied DALEL to explore binding specificity of SH3 domains in the budding yeast Saccharomyces cerevisiae. Using only the polypeptide sequences of SH3 domain binding proteins, we succeeded in identifying the majority of known SH3 binding sites previously discovered either in vitro or in vivo. Moreover, we discovered a number of sites with both non-canonical sequences and distinct properties that may serve ancillary roles in peptide recognition. We compared DALEL to a variety of state-of-the-art algorithms in the blind identification of known binding sites of the human Grb2 SH3 domain. We also benchmarked DALEL on curated biological motifs derived from the ELM database to evaluate the effect of increasing/decreasing the enrichment of the motifs. Our strategy can be applied in conjunction with experimental data of proteins interacting with a common partner to identify binding sites among them. Yet, our strategy can also be applied to any group of proteins of interest to identify enriched linear motifs or to exhaustively explore the space of linear information encoded in a polypeptide sequence. Finally, we have developed a webserver located at http://michnick.bcm.umontreal.ca/dalel, offering user-friendly interface and providing different scenarios utilizing DALEL.

  16. 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.

  17. Improving protein-protein interaction prediction using evolutionary information from low-quality MSAs.

    Science.gov (United States)

    Várnai, Csilla; Burkoff, Nikolas S; Wild, David L

    2017-01-01

    Evolutionary information stored in multiple sequence alignments (MSAs) has been used to identify the interaction interface of protein complexes, by measuring either co-conservation or co-mutation of amino acid residues across the interface. Recently, maximum entropy related correlated mutation measures (CMMs) such as direct information, decoupling direct from indirect interactions, have been developed to identify residue pairs interacting across the protein complex interface. These studies have focussed on carefully selected protein complexes with large, good-quality MSAs. In this work, we study protein complexes with a more typical MSA consisting of fewer than 400 sequences, using a set of 79 intramolecular protein complexes. Using a maximum entropy based CMM at the residue level, we develop an interface level CMM score to be used in re-ranking docking decoys. We demonstrate that our interface level CMM score compares favourably to the complementarity trace score, an evolutionary information-based score measuring co-conservation, when combined with the number of interface residues, a knowledge-based potential and the variability score of individual amino acid sites. We also demonstrate, that, since co-mutation and co-complementarity in the MSA contain orthogonal information, the best prediction performance using evolutionary information can be achieved by combining the co-mutation information of the CMM with co-conservation information of a complementarity trace score, predicting a near-native structure as the top prediction for 41% of the dataset. The method presented is not restricted to small MSAs, and will likely improve interface prediction also for complexes with large and good-quality MSAs.

  18. Common data model for natural language processing based on two existing standard information models: CDA+GrAF.

    Science.gov (United States)

    Meystre, Stéphane M; Lee, Sanghoon; Jung, Chai Young; Chevrier, Raphaël D

    2012-08-01

    An increasing need for collaboration and resources sharing in the Natural Language Processing (NLP) research and development community motivates efforts to create and share a common data model and a common terminology for all information annotated and extracted from clinical text. We have combined two existing standards: the HL7 Clinical Document Architecture (CDA), and the ISO Graph Annotation Format (GrAF; in development), to develop such a data model entitled "CDA+GrAF". We experimented with several methods to combine these existing standards, and eventually selected a method wrapping separate CDA and GrAF parts in a common standoff annotation (i.e., separate from the annotated text) XML document. Two use cases, clinical document sections, and the 2010 i2b2/VA NLP Challenge (i.e., problems, tests, and treatments, with their assertions and relations), were used to create examples of such standoff annotation documents, and were successfully validated with the XML schemata provided with both standards. We developed a tool to automatically translate annotation documents from the 2010 i2b2/VA NLP Challenge format to GrAF, and automatically generated 50 annotation documents using this tool, all successfully validated. Finally, we adapted the XSL stylesheet provided with HL7 CDA to allow viewing annotation XML documents in a web browser, and plan to adapt existing tools for translating annotation documents between CDA+GrAF and the UIMA and GATE frameworks. This common data model may ease directly comparing NLP tools and applications, combining their output, transforming and "translating" annotations between different NLP applications, and eventually "plug-and-play" of different modules in NLP applications. Copyright © 2011 Elsevier Inc. All rights reserved.

  19. The Protein Model Portal--a comprehensive resource for protein structure and model information.

    Science.gov (United States)

    Haas, Juergen; Roth, Steven; Arnold, Konstantin; Kiefer, Florian; Schmidt, Tobias; Bordoli, Lorenza; Schwede, Torsten

    2013-01-01

    The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access to structural information for proteins. Both experimental structures and theoretical models for a given protein can be searched simultaneously and analyzed for structural variability. By providing a comprehensive view on structural information, PMP offers the opportunity to apply consistent assessment and validation criteria to the complete set of structural models available for proteins. PMP is an open project so that new methods developed by the community can contribute to PMP, for example, new modeling servers for creating homology models and model quality estimation servers for model validation. The accuracy of participating modeling servers is continuously evaluated by the Continuous Automated Model EvaluatiOn (CAMEO) project. The PMP offers a unique interface to visualize structural coverage of a protein combining both theoretical models and experimental structures, allowing straightforward assessment of the model quality and hence their utility. The portal is updated regularly and actively developed to include latest methods in the field of computational structural biology. Database URL: http://www.proteinmodelportal.org.

  20. The Protein Model Portal—a comprehensive resource for protein structure and model information

    Science.gov (United States)

    Haas, Juergen; Roth, Steven; Arnold, Konstantin; Kiefer, Florian; Schmidt, Tobias; Bordoli, Lorenza; Schwede, Torsten

    2013-01-01

    The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access to structural information for proteins. Both experimental structures and theoretical models for a given protein can be searched simultaneously and analyzed for structural variability. By providing a comprehensive view on structural information, PMP offers the opportunity to apply consistent assessment and validation criteria to the complete set of structural models available for proteins. PMP is an open project so that new methods developed by the community can contribute to PMP, for example, new modeling servers for creating homology models and model quality estimation servers for model validation. The accuracy of participating modeling servers is continuously evaluated by the Continuous Automated Model EvaluatiOn (CAMEO) project. The PMP offers a unique interface to visualize structural coverage of a protein combining both theoretical models and experimental structures, allowing straightforward assessment of the model quality and hence their utility. The portal is updated regularly and actively developed to include latest methods in the field of computational structural biology. Database URL: http://www.proteinmodelportal.org PMID:23624946

  1. The Universal Protein Resource (UniProt): an expanding universe of protein information.

    Science.gov (United States)

    Wu, Cathy H; Apweiler, Rolf; Bairoch, Amos; Natale, Darren A; Barker, Winona C; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; Lopez, Rodrigo; Magrane, Michele; Martin, Maria J; Mazumder, Raja; O'Donovan, Claire; Redaschi, Nicole; Suzek, Baris

    2006-01-01

    The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/.

  2. 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.

  3. Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank.

    Science.gov (United States)

    Wako, Hiroshi; Endo, Shigeru

    2017-12-01

    Normal mode analysis (NMA) can facilitate quick and systematic investigation of protein dynamics using data from the Protein Data Bank (PDB). We developed an elastic network model-based NMA program using dihedral angles as independent variables. Compared to the NMA programs that use Cartesian coordinates as independent variables, key attributes of the proposed program are as follows: (1) chain connectivity related to the folding pattern of a polypeptide chain is naturally embedded in the model; (2) the full-atom system is acceptable, and owing to a considerably smaller number of independent variables, the PDB data can be used without further manipulation; (3) the number of variables can be easily reduced by some of the rotatable dihedral angles; (4) the PDB data for any molecule besides proteins can be considered without coarse-graining; and (5) individual motions of constituent subunits and ligand molecules can be easily decomposed into external and internal motions to examine their mutual and intrinsic motions. Its performance is illustrated with an example of a DNA-binding allosteric protein, a catabolite activator protein. In particular, the focus is on the conformational change upon cAMP and DNA binding, and on the communication between their binding sites remotely located from each other. In this illustration, NMA creates a vivid picture of the protein dynamics at various levels of the structures, i.e., atoms, residues, secondary structures, domains, subunits, and the complete system, including DNA and cAMP. Comparative studies of the specific protein in different states, e.g., apo- and holo-conformations, and free and complexed configurations, provide useful information for studying structurally and functionally important aspects of the protein.

  4. 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.

  5. 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.

  6. Information pertinent to the migration of radionuclides in ground water at the Nevada Test Site. Part 1. Review and analysis of existing information

    International Nuclear Information System (INIS)

    Borg, I.Y.; Stone, R.; Levy, H.B.; Ramspott, L.D.

    1976-01-01

    A history of NTS is given, the geologic and hydrologic setting is described, and the amount of radioactivity deposited within and near the main aquifers is estimated. The conclusions include: information currently available is insufficient to state categorically that radioactivity will never be carried off the Nevada Test Site by ground water movement; nonetheless, such a migration at levels above the maximum permissible concentration to existing wells and springs is considered unlikely; if offsite migration occurs, it will probably be from the southwestern margins of Pahute Mesa, where there is only a small chance of contaminating existing public water supplies; tritium is the most mobile radionuclide and may be the only long-lived isotope of concern. Highest priority is assigned to measurement of tritium and other radionuclides in large water samples taken from nuclear chimneys that water has re-entered after an explosion; expansion of the existing groundwater monitoring program at NTS to include wells with a higher probability of intersecting flow of contaminated water; measurement of groundwater flow velocities and other associated hydrologic parameters. High priority is assigned to production of an inventory of radionuclides deposited near NTS borders, especially beneath Pahute Mesa; determination of amounts of radioactivity deposited directly into the Lower Carbonate Aquifer; a sensitivity analysis of the many parameters that enter into transport calculations; a study of the many unplugged holes that penetrate the Tuff Aquitard; testing of the assumption that radionuclides deposited in the unsaturated zone are isolated from the saturated zone because of limited precipitation and downward movement of moisture; and determination of distribution coefficients for NTS alluvium, carbonate, and rhyolitic rocks, which are lacking or poorly represented in the literature. Twelve other recommendations of lesser priority are also given

  7. 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/ .

  8. 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

  9. 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

  10. 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

  11. 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 ...

  12. Purification of the spliced leader ribonucleoprotein particle from Leptomonas collosoma revealed the existence of an Sm protein in trypanosomes. Cloning the SmE homologue.

    Science.gov (United States)

    Goncharov, I; Palfi, Z; Bindereif, A; Michaeli, S

    1999-04-30

    Trans-splicing in trypanosomes involves the addition of a common spliced leader (SL) sequence, which is derived from a small RNA, the SL RNA, to all mRNA precursors. The SL RNA is present in the cell in the form of a ribonucleoprotein, the SL RNP. Using conventional chromatography and affinity selection with 2'-O-methylated RNA oligonucleotides at high ionic strength, five proteins of 70, 16, 13, 12, and 8 kDa were co-selected with the SL RNA from Leptomonas collosoma, representing the SL RNP core particle. Under conditions of lower ionic strength, additional proteins of 28 and 20 kDa were revealed. On the basis of peptide sequences, the gene coding for a protein with a predicted molecular weight of 11.9 kDa was cloned and identified as homologue of the cis-spliceosomal SmE. The protein carries the Sm motifs 1 and 2 characteristic of Sm antigens that bind to all known cis-spliceosomal uridylic acid-rich small nuclear RNAs (U snRNAs), suggesting the existence of Sm proteins in trypanosomes. This finding is of special interest because trypanosome snRNPs are the only snRNPs examined to date that are not recognized by anti-Sm antibodies. Because of the early divergence of trypanosomes from the eukaryotic lineage, the trypanosome SmE protein represents one of the primordial Sm proteins in nature.

  13. Deconstructing brain-derived neurotrophic factor actions in adult brain circuits to bridge an existing informational gap in neuro-cell biology

    Directory of Open Access Journals (Sweden)

    Heather Bowling

    2016-01-01

    Full Text Available Brain-derived neurotrophic factor (BDNF plays an important role in neurodevelopment, synaptic plasticity, learning and memory, and in preventing neurodegeneration. Despite decades of investigations into downstream signaling cascades and changes in cellular processes, the mechanisms of how BDNF reshapes circuits in vivo remain unclear. This informational gap partly arises from the fact that the bulk of studies into the molecular actions of BDNF have been performed in dissociated neuronal cultures, while the majority of studies on synaptic plasticity, learning and memory were performed in acute brain slices or in vivo. A recent study by Bowling-Bhattacharya et al., measured the proteomic changes in acute adult hippocampal slices following treatment and reported changes in proteins of neuronal and non-neuronal origin that may in concert modulate synaptic release and secretion in the slice. In this paper, we place these findings into the context of existing literature and discuss how they impact our understanding of how BDNF can reshape the brain.

  14. Worldwide Protein Data Bank validation information: usage and trends.

    Science.gov (United States)

    Smart, Oliver S; Horský, Vladimír; Gore, Swanand; Svobodová Vařeková, Radka; Bendová, Veronika; Kleywegt, Gerard J; Velankar, Sameer

    2018-03-01

    Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrends DB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

  15. Structure and expression of the maize (Zea mays L. SUN-domain protein gene family: evidence for the existence of two divergent classes of SUN proteins in plants

    Directory of Open Access Journals (Sweden)

    Simmons Carl R

    2010-12-01

    Full Text Available Abstract Background The nuclear envelope that separates the contents of the nucleus from the cytoplasm provides a surface for chromatin attachment and organization of the cortical nucleoplasm. Proteins associated with it have been well characterized in many eukaryotes but not in plants. SUN (Sad1p/Unc-84 domain proteins reside in the inner nuclear membrane and function with other proteins to form a physical link between the nucleoskeleton and the cytoskeleton. These bridges transfer forces across the nuclear envelope and are increasingly recognized to play roles in nuclear positioning, nuclear migration, cell cycle-dependent breakdown and reformation of the nuclear envelope, telomere-led nuclear reorganization during meiosis, and karyogamy. Results We found and characterized a family of maize SUN-domain proteins, starting with a screen of maize genomic sequence data. We characterized five different maize ZmSUN genes (ZmSUN1-5, which fell into two classes (probably of ancient origin, as they are also found in other monocots, eudicots, and even mosses. The first (ZmSUN1, 2, here designated canonical C-terminal SUN-domain (CCSD, includes structural homologs of the animal and fungal SUN-domain protein genes. The second (ZmSUN3, 4, 5, here designated plant-prevalent mid-SUN 3 transmembrane (PM3, includes a novel but conserved structural variant SUN-domain protein gene class. Mircroarray-based expression analyses revealed an intriguing pollen-preferred expression for ZmSUN5 mRNA but low-level expression (50-200 parts per ten million in multiple tissues for all the others. Cloning and characterization of a full-length cDNA for a PM3-type maize gene, ZmSUN4, is described. Peptide antibodies to ZmSUN3, 4 were used in western-blot and cell-staining assays to show that they are expressed and show concentrated staining at the nuclear periphery. Conclusions The maize genome encodes and expresses at least five different SUN-domain proteins, of which the PM3

  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. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-01-01

    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

  18. 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 existing literature, to establish a link between ventilation rate and key indoor air pollutants. Design characteristics of a mechanical ventilation system such as supply/exhaustairflow, system and design of supply and exhaust outlets were considered. The performance of various ventilation solutionswas......-house ventilation rate was reported below 0.5h-1 or 14 l/s·person in bedrooms, the concentrations of the pollutants elevated above minimum threshold limits (CO2>1350 ppm; TVOC >3000 μg/m3) defined by the standard. Insufficient or non-existent supply of air was related to significantly higher pollutant...

  19. Protein Sub-Nuclear Localization Prediction Using SVM and Pfam Domain Information

    Science.gov (United States)

    Kumar, Ravindra; Jain, Sohni; Kumari, Bandana; Kumar, Manish

    2014-01-01

    The nucleus is the largest and the highly organized organelle of eukaryotic cells. Within nucleus exist a number of pseudo-compartments, which are not separated by any membrane, yet each of them contains only a specific set of proteins. Understanding protein sub-nuclear localization can hence be an important step towards understanding biological functions of the nucleus. Here we have described a method, SubNucPred developed by us for predicting the sub-nuclear localization of proteins. This method predicts protein localization for 10 different sub-nuclear locations sequentially by combining presence or absence of unique Pfam domain and amino acid composition based SVM model. The prediction accuracy during leave-one-out cross-validation for centromeric proteins was 85.05%, for chromosomal proteins 76.85%, for nuclear speckle proteins 81.27%, for nucleolar proteins 81.79%, for nuclear envelope proteins 79.37%, for nuclear matrix proteins 77.78%, for nucleoplasm proteins 76.98%, for nuclear pore complex proteins 88.89%, for PML body proteins 75.40% and for telomeric proteins it was 83.33%. Comparison with other reported methods showed that SubNucPred performs better than existing methods. A web-server for predicting protein sub-nuclear localization named SubNucPred has been established at http://14.139.227.92/mkumar/subnucpred/. Standalone version of SubNucPred can also be downloaded from the web-server. PMID:24897370

  20. 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.

  1. 75 FR 16492 - Agency Information Collection Activities: Form G-28, and Form G-28I, Revision of an Existing...

    Science.gov (United States)

    2010-04-01

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services Agency Information... Attorney. OMB Control No. 1615-0105. The Department of Homeland Security, U.S. Citizenship and Immigration... of Homeland Security sponsoring the collection: Form G-28, and Form G-28I. U.S. Citizenship and...

  2. The RCSB protein data bank: integrative view of protein, gene and 3D structural information.

    Science.gov (United States)

    Rose, Peter W; Prlić, Andreas; Altunkaya, Ali; Bi, Chunxiao; Bradley, Anthony R; Christie, Cole H; Costanzo, Luigi Di; Duarte, Jose M; Dutta, Shuchismita; Feng, Zukang; Green, Rachel Kramer; Goodsell, David S; Hudson, Brian; Kalro, Tara; Lowe, Robert; Peisach, Ezra; Randle, Christopher; Rose, Alexander S; Shao, Chenghua; Tao, Yi-Ping; Valasatava, Yana; Voigt, Maria; Westbrook, John D; Woo, Jesse; Yang, Huangwang; Young, Jasmine Y; Zardecki, Christine; Berman, Helen M; Burley, Stephen K

    2017-01-04

    The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a 'Structural View of Biology.' Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Identification and characterization of novel ERC-55 interacting proteins: evidence for the existence of several ERC-55 splicing variants; including the cytosolic ERC-55-C.

    Science.gov (United States)

    Ludvigsen, Maja; Jacobsen, Christian; Maunsbach, Arvid B; Honoré, Bent

    2009-12-01

    ERC-55, encoded from RCN2, is localized in the ER and belongs to the CREC protein family. ERC-55 is involved in various diseases and abnormal cell behavior, however, the function is not well defined and it has controversially been reported to interact with a cytosolic protein, the vitamin D receptor. We have used a number of proteomic techniques to further our functional understanding of ERC-55. By affinity purification, we observed interaction with a large variety of proteins, including those secreted and localized outside of the secretory pathway, in the cytosol and also in various organelles. We confirm the existence of several ERC-55 splicing variants including ERC-55-C localized in the cytosol in association with the cytoskeleton. Localization was verified by immunoelectron microscopy and sub-cellular fractionation. Interaction of lactoferrin, S100P, calcyclin (S100A6), peroxiredoxin-6, kininogen and lysozyme with ERC-55 was further studied in vitro by SPR experiments. Interaction of S100P requires [Ca(2+)] of approximately 10(-7) M or greater, while calcyclin interaction requires [Ca(2+)] of >10(-5) M. Interaction with peroxiredoxin-6 is independent of Ca(2+). Co-localization of lactoferrin, S100P and calcyclin with ERC-55 in the perinuclear area was analyzed by fluorescence confocal microscopy. The functional variety of the interacting proteins indicates a broad spectrum of ERC-55 activities such as immunity, redox homeostasis, cell cycle regulation and coagulation.

  4. Potential application of remote sensing in monitoring informal settlements in South Africa where complimentary data does not exist

    CSIR Research Space (South Africa)

    Busgeeth, K

    2008-06-01

    Full Text Available as only the study conducted by Hofmann was available [7]. The study reported how informal settlements can be detected from other land-use-forms by describing typical characteristics of colour, texture, shape and context using remote sensed data from.... This approach may be appropriate for larger buildings, but Hofmann found that individual shacks could not be identified on IKONOS imagery [7]. QuickBird has a higher spatial resolution than IKONOS, at 0.6m vs 1m in the panchromatic band; this represents a...

  5. 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

  6. NASA's Indigenous Capacity Building Initiative: Balancing Traditional Knowledge and Existing Remote Sensing Training to Inform Management Decisions

    Science.gov (United States)

    McCullum, A. J. K.; Schmidt, C.; Palacios, S. L.; Ly, V.

    2017-12-01

    NASA's Indigenous Capacity Building Initiative is aimed to provide remote sensing training, mentoring, and research opportunities to the indigenous community. A key programmatic goal is the co-production of place-based trainings where participants have the opportunity to address specific natural resource research and management issues facing their tribal lands. Three primary strategies have been adopted to engage with our tribal partners, these include: (1) the use of existing tribal networks and conferences such as the National Tribal GIS Conference, (2) coordination with other federal agencies such as the Bureau of Indian Affairs (BIA) and tribal liaisons at regional Climate Science Centers, and (3) connecting with tribes directly. Regional partner visits with tribes, such as meetings with the Samish Indian Nation, are integral to cultivate trusting, collaborative, and sustained partnerships and an understanding of how Earth Observations can be applied to the unique set of challenges and goals each tribe faces. As the program continues to grow, we aim to increase our incorporation of Traditional Ecological Knowledge (TEK) into technical methods and to develop trainings tailored to thematic areas of interest to specific tribes. Engagement and feedback are encouraged to refine our approaches to increase capacity within the indigenous community to utilize NASA Earth Observations.

  7. 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.

  8. Inferring repeat-protein energetics from evolutionary information.

    Directory of Open Access Journals (Sweden)

    Rocío Espada

    2017-06-01

    Full Text Available Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing covariations in extant sequences. Still, many natural proteins that fold into the same structural topology show different stabilization energies, and these are often related to their physiological behavior. We propose a description for the energetic variation given by sequence modifications in repeat proteins, systems for which the overall problem is simplified by their inherent symmetry. We explicitly account for single amino acid and pair-wise interactions and treat higher order correlations with a single term. We show that the resulting evolutionary field can be interpreted with structural detail. We trace the variations in the energetic scores of natural proteins and relate them to their experimental characterization. The resulting energetic evolutionary field allows the prediction of the folding free energy change for several mutants, and can be used to generate synthetic sequences that are statistically indistinguishable from the natural counterparts.

  9. Additional phase information from UV damage of selenomethionine labelled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Sanctis, Daniele de [ESRF, Structural Biology Group, 6 rue Jules Horowitz, 38043 Grenoble Cedex (France); Tucker, Paul A.; Panjikar, Santosh, E-mail: panjikar@embl-hamburg.de [EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg (Germany)

    2011-05-01

    Successful examples of ultraviolet radiation-damage-induced phasing with anomalous scattering from selenomethionine protein crystals have been demonstrated. Currently, selenium is the most widely used phasing vehicle for experimental phasing, either by single anomalous scattering or multiple-wavelength anomalous dispersion (MAD) procedures. The use of the single isomorphous replacement anomalous scattering (SIRAS) phasing procedure with selenomethionine containing proteins is not so commonly used, as it requires isomorphous native data. Here it is demonstrated that isomorphous differences can be measured from intensity changes measured from a selenium labelled protein crystal before and after UV exposure. These can be coupled with the anomalous signal from the dataset collected at the selenium absorption edge to obtain SIRAS phases in a UV-RIPAS phasing experiment. The phasing procedure for two selenomethionine proteins, the feruloyl esterase module of xylanase 10B from Clostridium thermocellum and the Mycobacterium tuberculosis chorismate synthase, have been investigated using datasets collected near the absorption edge of selenium before and after UV radiation. The utility of UV radiation in measuring radiation damage data for isomorphous differences is highlighted and it is shown that, after such measurements, the UV-RIPAS procedure yields comparable phase sets with those obtained from the conventional MAD procedure. The results presented are encouraging for the development of alternative phasing approaches for selenomethionine proteins in difficult cases.

  10. 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...

  11. A method for partitioning the information contained in a protein sequence between its structure and function.

    Science.gov (United States)

    Possenti, Andrea; Vendruscolo, Michele; Camilloni, Carlo; Tiana, Guido

    2018-05-23

    Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance between the amount of information supplied by the sequence and that left after that the protein has folded into its structure. We study the amount of information necessary to specify the protein structure, providing an estimate that keeps into account the thermodynamic properties of protein folding. We thus show that the information remaining in the protein sequence after encoding for its structure (the 'information gap') is very close to what needed to encode for its function and interactions. Then, by predicting the information gap directly from the protein sequence, we show that it may be possible to use these insights from information theory to discriminate between ordered and disordered proteins, to identify unknown functions, and to optimize artificially-designed protein sequences. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

  12. Does representative wind information exist?

    NARCIS (Netherlands)

    Wieringa, J.

    1996-01-01

    Representativity requirements are discussed for various wind data users. It is shown that most applications can be dealt with by using data from wind stations when these are made to conform with WMO specifications. Methods to achieve this WMO normalization are reviewed, giving minimum specifications

  13. Protein Signaling Networks from Single Cell Fluctuations and Information Theory Profiling

    Science.gov (United States)

    Shin, Young Shik; Remacle, F.; Fan, Rong; Hwang, Kiwook; Wei, Wei; Ahmad, Habib; Levine, R.D.; Heath, James R.

    2011-01-01

    Protein signaling networks among cells play critical roles in a host of pathophysiological processes, from inflammation to tumorigenesis. We report on an approach that integrates microfluidic cell handling, in situ protein secretion profiling, and information theory to determine an extracellular protein-signaling network and the role of perturbations. We assayed 12 proteins secreted from human macrophages that were subjected to lipopolysaccharide challenge, which emulates the macrophage-based innate immune responses against Gram-negative bacteria. We characterize the fluctuations in protein secretion of single cells, and of small cell colonies (n = 2, 3,···), as a function of colony size. Measuring the fluctuations permits a validation of the conditions required for the application of a quantitative version of the Le Chatelier's principle, as derived using information theory. This principle provides a quantitative prediction of the role of perturbations and allows a characterization of a protein-protein interaction network. PMID:21575571

  14. Collection and analysis of existing information on applicability of investigation methods for estimation of beginning age of faulting in present faulting pattern

    International Nuclear Information System (INIS)

    Doke, Ryosuke; Yasue, Ken-ichi; Tanikawa, Shin-ichi; Nakayasu, Akio; Niizato, Tadafumi; Tanaka, Takenobu; Aoki, Michinori; Sekiya, Ayako

    2011-12-01

    In the field of R and D programs of a geological disposal of high level radioactive waste, it is great importance to develop a set of investigation and analysis techniques for the assessment of long-term geosphere stability over a geological time, which means that any changes of geological environment will not significantly impact on the long-term safety of a geological disposal system. In Japanese archipelago, crustal movements are so active that uplift and subsidence are remarkable in recent several hundreds of thousands of years. Therefore, it is necessary to assess the long-term geosphere stability taking into account a topographic change caused by crustal movements. One of the factors for the topographic change is the movement of an active fault, which is a geological process to release a strain accumulated by plate motion. A beginning age of the faulting in the present faulting pattern suggests the beginning age of neotectonic activities around the active fault, and also provides basic information to identifying the stage of a geomorphic development of mountains. Therefore, the age of faulting in the present faulting pattern is important information to estimate a topographic change in the future on the mountain regions of Japan. In this study, existing information related to methods for the estimation of the beginning age of the faulting in the present faulting pattern on the active fault were collected and reviewed. A principle of method, noticing points and technical know-hows in the application of the methods, data uncertainty, and so on were extracted from the existing information. Based on these extracted information, task-flows indicating working process on the estimation of the beginning age for the faulting of the active fault were illustrated on each method. Additionally, the distribution map of the beginning age with accuracy of faulting in the present faulting pattern on the active fault was illustrated. (author)

  15. 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.

  16. The presence of blogs in the field of Library and Information Sciences in Spain: Can we talk about the existence of a “Biblogsfera”?

    Directory of Open Access Journals (Sweden)

    Miguel Ángel Vera Baceta

    2014-03-01

    Full Text Available The blog phenomenon has meant a natural way of grouping and establishing communication amongst those who have similar concerns. This has happened the same way in the field of science, thus creating communities of special interest in a context in which blogs are consolidating as sources of information and extra tools for research. While the authors’ freedom to organise and offer their contents may be considered one of the main advantages and a trigger for the success of blogs, it is also one of their main drawbacks. The contents and communities of blogs are not easy to identify, classify and quantify, so that they constitute a vague concept under the name of “blogosphere”. This article is meant to identify the blogs related to the field of Library and Information Sciences in Spain, their authorship, their contents and their connections in order to clarify if we can really talk about the existence of a “Biblogsfera”.

  17. 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

    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......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...

  18. GPCRdb: an information system for G protein-coupled receptors.

    Science.gov (United States)

    Isberg, Vignir; Mordalski, Stefan; Munk, Christian; Rataj, Krzysztof; Harpsøe, Kasper; Hauser, Alexander S; Vroling, Bas; Bojarski, Andrzej J; Vriend, Gert; Gloriam, David E

    2016-01-04

    Recent developments in G protein-coupled receptor (GPCR) structural biology and pharmacology have greatly enhanced our knowledge of receptor structure-function relations, and have helped improve the scientific foundation for drug design studies. The GPCR database, GPCRdb, serves a dual role in disseminating and enabling new scientific developments by providing reference data, analysis tools and interactive diagrams. This paper highlights new features in the fifth major GPCRdb release: (i) GPCR crystal structure browsing, superposition and display of ligand interactions; (ii) direct deposition by users of point mutations and their effects on ligand binding; (iii) refined snake and helix box residue diagram looks; and (iii) phylogenetic trees with receptor classification colour schemes. Under the hood, the entire GPCRdb front- and back-ends have been re-coded within one infrastructure, ensuring a smooth browsing experience and development. GPCRdb is available at http://www.gpcrdb.org/ and it's open source code at https://bitbucket.org/gpcr/protwis. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Laboratory information management system for membrane protein structure initiative--from gene to crystal.

    Science.gov (United States)

    Troshin, Petr V; Morris, Chris; Prince, Stephen M; Papiz, Miroslav Z

    2008-12-01

    Membrane Protein Structure Initiative (MPSI) exploits laboratory competencies to work collaboratively and distribute work among the different sites. This is possible as protein structure determination requires a series of steps, starting with target selection, through cloning, expression, purification, crystallization and finally structure determination. Distributed sites create a unique set of challenges for integrating and passing on information on the progress of targets. This role is played by the Protein Information Management System (PIMS), which is a laboratory information management system (LIMS), serving as a hub for MPSI, allowing collaborative structural proteomics to be carried out in a distributed fashion. It holds key information on the progress of cloning, expression, purification and crystallization of proteins. PIMS is employed to track the status of protein targets and to manage constructs, primers, experiments, protocols, sample locations and their detailed histories: thus playing a key role in MPSI data exchange. It also serves as the centre of a federation of interoperable information resources such as local laboratory information systems and international archival resources, like PDB or NCBI. During the challenging task of PIMS integration, within the MPSI, we discovered a number of prerequisites for successful PIMS integration. In this article we share our experiences and provide invaluable insights into the process of LIMS adaptation. This information should be of interest to partners who are thinking about using LIMS as a data centre for their collaborative efforts.

  20. Elman RNN based classification of proteins sequences on account of their mutual information.

    Science.gov (United States)

    Mishra, Pooja; Nath Pandey, Paras

    2012-10-21

    In the present work we have employed the method of estimating residue correlation within the protein sequences, by using the mutual information (MI) of adjacent residues, based on structural and solvent accessibility properties of amino acids. The long range correlation between nonadjacent residues is improved by constructing a mutual information vector (MIV) for a single protein sequence, like this each protein sequence is associated with its corresponding MIVs. These MIVs are given to Elman RNN to obtain the classification of protein sequences. The modeling power of MIV was shown to be significantly better, giving a new approach towards alignment free classification of protein sequences. We also conclude that sequence structural and solvent accessible property based MIVs are better predictor. Copyright © 2012 Elsevier Ltd. All rights reserved.

  1. 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

  2. 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, B 12 , 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 B 12 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

  3. 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

  4. 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

    Energy Technology Data Exchange (ETDEWEB)

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

    2001-03-01

    A large protein superfamily with over 500 members has been discovered and analyzed using powerful new bioinformatics and information visualization methods. Evidence exists that these proteins generate a 5?-deoxyadenosyl radical by reductive cleavage of S-adenosylmethionine (SAM) through an unusual Fe-S center. Radical SAM superfamily proteins function in DNA precursor, vitamin, cofactor, antibiotic, and herbicide biosynthesis in a collection of basic and familiar pathways. One of the members is interferon-inducible and is considered a candidate drug target for osteoporosis. The identification of this superfamily suggests that radical-based catalysis is important in a number of previously well-studied but unresolved biochemical pathways.

  5. Defining the limits of homology modeling in information-driven protein docking

    NARCIS (Netherlands)

    Garcia Lopes Maia Rodrigues, João; Melquiond, A S J; Karaca, E; Trellet, M; van Dijk, M; van Zundert, G C P; Schmitz, C; de Vries, S J; Bordogna, A; Bonati, L; Kastritis, P L; Bonvin, Alexandre M J J; Garcia Lopes Maia Rodrigues, João

    2013-01-01

    Information-driven docking is currently one of the most successful approaches to obtain structural models of protein interactions as demonstrated in the latest round of CAPRI. While various experimental and computational techniques can be used to retrieve information about the binding mode, the

  6. Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.

    Science.gov (United States)

    Prlic, Andreas; Kalro, Tara; Bhattacharya, Roshni; Christie, Cole; Burley, Stephen K; Rose, Peter W

    2016-12-15

    The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules. To allow an interpretation of how PDB data relates to other publicly available annotations, we developed a novel data integration platform that maps 3D structural information across various datasets. This integration bridges from the human genome across protein sequence to 3D structure space. We developed novel software solutions for data management and visualization, while incorporating new libraries for web-based visualization using SVG graphics. The new views are available from http://www.rcsb.org and software is available from https://github.com/rcsb/. andreas.prlic@rcsb.orgSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  7. 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....... 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. Availability...... 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...

  8. Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

    Science.gov (United States)

    Ochoa, David; García-Gutiérrez, Ponciano; Juan, David; Valencia, Alfonso; Pazos, Florencio

    2013-01-27

    A widespread family of methods for studying and predicting protein interactions using sequence information is based on co-evolution, quantified as similarity of phylogenetic trees. Part of the co-evolution observed between interacting proteins could be due to co-adaptation caused by inter-protein contacts. In this case, the co-evolution is expected to be more evident when evaluated on the surface of the proteins or the internal layers close to it. In this work we study the effect of incorporating information on predicted solvent accessibility to three methods for predicting protein interactions based on similarity of phylogenetic trees. We evaluate the performance of these methods in predicting different types of protein associations when trees based on positions with different characteristics of predicted accessibility are used as input. We found that predicted accessibility improves the results of two recent versions of the mirrortree methodology in predicting direct binary physical interactions, while it neither improves these methods, nor the original mirrortree method, in predicting other types of interactions. That improvement comes at no cost in terms of applicability since accessibility can be predicted for any sequence. We also found that predictions of protein-protein interactions are improved when multiple sequence alignments with a richer representation of sequences (including paralogs) are incorporated in the accessibility prediction.

  9. Predicting protein folding rate change upon point mutation using residue-level coevolutionary information.

    Science.gov (United States)

    Mallik, Saurav; Das, Smita; Kundu, Sudip

    2016-01-01

    Change in folding kinetics of globular proteins upon point mutation is crucial to a wide spectrum of biological research, such as protein misfolding, toxicity, and aggregations. Here we seek to address whether residue-level coevolutionary information of globular proteins can be informative to folding rate changes upon point mutations. Generating residue-level coevolutionary networks of globular proteins, we analyze three parameters: relative coevolution order (rCEO), network density (ND), and characteristic path length (CPL). A point mutation is considered to be equivalent to a node deletion of this network and respective percentage changes in rCEO, ND, CPL are found linearly correlated (0.84, 0.73, and -0.61, respectively) with experimental folding rate changes. The three parameters predict the folding rate change upon a point mutation with 0.031, 0.045, and 0.059 standard errors, respectively. © 2015 Wiley Periodicals, Inc.

  10. The Coding of Biological Information: From Nucleotide Sequence to Protein Recognition

    Science.gov (United States)

    Štambuk, Nikola

    The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.

  11. The Mitochondrial Protein Atlas: A Database of Experimentally Verified Information on the Human Mitochondrial Proteome.

    Science.gov (United States)

    Godin, Noa; Eichler, Jerry

    2017-09-01

    Given its central role in various biological systems, as well as its involvement in numerous pathologies, the mitochondrion is one of the best-studied organelles. However, although the mitochondrial genome has been extensively investigated, protein-level information remains partial, and in many cases, hypothetical. The Mitochondrial Protein Atlas (MPA; URL: lifeserv.bgu.ac.il/wb/jeichler/MPA ) is a database that provides a complete, manually curated inventory of only experimentally validated human mitochondrial proteins. The MPA presently contains 911 unique protein entries, each of which is associated with at least one experimentally validated and referenced mitochondrial localization. The MPA also contains experimentally validated and referenced information defining function, structure, involvement in pathologies, interactions with other MPA proteins, as well as the method(s) of analysis used in each instance. Connections to relevant external data sources are offered for each entry, including links to NCBI Gene, PubMed, and Protein Data Bank. The MPA offers a prototype for other information sources that allow for a distinction between what has been confirmed and what remains to be verified experimentally.

  12. 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

  13. Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis.

    Science.gov (United States)

    Mahajan, Gaurang; Mande, Shekhar C

    2017-04-04

    A comprehensive map of the human-M. tuberculosis (MTB) protein interactome would help fill the gaps in our understanding of the disease, and computational prediction can aid and complement experimental studies towards this end. Several sequence-based in silico approaches tap the existing data on experimentally validated protein-protein interactions (PPIs); these PPIs serve as templates from which novel interactions between pathogen and host are inferred. Such comparative approaches typically make use of local sequence alignment, which, in the absence of structural details about the interfaces mediating the template interactions, could lead to incorrect inferences, particularly when multi-domain proteins are involved. We propose leveraging the domain-domain interaction (DDI) information in PDB complexes to score and prioritize candidate PPIs between host and pathogen proteomes based on targeted sequence-level comparisons. Our method picks out a small set of human-MTB protein pairs as candidates for physical interactions, and the use of functional meta-data suggests that some of them could contribute to the in vivo molecular cross-talk between pathogen and host that regulates the course of the infection. Further, we present numerical data for Pfam domain families that highlights interaction specificity on the domain level. Not every instance of a pair of domains, for which interaction evidence has been found in a few instances (i.e. structures), is likely to functionally interact. Our sorting approach scores candidates according to how "distant" they are in sequence space from known examples of DDIs (templates). Thus, it provides a natural way to deal with the heterogeneity in domain-level interactions. Our method represents a more informed application of local alignment to the sequence-based search for potential human-microbial interactions that uses available PPI data as a prior. Our approach is somewhat limited in its sensitivity by the restricted size and

  14. Integration of the Ovation Based Distributed Turbine Control System into the Existing Process Information System and Full Scope Simulator at NPP Krsko

    International Nuclear Information System (INIS)

    Cicvaric, D.

    2010-01-01

    Programmable Digital Electro Hydraulic System (PDEH) is Turbine Control System (TCS), built on Emerson OVATION Distributed Control System (DCS) platform and installed by the Westinghouse Electric Company at the Krsko Nuclear Power Plant as the replacement for the DEH Mod II turbine control system. Core of the PDEH system consist of three pairs of redundant controllers (ETS, OA/OPC and ATC/MSR) configured for the Turbine Generator (TG) set protection, control and monitoring functions. Existing serial data link between replaced DEH Mod II and Process Information System (PIS) was removed and replaced with redundant bi-directional Ethernet TCP/IP data link via two Data Link servers in client-server architecture configuration. All hardwired signals and some of the important calculated signals are being transferred from PDEH to PIS. Main purpose of PIS data link is trending utilization at the existing PIS workstations with pre-configured trend groups and centralized data archiving. Most of the PDEH display screens (mimics) were also replicated on the PIS platform, so that TG set monitoring and operation overview can be performed over the PIS network as well as over the Process Computer Network (PCN) with PMSNT-view utility. The simulator is implemented using a stimulated Windows based Ovation platform and a SGI IRIX based Plant Model Computer (PMC) using the L-3 MAPPS simulation software platform. Two PDEH stimulated systems are installed at the Krsko Full Scope Simulator (KFSS), one for foreground and another for background simulation. Stimulated PDEH hardware is essentially identical to that installed in the plant with the exception of hardware redundancy, isolation features and interface with physical plant I/O. The Ovation control logic sheets are executed with virtual controllers hosted on a simulator specific Virtual Controller Host (VCH) Workstation. The data interface between the simulator Ovation system and the PMC is accomplished through the Ethernet

  15. 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.

  16. MIPS: a database for protein sequences, homology data and yeast genome information.

    Science.gov (United States)

    Mewes, H W; Albermann, K; Heumann, K; Liebl, S; Pfeiffer, F

    1997-01-01

    The MIPS group (Martinsried Institute for Protein Sequences) at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, collects, processes and distributes protein sequence data within the framework of the tripartite association of the PIR-International Protein Sequence Database (,). MIPS contributes nearly 50% of the data input to the PIR-International Protein Sequence Database. The database is distributed on CD-ROM together with PATCHX, an exhaustive supplement of unique, unverified protein sequences from external sources compiled by MIPS. Through its WWW server (http://www.mips.biochem.mpg.de/ ) MIPS permits internet access to sequence databases, homology data and to yeast genome information. (i) Sequence similarity results from the FASTA program () are stored in the FASTA database for all proteins from PIR-International and PATCHX. The database is dynamically maintained and permits instant access to FASTA results. (ii) Starting with FASTA database queries, proteins have been classified into families and superfamilies (PROT-FAM). (iii) The HPT (hashed position tree) data structure () developed at MIPS is a new approach for rapid sequence and pattern searching. (iv) MIPS provides access to the sequence and annotation of the complete yeast genome (), the functional classification of yeast genes (FunCat) and its graphical display, the 'Genome Browser' (). A CD-ROM based on the JAVA programming language providing dynamic interactive access to the yeast genome and the related protein sequences has been compiled and is available on request. PMID:9016498

  17. 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

  18. Using Plain Language and Adding Communication Technology to an Existing Health-Related Questionnaire to Help Generate Accurate Information: Qualitative Study.

    Science.gov (United States)

    Welbie, Marlies; Wittink, Harriet; Westerman, Marjan J; Topper, Ilse; Snoei, Josca; Devillé, Walter Ljm

    2018-04-23

    Low-educated patients are disadvantaged in using questionnaires within the health care setting because most health-related questionnaires do not take the educational background of patients into account. The Dutch Talking Touch Screen Questionnaire (DTTSQ) was developed in an attempt to meet the needs of low-educated patients by using plain language and adding communication technology to an existing paper-based questionnaire. For physical therapists to use the DTTSQ as part of their intake procedure, it needs to generate accurate information from all of their patients, independent of educational level. The aim of this study was to get a first impression of the information that is generated by the DTTSQ. To achieve this goal, response processes of physical therapy patients with diverse levels of education were analyzed. The qualitative Three-Step Test-Interview method was used to collect observational data on actual response behavior of 24 physical therapy patients with diverse levels of education. The interviews included both think-aloud and retrospective probing techniques. Of the 24 respondents, 20 encountered one or more problems during their response process. The use of plain language and information and communication technology (ICT) appeared to have a positive effect on the comprehensibility of the DTTSQ. However, it also had some negative effects on the interpretation, retrieval, judgment, and response selection within the response processes of the participants in this study. No educational group in this research population stood out from the rest in the kind or number of problems that arose. All respondents recognized themselves in the outcomes of the questionnaire. The use of plain language and ICT within the DTTSQ had both positive and negative effects on the response processes of its target population. The results of this study emphasize the importance of earlier recommendations to accompany any adaption of any questionnaire to a new mode of delivery by

  19. Accurate protein structure modeling using sparse NMR data and homologous structure information.

    Science.gov (United States)

    Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

    2012-06-19

    While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

  20. 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/.

  1. 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

  2. Accessible surface area of proteins from purely sequence information and the importance of global features

    Science.gov (United States)

    Faraggi, Eshel; Zhou, Yaoqi; Kloczkowski, Andrzej

    2014-03-01

    We present a new approach for predicting the accessible surface area of proteins. The novelty of this approach lies in not using residue mutation profiles generated by multiple sequence alignments as descriptive inputs. Rather, sequential window information and the global monomer and dimer compositions of the chain are used. We find that much of the lost accuracy due to the elimination of evolutionary information is recouped by the use of global features. Furthermore, this new predictor produces similar results for proteins with or without sequence homologs deposited in the Protein Data Bank, and hence shows generalizability. Finally, these predictions are obtained in a small fraction (1/1000) of the time required to run mutation profile based prediction. All these factors indicate the possible usability of this work in de-novo protein structure prediction and in de-novo protein design using iterative searches. Funded in part by the financial support of the National Institutes of Health through Grants R01GM072014 and R01GM073095, and the National Science Foundation through Grant NSF MCB 1071785.

  3. pLoc-mVirus: Predict subcellular localization of multi-location virus proteins via incorporating the optimal GO information into general PseAAC.

    Science.gov (United States)

    Cheng, Xiang; Xiao, Xuan; Chou, Kuo-Chen

    2017-09-10

    Knowledge of subcellular locations of proteins is crucially important for in-depth understanding their functions in a cell. With the explosive growth of protein sequences generated in the postgenomic age, it is highly demanded to develop computational tools for timely annotating their subcellular locations based on the sequence information alone. The current study is focused on virus proteins. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions. This kind of multiplex proteins is particularly important for both basic research and drug design. Using the multi-label theory, we present a new predictor called "pLoc-mVirus" by extracting the optimal GO (Gene Ontology) information into the general PseAAC (Pseudo Amino Acid Composition). Rigorous cross-validation on a same stringent benchmark dataset indicated that the proposed pLoc-mVirus predictor is remarkably superior to iLoc-Virus, the state-of-the-art method in predicting virus protein subcellular localization. To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc-mVirus/, by which users can easily get their desired results without the need to go through the complicated mathematics involved. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. pLoc-mPlant: predict subcellular localization of multi-location plant proteins by incorporating the optimal GO information into general PseAAC.

    Science.gov (United States)

    Cheng, Xiang; Xiao, Xuan; Chou, Kuo-Chen

    2017-08-22

    One of the fundamental goals in cellular biochemistry is to identify the functions of proteins in the context of compartments that organize them in the cellular environment. To realize this, it is indispensable to develop an automated method for fast and accurate identification of the subcellular locations of uncharacterized proteins. The current study is focused on plant protein subcellular location prediction based on the sequence information alone. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most of the existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions. This kind of multiplex protein is particularly important for both basic research and drug design. Using the multi-label theory, we present a new predictor called "pLoc-mPlant" by extracting the optimal GO (Gene Ontology) information into the Chou's general PseAAC (Pseudo Amino Acid Composition). Rigorous cross-validation on the same stringent benchmark dataset indicated that the proposed pLoc-mPlant predictor is remarkably superior to iLoc-Plant, the state-of-the-art method for predicting plant protein subcellular localization. To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at , by which users can easily get their desired results without the need to go through the complicated mathematics involved.

  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. Prediction of glutathionylation sites in proteins using minimal sequence information and their experimental validation.

    Science.gov (United States)

    Pal, Debojyoti; Sharma, Deepak; Kumar, Mukesh; Sandur, Santosh K

    2016-09-01

    S-glutathionylation of proteins plays an important role in various biological processes and is known to be protective modification during oxidative stress. Since, experimental detection of S-glutathionylation is labor intensive and time consuming, bioinformatics based approach is a viable alternative. Available methods require relatively longer sequence information, which may prevent prediction if sequence information is incomplete. Here, we present a model to predict glutathionylation sites from pentapeptide sequences. It is based upon differential association of amino acids with glutathionylated and non-glutathionylated cysteines from a database of experimentally verified sequences. This data was used to calculate position dependent F-scores, which measure how a particular amino acid at a particular position may affect the likelihood of glutathionylation event. Glutathionylation-score (G-score), indicating propensity of a sequence to undergo glutathionylation, was calculated using position-dependent F-scores for each amino-acid. Cut-off values were used for prediction. Our model returned an accuracy of 58% with Matthew's correlation-coefficient (MCC) value of 0.165. On an independent dataset, our model outperformed the currently available model, in spite of needing much less sequence information. Pentapeptide motifs having high abundance among glutathionylated proteins were identified. A list of potential glutathionylation hotspot sequences were obtained by assigning G-scores and subsequent Protein-BLAST analysis revealed a total of 254 putative glutathionable proteins, a number of which were already known to be glutathionylated. Our model predicted glutathionylation sites in 93.93% of experimentally verified glutathionylated proteins. Outcome of this study may assist in discovering novel glutathionylation sites and finding candidate proteins for glutathionylation.

  7. Coulomb interactions between cytoplasmic electric fields and phosphorylated messenger proteins optimize information flow in cells.

    Directory of Open Access Journals (Sweden)

    Robert A Gatenby

    2010-08-01

    Full Text Available Normal cell function requires timely and accurate transmission of information from receptors on the cell membrane (CM to the nucleus. Movement of messenger proteins in the cytoplasm is thought to be dependent on random walk. However, Brownian motion will disperse messenger proteins throughout the cytosol resulting in slow and highly variable transit times. We propose that a critical component of information transfer is an intracellular electric field generated by distribution of charge on the nuclear membrane (NM. While the latter has been demonstrated experimentally for decades, the role of the consequent electric field has been assumed to be minimal due to a Debye length of about 1 nanometer that results from screening by intracellular Cl- and K+. We propose inclusion of these inorganic ions in the Debye-Huckel equation is incorrect because nuclear pores allow transit through the membrane at a rate far faster than the time to thermodynamic equilibrium. In our model, only the charged, mobile messenger proteins contribute to the Debye length.Using this revised model and published data, we estimate the NM possesses a Debye-Huckel length of a few microns and find this is consistent with recent measurement using intracellular nano-voltmeters. We demonstrate the field will accelerate isolated messenger proteins toward the nucleus through Coulomb interactions with negative charges added by phosphorylation. We calculate transit times as short as 0.01 sec. When large numbers of phosphorylated messenger proteins are generated by increasing concentrations of extracellular ligands, we demonstrate they generate a self-screening environment that regionally attenuates the cytoplasmic field, slowing movement but permitting greater cross talk among pathways. Preliminary experimental results with phosphorylated RAF are consistent with model predictions.This work demonstrates that previously unrecognized Coulomb interactions between phosphorylated messenger

  8. Enhancing the prediction of protein pairings between interacting families using orthology information

    Directory of Open Access Journals (Sweden)

    Pazos Florencio

    2008-01-01

    Full Text Available Abstract Background It has repeatedly been shown that interacting protein families tend to have similar phylogenetic trees. These similarities can be used to predicting the mapping between two families of interacting proteins (i.e. which proteins from one family interact with which members of the other. The correct mapping will be that which maximizes the similarity between the trees. The two families may eventually comprise orthologs and paralogs, if members of the two families are present in more than one organism. This fact can be exploited to restrict the possible mappings, simply by impeding links between proteins of different organisms. We present here an algorithm to predict the mapping between families of interacting proteins which is able to incorporate information regarding orthologues, or any other assignment of proteins to "classes" that may restrict possible mappings. Results For the first time in methods for predicting mappings, we have tested this new approach on a large number of interacting protein domains in order to statistically assess its performance. The method accurately predicts around 80% in the most favourable cases. We also analysed in detail the results of the method for a well defined case of interacting families, the sensor and kinase components of the Ntr-type two-component system, for which up to 98% of the pairings predicted by the method were correct. Conclusion Based on the well established relationship between tree similarity and interactions we developed a method for predicting the mapping between two interacting families using genomic information alone. The program is available through a web interface.

  9. 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

  10. Detection of Foot-and-mouth Disease Virus RNA and Capsid Protein in Lymphoid Tissues of Convalescent Pigs Does Not Indicate Existence of a Carrier State.

    Science.gov (United States)

    Stenfeldt, C; Pacheco, J M; Smoliga, G R; Bishop, E; Pauszek, S J; Hartwig, E J; Rodriguez, L L; Arzt, J

    2016-04-01

    A systematic study was performed to investigate the potential of pigs to establish and maintain persistent foot-and-mouth disease virus (FMDV) infection. Infectious virus could not be recovered from sera, oral, nasal or oropharyngeal fluids obtained after resolution of clinical infection with any of five FMDV strains within serotypes A, O and Asia-1. Furthermore, there was no isolation of live virus from tissue samples harvested at 28-100 days post-infection from convalescent pigs recovered from clinical or subclinical FMD. Despite lack of detection of infectious FMDV, there was a high prevalence of FMDV RNA detection in lymph nodes draining lesion sites harvested at 35 days post-infection, with the most frequent detection recorded in popliteal lymph nodes (positive detection in 88% of samples obtained from non-vaccinated pigs). Likewise, at 35 dpi, FMDV capsid antigen was localized within follicles of draining lymph nodes, but without concurrent detection of FMDV non-structural protein. There was a marked decline in the detection of FMDV RNA and antigen in tissue samples by 60 dpi, and no antigen or viral RNA could be detected in samples obtained at 100 dpi. The data presented herein provide the most extensive investigation of FMDV persistence in pigs. The overall conclusion is that domestic pigs are unlikely to be competent long-term carriers of infectious FMDV; however, transient persistence of FMDV protein and RNA in lymphoid tissues is common following clinical or subclinical infection. © Published 2014. This article is a US Government work and is in the public domain in the USA.

  11. 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…

  12. 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......The master two-dimensional gel database of human AMA cells currently lists 3801 cellular and secreted proteins, of which 371 cellular polypeptides (306 IEF; 65 NEPHGE) were added to the master images during the last 10 months. These include: (i) very basic and acidic proteins that do not focus...

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

    Directory of Open Access Journals (Sweden)

    Panwar Bharat

    2013-02-01

    Full Text Available Abstract 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

  14. IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.

    Science.gov (United States)

    Moal, Iain H; Barradas-Bautista, Didier; Jiménez-García, Brian; Torchala, Mieczyslaw; van der Velde, Arjan; Vreven, Thom; Weng, Zhiping; Bates, Paul A; Fernández-Recio, Juan

    2017-06-15

    In order to function, proteins frequently bind to one another and form 3D assemblies. Knowledge of the atomic details of these structures helps our understanding of how proteins work together, how mutations can lead to disease, and facilitates the designing of drugs which prevent or mimic the interaction. Atomic modeling of protein-protein interactions requires the selection of near-native structures from a set of docked poses based on their calculable properties. By considering this as an information retrieval problem, we have adapted methods developed for Internet search ranking and electoral voting into IRaPPA, a pipeline integrating biophysical properties. The approach enhances the identification of near-native structures when applied to four docking methods, resulting in a near-native appearing in the top 10 solutions for up to 50% of complexes benchmarked, and up to 70% in the top 100. IRaPPA has been implemented in the SwarmDock server ( http://bmm.crick.ac.uk/∼SwarmDock/ ), pyDock server ( http://life.bsc.es/pid/pydockrescoring/ ) and ZDOCK server ( http://zdock.umassmed.edu/ ), with code available on request. moal@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  15. 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.

  16. ProCKSI: a decision support system for Protein (Structure Comparison, Knowledge, Similarity and Information

    Directory of Open Access Journals (Sweden)

    Błażewicz Jacek

    2007-10-01

    Full Text Available Abstract Background We introduce the decision support system for Protein (Structure Comparison, Knowledge, Similarity and Information (ProCKSI. ProCKSI integrates various protein similarity measures through an easy to use interface that allows the comparison of multiple proteins simultaneously. It employs the Universal Similarity Metric (USM, the Maximum Contact Map Overlap (MaxCMO of protein structures and other external methods such as the DaliLite and the TM-align methods, the Combinatorial Extension (CE of the optimal path, and the FAST Align and Search Tool (FAST. Additionally, ProCKSI allows the user to upload a user-defined similarity matrix supplementing the methods mentioned, and computes a similarity consensus in order to provide a rich, integrated, multicriteria view of large datasets of protein structures. Results We present ProCKSI's architecture and workflow describing its intuitive user interface, and show its potential on three distinct test-cases. In the first case, ProCKSI is used to evaluate the results of a previous CASP competition, assessing the similarity of proposed models for given targets where the structures could have a large deviation from one another. To perform this type of comparison reliably, we introduce a new consensus method. The second study deals with the verification of a classification scheme for protein kinases, originally derived by sequence comparison by Hanks and Hunter, but here we use a consensus similarity measure based on structures. In the third experiment using the Rost and Sander dataset (RS126, we investigate how a combination of different sets of similarity measures influences the quality and performance of ProCKSI's new consensus measure. ProCKSI performs well with all three datasets, showing its potential for complex, simultaneous multi-method assessment of structural similarity in large protein datasets. Furthermore, combining different similarity measures is usually more robust than

  17. Complementary DNA and derived amino acid sequence of the α subunit of human complement protein C8: evidence for the existence of a separate α subunit messenger RNA

    International Nuclear Information System (INIS)

    Rao, A.G.; Howard, O.M.Z.; Ng, S.C.; Whitehead, A.S.; Colten, H.R.; Sodetz, J.M.

    1987-01-01

    The entire amino acid sequence of the α subunit (M/sub r/ 64,000) of the eight component of complement (C8) was determined by characterizing cDNA clones isolated from a human liver cDNA library. Two clones with overlapping inserts of net length 2.44 kilobases (kb) were isolated and found to contain the entire α coding region [1659 base pairs (bp)]. The 5' end consists of an untranslated region and a leader sequence of 30 amino acids. This sequence contains an apparent initiation Met, signal peptide, and propeptide which ends with an arginine-rich sequence that is characteristic of proteolytic processing sites found in the pro form of protein precursors. The 3' untranslated region contains two polyadenylation signals and a poly(A)sequence. RNA blot analysis of total cellular RNA from the human hepatoma cell line HepG2 revealed a message size of ∼2.5 kb. Features of the 5' and 3' sequences and the message size suggest that a separate mRNA codes for α and argues against the occurrence of a single-chain precursor form of the disulfide-linked α-λ subunit found in mature C8. Analysis of the derived amino acid sequence revealed several membrane surface seeking domains and a possible transmembrane domain. Analysis of the carbohydrate composition indicates 1 or 2 asparagine-linked but no O-linked oligosaccharide chains, a result consistent with predictions from the amino acid sequence. Most significantly, it exhibits a striking overall homology to human C9, with values of 24% on the basis of identity and 46% when conserved substitutions are allowed. As described in an accompanying report this homology also extends to the β subunit of C8

  18. pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information.

    Science.gov (United States)

    Cheng, Xiang; Xiao, Xuan; Chou, Kuo-Chen

    2018-05-01

    For in-depth understanding the functions of proteins in a cell, the knowledge of their subcellular localization is indispensable. The current study is focused on human protein subcellular location prediction based on the sequence information alone. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions that are particularly important for both basic research and drug design. Using the multi-label theory, we present a new predictor called 'pLoc-mHum' by extracting the crucial GO (Gene Ontology) information into the general PseAAC (Pseudo Amino Acid Composition). Rigorous cross-validations on a same stringent benchmark dataset have indicated that the proposed pLoc-mHum predictor is remarkably superior to iLoc-Hum, the state-of-the-art method in predicting the human protein subcellular localization. To maximize the convenience of most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc-mHum/, by which users can easily get their desired results without the need to go through the complicated mathematics involved. xcheng@gordonlifescience.org. Supplementary data are available at Bioinformatics online.

  19. Survey of the Effectiveness of Internet Information on Patient Education for Bone Morphogenetic Protein.

    Science.gov (United States)

    Huang, Meng; Briceño, Valentina; Lam, Sandi K; Luerssen, Thomas G; Jea, Andrew

    2016-03-01

    In light of recent reports of potential short- and long-term complications of bone morphogenetic protein (BMP) and increasing "off-label" use among spine surgeons, we wished to analyze online information on BMP and its controversial uses, as patients frequently search the Internet for medical information, even though the quality and accuracy of available information are highly variable. Between December 2014 and January 2015, we conducted a Google search to identify the 50 most accessed websites providing BMP information using the search phrase "bone morphogenetic protein." Websites were classified based on authorship. Each website was examined for the provision of appropriate patient inclusion and exclusion criteria, surgical and nonsurgical treatment alternatives, purported benefits, disclosure of common and potential complications, peer-reviewed literature citations, and discussion of off-label use. Two percent of websites were authored by private medical groups, 2% by academic medical groups, 10% by insurance companies, 16% by biomedical industries, 4% by news sources, 0% by lawyers, and 66% by others. Sixty-two percent referenced peer-reviewed literature. Benefits and complications were reported in 44% and 26% of websites, respectively. Surgical and nonsurgical treatment alternatives were mentioned in 16% and 4% of websites, respectively. Discussion of off-label BMP use occurred in 18% of websites. Our study showed the ineffectiveness of the Internet in reporting quality information on BMP use. We found that websites authored by insurance companies provide an acceptable foundation for patient education. This, however, cannot replace the need for a thorough dialogue between doctor and patient about risks, benefits, and indications. Copyright © 2016. Published by Elsevier Inc.

  20. 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.

  1. In_sight : Using Existing Wi-Fi networks to Provide Information on Occupancy and Exploitation of Educational Facilities using at Delft University of Technology

    NARCIS (Netherlands)

    van der Spek, S.C.; Verbree, E.; Meijers, B.M.; Bot, F.J.; Braaksma, H.H.; Braggaar, R.C.; Ligtvoet, B.R.; Staats, B.R.; Gartner, G.; Huang, H.

    2016-01-01

    The distribution of people in buildings, the occupancy of lecture-, work- and study places and the accessibility of facilities are essential information at university campuses who have to cope with limited and even shrinking budgets and huge, rising real estate costs. Only little insight is gained

  2. “How Can You Write About a Person Who Does Not Exist?”: Rethinking Pseudonymity and Informed Consent in Life History Research

    Directory of Open Access Journals (Sweden)

    Kate Mukungu

    2017-08-01

    Full Text Available This methodology paper recommends that, when possible, qualitative research on activism should be designed to enable each participant to choose between using a pseudonym and one’s actual name. The stance is informed by life history data collection encounters with women in post-conflict settings whose activism seeks to eliminate violence against women and girls (VAWG. The benefits of accommodating a mix of names make this a viable alternative to the prevalent practice of obscuring all participants’ identities with pseudonyms. Writing about participants in a way that does no harm to them depends on the care and attention with which the researcher ascribes or dissociates data to or from them, regardless of the name used. Process consent is desirable as participants’ consent is not fully informed prior to data collection. One aspect of informed consent worthy of attention is the need to explain the methods of data analysis and presentation of findings to life history participants. The above practices help ensure that negotiating informed consent with participants whilst acting towards the principle of doing no harm are tailored to the particular features of the life history method.

  3. Collection and analysis of existing information on applicability of investigation methods for characterizing natural events/processes in a coastal region

    International Nuclear Information System (INIS)

    Nakayasu, Akio; Niizato, Tadafumi; Yasue, Ken-ichi; Doke, Ryosuke; Shigehiro, Michiko; Tanaka, Takenobu; Aoki, Michinori; Sekiya, Ayako

    2011-02-01

    The investigation methods for characterizing natural events and processes in a coastal field have been extracted on the basis of analysis of previous research. Collected information is classified into three groups according to the characteristics of natural events/processes and investigation methods. First group is the methods for evaluation of uplift, subsidence and sedimentation rates. Second group is the methods for evaluation of denudation rates. The third group is the methods for reconstruction of the climatic and sea-level changes. Study area, timeframe of the investigation, work sequences, techniques for age-determination, index and objects for characterizing natural events/processes, etc. in each research example were arranged in an 'information spread sheet'. Information on applicability of the each investigation method was extracted from information spread sheet, and was arranged in tabular form. Based on an analysis of the above information, investigation method that can be applied to a coastal region was extracted. The methods and indices are as follows: Uplift rate: the heights of marine terraces are the most important index in an upheaval region. Subsidence and sedimentation rate: the depths of strata underlying an alluvial plain are main indices in a subsidence region. Denudation rate: the features of marine terrace are main indices and the inspection of denudation processes by the use of a numerical simulation is necessary. Climate change: lacustrine deposits are main object for investigation. Sea-level change: reconstruction of relative sea-level change curve including uplift/subsidence factor and paleogeography based on acoustic exploration and the investigation of marine terraces. (author)

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

    International Nuclear Information System (INIS)

    1995-01-01

    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 ampersand 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

  6. “How Can You Write About a Person Who Does Not Exist?”: Rethinking Pseudonymity and Informed Consent in Life History Research

    OpenAIRE

    Kate Mukungu

    2017-01-01

    This methodology paper recommends that, when possible, qualitative research on activism should be designed to enable each participant to choose between using a pseudonym and one’s actual name. The stance is informed by life history data collection encounters with women in post-conflict settings whose activism seeks to eliminate violence against women and girls (VAWG). The benefits of accommodating a mix of names make this a viable alternative to the prevalent practice of obscuring all partici...

  7. Music, movies and meaning: Communication in film-makers' Search for pre-existing music, and the implications for music information retrieval

    OpenAIRE

    Inskip, C.; Macfarlane, A.; Rafferty, P.

    2008-01-01

    While the use of music to accompany moving images is widespread, the information behaviour, communicative practice and decision making by creative professionals within this area of the music industry is an under-researched area. This investigation discusses the use of music in films and advertising focusing on communication and meaning of the music and introduces a reflexive communication model. The model is discussed in relation to interviews with a sample of music professionals who search f...

  8. Music, movies and meaning: communication in film-markers' search for pre-existing music, and the implications for music information retrieval

    OpenAIRE

    Inskip, C.; MacFarlane, A.; Rafferty, P.

    2008-01-01

    While the use of music to accompany moving images is widespread, the information behaviour, communicative practice and decision making by creative professionals within this area of the music industry is an under-researched area. This investigation discusses the use of music in films and advertising focusing on communication and meaning of the music and introduces a reflexive communication model. The model is discussed in relation to interviews with a sample of music professionals who search f...

  9. 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.

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

    KAUST Repository

    Gojobori, Takashi; Ikeo, Kazuho; Katayama, Yukie; Kawabata, Takeshi; Kinjo, Akira R.; Kinoshita, Kengo; Kwon, Yeondae; Migita, Ohsuke; Mizutani, Hisashi; Muraoka, Masafumi; Nagata, Koji; Omori, Satoshi; Sugawara, Hideaki; Yamada, Daichi; Yura, Kei

    2016-01-01

    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/.

  11. 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/.

  12. A systematic identification of species-specific protein succinylation sites using joint element features information

    Directory of Open Access Journals (Sweden)

    Hasan MM

    2017-08-01

    Full Text Available Md Mehedi Hasan,1 Mst Shamima Khatun,2 Md Nurul Haque Mollah,2 Cao Yong,3 Dianjing Guo1 1School of Life Sciences and the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territory, Hong Kong, People’s Republic of China; 2Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh; 3Department of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen Graduate School, Shenzhen, People’s Republic of China Abstract: Lysine succinylation, an important type of protein posttranslational modification, plays significant roles in many cellular processes. Accurate identification of succinylation sites can facilitate our understanding about the molecular mechanism and potential roles of lysine succinylation. However, even in well-studied systems, a majority of the succinylation sites remain undetected because the traditional experimental approaches to succinylation site identification are often costly, time-consuming, and laborious. In silico approach, on the other hand, is potentially an alternative strategy to predict succinylation substrates. In this paper, a novel computational predictor SuccinSite2.0 was developed for predicting generic and species-specific protein succinylation sites. This predictor takes the composition of profile-based amino acid and orthogonal binary features, which were used to train a random forest classifier. We demonstrated that the proposed SuccinSite2.0 predictor outperformed other currently existing implementations on a complementarily independent dataset. Furthermore, the important features that make visible contributions to species-specific and cross-species-specific prediction of protein succinylation site were analyzed. The proposed predictor is anticipated to be a useful computational resource for lysine succinylation site prediction. The integrated species-specific online tool of SuccinSite2.0 is publicly

  13. 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.

  14. 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.

  15. How best to assess quality of life in informal carers of people with dementia; A systematic review of existing outcome measures

    Science.gov (United States)

    Robinson, Jonah; Robalino, Shannon; Finch, Tracy; McColl, Elaine

    2018-01-01

    Background In the UK, there are currently 800 000 people living with dementia. This number is expected to double in the next 20 years. Two-thirds of people with dementia live in the community supported by informal carers. Caring for a person with dementia has adverse effects on psychological, physical, social wellbeing and quality of life. The measurement of quality of life of carers of people with dementia is increasingly of interest to health and social care practitioners and commissioners, policymakers, and carers themselves. However, there is lack of consensus on the most suitable instrument(s) for undertaking this. Methods A systematic review of the literature using COSMIN methodology. Searching of electronic databases (Medline, PsycINFO, CINAHL and Web of Science), reference list and citation searching of key papers was undertaken. COSMIN methodology was used to simultaneously extract data from and assess methodological quality of included studies, and make a recommendation for the instrument with the most high quality evidence for its measurement properties. Results Ten instruments were suitable for inclusion in this review. The Carer well-being and support questionnaire (CWS) has the best quality evidence for the greatest number of measurement of properties. The Caregiver Well-Being Scale is also worthy of consideration. There is not presently a measure which could be recommended for use in economic evaluations, however the Impact of Alzheimer’s Disease on the Caregiver questionnaire (IADCQ) could potentially be used following further investigation of its measurement properties in a representative population. Conclusion The CWS is the most appropriate instrument to recommend for the assessment of quality of life in informal carers of people with dementia at present. All instruments included in this review would benefit from more rigorous evaluation of their measurement properties. PMID:29538433

  16. 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.

  17. 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.

  18. 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....

  19. Greening Existing Tribal Buildings

    Science.gov (United States)

    Guidance about improving sustainability in existing tribal casinos and manufactured homes. Many steps can be taken to make existing buildings greener and healthier. They may also reduce utility and medical costs.

  20. AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins.

    Science.gov (United States)

    Ferro, Myriam; Brugière, Sabine; Salvi, Daniel; Seigneurin-Berny, Daphné; Court, Magali; Moyet, Lucas; Ramus, Claire; Miras, Stéphane; Mellal, Mourad; Le Gall, Sophie; Kieffer-Jaquinod, Sylvie; Bruley, Christophe; Garin, Jérôme; Joyard, Jacques; Masselon, Christophe; Rolland, Norbert

    2010-06-01

    Recent advances in the proteomics field have allowed a series of high throughput experiments to be conducted on chloroplast samples, and the data are available in several public databases. However, the accurate localization of many chloroplast proteins often remains hypothetical. This is especially true for envelope proteins. We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and envelope membranes. LC-MS/MS-based analyses first allowed building the AT_CHLORO database (http://www.grenoble.prabi.fr/protehome/grenoble-plant-proteomics/), a comprehensive repertoire of the 1323 proteins, identified by 10,654 unique peptide sequences, present in highly purified chloroplasts and their subfractions prepared from Arabidopsis thaliana leaves. This database also provides extensive proteomics information (peptide sequences and molecular weight, chromatographic retention times, MS/MS spectra, and spectral count) for a unique chloroplast protein accurate mass and time tag database gathering identified peptides with their respective and precise analytical coordinates, molecular weight, and retention time. We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). These data together with an in-depth investigation of the literature were compiled to provide accurate subplastidial localization of previously known and newly identified proteins. A unique knowledge base containing extensive information on the proteins identified in envelope fractions was thus obtained, allowing new insights into this membrane system to be revealed. Altogether, the data we obtained provide unexpected information about plastidial or subplastidial localization of some proteins that were not suspected to be associated to this membrane system. The spectral counting-based strategy was further

  1. 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.

  2. 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.

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

    International Nuclear Information System (INIS)

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

    2011-01-01

    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

  4. 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.

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

    OpenAIRE

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

    2008-01-01

    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 inter...

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

    Science.gov (United States)

    Konuma, Tsuyoshi; Harada, Erisa; Sugase, Kenji

    2015-12-01

    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.

  7. 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.

  8. 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.

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

    KAUST Repository

    Wang, Jim Jing-Yan; Gao, Xin

    2014-01-01

    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

  10. Why preeclampsia still exists?

    Science.gov (United States)

    Chelbi, Sonia T; Veitia, Reiner A; Vaiman, Daniel

    2013-08-01

    Preeclampsia (PE) is a deadly gestational disease affecting up to 10% of women and specific of the human species. Preeclampsia is clearly multifactorial, but the existence of a genetic basis for this disease is now clearly established by the existence of familial cases, epidemiological studies and known predisposing gene polymorphisms. PE is very common despite the fact that Darwinian pressure should have rapidly eliminated or strongly minimized the frequency of predisposing alleles. Consecutive pregnancies with the same partner decrease the risk and severity of PE. Here, we show that, due to this peculiar feature, preeclampsia predisposing-alleles can be differentially maintained according to the familial structure. Thus, we suggest that an optimal frequency of PE-predisposing alleles in human populations can be achieved as a result of a trade-off between benefits of exogamy, importance for maintaining genetic diversity and increase of the fitness owing to a stable paternal investment. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. 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...

  12. Existence of Projective Planes

    OpenAIRE

    Perrott, Xander

    2016-01-01

    This report gives an overview of the history of finite projective planes and their properties before going on to outline the proof that no projective plane of order 10 exists. The report also investigates the search carried out by MacWilliams, Sloane and Thompson in 1970 [12] and confirms their result by providing independent verification that there is no vector of weight 15 in the code generated by the projective plane of order 10.

  13. Does bioethics exist?

    Science.gov (United States)

    Turner, L

    2009-12-01

    Bioethicists disagree over methods, theories, decision-making guides, case analyses and public policies. Thirty years ago, the thinking of many scholars coalesced around a principlist approach to bioethics. That mid-level mode of moral reasoning is now one of many approaches to moral deliberation. Significant variation in contemporary approaches to the study of ethical issues related to medicine, biotechnology and health care raises the question of whether bioethics exists as widely shared method, theory, normative framework or mode of moral reasoning.

  14. Simplifying complex sequence information: a PCP-consensus protein binds antibodies against all four Dengue serotypes.

    Science.gov (United States)

    Bowen, David M; Lewis, Jessica A; Lu, Wenzhe; Schein, Catherine H

    2012-09-14

    Designing proteins that reflect the natural variability of a pathogen is essential for developing novel vaccines and drugs. Flaviviruses, including Dengue (DENV) and West Nile (WNV), evolve rapidly and can "escape" neutralizing monoclonal antibodies by mutation. Designing antigens that represent many distinct strains is important for DENV, where infection with a strain from one of the four serotypes may lead to severe hemorrhagic disease on subsequent infection with a strain from another serotype. Here, a DENV physicochemical property (PCP)-consensus sequence was derived from 671 unique sequences from the Flavitrack database. PCP-consensus proteins for domain 3 of the envelope protein (EdomIII) were expressed from synthetic genes in Escherichia coli. The ability of the purified consensus proteins to bind polyclonal antibodies generated in response to infection with strains from each of the four DENV serotypes was determined. The initial consensus protein bound antibodies from DENV-1-3 in ELISA and Western blot assays. This sequence was altered in 3 steps to incorporate regions of maximum variability, identified as significant changes in the PCPs, characteristic of DENV-4 strains. The final protein was recognized by antibodies against all four serotypes. Two amino acids essential for efficient binding to all DENV antibodies are part of a discontinuous epitope previously defined for a neutralizing monoclonal antibody. The PCP-consensus method can significantly reduce the number of experiments required to define a multivalent antigen, which is particularly important when dealing with pathogens that must be tested at higher biosafety levels. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. Companied P16 genetic and protein status together providing useful information on the clinical outcome of urinary bladder cancer.

    Science.gov (United States)

    Pu, Xiaohong; Zhu, Liya; Fu, Yao; Fan, Zhiwen; Zheng, Jinyu; Zhang, Biao; Yang, Jun; Guan, Wenyan; Wu, Hongyan; Ye, Qing; Huang, Qing

    2018-04-01

    SPEC P16/CEN3/7/17 Probe fluorescence-in-situ-hybridization (FISH) has become the most sensitive method in indentifying the urothelial tumors and loss of P16 has often been identified in low-grade urothelial lesions; however, little is known about the significations of other P16 genetic status (normal and amplification) in bladder cancer.We detected P16 gene status by FISH in 259 urine samples and divided these samples into 3 groups: 1, normal P16; 2, loss of P16; and 3, amplified P16. Meanwhile, p16 protein expression was measured by immunocytochemistry and we characterized the clinicopathologic features of cases with P16 gene status.Loss of P16 occurred in 26.2%, P16 amplification occurred in 41.3% and P16 gene normal occurred in 32.4% of all cases. P16 genetic status was significantly associated with tumor grade and primary tumor status (P = .008 and .017), but not with pathological tumor stage, overall survival, and p16 protein expression. However, P16 gene amplification accompanied protein high-expression has shorter overall survival compared with the overall patients (P = .023), and P16 gene loss accompanied loss of protein also had the tendency to predict bad prognosis (P = .067).Studies show that the genetic status of P16 has a close relation with the stages of bladder cancer. Loss of P16 is associated with low-grade urothelial malignancy while amplified P16 donotes high-grade. Neither P16 gene status nor p16 protein expression alone is an independent predictor of urothelial bladder carcinoma, but combine gene and protein status together providing useful information on the clinical outcome of these patients.

  16. Protein complex prediction in large ontology attributed protein-protein interaction networks.

    Science.gov (United States)

    Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng; Xu, Bo

    2013-01-01

    Protein complexes are important for unraveling the secrets of cellular organization and function. Many computational approaches have been developed to predict protein complexes in protein-protein interaction (PPI) networks. However, most existing approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology (GO) annotation information. In this paper, we constructed ontology attributed PPI networks with PPI data and GO resource. After constructing ontology attributed networks, we proposed a novel approach called CSO (clustering based on network structure and ontology attribute similarity). Structural information and GO attribute information are complementary in ontology attributed networks. CSO can effectively take advantage of the correlation between frequent GO annotation sets and the dense subgraph for protein complex prediction. Our proposed CSO approach was applied to four different yeast PPI data sets and predicted many well-known protein complexes. The experimental results showed that CSO was valuable in predicting protein complexes and achieved state-of-the-art performance.

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

    Science.gov (United States)

    2014-06-20

    studies that have reported antimalarial activities of azole compounds [39-43] lend support to our model predictions. The highest-scored non-malarial...Table 4, verapamil and cimetidine, do not have antimal- arial activities themselves but exhibit synergism when used in combination with antimalarial ... activators . Because of their high frequencies among the antimalarial drugs, according to Eq. 3, the drug-protein interactions contributing most to the

  18. O Ponto G Existe?

    Directory of Open Access Journals (Sweden)

    Carlos Alexandre Molina Noccioli

    2016-07-01

    Full Text Available Este trabalho busca analisar o tratamento linguístico-discursivo das informações acerca de um tópicotemático tradicionalmente visto como tabu, relacionado a questões sexuais, na notícia O ponto G existe?, publicada em 2008, na revista brasileira Superinteressante, destacando-se como o conhecimento em questão é representado socialmente ao se considerar a linha editorial da revista. A notícia caracteriza-se como um campo fértil para a análise das estratégias divulgativas, já que atrai, inclusive pelas escolhas temáticas, a curiosidade dos leitores. Imbuído de um tema excêntrico, o texto consegue angariar um público jovem interessado em discussões polêmicas relacionadas ao seu universo.

  19. 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.

  20. Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface.

    Science.gov (United States)

    Berlin, Konstantin; Longhini, Andrew; Dayie, T Kwaku; Fushman, David

    2013-12-01

    To facilitate rigorous analysis of molecular motions in proteins, DNA, and RNA, we present a new version of ROTDIF, a program for determining the overall rotational diffusion tensor from single- or multiple-field nuclear magnetic resonance relaxation data. We introduce four major features that expand the program's versatility and usability. The first feature is the ability to analyze, separately or together, (13)C and/or (15)N relaxation data collected at a single or multiple fields. A significant improvement in the accuracy compared to direct analysis of R2/R1 ratios, especially critical for analysis of (13)C relaxation data, is achieved by subtracting high-frequency contributions to relaxation rates. The second new feature is an improved method for computing the rotational diffusion tensor in the presence of biased errors, such as large conformational exchange contributions, that significantly enhances the accuracy of the computation. The third new feature is the integration of the domain alignment and docking module for relaxation-based structure determination of multi-domain systems. Finally, to improve accessibility to all the program features, we introduced a graphical user interface that simplifies and speeds up the analysis of the data. Written in Java, the new ROTDIF can run on virtually any computer platform. In addition, the new ROTDIF achieves an order of magnitude speedup over the previous version by implementing a more efficient deterministic minimization algorithm. We not only demonstrate the improvement in accuracy and speed of the new algorithm for synthetic and experimental (13)C and (15)N relaxation data for several proteins and nucleic acids, but also show that careful analysis required especially for characterizing RNA dynamics allowed us to uncover subtle conformational changes in RNA as a function of temperature that were opaque to previous analysis.

  1. 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

  2. Financial gap calculations for existing cogeneration 2008

    International Nuclear Information System (INIS)

    Hers, S.J.; Wetzels, W.; Seebregts, A.J.; Van der Welle, A.J.

    2008-05-01

    The Dutch SDE (abbreviation for the renewable energy incentive) subsidy scheme promotes the reduction of CO2 emissions which results from the use of Combined Heat and Power (CHP) plants. This report calculates the profitability of operation of existing CHP plants. This information can be used for decision making on the SDE subsidy for existing CHP plants in 2008 [nl

  3. 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/ .

  4. Information

    International Nuclear Information System (INIS)

    Boyard, Pierre.

    1981-01-01

    The fear for nuclear energy and more particularly for radioactive wastes is analyzed in the sociological context. Everybody agree on the information need, information is available but there is a problem for their diffusion. Reactions of the public are analyzed and journalists, scientists and teachers have a role to play [fr

  5. How to prove the existence of metabolons?

    DEFF Research Database (Denmark)

    Bassard, Jean-Étienne André; Halkier, Barbara Ann

    2017-01-01

    Sequential enzymes in biosynthetic pathways are organized in metabolons. It is challenging to provide experimental evidence for the existence of metabolons as biosynthetic pathways are composed of highly dynamic protein–protein interactions. Many different methods are being applied, each with str...

  6. 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

  7. DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.

    Science.gov (United States)

    Lu, Cheng-Tsung; Huang, Kai-Yao; Su, Min-Gang; Lee, Tzong-Yi; Bretaña, Neil Arvin; Chang, Wen-Chi; Chen, Yi-Ju; Chen, Yu-Ju; Huang, Hsien-Da

    2013-01-01

    Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.

  8. Local sequence information in cellular retinoic acid-binding protein I: specific residue roles in beta-turns.

    Science.gov (United States)

    Rotondi, Kenneth S; Gierasch, Lila M

    2003-01-01

    We have recently shown that two of the beta-turns (III and IV) in the ten-stranded, beta-clam protein, cellular retinoic acid-binding protein I (CRABP I), are favored in short peptide fragments, arguing that they are encoded by local interactions (K. S. Rotondi and L. M. Gierasch, Biochemistry, 2003, Vol. 42, pp. 7976-7985). In this paper we examine these turns in greater detail to dissect the specific local interactions responsible for their observed native conformational biases. Conformations of peptides corresponding to the turn III and IV fragments were examined under conditions designed to selectively disrupt stabilizing interactions, using pH variation, chaotrope addition, or mutagenesis to probe specific side-chain influences. We find that steric constraints imposed by excluded volume effects between near neighbor residues (i,i+2), favorable polar (i,i+2) interactions, and steric permissiveness of glycines are the principal factors accounting for the observed native bias in these turns. Longer-range stabilizing interactions across the beta-turns do not appear to play a significant role in turn stability in these short peptides, in contrast to their importance in hairpins. Additionally, our data add to a growing number of examples of the 3:5 type I turn with a beta-bulge as a class of turns with high propensity to form locally defined structure. Current work is directed at the interplay between the local sequence information in the turns and more long-range influences in the mechanism of folding of this predominantly beta-sheet protein. Copyright 2004 Wiley Periodicals, Inc.

  9. 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.

  10. Informe

    Directory of Open Access Journals (Sweden)

    Egon Lichetenberger

    1950-10-01

    Full Text Available Informe del doctor Egon Lichetenberger ante el Consejo Directivo de la Facultad, sobre el  curso de especialización en Anatomía Patológica patrocinado por la Kellogg Foundation (Departamento de Patología

  11. UN TOQUE ANTIGUO, QUIZÁS MÁS O MENOS NUEVO: RECONSIDERANDO LOS ENVENENAMIENTOS OFIDÍCOS Y PROTECTORES NATURALES PRESENTES EN PROTEÍNAS ENDÓGENAS DE MAMÍFEROS Y REPTILES I AN OLD TOUCH, MAY BE ROUGHLY NEW: RECONSIDERING OPHIDIC ENVENOMATIONS AND NATURAL PROTECTORS EXISTING IN ENDOGENOUS PROTEINS FROM MAMMALS AND REPTILES

    Directory of Open Access Journals (Sweden)

    Luis Manuel Salgueiro

    2015-07-01

    Full Text Available Based on the points discussed here, we can consider that all recent reports tend to suggest that there is more of a protein involved in inhibiting hemostatic activities in reptiles and mainly Didelphis gender of mammals. These proteins can exert its neutralizing ability in isolation, as units with high specificity for the enzyme. They could add their inhibitory capacity acting separately, as well as acting as sub-units under their coupling to promote its inhibition, existing as a mixture of specific inhibitors and nonspecific, acting separately or through a combination of some or all of the above.

  12. Whey Protein

    Science.gov (United States)

    ... reliable information about the safety of taking whey protein if you are pregnant or breast feeding. Stay on the safe side and avoid use. Milk allergy: If you are allergic to cow's milk, avoid using whey protein.

  13. Seismic assessment of existing nuclear chemical plants

    International Nuclear Information System (INIS)

    Merriman, P.A.

    1997-01-01

    This paper outlines the generic approach to the seismic assessment of existing structures. It describes the role of the safety case in determining the studies carried out by the functional departments on individual projects. There is an emphasis on the role of existing information and material tests to provide realistic properties for analysis to account for possible degradation effects. Finally, a case study of a concrete containment cell is shown to illustrate the approach. (author)

  14. Ontological Proofs of Existence and Non-Existence

    Czech Academy of Sciences Publication Activity Database

    Hájek, Petr

    2008-01-01

    Roč. 90, č. 2 (2008), s. 257-262 ISSN 0039-3215 R&D Projects: GA AV ČR IAA100300503 Institutional research plan: CEZ:AV0Z10300504 Keywords : ontological proofs * existence * non-existence * Gödel * Caramuel Subject RIV: BA - General Mathematics

  15. Existence theory in optimal control

    International Nuclear Information System (INIS)

    Olech, C.

    1976-01-01

    This paper treats the existence problem in two main cases. One case is that of linear systems when existence is based on closedness or compactness of the reachable set and the other, non-linear case refers to a situation where for the existence of optimal solutions closedness of the set of admissible solutions is needed. Some results from convex analysis are included in the paper. (author)

  16. 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

  17. Developing an Actuarial Track Utilizing Existing Resources

    Science.gov (United States)

    Rodgers, Kathy V.; Sarol, Yalçin

    2014-01-01

    Students earning a degree in mathematics often seek information on how to apply their mathematical knowledge. One option is to follow a curriculum with an actuarial emphasis designed to prepare students as an applied mathematician in the actuarial field. By developing only two new courses and utilizing existing courses for Validation by…

  18. 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.

  19. 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

  20. 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%,

  1. 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.

  2. HitPredict version 4: comprehensive reliability scoring of physical protein?protein interactions from more than 100 species

    OpenAIRE

    L?pez, Yosvany; Nakai, Kenta; Patil, Ashwini

    2015-01-01

    HitPredict is a consolidated resource of experimentally identified, physical protein?protein interactions with confidence scores to indicate their reliability. The study of genes and their inter-relationships using methods such as network and pathway analysis requires high quality protein?protein interaction information. Extracting reliable interactions from most of the existing databases is challenging because they either contain only a subset of the available interactions, or a mixture of p...

  3. A DArT marker genetic map of perennial ryegrass (Lolium perenne L.) integrated with detailed comparative mapping information; comparison with existing DArT marker genetic maps of Lolium perenne, L. multiflorum and Festuca pratensis.

    Science.gov (United States)

    King, Julie; Thomas, Ann; James, Caron; King, Ian; Armstead, Ian

    2013-07-03

    Ryegrasses and fescues (genera, Lolium and Festuca) are species of forage and turf grasses which are used widely in agricultural and amenity situations. They are classified within the sub-family Pooideae and so are closely related to Brachypodium distachyon, wheat, barley, rye and oats. Recently, a DArT array has been developed which can be used in generating marker and mapping information for ryegrasses and fescues. This represents a potential common marker set for ryegrass and fescue researchers which can be linked through to comparative genomic information for the grasses. A F2 perennial ryegrass genetic map was developed consisting of 7 linkage groups defined by 1316 markers and deriving a total map length of 683 cM. The marker set included 866 DArT and 315 gene sequence-based markers. Comparison with previous DArT mapping studies in perennial and Italian ryegrass (L. multiflorum) identified 87 and 105 DArT markers in common, respectively, of which 94% and 87% mapped to homoeologous linkage groups. A similar comparison with meadow fescue (F. pratensis) identified only 28 DArT markers in common, of which c. 50% mapped to non-homoelogous linkage groups. In L. perenne, the genetic distance spanned by the DArT markers encompassed the majority of the regions that could be described in terms of comparative genomic relationships with rice, Brachypodium distachyon, and Sorghum bicolor. DArT markers are likely to be a useful common marker resource for ryegrasses and fescues, though the success in aligning different populations through the mapping of common markers will be influenced by degrees of population interrelatedness. The detailed mapping of DArT and gene-based markers in this study potentially allows comparative relationships to be derived in future mapping populations characterised using solely DArT markers.

  4. 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

  5. Existing Steel Railway Bridges Evaluation

    Science.gov (United States)

    Vičan, Josef; Gocál, Jozef; Odrobiňák, Jaroslav; Koteš, Peter

    2016-12-01

    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.

  6. 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.

  7. Protein synthesis underlies post-retrieval memory consolidation to a restricted degree only when updated information is obtained

    OpenAIRE

    Rodriguez-Ortiz, Carlos J.; De la Cruz, Vanesa; Gutiérrez, Ranier; Bermudez-Rattoni, Federico

    2005-01-01

    Consolidation theory proposes that through the synthesis of new proteins recently acquired memories are strengthened over time into a stable long-term memory trace. However, evidence has accumulated suggesting that retrieved memory is susceptible to disruption, seeming to consolidate again (reconsolidate) to be retained in long-term storage. Here we show that intracortical blockade of protein synthesis in the gustatory cortex after retrieval of taste-recognition memory disrupts previously con...

  8. 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.

  9. 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 (pwomen with benign tumors/cysts and malignant ovarian 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 (

  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. A Deep Learning Framework for Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary Information.

    Science.gov (United States)

    Yi, Hai-Cheng; You, Zhu-Hong; Huang, De-Shuang; Li, Xiao; Jiang, Tong-Hai; Li, Li-Ping

    2018-06-01

    The interactions between non-coding RNAs (ncRNAs) and proteins play an important role in many biological processes, and their biological functions are primarily achieved by binding with a variety of proteins. High-throughput biological techniques are used to identify protein molecules bound with specific ncRNA, but they are usually expensive and time consuming. Deep learning provides a powerful solution to computationally predict RNA-protein interactions. In this work, we propose the RPI-SAN model by using the deep-learning stacked auto-encoder network to mine the hidden high-level features from RNA and protein sequences and feed them into a random forest (RF) model to predict ncRNA binding proteins. Stacked assembling is further used to improve the accuracy of the proposed method. Four benchmark datasets, including RPI2241, RPI488, RPI1807, and NPInter v2.0, were employed for the unbiased evaluation of five established prediction tools: RPI-Pred, IPMiner, RPISeq-RF, lncPro, and RPI-SAN. The experimental results show that our RPI-SAN model achieves much better performance than other methods, with accuracies of 90.77%, 89.7%, 96.1%, and 99.33%, respectively. It is anticipated that RPI-SAN can be used as an effective computational tool for future biomedical researches and can accurately predict the potential ncRNA-protein interacted pairs, which provides reliable guidance for biological research. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  13. Predicting protein complexes from weighted protein-protein interaction graphs with a novel unsupervised methodology: Evolutionary enhanced Markov clustering.

    Science.gov (United States)

    Theofilatos, Konstantinos; Pavlopoulou, Niki; Papasavvas, Christoforos; Likothanassis, Spiros; Dimitrakopoulos, Christos; Georgopoulos, Efstratios; Moschopoulos, Charalampos; Mavroudi, Seferina

    2015-03-01

    Proteins are considered to be the most important individual components of biological systems and they combine to form physical protein complexes which are responsible for certain molecular functions. Despite the large availability of protein-protein interaction (PPI) information, not much information is available about protein complexes. Experimental methods are limited in terms of time, efficiency, cost and performance constraints. Existing computational methods have provided encouraging preliminary results, but they phase certain disadvantages as they require parameter tuning, some of them cannot handle weighted PPI data and others do not allow a protein to participate in more than one protein complex. In the present paper, we propose a new fully unsupervised methodology for predicting protein complexes from weighted PPI graphs. The proposed methodology is called evolutionary enhanced Markov clustering (EE-MC) and it is a hybrid combination of an adaptive evolutionary algorithm and a state-of-the-art clustering algorithm named enhanced Markov clustering. EE-MC was compared with state-of-the-art methodologies when applied to datasets from the human and the yeast Saccharomyces cerevisiae organisms. Using public available datasets, EE-MC outperformed existing methodologies (in some datasets the separation metric was increased by 10-20%). Moreover, when applied to new human datasets its performance was encouraging in the prediction of protein complexes which consist of proteins with high functional similarity. In specific, 5737 protein complexes were predicted and 72.58% of them are enriched for at least one gene ontology (GO) function term. EE-MC is by design able to overcome intrinsic limitations of existing methodologies such as their inability to handle weighted PPI networks, their constraint to assign every protein in exactly one cluster and the difficulties they face concerning the parameter tuning. This fact was experimentally validated and moreover, new

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

    OpenAIRE

    Maréchal Eric; Ortet Philippe; Roy Sylvaine; Bastien Olivier

    2005-01-01

    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 recon...

  15. The Protein Model Portal.

    Science.gov (United States)

    Arnold, Konstantin; Kiefer, Florian; Kopp, Jürgen; Battey, James N D; Podvinec, Michael; Westbrook, John D; Berman, Helen M; Bordoli, Lorenza; Schwede, Torsten

    2009-03-01

    Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Thereby, experimental structure determination efforts and homology modeling complement each other in the exploration of the protein structure space. One of the challenges in using model information effectively has been to access all models available for a specific protein in heterogeneous formats at different sites using various incompatible accession code systems. Often, structure models for hundreds of proteins can be derived from a given experimentally determined structure, using a variety of established methods. This has been done by all of the PSI centers, and by various independent modeling groups. The goal of the Protein Model Portal (PMP) is to provide a single portal which gives access to the various models that can be leveraged from PSI targets and other experimental protein structures. A single interface allows all existing pre-computed models across these various sites to be queried simultaneously, and provides links to interactive services for template selection, target-template alignment, model building, and quality assessment. The current release of the portal consists of 7.6 million model structures provided by different partner resources (CSMP, JCSG, MCSG, NESG, NYSGXRC, JCMM, ModBase, SWISS-MODEL Repository). The PMP is available at http://www.proteinmodelportal.org and from the PSI Structural Genomics Knowledgebase.

  16. 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

  17. The Greenhouse Effect Does Exist!

    OpenAIRE

    Ebel, Jochen

    2009-01-01

    In particular, without the greenhouse effect, essential features of the atmospheric temperature profile as a function of height cannot be described, i.e., the existence of the tropopause above which we see an almost isothermal temperature curve, whereas beneath it the temperature curve is nearly adiabatic. The relationship between the greenhouse effect and observed temperature curve is explained and the paper by Gerlich and Tscheuschner [arXiv:0707.1161] critically analyzed. Gerlich and Tsche...

  18. Europe - space for transcultural existence?

    OpenAIRE

    Tamcke, Martin; Janny, de Jong; Klein, Lars; Waal, Margriet

    2013-01-01

    Europe - Space for Transcultural Existence? is the first volume of the new series, Studies in Euroculture, published by Göttingen University Press. The series derives its name from the Erasmus Mundus Master of Excellence Euroculture: Europe in the Wider World, a two year programme offered by a consortium of eight European universities in collaboration with four partner universities outside Europe. This master highlights regional, national and supranational dimensions of the European democrati...

  19. Existence of undiscovered Uranian satellites

    International Nuclear Information System (INIS)

    Boice, D.C.

    1986-04-01

    Structure in the Uranian ring system as observed in recent occultations may contain indirect evidence for the existence of undiscovered satellites. Using the Alfven and Arrhenius (1975, 1976) scenario for the formation of planetary systems, the orbital radii of up to nine hypothetical satellites interior to Miranda are computed. These calculations should provide interesting comparisons when the results from the Voyager 2 encounter with Uranus are made public. 15 refs., 1 fig., 1 tab

  20. UNCITRAL: Changes to existing law

    OpenAIRE

    Andersson, Joakim

    2008-01-01

    The UNCITRAL Convention on Contracts for the International Carriage of Goods [wholly or partly] by Sea has an ambition of replacing current maritime regimes and expands the application of the Convention to include also multimodal transport. This thesis questions what changes to existing law, in certain areas, the new Convention will bring compared to the current regimes. In the initial part, the thesis provides for a brief background and history of international maritime regulations and focus...

  1. Existence Results for Incompressible Magnetoelasticity

    Czech Academy of Sciences Publication Activity Database

    Kružík, Martin; Stefanelli, U.; Zeman, J.

    2015-01-01

    Roč. 35, č. 6 (2015), s. 2615-2623 ISSN 1078-0947 R&D Projects: GA ČR GA13-18652S Institutional support: RVO:67985556 Keywords : magnetoelasticity * magnetostrictive solids * incompressibility * existence of minimizers * quasistatic evolution * energetic solution Subject RIV: BA - General Mathematics Impact factor: 1.127, year: 2015 http://library.utia.cas.cz/separaty/2015/MTR/kruzik-0443017.pdf

  2. 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.

  3. Protein Synthesis Underlies Post-Retrieval Memory Consolidation to a Restricted Degree Only when Updated Information Is Obtained

    Science.gov (United States)

    Rodriguez-Ortiz, Carlos J.; De la Cruz, Vanesa; Gutierrez, Ranier; Bermudez-Rattoni, Federico

    2005-01-01

    Consolidation theory proposes that through the synthesis of new proteins recently acquired memories are strengthened over time into a stable long-term memory trace. However, evidence has accumulated suggesting that retrieved memory is susceptible to disruption, seeming to consolidate again (reconsolidate) to be retained in long-term storage. Here…

  4. 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.

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

    Science.gov (United States)

    Bastien, Olivier; Ortet, Philippe; Roy, Sylvaine; Maréchal, Eric

    2005-03-10

    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. 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. 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.

  6. 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.

  7. Hepatitis C virus core protein induces dysfunction of liver sinusoidal endothelial cell by down-regulation of silent information regulator 1.

    Science.gov (United States)

    Sun, Li-Jie; Yu, Jian-Wu; Shi, Yu-Guang; Zhang, Xiao-Yu; Shu, Meng-Ni; Chen, Mo-Yang

    2018-05-01

    Hepatic fibrosis is a frequent feature of chronic hepatitis C virus (HCV) infection. Some evidence has suggested the potential role of silent information regulator 1 (SIRT1) in organ fibrosis. The aim of this study was to investigate the effect of HCV core protein on expression of SIRT1 of liver sinusoidal endothelial cell (LSEC) and function of LSEC. LSECs were co-cultured with HepG2 cells or HepG2 cells expressing HCV core protein and LSECs cultured alone were used as controls. After co-culture, the activity and expression levels of mRNA and protein of SIRT1 in LSEC were detected by a SIRT1 fluorometric assay kit, real time-PCR (RT-PCR), Western blot, respectively. The levels of adiponectin receptor 2 (AdipoR2), endothelial nitric oxide synthase (eNOS) and vascular endothelial growth factor (VEGF) were measured by Western blot. Cluster of differentiation 31 (CD31), CD14, and von Willebrand factor (vWf) of LSECs was performed by flow cytometry. The level of reactive oxygen species (ROS) was assayed. Malondialdehyde (MDA), superoxide dismutase (SOD), adiponectin, nitric oxide (NO), and endothelin-1 (ET-1) levels in the co-culture supernatant were measured. The co-culture supernatant was then used to cultivate LX-2 cells. The levels of α-smooth muscle actin (ASMA) and transforming growth factor-β1 (TGF-β1) protein in LX-2 cells were measured by Western blot. Compared with LSEC co-cultured with HepG2 cells group, in LSEC co-cultured with HepG2-core cells group, the activity and expression level of mRNA and protein of SIRT1 reduced; the level of adiponectin reduced and the expression level of AdipoR2 protein decreased; ROS levels increased; the expression level of eNOS, VEGF protein decreased; and the expression level of CD14 decreased; the expression level of vWf and CD31 increased; NO and SOD levels decreased; whereas ET-1 and MDA levels increased; the levels of ASMA and TGF-β1 protein in LX-2 cells increased. SIRT1 activator improved the above-mentioned changes

  8. Quantum logics with existence property

    International Nuclear Information System (INIS)

    Schindler, C.

    1991-01-01

    A quantum logic (σ-orthocomplete orthomodular poset L with a convex, unital, and separating set Δ of states) is said to have the existence property if the expectation functionals on lin(Δ) associated with the bounded observables of L form a vector space. Classical quantum logics as well as the Hilbert space logics of traditional quantum mechanics have this property. The author shows that, if a quantum logic satisfies certain conditions in addition to having property E, then the number of its blocks (maximal classical subsystems) must either be one (classical logics) or uncountable (as in Hilbert space logics)

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

    African Journals Online (AJOL)

    spamer

    emitting diodes in the blue, green and red part of the visible spectrum ..... highly affected by sun angle, cloud cover and time of .... for Detecting Large-Scale Environmental Change. Kahru, ... Oceanographic Commission Technical Series. No.

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

    Science.gov (United States)

    1987-07-01

    copper-clad steel rod, unspeci- fied rod or pipe. 3. Structures - massive retaining walls, abutments and piers of large bridges, tunnels, massive...rods, posts. reber t Stable, granular or cohe-- with caps, disks Fig. 61.39, Table 53 NA Siv* soils. - without caps, disks Fig. C12 NA - prefabricated ...particular point on a structure (preferably founded on bedrock), i.e., dams, spillways, bridge piers or abutments . 3. Concrete structure (third choice

  11. 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...

  12. Does cold nuclear fusion exist?

    International Nuclear Information System (INIS)

    Brudanin, V.B.; Bystritskij, V.M.; Egorov, V.G.; Shamsutdinov, S.G.; Shyshkin, A.L.; Stolupin, V.A.; Yutlandov, I.A.

    1989-01-01

    The results of investigation of cold nuclear fusion on palladium are given both for electrolysis of heavy water D 2 O and mixture D 2 O + H 2 O) (1:1) and for palladium saturation with gaseous deuterium. The possibility of existance of this phenomenon was examined by detection of neutrons and gamma quanta from reactions: d + d → 3 He + n + 3.27 MeV, p + d → 3 He + γ + 5.5 MeV. Besides these reactions were identified by measuring the characteristic X radiation of palladium due to effect of charged products 3 He, p, t. The upper limits of the intensities of hypothetical sources of neutrons and gamma quanta at the 95% confidence level were obtained to be Q n ≤ 2x10 -2 n/sxcm 3 Pd, Q γ ≤ 2x10 -3 γ/sxcm 3 Pd. 2 refs.; 4 figs.; 2 tabs

  13. 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

  14. Why do interstellar grains exist

    International Nuclear Information System (INIS)

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

  15. SAS-Based Studies of Protein Fibrillation

    DEFF Research Database (Denmark)

    Marasini, Carlotta; Vestergaard, Bente

    2017-01-01

    Protein fibrillation is associated with a number of fatal amyloid diseases (e.g. Alzheimer's and Parkinson's diseases). From a structural point of view, the aggregation process starts from an ensemble of native states that convert into transiently formed oligomers, higher order assemblies and pro...... and highlight existing reports, exemplifying the wealth of information that can be derived from the method....

  16. 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.

  17. Existe sujeito em Michel Maffesoli?

    Directory of Open Access Journals (Sweden)

    Marli Appel da Silva

    2010-06-01

    Full Text Available Este ensaio discute a concepção de sujeito na abordagem teórica de Michel Maffesoli. As ideias desse autor estão em voga em alguns meios acadêmicos no Brasil e são difundidas por algumas mídias de grande circulação nacional. Entretanto, ao longo de suas obras, os pressupostos que definem quem é o sujeito maffesoliano se encontram pouco clarificados. Portanto, para alcançar o objetivo a que se propõe, este ensaio desenvolve uma análise da epistemologia e da ontologia maffesoliana com a finalidade de compreender as origens dos pressupostos desse autor, ou seja, as teorias e os autores em que Maffesoli se baseou para desenvolver uma visão de sujeito. Com essa compreensão, pretende-se responder à questão: existe sujeito na abordagem teórica de Maffesoli.

  18. Diversity and evolution of ABC proteins in basidiomycetes.

    Science.gov (United States)

    Kovalchuk, Andriy; Lee, Yong-Hwan; Asiegbu, Fred O

    2013-01-01

    ABC proteins constitute one of the largest families of proteins. They are implicated in wide variety of cellular processes ranging from ribosome biogenesis to multidrug resistance. With the advance of fungal genomics, the number of known fungal ABC proteins increases rapidly but the information on their biological functions remains scarce. In this work we extended the previous analysis of fungal ABC proteins to include recently sequenced species of basidiomycetes. We performed an identification and initial cataloging of ABC proteins from 23 fungal species representing 10 orders within class Agaricomycotina. We identified more than 1000 genes coding for ABC proteins. Comparison of sets of ABC proteins present in basidiomycetes and ascomycetes revealed the existence of two groups of ABC proteins specific for basidiomycetes. Results of survey should contribute to the better understanding of evolution of ABC proteins in fungi and support further experimental work on their characterization.

  19. 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...

  20. Summary of existing uncertainty methods

    International Nuclear Information System (INIS)

    Glaeser, Horst

    2013-01-01

    A summary of existing and most used uncertainty methods is presented, and the main features are compared. One of these methods is the order statistics method based on Wilks' formula. It is applied in safety research as well as in licensing. This method has been first proposed by GRS for use in deterministic safety analysis, and is now used by many organisations world-wide. Its advantage is that the number of potential uncertain input and output parameters is not limited to a small number. Such a limitation was necessary for the first demonstration of the Code Scaling Applicability Uncertainty Method (CSAU) by the United States Regulatory Commission (USNRC). They did not apply Wilks' formula in their statistical method propagating input uncertainties to obtain the uncertainty of a single output variable, like peak cladding temperature. A Phenomena Identification and Ranking Table (PIRT) was set up in order to limit the number of uncertain input parameters, and consequently, the number of calculations to be performed. Another purpose of such a PIRT process is to identify the most important physical phenomena which a computer code should be suitable to calculate. The validation of the code should be focused on the identified phenomena. Response surfaces are used in some applications replacing the computer code for performing a high number of calculations. The second well known uncertainty method is the Uncertainty Methodology Based on Accuracy Extrapolation (UMAE) and the follow-up method 'Code with the Capability of Internal Assessment of Uncertainty (CIAU)' developed by the University Pisa. Unlike the statistical approaches, the CIAU does compare experimental data with calculation results. It does not consider uncertain input parameters. Therefore, the CIAU is highly dependent on the experimental database. The accuracy gained from the comparison between experimental data and calculated results are extrapolated to obtain the uncertainty of the system code predictions

  1. Affinity-based, biophysical methods to detect and analyze ligand binding to recombinant proteins: matching high information content with high throughput.

    Science.gov (United States)

    Holdgate, Geoff A; Anderson, Malcolm; Edfeldt, Fredrik; Geschwindner, Stefan

    2010-10-01

    Affinity-based technologies have become impactful tools to detect, monitor and characterize molecular interactions using recombinant target proteins. This can aid the understanding of biological function by revealing mechanistic details, and even more importantly, enables the identification of new improved ligands that can modulate the biological activity of those targets in a desired fashion. The selection of the appropriate technology is a key step in that process, as each one of the currently available technologies offers a characteristic type of biophysical information about the ligand-binding event. Alongside the indisputable advantages of each of those technologies they naturally display diverse restrictions that are quite frequently related to the target system to be studied but also to the affinity, solubility and molecular size of the ligands. This paper discusses some of the theoretical and experimental aspects of the most common affinity-based methods, what type of information can be gained from each one of those approaches, and what requirements as well as limitations are expected from working with recombinant proteins on those platforms and how those can be optimally addressed.

  2. Cost-effectiveness of point-of-care C-reactive protein testing to inform antibiotic prescribing decisions

    Science.gov (United States)

    Oppong, Raymond; Jit, Mark; Smith, Richard D; Butler, Christopher C; Melbye, Hasse; Mölstad, Sigvard; Coast, Joanna

    2013-01-01

    Background Point-of-care C-reactive protein (POCCRP) is a biomarker of inflammation that offers clinicians a rapid POC test to guide antibiotic prescribing decisions for acute cough and lower respiratory tract infections (LRTI). However, evidence that POCCRP is cost-effective is limited, particularly outside experimental settings. Aim To assess the cost-effectiveness of POCCRP as a diagnostic tool for acute cough and LRTI from the perspective of the health service. Design and setting Observational study of the presentation, management, and outcomes of patients with acute cough and LRTI in primary care settings in Norway and Sweden. Method Using hierarchical regression, data were analysed in terms of the effect on antibiotic use, cost, and patient outcomes (symptom severity after 7 and 14 days, time to recovery, and EQ-5D), while controlling for patient characteristics (self-reported symptom severity, comorbidities, and health-related quality of life) at first attendance. Results POCCRP testing is associated with non-significant positive reductions in antibiotic prescribing (P = 0.078) and increased cost (P = 0.092). Despite the uncertainty, POCCRP testing is also associated with a cost per quality-adjusted life year (QALY) gain of €9391. At a willingness-to-pay threshold of €30 000 per QALY gained, there is a 70% probability of CRP being cost-effective. Conclusion POCCRP testing is likely to provide a cost-effective diagnostic intervention both in terms of reducing antibiotic prescribing and in terms of QALYs gained. PMID:23834883

  3. Construction of ontology augmented networks for protein complex prediction.

    Science.gov (United States)

    Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian

    2013-01-01

    Protein complexes are of great importance in understanding the principles of cellular organization and function. The increase in available protein-protein interaction data, gene ontology and other resources make it possible to develop computational methods for protein complex prediction. Most existing methods focus mainly on the topological structure of protein-protein interaction networks, and largely ignore the gene ontology annotation information. In this article, we constructed ontology augmented networks with protein-protein interaction data and gene ontology, which effectively unified the topological structure of protein-protein interaction networks and the similarity of gene ontology annotations into unified distance measures. After constructing ontology augmented networks, a novel method (clustering based on ontology augmented networks) was proposed to predict protein complexes, which was capable of taking into account the topological structure of the protein-protein interaction network, as well as the similarity of gene ontology annotations. Our method was applied to two different yeast protein-protein interaction datasets and predicted many well-known complexes. The experimental results showed that (i) ontology augmented networks and the unified distance measure can effectively combine the structure closeness and gene ontology annotation similarity; (ii) our method is valuable in predicting protein complexes and has higher F1 and accuracy compared to other competing methods.

  4. 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

  5. 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.

  6. Existing and new techniques in uranium exploration

    International Nuclear Information System (INIS)

    Bowie, S.H.U.; Cameron, J.

    1976-01-01

    The demands on uranium exploration over the next 25 years will be very great indeed and will call for every possible means of improvement in exploration capability. The first essential is to increase geological knowledge of the mode of occurrence of uranium ore deposits. The second is to improve existing exploration techniques and instrumentation while, at the same time, promoting research and development on new methods to discover uranium ore bodies on the earth's surface and at depth. The present symposium is an effort to increase co-operation and the exchange of information in the critical field of uranium exploration techniques and instrumentation. As an introduction to the symposium a brief review is presented, firstly of what can be considered as existing techniques and, secondly, of techniques which have not yet been used on an appreciable scale. Some fourteen techniques used over the last 30 years are identified and their appropriate application, advantages and limitations are briefly summarized and the possibilities of their further development considered. The aim of future research on new techniques, in addition to finding new ways and means of identifying surface deposits, should be mainly directed to devising methods and instrumentation capable of detecting buried ore bodies that do not give a gamma signal at the surface. To achieve this aim, two contributory factors are essential: adequate financial support for research and development and increased specialized training in uranium exploration and instrumentation design. The papers in this symposium describe developments in the existing techniques, proposals for future research and development and case histories of exploration programmes

  7. Integrating existing software toolkits into VO system

    Science.gov (United States)

    Cui, Chenzhou; Zhao, Yong-Heng; Wang, Xiaoqian; Sang, Jian; Luo, Ze

    2004-09-01

    Virtual Observatory (VO) is a collection of interoperating data archives and software tools. Taking advantages of the latest information technologies, it aims to provide a data-intensively online research environment for astronomers all around the world. A large number of high-qualified astronomical software packages and libraries are powerful and easy of use, and have been widely used by astronomers for many years. Integrating those toolkits into the VO system is a necessary and important task for the VO developers. VO architecture greatly depends on Grid and Web services, consequently the general VO integration route is "Java Ready - Grid Ready - VO Ready". In the paper, we discuss the importance of VO integration for existing toolkits and discuss the possible solutions. We introduce two efforts in the field from China-VO project, "gImageMagick" and "Galactic abundance gradients statistical research under grid environment". We also discuss what additional work should be done to convert Grid service to VO service.

  8. 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...

  9. Information and Informality

    DEFF Research Database (Denmark)

    Larsson, Magnus; Segerstéen, Solveig; Svensson, Cathrin

    2011-01-01

    leaders on the basis of their possession of reliable knowledge in technical as well as organizational domains. The informal leaders engaged in interpretation and brokering of information and knowledge, as well as in mediating strategic values and priorities on both formal and informal arenas. Informal...... 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...... contributed to task structuring through sensemaking activities, while formal leaders focused on aspects such as clarifying output expectations, providing feedback, project structure, and diversity....

  10. 10 CFR 4.127 - Existing facilities.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Existing facilities. 4.127 Section 4.127 Energy NUCLEAR... 1973, as Amended Discriminatory Practices § 4.127 Existing facilities. (a) Accessibility. A recipient... make each of its existing facilities or every part of an existing facility accessible to and usable by...

  11. Existing reflection seismic data re-processing

    International Nuclear Information System (INIS)

    Higashinaka, Motonori; Sano, Yukiko; Kozawa, Takeshi

    2005-08-01

    This document is to report the results of existing seismic data re-processing around Horonobe town, Hokkaido, Japan, which is a part of the Horonobe Underground Research Project. The main purpose of this re-processing is to recognize the subsurface structure of Omagari Fault and fold system around Omagari Fault. The seismic lines for re-processing are TYHR-A3 line and SHRB-2 line, which JAPEX surveyed in 1975. Applying weathering static correction using refraction analysis and noise suppression procedure, we have much enhanced seismic profile. Following information was obtained from seismic re-processing results. TYHR-A3 line: There are strong reflections, dipping to the west. These reflections are corresponding western limb of anticline to the west side of Omagari Fault. SHRB-2 line: There are strong reflections, dipping to the west, at CDP 60-140, while there are reflections, dipping to the east, to the east side of CDP 140. These reflections correspond to the western limb and the eastern limb of the anticline, which is parallel to Omagari FAULT. This seismic re-processing provides some useful information to know the geological structure around Omagari Fault. (author)

  12. Bibliography - Existing Guidance for External Hazard Modelling

    International Nuclear Information System (INIS)

    Decker, Kurt

    2015-01-01

    The bibliography of deliverable D21.1 includes existing international and national guidance documents and standards on external hazard assessment together with a selection of recent scientific papers, which are regarded to provide useful information on the state of the art of external event modelling. The literature database is subdivided into International Standards, National Standards, and Science Papers. The deliverable is treated as a 'living document' which is regularly updated as necessary during the lifetime of ASAMPSA-E. The current content of the database is about 140 papers. Most of the articles are available as full-text versions in PDF format. The deliverable is available as an EndNote X4 database and as text files. The database includes the following information: Reference, Key words, Abstract (if available), PDF file of the original paper (if available), Notes (comments by the ASAMPSA-E consortium if available) The database is stored at the ASAMPSA-E FTP server hosted by IRSN. PDF files of original papers are accessible through the EndNote software

  13. 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/.

  14. 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.

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

    Science.gov (United States)

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

    2010-01-01

    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. PMID:21152409

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

    Science.gov (United States)

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

    2010-11-30

    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. 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.

  17. 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.

  18. 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.

  19. 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

  20. Existing ingestion guidance: Problems and recommendations

    Energy Technology Data Exchange (ETDEWEB)

    Mooney, Robert R; Ziegler, Gordon L; Peterson, Donald S [Environmental Radiation Section, Division of Radiation Protection, WA (United States)

    1989-09-01

    accident. Washington's new computer model is consistent with informal guidance received in 1988 from FDA. An important change of philosophy made in this process was to establish CGs which define foods that may be marketed, whereas current CGs define food which must be interdicted. The concept of food (contaminated with radioactivity) being consumed by the public creates a totally different mindset from the concept of contaminated food being embargoed. This experience has led us to identify a number of problems with existing federal ingestion guidance, as well as some recommendations for resolving these problems.

  1. Existing ingestion guidance: Problems and recommendations

    International Nuclear Information System (INIS)

    Mooney, Robert R.; Ziegler, Gordon L.; Peterson, Donald S.

    1989-01-01

    accident. Washington's new computer model is consistent with informal guidance received in 1988 from FDA. An important change of philosophy made in this process was to establish CGs which define foods that may be marketed, whereas current CGs define food which must be interdicted. The concept of food (contaminated with radioactivity) being consumed by the public creates a totally different mindset from the concept of contaminated food being embargoed. This experience has led us to identify a number of problems with existing federal ingestion guidance, as well as some recommendations for resolving these problems

  2. 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.

  3. Do Elementary Particles Have an Objective Existence?

    OpenAIRE

    Nissenson, Bilha

    2007-01-01

    The formulation of quantum theory does not comply with the notion of objective existence of elementary particles. Objective existence independent of observation implies the distinguishability of elementary particles. In other words: If elementary particles have an objective existence independent of observations, then they are distinguishable. Or if elementary particles are indistinguishable then matter cannot have existence independent of our observation. This paper presents a simple deductio...

  4. Seismic evaluation of existing nuclear facilities. Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-07-01

    Programmes for re-evaluation and upgrading of safety of existing nuclear facilities are presently under way in a number of countries around the world. An important component of these programmes is the re-evaluation of the seismic safety through definition of new seismic parameters at the site and evaluation of seismic capacity of structures, equipment and distribution systems following updated information and criteria. The Seminar is intended to provide a forum for the exchange of information and discussion of the state-of-the-art on seismic safety of nuclear facilities in operation or under construction. Both analytical and experimental techniques for the evaluation of seismic capacity of structures, equipment and distribution systems are discussed. Full scale and field tests of structures and components using shaking tables, mechanical exciters, explosive and shock tests, and ambient vibrations are included in the seminar programme with emphasis on recent case histories. Presentations at the Seminar also include analytical techniques for the determination of dynamic properties of soil-structure systems from experiments as well as calibration of numerical models. Methods and criteria for seismic margin assessment based on experience data obtained from the behaviour of structures and components in real earthquakes are discussed. Guidelines for defining technical requirements for capacity re-evaluation (i.e. acceptable behaviour limits and design and implementation of structure and components upgrades are also presented and discussed. The following topics were covered during 7 sessions: earthquake experience and seismic re-evaluation; country experience in seismic re-evaluation programme; generic WWER studies; analytical methods for seismic capacity re-evaluation; experimental methods for seismic capacity re-evaluation; case studies.

  5. Seismic evaluation of existing nuclear facilities. Proceedings

    International Nuclear Information System (INIS)

    1995-01-01

    Programmes for re-evaluation and upgrading of safety of existing nuclear facilities are presently under way in a number of countries around the world. An important component of these programmes is the re-evaluation of the seismic safety through definition of new seismic parameters at the site and evaluation of seismic capacity of structures, equipment and distribution systems following updated information and criteria. The Seminar is intended to provide a forum for the exchange of information and discussion of the state-of-the-art on seismic safety of nuclear facilities in operation or under construction. Both analytical and experimental techniques for the evaluation of seismic capacity of structures, equipment and distribution systems are discussed. Full scale and field tests of structures and components using shaking tables, mechanical exciters, explosive and shock tests, and ambient vibrations are included in the seminar programme with emphasis on recent case histories. Presentations at the Seminar also include analytical techniques for the determination of dynamic properties of soil-structure systems from experiments as well as calibration of numerical models. Methods and criteria for seismic margin assessment based on experience data obtained from the behaviour of structures and components in real earthquakes are discussed. Guidelines for defining technical requirements for capacity re-evaluation (i.e. acceptable behaviour limits and design and implementation of structure and components upgrades are also presented and discussed. The following topics were covered during 7 sessions: earthquake experience and seismic re-evaluation; country experience in seismic re-evaluation programme; generic WWER studies; analytical methods for seismic capacity re-evaluation; experimental methods for seismic capacity re-evaluation; case studies

  6. 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

  7. 34 CFR 104.22 - Existing facilities.

    Science.gov (United States)

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Existing facilities. 104.22 Section 104.22 Education... Accessibility § 104.22 Existing facilities. (a) Accessibility. A recipient shall operate its program or activity.... This paragraph does not require a recipient to make each of its existing facilities or every part of a...

  8. 45 CFR 1170.32 - Existing facilities.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 3 2010-10-01 2010-10-01 false Existing facilities. 1170.32 Section 1170.32... ASSISTED PROGRAMS OR ACTIVITIES Accessibility § 1170.32 Existing facilities. (a) Accessibility. A recipient... require a recipient to make each of its existing facilities or every part of a facility accessible to and...

  9. 45 CFR 605.22 - Existing facilities.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 3 2010-10-01 2010-10-01 false Existing facilities. 605.22 Section 605.22 Public... Accessibility § 605.22 Existing facilities. (a) Accessibility. A recipient shall operate each program or... existing facilities or every part of a facility accessible to and usable by qualified handicapped persons...

  10. 14 CFR 1251.301 - Existing facilities.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 5 2010-01-01 2010-01-01 false Existing facilities. 1251.301 Section 1251... HANDICAP Accessibility § 1251.301 Existing facilities. (a) Accessibility. A recipient shall operate each... existing facilities or every part of a facility accessible to and usable by handicapped persons. (b...

  11. 45 CFR 1151.22 - Existing facilities.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 3 2010-10-01 2010-10-01 false Existing facilities. 1151.22 Section 1151.22... Prohibited Accessibility § 1151.22 Existing facilities. (a) A recipient shall operate each program or... make each of its existing facilities or every part of a facility accessible to and usable by...

  12. 10 CFR 611.206 - Existing facilities.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Existing facilities. 611.206 Section 611.206 Energy... PROGRAM Facility/Funding Awards § 611.206 Existing facilities. The Secretary shall, in making awards to those manufacturers that have existing facilities, give priority to those facilities that are oldest or...

  13. 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...

  14. 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.

  15. 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.

  16. 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.

  17. Exploration of the dynamic properties of protein complexes predicted from spatially constrained protein-protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Eric A Yen

    2014-05-01

    Full Text Available Protein complexes are not static, but rather highly dynamic with subunits that undergo 1-dimensional diffusion with respect to each other. Interactions within protein complexes are modulated through regulatory inputs that alter interactions and introduce new components and deplete existing components through exchange. While it is clear that the structure and function of any given protein complex is coupled to its dynamical properties, it remains a challenge to predict the possible conformations that complexes can adopt. Protein-fragment Complementation Assays detect physical interactions between protein pairs constrained to ≤8 nm from each other in living cells. This method has been used to build networks composed of 1000s of pair-wise interactions. Significantly, these networks contain a wealth of dynamic information, as the assay is fully reversible and the proteins are expressed in their natural context. In this study, we describe a method that extracts this valuable information in the form of predicted conformations, allowing the user to explore the conformational landscape, to search for structures that correlate with an activity state, and estimate the abundance of conformations in the living cell. The generator is based on a Markov Chain Monte Carlo simulation that uses the interaction dataset as input and is constrained by the physical resolution of the assay. We applied this method to an 18-member protein complex composed of the seven core proteins of the budding yeast Arp2/3 complex and 11 associated regulators and effector proteins. We generated 20,480 output structures and identified conformational states using principle component analysis. We interrogated the conformation landscape and found evidence of symmetry breaking, a mixture of likely active and inactive conformational states and dynamic exchange of the core protein Arc15 between core and regulatory components. Our method provides a novel tool for prediction and

  18. AFAL: a web service for profiling amino acids surrounding ligands in proteins

    Science.gov (United States)

    Arenas-Salinas, Mauricio; Ortega-Salazar, Samuel; Gonzales-Nilo, Fernando; Pohl, Ehmke; Holmes, David S.; Quatrini, Raquel

    2014-11-01

    With advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein-ligand interactions. Herein, a new web service is presented termed amino acid frequency around ligand (AFAL) for determining amino acids type and frequencies surrounding ligands within proteins deposited in the Protein Data Bank and for assessing the atoms and atom-ligand distances involved in each interaction (availability: http://structuralbio.utalca.cl/AFAL/index.html). AFAL allows the user to define a wide variety of filtering criteria (protein family, source organism, resolution, sequence redundancy and distance) in order to uncover trends and evolutionary differences in amino acid preferences that define interactions with particular ligands. Results obtained from AFAL provide valuable statistical information about amino acids that may be responsible for establishing particular ligand-protein interactions. The analysis will enable investigators to compare ligand-binding sites of different proteins and to uncover general as well as specific interaction patterns from existing data. Such patterns can be used subsequently to predict ligand binding in proteins that currently have no structural information and to refine the interpretation of existing protein models. The application of AFAL is illustrated by the analysis of proteins interacting with adenosine-5'-triphosphate.

  19. Existence of equilibria in articulated bearings

    Science.gov (United States)

    Buscaglia, G.; Ciuperca, I.; Hafidi, I.; Jai, M.

    2007-04-01

    The existence of equilibrium solutions for a lubricated system consisting of an articulated body sliding over a flat plate is considered. Though this configuration is very common (it corresponds to the popular tilting-pad thrust bearings), the existence problem has only been addressed in extremely simplified cases, such as planar sliders of infinite width. Our results show the existence of at least one equilibrium for a quite general class of (nonplanar) slider shapes. We also extend previous results concerning planar sliders.

  20. 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

  1. 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.

  2. Protein-protein interaction inference based on semantic similarity of Gene Ontology terms.

    Science.gov (United States)

    Zhang, Shu-Bo; Tang, Qiang-Rong

    2016-07-21

    Identifying protein-protein interactions is important in molecular biology. Experimental methods to this issue have their limitations, and computational approaches have attracted more and more attentions from the biological community. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most powerful indicators for protein interaction. However, conventional methods based on GO similarity fail to take advantage of the specificity of GO terms in the ontology graph. We proposed a GO-based method to predict protein-protein interaction by integrating different kinds of similarity measures derived from the intrinsic structure of GO graph. We extended five existing methods to derive the semantic similarity measures from the descending part of two GO terms in the GO graph, then adopted a feature integration strategy to combines both the ascending and the descending similarity scores derived from the three sub-ontologies to construct various kinds of features to characterize each protein pair. Support vector machines (SVM) were employed as discriminate classifiers, and five-fold cross validation experiments were conducted on both human and yeast protein-protein interaction datasets to evaluate the performance of different kinds of integrated features, the experimental results suggest the best performance of the feature that combines information from both the ascending and the descending parts of the three ontologies. Our method is appealing for effective prediction of protein-protein interaction. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. 47 CFR 17.17 - Existing structures.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Existing structures. 17.17 Section 17.17... STRUCTURES Federal Aviation Administration Notification Criteria § 17.17 Existing structures. (a) The requirements found in § 17.23 relating to painting and lighting of antenna structures shall not apply to those...

  4. 10 CFR 1040.72 - Existing facilities.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Existing facilities. 1040.72 Section 1040.72 Energy... § 1040.72 Existing facilities. (a) Accessibility. A recipient shall operate any program or activity to... facilities or every part of a facility accessible to and useable by handicapped persons. (b) Methods. A...

  5. 45 CFR 84.22 - Existing facilities.

    Science.gov (United States)

    2010-10-01

    ... HANDICAP IN PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Accessibility § 84.22 Existing facilities. (a) Accessibility. A recipient shall operate its program or activity so that when each part is..., welfare, or other social services at alternate accessible sites, alteration of existing facilities and...

  6. 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...

  7. 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 ...is a lack of standardization – from the tactical to the strategic level – with integrating and employing IRCs and these SMEs. This along with other...organization strategic goals and objectives, and/or a lack of senior leader advocacy. Practical approaches such as the IRCs Integration Continuum acts as a

  8. 76 FR 52961 - Agency Information Collection Activities: Form N-300; Revision of an Existing Information...

    Science.gov (United States)

    2011-08-24

    ... documentary requirements for those seeking to work in certain occupations or professions, or to obtain various... 18, 2011. Liana Miranda-Valido, Management and Program Analyst, Regulatory Products Division, Office...

  9. 76 FR 20996 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2011-04-14

    ... burden and associated response time should be directed to the Office of the Chief Financial Officer/OAA... Chief Financial Officer/OAA/Records Branch, U.S. Immigration and Customs Enforcement, 500 12th Street...

  10. 75 FR 54646 - Agency Information Collection Activities: Form I-914; Extension of an Existing Information...

    Science.gov (United States)

    2010-09-08

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services [OMB Control No. 1615.... 1615-0099. The Department of Homeland Security, U.S. Citizenship and Immigration Services (USCIS) will... Homeland Security sponsoring the collection: Form I-914; U.S. Citizenship and Immigration Services (USCIS...

  11. 75 FR 51095 - Agency Information Collection Activities: Form N-336; Extension of an Existing Information...

    Science.gov (United States)

    2010-08-18

    ... DEPARTMENT OF HOMELAND SECURITY U.S. Citizenship and Immigration Services [OMB Control No. 1615...-0050. The Department of Homeland Security, U.S. Citizenship and Immigration Services (USCIS) will be... sponsoring the collection: Form N-336; U.S. Citizenship and Immigration Services (USCIS). (4) Affected public...

  12. 77 FR 27473 - Agency Information Collection Activities: Form I-924; Extension of an Existing Information...

    Science.gov (United States)

    2012-05-10

    ... Immigrant Investor Pilot Program. The Department of Homeland Security (DHS), U.S. Citizenship and... is published to obtain comments from the public and affected agencies. Comments are encouraged and... whether to revise the Application for Regional Center Under the Immigrant Investor Pilot Program, Form I...

  13. 78 FR 23577 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2013-04-19

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency.... Comments should be addressed to OMB Desk Officer, for United States Immigration and Customs Enforcement... Desk Officer, for United States Immigration and Customs Enforcement, Department of Homeland Security...

  14. 77 FR 47656 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-08-09

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... Immigration and Nationality Act (8 U.S.C. 1101 note) provides for the reimbursement to States and localities...; OMB Control No. 1653-0037. The Department of Homeland Security, U.S. Immigration and Customs...

  15. 77 FR 33478 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-06-06

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... Management and Budget. Comments should be addressed to OMB Desk Officer, for United States Immigration and... Immigration and Nationality Act (8 U.S.C. 1101 note) provides for the reimbursement to States and localities...

  16. 77 FR 50145 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-08-20

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... (F-2, M-2 or J-2) is admitted to the United States as a nonimmigrant alien under section 101(a)(15...; OMB Control No. 1653-0037. The Department of Homeland Security, U.S. Immigration and Customs...

  17. 77 FR 38651 - Agency Information Collection Activities: Extension, With Change, of an Existing Information...

    Science.gov (United States)

    2012-06-28

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... States and localities for assistance provided in meeting an immigration emergency. This collection of...; OMB Control No. 1653-0043. The Department of Homeland Security, U.S. Immigration and Customs...

  18. 75 FR 68371 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2010-11-05

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... Government. Section 404(b) of the Immigration and Naturalization Act provides for the reimbursement to States... Assistance; OMB Control No. 1653-0019. The Department of Homeland Security, U.S. Immigration and Customs...

  19. 77 FR 65901 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-10-31

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency..., Office of Management and Budget. Comments should be addressed to OMB Desk Officer, for United States... of persons in the United States or abroad regarding the whereabouts of the alien. (5) An estimate of...

  20. 76 FR 79204 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2011-12-21

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency...) of the Immigration and Nationality Act (8 U.S.C. 1101 note) provides for the reimbursement to States... Assistance; OMB Control No. 1653-0019. [[Page 79205

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

    Science.gov (United States)

    2011-01-27

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... should be addressed to OMB Desk Officer, for United States Immigration and Customs Enforcement...: Primary: State, Local or Tribal Government. Section 404(b) of the Immigration and Naturalization Act...

  2. 75 FR 53322 - Agency Information Collection Activities: Extension of an Existing Information Collection...

    Science.gov (United States)

    2010-08-31

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... should be addressed to OMB Desk Officer, for United States Immigration and Customs Enforcement... school; and at the time they leave the United States. (5) An estimate of the total number of respondents...

  3. 77 FR 42322 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-07-18

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... Immigration and Nationality Act (8 U.S.C. 1101 note) provides for the reimbursement to States and localities... Control No. 1615-0019. The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE...

  4. 77 FR 49823 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-08-17

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... United States ICE for Collateral Accepted as Security; OMB Control No. 1653-0045. The Department of...: Affidavit in Lieu of Lost Receipt of United States for Collateral Accepted as Security. (3) Agency form...

  5. 77 FR 66862 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-11-07

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... United States Immigration and Customs Enforcement, Department of Homeland Security, and sent via... Lost Receipt of United States ICE for Collateral Accepted as Security; OMB Control No. 1653-0045. The...

  6. 76 FR 8373 - Agency Information Collection Activities: Revision of an Existing Information Collection; Comment...

    Science.gov (United States)

    2011-02-14

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... Management and Budget. Comments should be addressed to OMB Desk Officer, for United States Immigration and... (SEVIS); OMB Control No. 1653-0038, * * * * * The Department of Homeland Security, U.S. Immigration and...

  7. 77 FR 38651 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2012-06-28

    ... DEPARTMENT OF HOMELAND SECURITY United States Immigration and Customs Enforcement Agency... Immigration and Nationality Act (8 U.S.C. 1101 note) provides for the reimbursement to States and localities.... 1653-0020. The Department of Homeland Security, U.S. Immigration and Customs Enforcement (ICE), will...

  8. 76 FR 36560 - Agency Information Collection Activities; Form N-300; Extension of an Existing Information...

    Science.gov (United States)

    2011-06-22

    ... Management and Budget (OMB) for review and clearance in accordance with the Paperwork Reduction Act of 1995... (DHS), and to the Office of Management and Budget (OMB) USCIS Desk Officer. Comments may be submitted... documentary requirements for those seeking to work in certain occupations or professions, or to obtain various...

  9. 78 FR 11216 - Agency Information Collection Activities: Extension, Without Change, of an Existing Information...

    Science.gov (United States)

    2013-02-15

    ... regard to the estimated public burden and associated response time should be directed to the Department of Homeland Security (DHS), Scott Elmore, Forms Managment, U.S. Immigration and Customs Enforcement... bond form manually. (5) An estimate of the total number of respondents and the amount of time estimated...

  10. ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval.

    Science.gov (United States)

    Wang, Jingyan; Gao, Xin; Wang, Quanquan; Li, Yongping

    2012-05-08

    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. 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 the Protein Hierarchial

  11. 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

  12. Insulin-Like Growth Factor Binding Protein 4 Fragments Provide Incremental Prognostic Information on Cardiovascular Events in Patients With ST-Segment Elevation Myocardial Infarction

    DEFF Research Database (Denmark)

    Hjortebjerg, Rikke; Lindberg, Søren; Pedersen, Sune

    2017-01-01

    BACKGROUND: Fragments of insulin-like growth factor binding protein 4 (IGFBP-4) are potential new biomarkers for cardiac risk assessment. The fragments are generated on specific cleavage by pregnancy-associated plasma protein-A, which exerts proatherogenic activity. This study investigated the pr...

  13. The existence of trajectories joining critical points

    International Nuclear Information System (INIS)

    Yu Shuxiang.

    1985-01-01

    In this paper, using the notion of an isolating block and the concept of canonical regions, three existence criteria of trajectories connecting a pair of critical points of planar differential equations are given. (author)

  14. 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...

  15. Solar Panel Installations on Existing Structures

    OpenAIRE

    Tim D. Sass; Pe; Leed

    2013-01-01

    The rising price of fossil fuels, government incentives and growing public aware-ness for the need to implement sustainable energy supplies has resulted in a large in-crease in solar panel installations across the country. For many sites the most eco-nomical solar panel installation uses existing, southerly facing rooftops. Adding solar panels to an existing roof typically means increased loads that must be borne by the building-s structural elements. The structural desig...

  16. The global existence problem in general relativity

    CERN Document Server

    Andersson, L

    2000-01-01

    We survey some known facts and open questions concerning the global properties of 3+1 dimensional space--times containing a compact Cauchy surface. We consider space--times with an $\\ell$--dimensional Lie algebra of space--like Killing fields. For each $\\ell \\leq 3$, we give some basic results and conjectures on global existence and cosmic censorship. For the case of the 3+1 dimensional Einstein equations without symmetries, a new small data global existence result is announced.

  17. Predicting protein-protein interactions from multimodal biological data sources via nonnegative matrix tri-factorization.

    Science.gov (United States)

    Wang, Hua; Huang, Heng; Ding, Chris; Nie, Feiping

    2013-04-01

    Protein interactions are central to all the biological processes and structural scaffolds in living organisms, because they orchestrate a number of cellular processes such as metabolic pathways and immunological recognition. Several high-throughput methods, for example, yeast two-hybrid system and mass spectrometry method, can help determine protein interactions, which, however, suffer from high false-positive rates. Moreover, many protein interactions predicted by one method are not supported by another. Therefore, computational methods are necessary and crucial to complete the interactome expeditiously. In this work, we formulate the problem of predicting protein interactions from a new mathematical perspective--sparse matrix completion, and propose a novel nonnegative matrix factorization (NMF)-based matrix completion approach to predict new protein interactions from existing protein interaction networks. Through using manifold regularization, we further develop our method to integrate different biological data sources, such as protein sequences, gene expressions, protein structure information, etc. Extensive experimental results on four species, Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, and Caenorhabditis elegans, have shown that our new methods outperform related state-of-the-art protein interaction prediction methods.

  18. 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.

  19. 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...

  20. 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...... on thecomponentwise calculations done in the course of the iteration. These componentwisetests are useful for parallel implementation of the search, sincethe tests can then be performed local to each processor and only when a test issuccessful do a processor communicate this result to other processors....

  1. Seismic reevaluation of existing nuclear power plants

    International Nuclear Information System (INIS)

    Hennart, J.C.

    1978-01-01

    The codes and regulations governing Nuclear Power Plant seismic analysis are continuously becoming more stringent. In addition, design ground accelerations of existing plants must sometimes be increased as a result of discovery of faulting zones or recording of recent earthquakes near the plant location after plant design. These new factors can result in augmented seismic design criteria. Seismic reanalysius of the existing Nuclear Power Plant structures and equipments is necessary to prevent the consequences of newly postulated accidents that could cause undue risk to the health or safety of the public. This paper reviews the developments of seismic analysis as applied to Nuclear Power Plants and the methods used by Westinghouse to requalify existing plants to the most recent safety requirements. (author)

  2. 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.

  3. Radiation protection programme for existing exposure situation

    International Nuclear Information System (INIS)

    Ramadhani, Hilali Hussein

    2016-04-01

    This study was conducted to develop the Radiation protection Programme (RPP) to ensure that measures are in place for protection of individuals from the existing source of exposure. The study established a number of protective and remedial actions to be considered by the responsible regulatory Authority, licensee for existing exposure in workplace and dwellings. Tanzania is endowed with a number NORMs processing industries with an experience of uncontrolled exploration and extraction of minerals and the use of unsafe mining methods leading to severe environmental damage and appalling living conditions in the mining communities. Some of NORMs industries have been abandoned due to lack of an effect management infrastructure. The residual radioactive materials have been found to be the most import source of existing exposure resulted from NORMs industries. The Radon gas and its progeny have also been found to be a source of existing exposure from natural source as well as the major source of risk and health effects associated with existing exposure situation. The following measures have been discovered to play a pivotal role in avoiding or reducing the source of exposure to individuals such as restriction of the use of the construction materials, restriction on the consumption of foodstuffs and restriction on the access to the land and buildings, the removal of the magnitude of the source in terms of activity concentration as well as improvement of ventilation in dwellings. Therefore, the regulatory body (Tanzania Atomic Energy Commission) should examine the major areas outlined in the established RRP for existing exposure situation resulted from the NORMs industries and natural sources so as to develop strategies that will ensure the adequate protection of members of the public and the environment as well as guiding operating organizations to develop radiation protection and safety measures for workers. (au)

  4. Automated quantitative assessment of proteins' biological function in protein knowledge bases.

    Science.gov (United States)

    Mayr, Gabriele; Lepperdinger, Günter; Lackner, Peter

    2008-01-01

    Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

  5. Automated Quantitative Assessment of Proteins' Biological Function in Protein Knowledge Bases

    Directory of Open Access Journals (Sweden)

    Gabriele Mayr

    2008-01-01

    Full Text Available Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

  6. A Type-2 fuzzy data fusion approach for building reliable weighted protein interaction networks with application in protein complex detection.

    Science.gov (United States)

    Mehranfar, Adele; Ghadiri, Nasser; Kouhsar, Morteza; Golshani, Ashkan

    2017-09-01

    Detecting the protein complexes is an important task in analyzing the protein interaction networks. Although many algorithms predict protein complexes in different ways, surveys on the interaction networks indicate that about 50% of detected interactions are false positives. Consequently, the accuracy of existing methods needs to be improved. In this paper we propose a novel algorithm to detect the protein complexes in 'noisy' protein interaction data. First, we integrate several biological data sources to determine the reliability of each interaction and determine more accurate weights for the interactions. A data fusion component is used for this step, based on the interval type-2 fuzzy voter that provides an efficient combination of the information sources. This fusion component detects the errors and diminishes their effect on the detection protein complexes. So in the first step, the reliability scores have been assigned for every interaction in the network. In the second step, we have proposed a general protein complex detection algorithm by exploiting and adopting the strong points of other algorithms and existing hypotheses regarding real complexes. Finally, the proposed method has been applied for the yeast interaction datasets for predicting the interactions. The results show that our framework has a better performance regarding precision and F-measure than the existing approaches. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Protein Inference from the Integration of Tandem MS Data and Interactome Networks.

    Science.gov (United States)

    Zhong, Jiancheng; Wang, Jianxing; Ding, Xiaojun; Zhang, Zhen; Li, Min; Wu, Fang-Xiang; Pan, Yi

    2017-01-01

    Since proteins are digested into a mixture of peptides in the preprocessing step of tandem mass spectrometry (MS), it is difficult to determine which specific protein a shared peptide belongs to. In recent studies, besides tandem MS data and peptide identification information, some other information is exploited to infer proteins. Different from the methods which first use only tandem MS data to infer proteins and then use network information to refine them, this study proposes a protein inference method named TMSIN, which uses interactome networks directly. As two interacting proteins should co-exist, it is reasonable to assume that if one of the interacting proteins is confidently inferred in a sample, its interacting partners should have a high probability in the same sample, too. Therefore, we can use the neighborhood information of a protein in an interactome network to adjust the probability that the shared peptide belongs to the protein. In TMSIN, a multi-weighted graph is constructed by incorporating the bipartite graph with interactome network information, where the bipartite graph is built with the peptide identification information. Based on multi-weighted graphs, TMSIN adopts an iterative workflow to infer proteins. At each iterative step, the probability that a shared peptide belongs to a specific protein is calculated by using the Bayes' law based on the neighbor protein support scores of each protein which are mapped by the shared peptides. We carried out experiments on yeast data and human data to evaluate the performance of TMSIN in terms of ROC, q-value, and accuracy. The experimental results show that AUC scores yielded by TMSIN are 0.742 and 0.874 in yeast dataset and human dataset, respectively, and TMSIN yields the maximum number of true positives when q-value less than or equal to 0.05. The overlap analysis shows that TMSIN is an effective complementary approach for protein inference.

  8. 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.

  9. Structural behaviour characterization of existing adobe constructions in Aveiro

    OpenAIRE

    Varum, H.; Costa, A.; Martins, T.; Pereira, H.; Almeida, J.; Rodrigues, H.; Silveira, D.

    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...

  10. 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…

  11. Conditions for the Existence of Market Equilibrium.

    Science.gov (United States)

    Bryant, William D. A.

    1997-01-01

    Maintains that most graduate-level economics textbooks rarely mention the need for consumers to be above their minimum wealth position as a condition for market equilibrium. Argues that this omission leaves students with a mistaken sense about the range of circumstances under which market equilibria can exist. (MJP)

  12. 22 CFR 142.16 - Existing facilities.

    Science.gov (United States)

    2010-04-01

    ... OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Accessibility § 142.16 Existing facilities. (a) Accessibility. A recipient shall operate each program or activity to which this part applies so that when each...., telecommunication device for the deaf) redesign of equipment, reassignment of classes or other services to...

  13. Transportation capabilities of the existing cask fleet

    International Nuclear Information System (INIS)

    Johnson, P.E.; Joy, D.S.; Wankerl, M.W.

    1991-01-01

    This paper describes a number of scenarios estimating the amount of spent nuclear fuel that could be transported to a Monitored Retrievable Storage (MRS) Facility by various combinations of existing cask fleets. To develop the scenarios, the data provided by the Transportation System Data Base (TSDB) were modified to reflect the additional time for cask turnaround resulting from various startup and transportation issues. With these more realistic speed and cask-handling assumptions, the annual transportation capability of a fleet consisting of all of the existing casks is approximately 46 metric tons of uranium (MTU). The most likely fleet of existing casks that would be made available to the Department of Energy (DOE) consists of two rail, three overweight truck, and six legal weight truck casks. Under the same transportation assumptions, this cask fleet is capable of approximately transporting 270 MTU/year. These ranges of capability is a result of the assumptions pertaining to the number of casks assumed to be available. It should be noted that this assessment assumes additional casks based on existing certifications are not fabricated. 5 refs., 4 tabs

  14. Conservation and Development Options existing on Uluguru ...

    African Journals Online (AJOL)

    Effective management of projects on Uluguru Mountains requires that both development and conservation options are weighed and that opportunities and challenges are considered. This study identified various conservation and development options existing on Uluguru Mountains and assessed the perceptions of the local ...

  15. Transportation capabilities of the existing cask fleet

    International Nuclear Information System (INIS)

    Johnson, P.E.; Wankerl, M.W.; Joy, D.S.

    1991-01-01

    This paper describes a number of scenarios estimating the amount of spent nuclear fuel that could be transported to a Monitored Retrievable Storage (MRS) Facility by various combinations of existing cask fleets. To develop the scenarios, the data provided by the Transportation System Data Base (TSDB) were modified to reflect the additional time for cask turnaround resulting from various startup and transportation issues. With these more realistic speed and cask-handling assumptions, the annual transportation capability of a fleet consisting of all of the existing casks is approximately 465 metric tons of uranium (MTU). The most likely fleet of existing casks that would be made available to the DOE consists of two rail, three overweight truck, and six legal weight truck casks. Under the same transportation assumptions, this cask fleet is capable of approximately transporting 270 MTU/year. These ranges of capability is a result of the assumptions pertaining to the number of casks assumed to be available. It should be noted that this assessment assumes additional casks based on existing certifications are not fabricated

  16. Does the Kuleshov Effect really Exist?

    DEFF Research Database (Denmark)

    Barratt, Daniel; Cabak Rédei, Anna

    2013-01-01

    with a doll, a dead woman in a coffin, and a bowl of soup; the viewers of the three sequences were reported to have perceived Mozhukin’s face as expressing happiness, sadness, and hunger/thoughtfulness respectively. It is not clear, however, whether or not the socalled “Kuleshov effect” really exists...

  17. COMPARATIVE ANALYSIS OF SOME EXISTING KINETIC MODELS ...

    African Journals Online (AJOL)

    The biosorption of three heavy metal ions namely; Zn2+, Cu2+ and Mn2+ using five microorganisms namely; Bacillus circulans, Pseudomonas aeruginosa, Staphylococcus xylosus, Streptomyces rimosus and Yeast (Saccharomyces sp.) were studied. In this paper, the effectiveness of six existing and two proposed kinetic ...

  18. Do ‘African’ universities exist?

    DEFF Research Database (Denmark)

    Jensen, Stig; Adriansen, Hanne Kirstine; Madsen, Lene Møller

    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 subseq...

  19. Do Biopositive Effects of Ionizing Radiations Exist

    International Nuclear Information System (INIS)

    Broda, E.

    1983-01-01

    The claim that radiations, e.g, in spas, can have biopositive actions on humans is unproven and unplausible. It also conflicts with the contents of the standard handbooks and with national legislation everywhere. Further, stimulation of plants by radiation is badly reproducible. But even if existing it need not be beneficial to the plant itself ("selfpositive"). (author)

  20. Repurposing Existing Material for Performance Support.

    Science.gov (United States)

    Harvey, Francis A.; Nelson, Adam

    1995-01-01

    Presents an overview of performance support systems (PSS), describes their role in promoting productivity in agile organizations, and discusses issues related to developing effective performance support using existing orientation, training, or procedural manuals. Topics include strategic principles of agility, and adding value when incorporating…

  1. Global existence proof for relativistic Boltzmann equation

    International Nuclear Information System (INIS)

    Dudynski, M.; Ekiel-Jezewska, M.L.

    1992-01-01

    The existence and causality of solutions to the relativistic Boltzmann equation in L 1 and in L loc 1 are proved. The solutions are shown to satisfy physically natural a priori bounds, time-independent in L 1 . The results rely upon new techniques developed for the nonrelativistic Boltzmann equation by DiPerna and Lions

  2. 38 CFR 18.422 - Existing facilities.

    Science.gov (United States)

    2010-07-01

    ... THE CIVIL RIGHTS ACT OF 1964 Nondiscrimination on the Basis of Handicap Accessibility § 18.422 Existing facilities. (a) Accessibility. A recipient shall operate each program or activity to which this... visits, delivery of health, or other social services at alternate accessible sites, alteration of...

  3. 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 Regulations of the Department of Agriculture (Continued) RURAL UTILITIES SERVICE, DEPARTMENT OF AGRICULTURE LOAN SECURITY DOCUMENTS FOR ELECTRIC BORROWERS Mortgage for Distribution Borrowers § 1718.52...

  4. 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.

  5. Psychology's struggle for existence: Second edition, 1913.

    Science.gov (United States)

    Wundt, Wilhelm; Lamiell, James T

    2013-08-01

    Presents an English translation of Wilhelm Wundt's Psychology's struggle for existence: Second edition, 1913, by James T. Lamiell in August, 2012. In his essay, Wundt advised against the impending divorce of psychology from philosophy. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

  6. Altering existing buildings in the UK

    International Nuclear Information System (INIS)

    Roberts, Simon

    2008-01-01

    The profiles of both existing housing and existing public and commercial buildings show that many have very poor thermal efficiency. The UK housing stock is replaced at a low rate of about 1% a year, so to cut energy use it is essential to address the challenges of existing buildings. This will involve reducing energy demand through passive measures such as retrofitted insulation, replacement of windows and proper airtightness, while ensuring adequate ventilation. Active measures include upgrading improved boilers and adding locally produced energy from wind, biomass, solar power and other sources. The introduction of Display Energy Certificates will increase energy awareness but there will also need to be a programme of increased demolition for the worst-performing homes. In addition, buildings will need to be adapted to cope with worse weather, higher temperatures and increased flood risk as climate change takes effect. Overheating, rather than excessive cold, is set to become a growing problem for householders and employees in existing UK buildings

  7. Adding Semantic Support to Existing UDDI Infrastructure

    National Research Council Canada - National Science Library

    Luo, Jim; Montrose, Bruce; Kang, Myong

    2005-01-01

    .... The advantage is that it is completely backward compatible. The add-on modules only need to be installed on the clients of users who wish to take advantage of semantic markups. They can be integrated seamlessly into existing systems and operations without any modification of the infrastructure.

  8. 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.

  9. 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.

  10. 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.

  11. Protein docking prediction using predicted protein-protein interface.

    Science.gov (United States)

    Li, Bin; Kihara, Daisuke

    2012-01-10

    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. 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. 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.

  12. Essence and Existence in Avicenna and Averroes

    Directory of Open Access Journals (Sweden)

    Belo, Catarina

    2009-12-01

    Full Text Available This article explores the views on existence of medieval Muslim philosophers Avicenna (d. 1037 and Averroes (d. 1198, whose works followed closely the philosophy of Aristotle. In addition to the Aristotelian influence, which permeated all medieval Islamic philosophy, Avicenna and Averroes were also inspired by Islamic theology, known in Arabic as kalām. The distinction between essence and existence is one of the most central and controversial aspects of Avicenna’s philosophy, together with his claim that existence is an accident. Averroes in turn has a radically different conception of existence, identifying it with existing beings rather than considering it as something in itself. With the Latin translation of Avicenna’s metaphysical works in the 12th century, the Avicennian distinction went on to shape much of the debate on existence in medieval Scholastic philosophy and beyond. This article assesses the meaning of the distinction in Avicenna as well as Averroes’ criticism. In explicating their radically different views on existence, it also touches on later discussions concerning existence, for example the issue whether existence is a predicate, in the Modern Age.

    El presente artículo explora las percepciones sobre la existencia de los filósofos medievales musulmanes Avicena (m. 1037 y Averroes (m. 1198, cuyas obras se encuentran muy próximas a la filosofía de Aristóteles. Además de la influencia aristotélica, que caló en toda la filosofía islámica medieval, Avicena y Averroes estuvieron inspirados por la teología islámica, conocida en árabe como Kalām. La distinción entre esencia y existencia es uno de los más fundamentales y controvertidos aspectos de la filosofía de Avicena junto a su aseveración de que la existencia es un accidente. Averroes, en cambio, concibe de forma radicalmente diferente la existencia, identificándola con los seres existentes más que considerarla como algo en

  13. Biases in the experimental annotations of protein function and their effect on our understanding of protein function space.

    Directory of Open Access Journals (Sweden)

    Alexandra M Schnoes

    Full Text Available The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data. However, with the increasing use of high-throughput experimental assays, a small number of experimental studies dominate the functional protein annotations collected in databases. Here, we investigate just how prevalent is the "few articles - many proteins" phenomenon. We examine the experimentally validated annotation of proteins provided by several groups in the GO Consortium, and show that the distribution of proteins per published study is exponential, with 0.14% of articles providing the source of annotations for 25% of the proteins in the UniProt-GOA compilation. Since each of the dominant articles describes the use of an assay that can find only one function or a small group of functions, this leads to substantial biases in what we know about the function of many proteins. Mass-spectrometry, microscopy and RNAi experiments dominate high throughput experiments. Consequently, the functional information derived from these experiments is mostly of the subcellular location of proteins, and of the participation of proteins in embryonic developmental pathways. For some organisms, the information provided by different studies overlap by a large amount. We also show that the information provided by high throughput experiments is less specific than those provided by low throughput experiments. Given the experimental techniques available, certain biases in protein function annotation due to high-throughput experiments are unavoidable. Knowing that these biases exist and understanding their characteristics and extent is important for database curators, developers of function annotation programs, and anyone who uses protein function annotation data to plan experiments.

  14. 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.

  15. Co-existence in multispecies biofilm communities

    DEFF Research Database (Denmark)

    Røder, Henriette Lyng

    of these emergent properties which are relevant to as diverse areas as clinical settings and natural systems. In this thesis, I have attempted to contribute to our knowledge on the multispecies interactions with a special focus on biofilm communities. I was especially interested in how co-existing species affect...... each other and in understanding the key mechanisms and interactions involved. In the introduction of this thesis the most important concepts of multi-species interactions and biofilm development are explained. After this the topic changes to the various ways of examining community interactions...... 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...

  16. 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...

  17. Leveraging Existing Laboratory Capacity towards Universal Health ...

    African Journals Online (AJOL)

    Background: The provision of quality health care is influenced by ... Laboratory support is urgently needed to enhance service delivery in the ... Information generated through ... professionals using simple rapid technology have been adopted.

  18. 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.

  19. 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.

  20. Existence and Comparability of data sources

    OpenAIRE

    KUHNIMHOF, T; ARMOOGUM, J

    2007-01-01

    The deliverable at hand comprises a comprehensive overview over existing data sources which can be used for analysis of long distance travel demand. This encompasses both national and international data sources with a focus on household travel surveys. Three types of relevant surveys were identified: - National travel surveys with focus on daily mobility - Travel survey elements dedicated to long distance mobility - Long distance travel surveys. RAPPORT DE CONTRAT

  1. Transgender Parenting: A Review of Existing Research

    OpenAIRE

    Stotzer, Rebecca L; Herman, Jody L; Hasenbush, Amira

    2014-01-01

    The authors of this report reviewed 51 studies that analyze data about transgender parents. This report reviews the existing research on the prevalence and characteristics of transgender people who are parents, the quality of relationships between transgender parents and their children, outcomes for children with a transgender parent, and the reported needs of transgender parents. Overall, the authors found that substantial numbers of transgender people are parents, though at rates below the ...

  2. Streamlining Research by Using Existing Tools

    OpenAIRE

    Greene, Sarah M.; Baldwin, Laura-Mae; Dolor, Rowena J.; Thompson, Ella; Neale, Anne Victoria

    2011-01-01

    Over the past two decades, the health research enterprise has matured rapidly, and many recognize an urgent need to translate pertinent research results into practice, to help improve the quality, accessibility, and affordability of U.S. health care. Streamlining research operations would speed translation, particularly for multi-site collaborations. However, the culture of research discourages reusing or adapting existing resources or study materials. Too often, researchers start studies and...

  3. Seismic evaluation of existing nuclear power plants

    International Nuclear Information System (INIS)

    2003-01-01

    The IAEA nuclear safety standards publications address the site evaluation and the design of new nuclear power plants (NPPs), including seismic hazard assessment and safe seismic design, at the level of the Safety Requirements as well as at the level of dedicated Safety Guides. It rapidly became apparent that the existing nuclear safety standards documents were not adequate for handling specific issues in the seismic evaluation of existing NPPs, and that a dedicated document was necessary. This is the purpose of this Safety Report, which is written in the spirit of the nuclear safety standards and can be regarded as guidance for the interpretation of their intent. Worldwide experience shows that an assessment of the seismic capacity of an existing operating facility can be prompted for the following: (a) Evidence of a greater seismic hazard at the site than expected before, owing to new or additional data and/or to new methods; (b) Regulatory requirements, such as periodic safety reviews, to ensure that the plant has adequate margins for seismic loads; (c) Lack of anti-seismic design or poor anti-seismic design; (d) New technical finding such as vulnerability of some structures (masonry walls) or equipment (relays), other feedback and new experience from real earthquakes. Post-construction evaluation programmes evaluate the current capability of the plant to withstand the seismic concern and identify any necessary upgrades or changes in operating procedures. Seismic qualification is distinguished from seismic evaluation primarily in that seismic qualification is intended to be performed at the design stage of a plant, whereas seismic evaluation is intended to be applied after a plant has been constructed. Although some guidelines do exist for the evaluation of existing NPPs, these are not established at the level of a regulatory guide or its equivalent. Nevertheless, a number of existing NPPs throughout the world have been and are being subjected to review of their

  4. Analysis of protein folds using protein contact networks

    Indian Academy of Sciences (India)

    is a well-recognized classification system of proteins, which is based on manual in- ... can easily correspond to the information in the 2D matrix. ..... [7] U K Muppirala and Zhijun Li, Protein Engineering, Design & Selection 19, 265 (2006).

  5. Protein sequence comparison and protein evolution

    Energy Technology Data Exchange (ETDEWEB)

    Pearson, W.R. [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Biochemistry

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.

  6. 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....

  7. 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.

  8. Analysis of field errors in existing undulators

    International Nuclear Information System (INIS)

    Kincaid, B.M.

    1990-01-01

    The Advanced Light Source (ALS) and other third generation synchrotron light sources have been designed for optimum performance with undulator insertion devices. The performance requirements for these new undulators are explored, with emphasis on the effects of errors on source spectral brightness. Analysis of magnetic field data for several existing hybrid undulators is presented, decomposing errors into systematic and random components. An attempts is made to identify the sources of these errors, and recommendations are made for designing future insertion devices. 12 refs., 16 figs

  9. 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

  10. 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.

  11. Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

    Science.gov (United States)

    Schnoes, Alexandra M.; Ream, David C.; Thorman, Alexander W.; Babbitt, Patricia C.; Friedberg, Iddo

    2013-01-01

    The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data. However, with the increasing use of high-throughput experimental assays, a small number of experimental studies dominate the functional protein annotations collected in databases. Here, we investigate just how prevalent is the “few articles - many proteins” phenomenon. We examine the experimentally validated annotation of proteins provided by several groups in the GO Consortium, and show that the distribution of proteins per published study is exponential, with 0.14% of articles providing the source of annotations for 25% of the proteins in the UniProt-GOA compilation. Since each of the dominant articles describes the use of an assay that can find only one function or a small group of functions, this leads to substantial biases in what we know about the function of many proteins. Mass-spectrometry, microscopy and RNAi experiments dominate high throughput experiments. Consequently, the functional information derived from these experiments is mostly of the subcellular location of proteins, and of the participation of proteins in embryonic developmental pathways. For some organisms, the information provided by different studies overlap by a large amount. We also show that the information provided by high throughput experiments is less specific than those provided by low throughput experiments. Given the experimental techniques available, certain biases in protein function annotation due to high-throughput experiments are unavoidable. Knowing that these biases exist and understanding their characteristics and extent is important for database curators, developers of function annotation programs, and anyone who uses protein function annotation data to plan experiments. PMID:23737737

  12. 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

  13. 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, ...

  14. LDEF data: Comparisons with existing models

    Science.gov (United States)

    Coombs, Cassandra R.; Watts, Alan J.; Wagner, John D.; Atkinson, Dale R.

    1993-04-01

    The relationship between the observed cratering impact damage on the Long Duration Exposure Facility (LDEF) versus the existing models for both the natural environment of micrometeoroids and the man-made debris was investigated. Experimental data was provided by several LDEF Principal Investigators, Meteoroid and Debris Special Investigation Group (M&D SIG) members, and by the Kennedy Space Center Analysis Team (KSC A-Team) members. These data were collected from various aluminum materials around the LDEF satellite. A PC (personal computer) computer program, SPENV, was written which incorporates the existing models of the Low Earth Orbit (LEO) environment. This program calculates the expected number of impacts per unit area as functions of altitude, orbital inclination, time in orbit, and direction of the spacecraft surface relative to the velocity vector, for both micrometeoroids and man-made debris. Since both particle models are couched in terms of impact fluxes versus impactor particle size, and much of the LDEF data is in the form of crater production rates, scaling laws have been used to relate the two. Also many hydrodynamic impact computer simulations were conducted, using CTH, of various impact events, that identified certain modes of response, including simple metallic target cratering, perforations and delamination effects of coatings.

  15. Eternally existing self-reproducing inflationary universe

    International Nuclear Information System (INIS)

    Linde, A.D.

    1986-05-01

    It is shown that the large-scale quantum fluctuations of the scalar field φ generated in the chaotic inflation scenario lead to an infinite process of self-reproduction of inflationary mini-universes. A model of eternally existing chaotic inflationary universe is suggested. It is pointed out that whereas the universe locally is very homogeneous as a result of inflation, which occurs at the classical level, the global structure of the universe is determined by quantum effects and is highly non-trivial. The universe consists of exponentially large number of different mini-universes, inside which all possible (metastable) vacuum states and all possible types of compactification are realized. The picture differs crucially from the standard picture of a one-domain universe in a ''true'' vacuum state. Our results may serve as a justification of the anthropic principle in the inflationary cosmology. These results may have important implications for the elementary particle theory as well. Namely, since all possible types of mini-universes, in which inflation may occur, should exist in our universe, there is no need to insist (as it is usually done) that in realistic theories the vacuum state of our type should be the only possible one or the best one. (author)

  16. A comparative analysis of existing oligonucleotides selection ...

    African Journals Online (AJOL)

    SERVER

    2007-07-04

    Jul 4, 2007 ... Available online at http://www.academicjournals.org/AJB ... Department of Computer and Information Sciences, Covenant University P. M. B 1023, Ota, Nigeria. ... Key words: System biology, microarray technology, oligo, genome, coding sequence, ... ficity) and efficiency (computer speed and memory requi-.

  17. 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.

  18. A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

    Directory of Open Access Journals (Sweden)

    Meijing Li

    2015-01-01

    Full Text Available Many researchers focus on developing protein-named entity recognition (Protein-NER or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM and parsing tree. PPIMiner consists of three main models: natural language processing (NLP model, Protein-NER model, and PPI discovery model. The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method. ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems. The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods. In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools. PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction. We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER.

  19. Analyzing the security of an existing computer system

    Science.gov (United States)

    Bishop, M.

    1986-01-01

    Most work concerning secure computer systems has dealt with the design, verification, and implementation of provably secure computer systems, or has explored ways of making existing computer systems more secure. The problem of locating security holes in existing systems has received considerably less attention; methods generally rely on thought experiments as a critical step in the procedure. The difficulty is that such experiments require that a large amount of information be available in a format that makes correlating the details of various programs straightforward. This paper describes a method of providing such a basis for the thought experiment by writing a special manual for parts of the operating system, system programs, and library subroutines.

  20. Guidance for closure of existing DOE LLW disposal sites

    International Nuclear Information System (INIS)

    Blanchfield, L.

    1987-01-01

    During FY 1986, a closure guidance document was developed. The purpose of this document is to provide guidance in support of DOE Order 5820.2 to site operating contractors for the stabilization and closure of existing low-level waste (LLW) shallow land disposal sites at US Department of Energy (DOE) facilities. Guidance is provided to aid operators in placing existing LLW sites in a closed conditions, i.e., a condition in which a nonoperational site meets postclosure performance requirements and can be shown, within a high degree of confidence, to perform as anticipated in the future, under the most cost-effective maintenance approach. Guidance is based on the philosophy that closure should be planned and performed using a systems approach. Plans for FY 1987 call for revision of the document to incorporate more information on closure of LLW sites also containing radioactive mixed waste and/or transuranic waste. 4 references, 3 figures, 2 tables

  1. Introduction of the EISA-PC into existing fusion experiments

    International Nuclear Information System (INIS)

    Tenten, W.; Bertschinger, G.; Mueller, K.D.; Reinhart, P.; Rongen, F.

    1995-01-01

    A general problem in the data acquisition field in fusion research is the lack of sufficient local memory for the storage of information acquired during a single discharge. While it is absolutely necessary to keep these data locally before transferring them to a central node, there has been a steadily increasing demand for more capacity. The introduction of an EISA-Personal-Computer with its vast and cheap memory resources is presenting a very interesting solution for the upgrade of existing installations and the design of new experiments. An innovative PC interface using Programmable Logic techniques was developed that allows easy and fast integration of a PC into an existing experimental setup. Several typical applications of this method are presented, that are of special interest for fusion experiments. (orig.)

  2. 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.

  3. A protein-dependent side-chain rotamer library.

    KAUST Repository

    Bhuyan, M.S.; Gao, Xin

    2011-01-01

    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.

  4. Growing functional modules from a seed protein via integration of protein interaction and gene expression data

    Directory of Open Access Journals (Sweden)

    Dimitrakopoulou Konstantina

    2007-10-01

    Full Text Available Abstract Background Nowadays modern biology aims at unravelling the strands of complex biological structures such as the protein-protein interaction (PPI networks. A key concept in the organization of PPI networks is the existence of dense subnetworks (functional modules in them. In recent approaches clustering algorithms were applied at these networks and the resulting subnetworks were evaluated by estimating the coverage of well-established protein complexes they contained. However, most of these algorithms elaborate on an unweighted graph structure which in turn fails to elevate those interactions that would contribute to the construction of biologically more valid and coherent functional modules. Results In the current study, we present a method that corroborates the integration of protein interaction and microarray data via the discovery of biologically valid functional modules. Initially the gene expression information is overlaid as weights onto the PPI network and the enriched PPI graph allows us to exploit its topological aspects, while simultaneously highlights enhanced functional association in specific pairs of proteins. Then we present an algorithm that unveils the functional modules of the weighted graph by expanding a kernel protein set, which originates from a given 'seed' protein used as starting-point. Conclusion The integrated data and the concept of our approach provide reliable functional modules. We give proofs based on yeast data that our method manages to give accurate results in terms both of structural coherency, as well as functional consistency.

  5. 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.

  6. Seismic review of existing nuclear power plants

    International Nuclear Information System (INIS)

    Yanev, P.I.; Mayes, R.L.; Jones, L.R.

    1975-01-01

    Because of developments in the fields of earthquake and structural engineering over the last two decades, the codes, standards and design criteria for Nuclear Power Plants and other critical structures have changed substantially. As a result, plants designed only a few years ago do not satisfy the requirements for new plants. Accordingly, the Regulatory Agencies are requiring owners of older Nuclear Power Plants to re-qualify the plants seismically, using codes, standards, analytical techniques and knowledge developed in recent years. Seismic review consists of three major phases: establishing the design and performance criteria, re-qualifying the structures, and re-qualifying the equipment. The authors of the paper have been recently involved in the seismic review of existing nuclear power plants in the United States. This paper is a brief summary of their experiences

  7. 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.

  8. 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.

  9. On the existence of hot positronium reactions

    International Nuclear Information System (INIS)

    Lazzarini, E.

    1984-01-01

    The existence of hot Ps reactions is nowadays questioned; the controversy arises from the two models (the Ore gap and the spur theories) advanced in order to explain the mechanism of the positronium formation and of its inhibition in liquids by dissolution of certain compounds. The hypothesis of the hot Ps reactions was initially advanced as an additional statement for explaining the inhibition phenomenon within the framework of the Ore gap theory, but it is not considered necessary for the spur theory. The present paper is chiefly intended as a presentation of this particular aspect of Ps chemistry to hot atom chemists unspecialized in the field. The reader is assumed to be familiar with the basic physics and experimental methods used in positronium chemistry. Contents: positrons and positronium formation; inhibition and enhancement of Ps formation in solutions; positronium reactions in gases. (Auth.)

  10. Sustainability in the existing building stock

    DEFF Research Database (Denmark)

    Elle, Morten; Nielsen, Susanne Balslev; Hoffmann, Birgitte

    2005-01-01

    , 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......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...... management is a concept relevant to others than large companies. Managing the flows of energy and other resources is a part of facilities management, and an increased professionalism could lead to the reduction of the use of energy and water and the generation of waste and wastewater. This is, however...

  11. 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.

  12. [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.

  13. 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

  14. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    International Nuclear Information System (INIS)

    Yu, P.

    2007-01-01

    The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  15. How many N = 4 strings exist?

    International Nuclear Information System (INIS)

    Ketov, S.V.

    1994-09-01

    Possible ways of constructing extended fermionic strings with N=4 world-sheet supersymmetry are reviewed. String theory constraints form, in general, a non-linear quasi(super)conformal algebra, and can have conformal dimensions ≥1. When N=4, the most general N=4 quasi-superconformal algebra to consider for string theory building is D(1, 2; α), whose linearisation is the so-called ''large'' N=4 superconformal algebra. The D(1, 2; α) algebra has su(2)sub(κ + )+su(2)sub(κ - )+u(1) Kac-Moody component, and α=κ - /κ + . We check the Jacobi identities and construct a BRST charge for the D(1, 2; α) algebra. The quantum BRST operator can be made nilpotent only when κ + =κ - =-2. The D(1, 2; 1) algebra is actually isomorphic to the SO(4)-based Bershadsky-Knizhnik non-linear quasi-superconformal algebra. We argue about the existence of a string theory associated with the latter, and propose the (non-covariant) hamiltonian action for this new N=4 string theory. Our results imply the existence of two different N=4 fermionic string theories: the old one based on the ''small'' linear N=4 superconformal algebra and having the total ghost central charge c gh =+12, and the new one with non-linearly realised N=4 supersymmetry, based on the SO(4) quasi-superconformal algebra and having c gh =+6. Both critical string theories have negative ''critical dimensions'' and do not admit unitary matter representations. (orig.)

  16. Protein - Which is Best?

    Science.gov (United States)

    Hoffman, Jay R; Falvo, Michael J

    2004-09-01

    Protein intake that exceeds the recommended daily allowance is widely accepted for both endurance and power athletes. However, considering the variety of proteins that are available much less is known concerning the benefits of consuming one protein versus another. The purpose of this paper is to identify and analyze key factors in order to make responsible recommendations to both the general and athletic populations. Evaluation of a protein is fundamental in determining its appropriateness in the human diet. Proteins that are of inferior content and digestibility are important to recognize and restrict or limit in the diet. Similarly, such knowledge will provide an ability to identify proteins that provide the greatest benefit and should be consumed. The various techniques utilized to rate protein will be discussed. Traditionally, sources of dietary protein are seen as either being of animal or vegetable origin. Animal sources provide a complete source of protein (i.e. containing all essential amino acids), whereas vegetable sources generally lack one or more of the essential amino acids. Animal sources of dietary protein, despite providing a complete protein and numerous vitamins and minerals, have some health professionals concerned about the amount of saturated fat common in these foods compared to vegetable sources. The advent of processing techniques has shifted some of this attention and ignited the sports supplement marketplace with derivative products such as whey, casein and soy. Individually, these products vary in quality and applicability to certain populations. The benefits that these particular proteins possess are discussed. In addition, the impact that elevated protein consumption has on health and safety issues (i.e. bone health, renal function) are also reviewed. Key PointsHigher protein needs are seen in athletic populations.Animal proteins is an important source of protein, however potential health concerns do exist from a diet of protein

  17. Metabolic fingerprinting of high-fat plasma samples processed by centrifugation- and filtration-based protein precipitation delineates significant differences in metabolite information coverage.

    Science.gov (United States)

    Barri, Thaer; Holmer-Jensen, Jens; Hermansen, Kjeld; Dragsted, Lars O

    2012-03-09

    Metabolomics and metabolic fingerprinting are being extensively employed for improved understanding of biological changes induced by endogenous or exogenous factors. Blood serum or plasma samples are often employed for metabolomics studies. Plasma protein precipitation (PPP) is currently performed in most laboratories before LC-MS analysis. However, the impact of fat content in plasma samples on metabolite coverage has not previously been investigated. Here, we have studied whether PPP procedures influence coverage of plasma metabolites from high-fat plasma samples. An optimized UPLC-QTOF/MS metabolic fingerprinting approach and multivariate modeling (PCA and OPLS-DA) were utilized for finding characteristic metabolite changes induced by two PPP procedures; centrifugation and filtration. We used 12-h fasting samples and postprandial samples collected at 2h after a standardized high-fat protein-rich meal in obese non-diabetic subjects recruited in a dietary intervention. The two PPP procedures as well as external and internal standards (ISs) were used to track errors in response normalization and quantification. Remarkably and sometimes uniquely, the fPPP, but not the cPPP approach, recovered not only high molecular weight (HMW) lipophilic metabolites, but also small molecular weight (SMW) relatively polar metabolites. Characteristic SMW markers of postprandial samples were aromatic and branched-chain amino acids that were elevated (p<0.001) as a consequence of the protein challenge. In contrast, some HMW lipophilic species, e.g. acylcarnitines, were moderately lower (p<0.001) in postprandial samples. LysoPCs were largely unaffected. In conclusion, the fPPP procedure is recommended for processing high-fat plasma samples in metabolomics studies. While method improvements presented here were clear, use of several ISs revealed substantial challenges to untargeted metabolomics due to large and variable matrix effects. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. Applying new safeguards technology to existing nuclear facilities

    International Nuclear Information System (INIS)

    Johnson, C.E.; Wagner, E.P.

    1979-01-01

    The application and operation of safeguards instrumentation in a facility containing special nuclear material is most successful when the installation is designed for the operation of the specific facility. Experience at the Idaho National Engineering Laboratory demonstrates that installation designs must consider both Safeguards and Production requirements of specific facilities. Equipment selection and installation design influenced by the training and experience of production operations and safeguards personnel at a specific facility help assure successful installation, reliable operation, and minimal operator training. This minimizes impacts on existing plant production activities while maximizing utility of the safeguards information obtained

  19. Applying new safeguards technology to existing nuclear facilities

    International Nuclear Information System (INIS)

    Harris, W.J.; Wagner, E.P.

    1979-01-01

    The application and operation of safeguards instrumentation in a facility containing special nuclear material is most successful when the installation is desinged for the operation of the specific facility. Experience at the Idaho National Engineering Laboratory demonstrates that installation designs must consider both safeguards and production requirements of specific facilities. Equipment selection and installation design influenced by the training and experience of production operations and safeguards personnel at a specific facility help assure successful installation, reliable operation, and minimal operator training. This minimizes impacts on existing plant production activities while maximizing utility of the safeguards information obtained

  20. 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.)

  1. Automatic annotation of protein motif function with Gene Ontology terms

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Vanathi

    2004-09-01

    Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.

  2. A computational approach to finding novel targets for existing drugs.

    Directory of Open Access Journals (Sweden)

    Yvonne Y Li

    2011-09-01

    Full Text Available Repositioning existing drugs for new therapeutic uses is an efficient approach to drug discovery. We have developed a computational drug repositioning pipeline to perform large-scale molecular docking of small molecule drugs against protein drug targets, in order to map the drug-target interaction space and find novel interactions. Our method emphasizes removing false positive interaction predictions using criteria from known interaction docking, consensus scoring, and specificity. In all, our database contains 252 human protein drug targets that we classify as reliable-for-docking as well as 4621 approved and experimental small molecule drugs from DrugBank. These were cross-docked, then filtered through stringent scoring criteria to select top drug-target interactions. In particular, we used MAPK14 and the kinase inhibitor BIM-8 as examples where our stringent thresholds enriched the predicted drug-target interactions with known interactions up to 20 times compared to standard score thresholds. We validated nilotinib as a potent MAPK14 inhibitor in vitro (IC50 40 nM, suggesting a potential use for this drug in treating inflammatory diseases. The published literature indicated experimental evidence for 31 of the top predicted interactions, highlighting the promising nature of our approach. Novel interactions discovered may lead to the drug being repositioned as a therapeutic treatment for its off-target's associated disease, added insight into the drug's mechanism of action, and added insight into the drug's side effects.

  3. Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information.

    Science.gov (United States)

    Karczyńska, Agnieszka S; Mozolewska, Magdalena A; Krupa, Paweł; Giełdoń, Artur; Liwo, Adam; Czaplewski, Cezary

    2018-03-01

    A new approach to assisted protein-structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics simulations with the coarse-grained UNRES force field with restraints derived from knowledge-based models and distance distribution from small angle X-ray scattering (SAXS) measurements. The latter restraints are incorporated into the target function as a maximum-likelihood term that guides the shape of the simulated structures towards that defined by SAXS. The approach was first verified with the 1KOY protein, for which the distance distribution was calculated from the experimental structure, and subsequently used to predict the structures of 11 data-assisted targets in the CASP12 experiment. Major improvement of the GDT_TS was obtained for 2 targets, minor improvement for other 2 while, for 6 target GDT_TS deteriorated compared with that calculated for predictions without the SAXS data, partly because of assuming a wrong multimeric state (for Ts866) or because the crystal conformation was more compact than the solution conformation (for Ts942). Particularly good results were obtained for Ts909, in which use of SAXS data resulted in the selection of a correctly packed trimer and, subsequently, increased the GDT_TS of monomer prediction. It was found that running simulations with correct oligomeric state is essential for the success in SAXS-data-assisted prediction. © 2017 Wiley Periodicals, Inc.

  4. 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....

  5. Building on existing institutions to perpetuate knowledge of waste repositories

    International Nuclear Information System (INIS)

    Weitzberg, A.

    1982-08-01

    Purpose of this report is to examine the function of several existing institutions and to show how they could be effectively used to transmit information about waste repositories for long times into the future. Scope of this report is limited to a discussion of four institutional approaches to the dissemination and retention of information: Widely distributed maps, the marker system of the National Geodetic Survey, the archiving of documents, and one-call systems designed to protect underground utility installations from inadvertent damage by the public. Each of these approaches is discussed in an independent section that describes the background of the institutional approach, discusses methods for applying it to waste repositories, and assesses its potential value. The sole intent of this report is to present supporting data for future decisions about the kinds of communication measures that should be implemented to advise future generations about the locations and hazards of waste repositories

  6. Effectiveness of Existing International Nuclear Liability Regime

    International Nuclear Information System (INIS)

    Al-Doais, Salwa; Kessel, Daivd

    2015-01-01

    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

  7. Existing facilities and past practices: Lessons learned

    International Nuclear Information System (INIS)

    Huizenga, D.; Tonkay, D.W.; Owens, K.

    2000-01-01

    Article 12 of the Joint Convention on the Safety of Spent Fuel Management and on the Safety of Radioactive Waste Management (Joint Convention) requires parties to the Joint Convention to review the safety of existing radioactive waste management facilities 'to ensure that, if necessary, all reasonably practicable improvements are made to upgrade the safety of such a facility'. Also required is a review of the results of past practices to determine 'whether any intervention is needed for reasons of radiation protection' and to consider whether the benefits of the intervention or remediation are sufficient, with regard to the costs and the impact on workers, the public and the environment. This paper discusses the experience of the United States Department of Energy in terms of the lessons learned from operating radioactive waste management facilities and from undertaking intervention or remedial action, and from decision making in an international context. Overarching safety principles are discussed, including integrating safety into all work practices and minimizing the generation of waste. Safety review lessons learned with existing facilities are discussed with respect to: applying new requirements to old facilities, taking a life-cycle perspective of waste management, improving high level waste facility management, and blending current and past practices with respect to the process used to arrive at decisions for intervention. Special emphasis is placed on the need to provide for early and substantive input from the involved regulatory agencies, Native American tribes, and those citizens and groups with an interest in the decisions. Examples of intervention decisions are discussed, including examples taken from uranium mill tailings operations, from cleanup of a former uranium processing plant site, from evaluation of pre-1970 buried 'transuranic waste' sites, and from decommissioning or closure of high level waste storage tanks. The paper concludes that on the

  8. 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

  9. 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

  10. cuticleDB: a relational database of Arthropod cuticular proteins

    Directory of Open Access Journals (Sweden)

    Willis Judith H

    2004-09-01

    Full Text Available Abstract Background The insect exoskeleton or cuticle is a bi-partite composite of proteins and chitin that provides protective, skeletal and structural functions. Little information is available about the molecular structure of this important complex that exhibits a helicoidal architecture. Scores of sequences of cuticular proteins have been obtained from direct protein sequencing, from cDNAs, and from genomic analyses. Most of these cuticular protein sequences contain motifs found only in arthropod proteins. Description cuticleDB is a relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the Drosophila melanogaster and the Anopheles gambiae genomes, that have been predicted to be cuticular proteins, based on a Pfam motif (PF00379 responsible for chitin binding in Arthropod cuticle. The total number of the database entries is 445: 370 derive from insects, 60 from Crustacea and 15 from Chelicerata. The database can be accessed from our web server at http://bioinformatics.biol.uoa.gr/cuticleDB. Conclusions CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin.

  11. 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.

  12. Does the chromatic Mach bands effect exist?

    Science.gov (United States)

    Tsofe, Avital; Spitzer, Hedva; Einav, Shmuel

    2009-06-30

    The achromatic Mach bands effect is a well-known visual illusion, discovered over a hundred years ago. This effect has been investigated thoroughly, mainly for its brightness aspect. The existence of Chromatic Mach bands, however, has been disputed. In recent years it has been reported that Chromatic Mach bands are not perceived under controlled iso-luminance conditions. However, here we show that a variety of Chromatic Mach bands, consisting of chromatic and achromatic regions, separated by a saturation ramp, can be clearly perceived under iso-luminance and iso-brightness conditions. In this study, observers' eye movements were recorded under iso-brightness conditions. Several observers were tested for their ability to perceive the Chromatic Mach bands effect and its magnitude, across different cardinal and non-cardinal Chromatic Mach bands stimuli. A computational model of color adaptation, which predicted color induction and color constancy, successfully predicts this variation of Chromatic Mach bands. This has been tested by measuring the distance of the data points from the "achromatic point" and by calculating the shift of the data points from predicted complementary lines. The results suggest that the Chromatic Mach bands effect is a specific chromatic induction effect.

  13. 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.

  14. On the existence of tropical anvil clouds

    Science.gov (United States)

    Seeley, J.; Jeevanjee, N.; Langhans, W.; Romps, D.

    2017-12-01

    In the deep tropics, extensive anvil clouds produce a peak in cloud cover below the tropopause. The dominant paradigm for cloud cover attributes this anvil peak to a layer of enhanced mass convergence in the clear-sky upper-troposphere, which is presumed to force frequent detrainment of convective anvils. However, cloud cover also depends on the lifetime of cloudy air after it detrains, which raises the possibility that anvil clouds may be the signature of slow cloud decay rather than enhanced detrainment. Here we measure the cloud decay timescale in cloud-resolving simulations, and find that cloudy updrafts that detrain in the upper troposphere take much longer to dissipate than their shallower counterparts. We show that cloud lifetimes are long in the upper troposphere because the saturation specific humidity becomes orders of magnitude smaller than the typical condensed water loading of cloudy updrafts. This causes evaporative cloud decay to act extremely slowly, thereby prolonging cloud lifetimes in the upper troposphere. As a consequence, extensive anvil clouds still occur in a convecting atmosphere that is forced to have no preferential clear-sky convergence layer. On the other hand, when cloud lifetimes are fixed at a characteristic lower-tropospheric value, extensive anvil clouds do not form. Our results support a revised understanding of tropical anvil clouds, which attributes their existence to the microphysics of slow cloud decay rather than a peak in clear-sky convergence.

  15. Personal anticipated information need

    OpenAIRE

    H. Bruce

    2005-01-01

    Background. The role of personal information collections is a well known feature of personal information management. The World Wide Web has introduced to such collections ideas such as filing Web pages or noting their existence in 'Bookmarks' and 'Favourites'. Argument. It is suggested that personal information collections are created in anticipation of some future need for that information-personal, anticipated information need, which also underlies the design of formal information systems. ...

  16. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

    International Nuclear Information System (INIS)

    Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei

    2013-01-01

    We introduce a Python-based program that utilizes the large database of 13 C and 15 N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13 C– 13 C, 15 N– 13 C, or 3D 15 N– 13 C– 13 C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13 C– 13 C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

  17. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

    Energy Technology Data Exchange (ETDEWEB)

    Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry (United States)

    2013-06-15

    We introduce a Python-based program that utilizes the large database of {sup 13}C and {sup 15}N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D {sup 13}C-{sup 13}C, {sup 15}N-{sup 13}C, or 3D {sup 15}N-{sup 13}C-{sup 13}C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D {sup 13}C-{sup 13}C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the C{alpha} and C{beta} chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-C{alpha}-C{beta} or N-C{alpha}-C{beta}), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

  18. 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.

  19. 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.

  20. ProteinTracker: an application for managing protein production and purification.

    Science.gov (United States)

    Ponko, Stefan C; Bienvenue, David

    2012-05-10

    Laboratories that produce protein reagents for research and development face the challenge of deciding whether to track batch-related data using simple file based storage mechanisms (e.g. spreadsheets and notebooks), or commit the time and effort to install, configure and maintain a more complex laboratory information management system (LIMS). Managing reagent data stored in files is challenging because files are often copied, moved, and reformatted. Furthermore, there is no simple way to query the data if/when questions arise. Commercial LIMS often include additional modules that may be paid for but not actually used, and often require software expertise to truly customize them for a given environment. This web-application allows small to medium-sized protein production groups to track data related to plasmid DNA, conditioned media samples (supes), cell lines used for expression, and purified protein information, including method of purification and quality control results. In addition, a request system was added that includes a means of prioritizing requests to help manage the high demand of protein production resources at most organizations. ProteinTracker makes extensive use of existing open-source libraries and is designed to track essential data related to the production and purification of proteins. ProteinTracker is an open-source web-based application that provides organizations with the ability to track key data involved in the production and purification of proteins and may be modified to meet the specific needs of an organization. The source code and database setup script can be downloaded from http://sourceforge.net/projects/proteintracker. This site also contains installation instructions and a user guide. A demonstration version of the application can be viewed at http://www.proteintracker.org.

  1. ProteinTracker: an application for managing protein production and purification

    Directory of Open Access Journals (Sweden)

    Ponko Stefan C

    2012-05-01

    Full Text Available Abstract Background Laboratories that produce protein reagents for research and development face the challenge of deciding whether to track batch-related data using simple file based storage mechanisms (e.g. spreadsheets and notebooks, or commit the time and effort to install, configure and maintain a more complex laboratory information management system (LIMS. Managing reagent data stored in files is challenging because files are often copied, moved, and reformatted. Furthermore, there is no simple way to query the data if/when questions arise. Commercial LIMS often include additional modules that may be paid for but not actually used, and often require software expertise to truly customize them for a given environment. Findings This web-application allows small to medium-sized protein production groups to track data related to plasmid DNA, conditioned media samples (supes, cell lines used for expression, and purified protein information, including method of purification and quality control results. In addition, a request system was added that includes a means of prioritizing requests to help manage the high demand of protein production resources at most organizations. ProteinTracker makes extensive use of existing open-source libraries and is designed to track essential data related to the production and purification of proteins. Conclusions ProteinTracker is an open-source web-based application that provides organizations with the ability to track key data involved in the production and purification of proteins and may be modified to meet the specific needs of an organization. The source code and database setup script can be downloaded from http://sourceforge.net/projects/proteintracker. This site also contains installation instructions and a user guide. A demonstration version of the application can be viewed at http://www.proteintracker.org.

  2. ProteinTracker: an application for managing protein production and purification

    Science.gov (United States)

    2012-01-01

    Background Laboratories that produce protein reagents for research and development face the challenge of deciding whether to track batch-related data using simple file based storage mechanisms (e.g. spreadsheets and notebooks), or commit the time and effort to install, configure and maintain a more complex laboratory information management system (LIMS). Managing reagent data stored in files is challenging because files are often copied, moved, and reformatted. Furthermore, there is no simple way to query the data if/when questions arise. Commercial LIMS often include additional modules that may be paid for but not actually used, and often require software expertise to truly customize them for a given environment. Findings This web-application allows small to medium-sized protein production groups to track data related to plasmid DNA, conditioned media samples (supes), cell lines used for expression, and purified protein information, including method of purification and quality control results. In addition, a request system was added that includes a means of prioritizing requests to help manage the high demand of protein production resources at most organizations. ProteinTracker makes extensive use of existing open-source libraries and is designed to track essential data related to the production and purification of proteins. Conclusions ProteinTracker is an open-source web-based application that provides organizations with the ability to track key data involved in the production and purification of proteins and may be modified to meet the specific needs of an organization. The source code and database setup script can be downloaded from http://sourceforge.net/projects/proteintracker. This site also contains installation instructions and a user guide. A demonstration version of the application can be viewed at http://www.proteintracker.org. PMID:22574679

  3. Interim Storage of Plutonium in Existing Facilities

    International Nuclear Information System (INIS)

    Woodsmall, T.D.

    1999-01-01

    'In this era of nuclear weapons disarmament and nonproliferation treaties, among many problems being faced by the Department of Energy is the safe disposal of plutonium. There is a large stockpile of plutonium at the Rocky Flats Environmental Technology Center and it remains politically and environmentally strategic to relocate the inventory closer to a processing facility. Savannah River Site has been chosen as the final storage location, and the Actinide Packaging and Storage Facility (APSF) is currently under construction for this purpose. With the ability of APSF to receive Rocky Flats material an estimated ten years away, DOE has decided to use the existing reactor building in K-Area of SRS as temporary storage to accelerate the removal of plutonium from Rocky Flats. There are enormous cost savings to the government that serve as incentive to start this removal as soon as possible, and the KAMS project is scheduled to receive the first shipment of plutonium in January 2000. The reactor building in K-Area was chosen for its hardened structure and upgraded seismic qualification, both resulting from an effort to restart the reactor in 1991. The KAMS project has faced unique challenges from Authorization Basis and Safety Analysis perspectives. Although modifying a reactor building from a production facility to a storage shelter is not technically difficult, the nature of plutonium has caused design and safety analysis engineers to make certain that the design of systems, structures and components included will protect the public, SRS workers, and the environment. A basic overview of the KAMS project follows. Plutonium will be measured and loaded into DOT Type-B shipping packages at Rocky Flats. The packages are 35-gallon stainless steel drums with multiple internal containment boundaries. DOE transportation vehicles will be used to ship the drums to the KAMS facility at SRS. They will then be unloaded, stacked and stored in specific locations throughout the

  4. 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.

  5. Virtual existence in contemporary Serbian novel

    Directory of Open Access Journals (Sweden)

    Gordić-Petković Vladislava S.

    2017-01-01

    Full Text Available The paper sets out to explore the perspectives and strategies of virtual existence in contemporary Serbian novel in order to illustrate radical changes in the concept of reality and writers' concern with the fidelity to experience. A new surge of the so-called digital realism emerges simultaneously with the increase of awareness that the line between our digital selves and our real-world selves has become blurred and difficult to explain, while new technologies are required to go beyond what our human senses can encompass and deliver. The fictional realism of the digital age will also commit itself to young or middle-aged individuals that passionately attempt to define their aims and objectives so that they could fit into a newly constructed and acquired concept of reality. This is the case with the protagonists in the novels by Ivančica Đerić, Tamara Jecić and Aleksandar Ilić, all of them questioning both their offline and online identities. Their everyday life in a postmillennial world includes many intersecting empirical and virtual realities: love, career and sex take place in a dimension which ignores geography and physical distance and ultimately alters the concepts of time and space, as well the concepts of privacy and intimacy. The paper intends to examine the ways new digital technologies contribute to representations of reality in the novels of both accomplished and aspiring authors whose novels deal with ways of life amid social networks. The novels we analyzed show that the distinction between the virtual and the real world narrows, as the narratives range from intimate confession in letters and journals to tweets, notes and statuses, introducing verbal and structural experimental practices which involve shifting points of view.

  6. Thallium exists in opioid poisoned patients.

    Science.gov (United States)

    Ghaderi, Amir; Vahdati-Mashhadian, Naser; Oghabian, Zohreh; Moradi, Valiallah; Afshari, Reza; Mehrpour, Omid

    2015-08-01

    Thallium (Tl) is a toxic heavy metal that exists in nature. Tl poisoning (thallotoxicosis) may occur in opioid addicts. This study was designed to evaluate the frequency and level of urinary Tl in opioid abusers. In addition, clinical findings were evaluated. A total of 150 subjects were examined. Cases with a history of at least 3 years of abuse were admitted in the Imam Reza Hospital as the case group; 50 non-opioid abusers from the target population were included as the control group. Twenty-four hour urinary qualitative and quantitative Tl analyses were performed on both groups. Out of the 150 subjects, 128 (85 %) were negative for qualitative urinary Tl, followed by 5 % (trace), 7 % (1+), 2 % (2+), and 1 % (3+). Mean (standard error (SE), Min-Max) quantitative urinary Tl level was 14 μg/L (3.5 μg/L, 0-346 μg/L). Mean urinary Tl level in the case group was 21 μg/L (5 μg/L, 0-346 μg/L) and that in the controls was 1 μg/L (0.14 μg/L, 0-26 μg/L), which were significantly different (P = 0.001). The most frequent clinical findings were ataxia (86 %), sweating (81 %), and constipation (54 %). In all cases (n = 150), the mean (SE) value for cases with positive qualitative urinary Tl was 26.8 μg/L (0.9 μg/L) and that in the negative cases was 2.3 μg/L (0.2 μg/L), which were significantly different (P = 0.002). This study showed that long-term opioid abuse may lead to Tl exposure. In opioid abusers with the clinical manifestation of thallotoxicosis, urinary Tl should be determined.

  7. Ensemble Linear Neighborhood Propagation for Predicting Subchloroplast Localization of Multi-Location Proteins.

    Science.gov (United States)

    Wan, Shibiao; Mak, Man-Wai; Kung, Sun-Yuan

    2016-12-02

    In the postgenomic era, the number of unreviewed protein sequences is remarkably larger and grows tremendously faster than that of reviewed ones. However, existing methods for protein subchloroplast localization often ignore the information from these unlabeled proteins. This paper proposes a multi-label predictor based on ensemble linear neighborhood propagation (LNP), namely, LNP-Chlo, which leverages hybrid sequence-based feature information from both labeled and unlabeled proteins for predicting localization of both single- and multi-label chloroplast proteins. Experimental results on a stringent benchmark dataset and a novel independent dataset suggest that LNP-Chlo performs at least 6% (absolute) better than state-of-the-art predictors. This paper also demonstrates that ensemble LNP significantly outperforms LNP based on individual features. For readers' convenience, the online Web server LNP-Chlo is freely available at http://bioinfo.eie.polyu.edu.hk/LNPChloServer/ .

  8. 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)

  9. Texturized dairy proteins.

    Science.gov (United States)

    Onwulata, Charles I; Phillips, John G; Tunick, Michael H; Qi, Phoebi X; Cooke, Peter H

    2010-03-01

    Dairy proteins are amenable to structural modifications induced by high temperature, shear, and moisture; in particular, whey proteins can change conformation to new unfolded states. The change in protein state is a basis for creating new foods. The dairy products, nonfat dried milk (NDM), whey protein concentrate (WPC), and whey protein isolate (WPI) were modified using a twin-screw extruder at melt temperatures of 50, 75, and 100 degrees C, and moistures ranging from 20 to 70 wt%. Viscoelasticity and solubility measurements showed that extrusion temperature was a more significant (P extruded dairy protein ranged from rigid (2500 N) to soft (2.7 N). Extruding at or above 75 degrees C resulted in increased peak force for WPC (138 to 2500 N) and WPI (2.7 to 147.1 N). NDM was marginally texturized; the presence of lactose interfered with its texturization. WPI products extruded at 50 degrees C were not texturized; their solubility values ranged from 71.8% to 92.6%. A wide possibility exists for creating new foods with texturized dairy proteins due to the extensive range of states achievable. Dairy proteins can be used to boost the protein content in puffed snacks made from corn meal, but unmodified, they bind water and form doughy pastes with starch. To minimize the water binding property of dairy proteins, WPI, or WPC, or NDM were modified by extrusion processing. Extrusion temperature conditions were adjusted to 50, 75, or 100 degrees C, sufficient to change the structure of the dairy proteins, but not destroy them. Extrusion modified the structures of these dairy proteins for ease of use in starchy foods to boost nutrient levels. Dairy proteins can be used to boost the protein content in puffed snacks made from corn meal, but unmodified, they bind water and form doughy pastes with starch. To minimize the water binding property of dairy proteins, whey protein isolate, whey protein concentrate, or nonfat dried milk were modified by extrusion processing. Extrusion

  10. The ethical use of existing samples for genome research.

    Science.gov (United States)

    Bathe, Oliver F; McGuire, Amy L

    2009-10-01

    Modern biobanking efforts consist of prospective collections of tissues linked to clinical data for patients who have given informed consent for the research use of their specimens and data, including their DNA. In such efforts, patient autonomy and privacy are well respected because of the prospective nature of the informed consent process. However, one of the richest sources of tissue for research continues to be the millions of archived samples collected by pathology departments during normal clinical care or for research purposes without specific consent for future research or genetic analysis. Because specific consent was not obtained a priori, issues related to individual privacy and autonomy are much more complicated. A framework for accessing these existing samples and related clinical data for research is presented. Archival tissues may be accessed only when there is a reasonable likelihood of generating beneficial and scientifically valid information. To minimize risks, databases containing information related to the tissue and to clinical data should be coded, no personally identifying phenotypic information should be included, and access should be restricted to bona fide researchers for legitimate research purposes. These precautions, if implemented appropriately, should ensure that the research use of archival tissue and data are no more than minimal risk. A waiver of the requirement for informed consent would then be justified if reconsent is shown to be impracticable. A waiver of consent should not be granted, however, if there is a significant risk to privacy, if the proposed research use is inconsistent with the original consent (where there is one), or if the potential harm from a privacy breach is considerable.

  11. Time-resolved infrared studies of protein conformational dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Woodruff, W.H.; Causgrove, T.P.; Dyer, R.B. [Los Alamos National Laboratory, NM (United States); Callender, R.H. [Univ. of New York, NY (United States)

    1994-12-01

    We have demonstrated that TRIR in the amide I region gives structural information regarding protein conformational changes in realtime, both on processes involved in the development of the functional structure (protein folding) and on protein structural changes that accompany the functional dynamics of the native structure. Assignment of many of the amide I peaks to specific amide or sidechain structures will require much additional effort. Specifically, the congestion and complexity of the protein vibrational spectra dictate that isotope studies are an absolute requirement for more than a qualitative notion of the structural interpretation of these measurements. It is clear, however, that enormous potential exists for elucidating structural relaxation dynamics and energetics with a high degree of structural specificity using this approach.

  12. Triplet Excited States as a Source of Relevant (Bio)Chemical Information

    OpenAIRE

    Jiménez Molero, María Consuelo; Miranda Alonso, Miguel Ángel

    2014-01-01

    The properties of triplet excited states are markedly medium-dependent, which turns this species into valuable tools for investigating the microenvironments existing in protein binding pockets. Monitoring of the triplet excited state behavior of drugs within transport proteins (serum albumins and alpha(1)-acid glycoproteins) by laser flash photolysis constitutes a valuable source of information on the strength of interaction, conformational freedom and protection from oxygen or other external...

  13. 77 FR 57080 - Proposed Agency Information Collection

    Science.gov (United States)

    2012-09-17

    ...-0149: Existing; (2) Information Collection Request Title: Evaluation of the Financial Reporting System... existing data collection, the Financial Reporting System, EIA-28. This is not a request to collect data... DEPARTMENT OF ENERGY Energy Information Administration Proposed Agency Information Collection...

  14. Does GaH5 exist?

    Science.gov (United States)

    Speakman, Lucas D.; Turney, Justin M.; Schaefer, Henry F.

    2005-11-01

    The existence or nonexistence of GaH5 has been widely discussed [N. M. Mitzel, Angew. Chem. Int. Ed. 42, 3856 (2003)]. Seven possible structures for gallium pentahydride have been systematically investigated using ab initio electronic structure theory. Structures and vibrational frequencies have been determined employing self-consistent field, coupled cluster including all single and double excitations (CCSD), and CCSD with perturbative triples levels of theory, with at least three correlation-consistent polarized-valence-(cc-pVXZ and aug-cc-pVXZ) type basis sets. The X˜A'1 state for GaH5 is predicted to be weakly bound complex 1 between gallane and molecular hydrogen, with Cs symmetry. The dissociation energy corresponding to GaH5→GaH3+H2 is predicted to be De=2.05kcalmol-1. The H-H stretching fundamental is predicted to be v =4060cm-1, compared to the tentatively assigned experimental feature of Wang and Andrews [J. Phys. Chem. A 107, 11371 (2003)] at 4087cm-1. A second Cs structure 2 with nearly equal energy is predicted to be a transition state, corresponding to a 90° rotation of the H2 bond. Thus the rotation of the hydrogen molecule is essentially free. However, hydrogen scrambling through the C2v structure 3 seems unlikely, as the activation barrier for scrambling is at least 30kcalmol-1 higher in energy than that for the dissociation of GaH5 to GaH3 and H2. Two additional structures consisting of GaH3 with a dihydrogen bond perpendicular to gallane (C3v structure 4) and an in-plane dihydrogen bond [Cs(III) structure 5] were also examined. A C3v symmetry second-order saddle point has nearly the same energy as the GaH3+H2 dissociation limit, while the Cs(III) structure 5 is a transition structure to the C3v structure. The C4v structure 6 and the D3h structure 7 are much higher in energy than GaH3+H2 by 88 and 103kcalmol-1, respectively.

  15. PASSCLAIM - Synthesis and review of existing processes.

    Science.gov (United States)

    Richardson, David P; Affertsholt, Tage; Asp, Nils-Georg; Bruce, Ake; Grossklaus, Rolf; Howlett, John; Pannemans, Daphne; Ross, Richard; Verhagen, Hans; Viechtbauer, Volker

    2003-03-01

    Several approaches to the use of health claims on foods have been made around the world, and the common theme is that any health claim will require scientific validation and substantiation. There is also broad consensus that any regulatory framework should protect the consumer, promote fair trade and encourage innovation in the food industry.This paper is based on a critical evaluation of existing international approaches to the scientific substantiation of health claims, with a view to identifying common new ideas, definitions, best practice and a methodology to underpin current and future developments. There is a clear need to have uniform understanding, terminology and description of types of nutrition and health claims. Two broad categories were defined: Nutrition Claims, i. e. what the product contains, and Health Claims, i. e. relating to health, well-being and/or performance, including well-established nutrient function claims, enhanced function claims and disease risk reduction claims. Such health claims relate to what the food or food components does or do. The categories of health claims are closely and progressively related and are, in practice, part of a continuum. Provision is also made for "generic" or well-established, generally accepted claims and for "innovative" or "product-specific" claims. Special attention was paid to reflect the health-promoting properties of a food or food component in such a way as to facilitate the making of risk reduction claims outside the medical scope of the term prevention. The paper sets out basic principles and guidelines for communication of health claims and principles of nutritional safety. The main body of the work examines the process for the assessment of scientific support for health claims on food and emphasises an evidence-based approach consisting of: Identification of all relevant studies exploring the collection of evidence, data searches, the nature of the scientific evidence, sources of scientific data

  16. A precariedade humana e a existência estilizada Human precariousness and stylized existence

    Directory of Open Access Journals (Sweden)

    Rita Paiva

    2013-04-01

    Full Text Available Este artigo tematiza o desamparo vivenciado pela consciência ante a ausência de bases sólidas para seus anseios de felicidade e para suas representações simbólicas. Com esse propósito, toma como objeto de reflexão um dos ensaios filosóficos de Albert Camus, O mito de Sísifo, equacionando a possibilidade de uma ética que estilize a vida, sem que se minimize a dolorosa precariedade da existência humana. Posteriormente, em diálogo com alguns textos de M. Foucault, a reflexão procura estabelecer os vínculos possíveis entre a ética camusiana e a ética como uma estética da existência, tal como pensada entre os gregos antigos.This article discusses the helplessness experienced by the consciousness vis-à-vis the absence of solid bases for its longings for happiness and for its symbolic representations. For this purpose, the object of reflection of the article is one of Albert Camus' philosophical essays, The Myth of Sisyphus, and we inquire into the possibility of an ethics that stylizes life without minimizing the painful precariousness of human existence. Making reference to certain texts by Foucault, we attempt to establish possible connections between Camus' ethics and an ethics of the aesthetics of existence as found in the thinkers of ancient Greece.

  17. Existence and non-existence of solutions for a singular problem with variable potentials

    Directory of Open Access Journals (Sweden)

    Kamel Saoudi

    2017-11-01

    Full Text Available The purpose of this article is to prove some existence and nonexistence theorems for the inhomogeneous singular Dirichlet problem $$ - \\Delta_p u = \\frac{\\lambda k(x}{u^\\delta}\\pm h(x u^q. $$ For proving our results we use the sub and super solution method, and monotonicity arguments.

  18. 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.

  19. Cell-specific monitoring of protein synthesis in vivo.

    Directory of Open Access Journals (Sweden)

    Nikos Kourtis

    Full Text Available Analysis of general and specific protein synthesis provides important information, relevant to cellular physiology and function. However, existing methodologies, involving metabolic labelling by incorporation of radioactive amino acids into nascent polypeptides, cannot be applied to monitor protein synthesis in specific cells or tissues, in live specimens. We have developed a novel approach for monitoring protein synthesis in specific cells or tissues, in vivo. Fluorescent reporter proteins such as GFP are expressed in specific cells and tissues of interest or throughout animals using appropriate promoters. Protein synthesis rates are assessed by following fluorescence recovery after partial photobleaching of the fluorophore at targeted sites. We evaluate the method by examining protein synthesis rates in diverse cell types of live, wild type or mRNA translation-defective Caenorhabditis elegans animals. Because it is non-invasive, our approach allows monitoring of protein synthesis in single cells or tissues with intrinsically different protein synthesis rates. Furthermore, it can be readily implemented in other organisms or cell culture systems.

  20. HIV protein sequence hotspots for crosstalk with host hub proteins.

    Directory of Open Access Journals (Sweden)

    Mahdi Sarmady

    Full Text Available HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of host proteins in their interaction with hub proteins, drastically affecting cell physiology. Functional genomics and interactome datasets can be used to quantify the sequence hotspots on the HIV proteome mediating interactions with host hub proteins. In this study, we used the HIV and human interactome databases to identify HIV targeted host hub proteins and their host binding partners (H2. We developed a high throughput computational procedure utilizing motif discovery algorithms on sets of protein sequences, including sequences of HIV and H2 proteins. We identified as HIV sequence hotspots those linear motifs that are highly conserved on HIV sequences and at the same time have a statistically enriched presence on the sequences of H2 proteins. The HIV protein motifs discovered in this study are expressed by subsets of H2 host proteins potentially outcompeted by HIV proteins. A large subset of these motifs is involved in cleavage, nuclear localization, phosphorylation, and transcription factor binding events. Many such motifs are clustered on an HIV sequence in the form of hotspots. The sequential positions of these hotspots are consistent with the curated literature on phenotype altering residue mutations, as well as with existing binding site data. The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes.